
                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb12e8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb12e8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb15c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb15c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.356

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a14_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a14_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a2y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a2y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a3r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a3r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a5f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a5f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.430

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.327
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a6u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a6u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a7r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a7r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1a8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1a8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.309
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1acy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1acy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.317

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.087

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.073
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ad9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ad9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1adq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1adq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ae6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ae6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.303

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.266
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1afv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1afv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.353
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ahw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ahw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ai1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ai1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.297
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aif_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aif_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.347

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.077
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1aqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1aqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ar1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ar1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.297

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1axt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1axt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.301

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ay1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ay1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b0w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b0w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b0w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b0w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b0w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b0w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.292
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b2w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b2w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.318

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b4j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b4j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b6d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b6d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b6d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b6d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1b6d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1b6d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.335
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1baf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1baf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.334
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.387
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bey_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bey_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.408
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.343
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bgx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bgx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.321

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.092
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.289
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.360

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bjm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bjm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bjm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bjm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bjm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bjm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bln_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bln_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bog_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bog_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.315
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bre_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bre_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bre_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bre_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bre_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bre_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.096
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bvl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bvl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bww_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bww_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bww_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bww_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bww_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bww_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.086

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.317

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bzq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bzq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bzq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bzq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.354
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1bzq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1bzq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c08_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c08_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c12_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c12_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c1e_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c1e_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.298

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1c5d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1c5d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.079
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ce1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ce1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cf8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cf8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cft_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cft_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cgs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cgs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.332

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cic_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cic_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.325

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cly_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cly_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1clz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1clz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cr9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cr9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ct8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ct8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cu4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cu4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.292
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.308
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1cz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1cz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.340
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1d6v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1d6v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dba_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dba_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.316
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.355

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.344
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.308
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.283
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.304
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.366
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dl7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dl7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.560

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.079
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.078
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dn0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dn0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.385

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.306
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.326
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dql_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dql_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dqq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dqq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1dsf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1dsf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.367

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.306

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1e6o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1e6o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.382

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eap_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eap_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eeu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eeu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1efq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1efq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1efq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1efq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1efq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1efq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.257
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1egj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1egj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ehl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ehl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ejo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ejo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ek3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ek3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ek3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ek3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ek3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ek3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.314
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1emt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1emt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.335
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1eo8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1eo8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1etz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1etz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.089
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ezv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ezv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f11_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f11_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.246
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.296
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.344
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f4y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f4y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f6l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f6l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f6l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f6l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f6l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f6l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.082
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f8t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f8t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1f90_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1f90_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.297

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.272
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fbi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fbi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.327
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fdl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fdl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fe8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fe8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.406
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.284
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.302
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.315
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.338
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.320

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fj1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fj1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fl6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fl6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.411
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.324
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.382
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.320

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.296
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.088
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fns_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fns_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.303
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1for_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1for_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1frg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1frg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fsk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fsk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.405
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.348
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fvd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fvd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1fve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1fve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.257
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.331
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1g9n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1g9n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gaf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gaf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.329
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gc1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gc1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ggi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ggi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gig_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gig_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1gpo_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1gpo_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h0d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h0d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h3p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h3p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8s_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8s_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8s_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8s_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1h8s_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1h8s_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hez_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hez_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.087
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.081
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hh9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hh9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.090
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hi6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hi6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1him_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1him_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.312

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hin_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hin_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hkl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hkl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.082
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hq4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hq4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hys_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hys_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1hzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1hzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.266

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3g_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3g_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3u_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3u_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.340
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i3v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i3v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.557

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.394
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i7z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i7z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.371

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.089
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.301
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.305
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1i9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1i9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iai_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iai_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.328
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ibg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ibg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ic7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ic7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ifh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ifh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.303
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.368
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.286
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.339
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.288
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.386

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.096
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.479

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1igy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1igy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.331

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.326
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ikf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ikf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1il1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1il1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ind_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ind_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ine_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ine_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.351

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1iqw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1iqw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1it9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1it9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ivl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ivl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ivl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ivl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ivl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ivl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j1x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j1x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1j5o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1j5o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jfq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jfq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.268

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.272
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jhl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jhl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jn6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jn6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jnn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jnn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jps_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jps_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jpt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jpt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jrh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jrh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jto_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jto_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jto_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jto_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jto_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jto_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.486
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.513
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.666
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jtt_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jtt_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1jvk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1jvk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.092
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k4d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k4d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1k6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1k6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.392
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kb5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kb5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kc5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kc5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kcv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kcv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1keg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1keg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.270
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kem_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kem_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.379
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ken_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ken_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.346

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.391

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kip_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kip_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kiq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kiq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kn4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kn4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.270

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.275
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1kno_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1kno_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ktr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ktr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1l7t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1l7t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lgv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lgv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lhz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lhz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lhz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lhz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lhz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lhz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.372
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lil_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lil_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.348
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lk3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lk3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lo4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lo4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m71_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m71_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7d_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7d_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.246
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1m7i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1m7i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.390
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mce_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mce_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.321
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mce_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mce_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mce_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mce_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.326

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mch_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mch_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mch_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mch_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.342
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mch_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mch_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.306

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mci_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mci_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mci_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mci_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mci_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mci_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.318
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mck_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mck_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mck_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mck_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mck_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mck_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.381
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.300
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.348
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mco_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mco_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.317
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.322
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.324

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.313
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.313
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mcw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mcw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mf2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mf2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.307
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mfe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mfe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mh5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mh5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mhp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mhp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mie_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mie_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mie_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mie_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mie_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mie_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mj8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mj8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mjj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mjj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.086
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mju_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mju_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mlc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mlc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.354
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mnu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mnu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.363

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mqk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mqk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.520
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.760
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1mvu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1mvu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.082
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.265
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.295
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n4x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n4x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n5y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n5y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.358

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n64_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n64_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.272
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.309
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n6q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n6q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1n8z_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1n8z_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.304
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nby_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nby_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nbz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nbz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nc4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nc4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.332
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ncw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ncw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.284
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ndm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ndm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.268
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.083
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.314
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.081
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngy_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngy_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ngz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ngz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nl0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nl0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nlb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nlb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nld_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nld_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nma_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nma_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.084
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1nmc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1nmc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.290
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.085
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oak_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oak_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oar_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oar_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oau_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oau_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oax_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oax_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oay_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oay_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.257
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1oaz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1oaz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ob1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ob1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.313
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ocw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ocw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.661

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ohq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ohq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ohq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ohq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ohq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ohq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ol0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ol0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ol0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ol0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ol0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ol0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1om3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1om3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.100
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.310
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.296
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1op9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1op9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1opg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1opg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.287
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1orq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1orq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.303
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ors_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ors_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1osp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1osp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ots_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ots_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.271
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ott_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ott_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.338

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1otu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1otu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.301

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p2c_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p2c_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.317
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1p4i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1p4i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.314

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pg7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pg7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.384
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1plg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1plg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1psk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1psk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1pz5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1pz5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.102
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0x_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0x_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q0y_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q0y_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q1j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q1j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.325
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9r_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9r_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9t_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9t_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9v_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9v_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1q9w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1q9w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qbm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qbm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qd0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qd0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qfu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qfu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qkz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qkz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qle_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qle_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.287
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.469
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qlr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qlr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.039
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.075
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qnz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qnz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qp1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qp1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qp1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qp1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qp1_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qp1_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.079

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1qyg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1qyg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r0a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r0a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.088
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1r3l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1r3l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.399
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.405
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.294
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rfd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rfd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rhh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rhh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.344

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rih_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rih_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.278
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riu_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riu_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1riv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1riv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.403
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.272
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rum_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rum_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rup_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rup_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ruq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ruq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rur_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rur_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.261
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.494

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.327
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.454

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.280
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.343

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.289
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1rzk_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1rzk_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.118
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s3k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s3k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.313

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.088
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.089
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s5i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s5i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.087
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1s78_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1s78_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.321

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sbs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sbs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1seq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1seq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1shm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1shm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1shm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1shm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1shm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1shm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sjx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sjx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sjx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sjx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sjx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sjx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sm3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sm3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.270
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1sy6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1sy6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.144
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.314
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t03_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t03_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.315

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t04_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t04_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.293

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.084
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t2q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t2q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.096
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t3f_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t3f_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.081
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t4k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t4k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1t66_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1t66_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tet_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tet_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.284

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tjh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tjh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.347

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tji_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tji_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.327

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1txv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1txv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.229

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.224
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.192
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.287
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.266
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ty7_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ty7_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.240

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.227
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1tzi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1tzi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u0q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u0q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8h_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8h_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8i_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8i_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8j_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8j_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.201
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8k_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8k_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.266
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.110
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.246
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8o_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8o_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.300
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.257

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.268
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u8q_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u8q_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.251

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.284
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u91_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u91_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u92_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u92_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.245

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u93_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u93_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.115
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1u95_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1u95_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.260

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.100
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ua6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ua6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.191
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uac_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uac_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ub6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ub6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   Error==> Number of residues in zone does not match.
           H95    to H102   with H95    to H102   (Residue numbering)
            Reference: 129, Mobile: 16

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ucb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ucb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uj3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uj3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.078
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.101
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.082
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.070
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1um6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1um6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.306

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.064
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.080
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.082
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.104
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uwx_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uwx_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.077
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.090
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.276
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uyw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uyw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz6_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz6_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.098
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.070
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1uz8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1uz8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.083

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.190
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7m_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7m_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1v7n_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1v7n_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1vge_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1vge_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1w72_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1w72_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.283
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wt5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wt5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wtl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wtl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wtl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wtl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1wtl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1wtl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.457
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.248
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xcq_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xcq_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.173
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.293
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1xf5_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1xf5_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.085

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y0l_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y0l_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1y18_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1y18_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.103
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.239
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yec_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yec_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.288

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.083
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yed_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yed_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.100
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.214
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yee_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yee_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.232
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yef_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yef_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.272

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.093
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.275

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.247
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yeh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yeh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yei_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yei_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.105
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yej_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yej_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.236

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.230
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yek_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yek_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.267

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.124
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.112
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yjd_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yjd_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.231
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.262
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.284
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1ymh_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1ymh_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yqv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yqv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.128
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.307
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.216
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.123
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yy9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yy9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.270
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.254
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yyl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yyl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.113
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.242
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yym_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yym_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yzz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yzz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.285
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yzz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yzz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.751
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1yzz_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1yzz_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.517

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.180
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.092
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.183
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.149
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb1za3_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb1za3_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.194

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.269
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb25c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb25c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.085
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.133
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.061
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.111
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a1w_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a1w_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.321

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2a77_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2a77_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.308

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.108
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.177
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ap2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ap2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.207
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.274
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bfv_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bfv_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.114
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.080
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2bob_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2bob_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.246
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.277
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.090
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.234
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2boc_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2boc_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.138
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2cgr_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2cgr_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.130
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.150

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.203
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.233
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.178
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dbl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dbl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.288

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.075
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.088
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.109
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2dlf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2dlf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.228
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f19_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f19_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.446

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.176
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.332
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.376

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.092
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.179
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.215
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5a_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5a_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.388

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.107
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.220
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.167
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2f5b_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2f5b_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.145
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fb4_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fb4_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.266
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.246
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fbj_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fbj_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.200
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.259
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.181
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.328
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2fgw_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2fgw_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.428

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.257
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.120
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2gfb_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2gfb_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.237
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.282
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2h1p_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2h1p_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.097
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.081
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.154
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hmi_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hmi_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.142
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.223
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2hrp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2hrp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.322

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.170
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.270
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.221
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2iff_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2iff_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.100
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.143
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.136
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.121
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2ig2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2ig2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.159
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.296
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.218
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.166
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2igf_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2igf_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.264

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2imn_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2imn_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.163

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.139
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.091
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.263
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2jel_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2jel_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.157
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.193
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.250
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.244

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.241
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.211
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.225
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2mpa_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2mpa_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.169
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.125
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.235
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2pcp_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2pcp_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.199

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.099
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rcs_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rcs_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rhe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rhe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.208
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rhe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rhe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.222
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2rhe_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2rhe_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.153

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.158
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.311
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.132
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vir_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vir_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.186
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.300
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.226
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.209
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vis_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vis_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.147
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.281
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.213
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.134
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.195
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb2vit_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb2vit_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.185

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.151
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.086
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.172
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb32c2_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb32c2_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.155

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.131
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.286
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.273
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb35c8_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb35c8_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.119

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.287
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.238
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.189

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.129
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.174
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.095
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.165
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.161
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3ck0_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3ck0_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.175

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.122
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.243
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.160
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3f58_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3f58_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.279

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.206
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.106
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.184
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.256
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3fct_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3fct_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.188

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.202
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.137
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.289
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.258
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3hfm_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3hfm_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.205

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.140
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.196
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.117

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.249
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.204
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb3mcg_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb3mcg_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.253

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.162
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.198
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.094
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.156
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43c9_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43c9_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.116

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.219
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.168
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.126
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.327
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb43ca_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb43ca_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.152

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.210
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.255
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4bjl_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4bjl_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.298

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.342
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.182
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.268
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.332
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.217
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.135

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.127
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.252
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb4lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb4lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.141

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb5lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb5lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.148
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb5lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb5lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.212
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb5lve_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb5lve_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.146

                  PPPPP                FFFFFF ii   tt
                  PP  PP               FF          tt
                  PP  PP rrrrr   oooo  FF     ii  ttttt
                  PPPPP  rr  rr oo  oo FFFF   ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr     oo  oo FF     ii   tt
                  PP     rr      oooo  FF      ii   ttt

                      Protein Least Squares Fitting

                               Version 2.5.1

      Copyright (c) Dr. Andrew C.R. Martin, SciTech Software 1992-2005

   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.164
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.349
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.171
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.187
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.334
   Unrecognised keyword: /home/arvind/simulations/RAM/pdbfiles/pdb6fab_chothia.pdb /home/arvind/simulations/RAM/pdbfiles/idealized/pdb6fab_chothia.pdb
   Reading reference structure...
   Reading mobile structure...
   RMS: 0.197
