core.init: Mini-Rosetta version 43134M from https://svn.rosettacommons.org/source/trunk/mini
core.init: command: ../../bin/AbinitioRelax.linuxgccrelease @flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-540226944 seed_offset=0 real_seed=-540226944
core.init.random: RandomGenerator:init: Normal mode, seed=-540226944 RG_type=mt19937
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 4101 residue types
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU_p:NtermProteinFull 1
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name  CG 
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: CEN6_mem_env_log.txt
basic.io.database: Database file opened: CEN10_mem_env_log.txt
basic.io.database: Database file opened: memcbeta_den.txt
basic.io.database: Database file opened: mem_pair_log.txt
basic.io.database: Database file opened: P_AA
basic.io.database: Database file opened: P_AA_n
basic.io.database: Database file opened: P_AA_pp
basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
core.pack.dunbrack: Dunbrack library took 0.06 seconds to load from binary
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 13 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 840 bytes
core.chemical.ResidueTypeSet: Finished initializing centroid residue type set.  Created 1202 residue types
protocols.abinitio.AbrelaxApplication: read fasta sequence: 117 residues
EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CG  on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD  on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE1 on residue GLU_p:NtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OE2 on residue GLU_p:NtermProteinFull 1
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name  CG 
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 13 rotamers at 1 positions.
core.pack.pack_rotamers: IG: 840 bytes
core.io.fragments: reading fragments from file: ./input_files/aa1elwA09_05.200_v1_3 ... 
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... 
core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file ./input_files/aa1elwA09_05.200_v1_3
core.io.fragments: reading fragments from file: ./input_files/aa1elwA03_05.200_v1_3 ... 
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... 
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ./input_files/aa1elwA03_05.200_v1_3
core.fragment: compute strand/loop fractions for 117 residues... 
protocols.abinitio.AbrelaxApplication: run ClassicAbinitio.....
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: phi.theta.36.HS.resmooth
basic.io.database: Database file opened: phi.theta.36.SS.resmooth
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jobdist.JobDistributors: Looking for an available job: 1 1  1
protocols.relax.ClassicRelax: Setting up default relax setting
protocols::checkpoint: Deleting checkpoints of ClassicRelax
protocols.abinitio: 
===================================================================
   Stage 1                                                         
   Folding with score0 for max of 20000
protocols.abinitio: Replaced extended chain after 95 cycles.
protocols.moves.MonteCarlo: ClassicFragmentM trials=     95;  accepts= 0.7474;  energy_drop/trial=   0.01215
protocols.abinitio: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 vdw                          0.100      11.539       1.154
---------------------------------------------------
 Total weighted score:                        1.154

===================================================================
   Stage 2                                                         
   Folding with score1 for 20000
protocols.moves.MonteCarlo: ClassicFragmentM trials=  20000;  accepts= 0.4688;  energy_drop/trial=  -0.00117
protocols.abinitio: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 vdw                          1.000       0.961       0.961
 pair                         1.000      -3.636      -3.636
 env                          1.000     -18.210     -18.210
 hs_pair                      1.000       0.000       0.000
 ss_pair                      0.300       0.000       0.000
 sheet                        1.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                      -20.885

===================================================================
   Stage 3                                                         
   Folding with score2 and score5 for 20000
protocols.moves.MonteCarlo: ClassicFragmentM trials= 200000;  accepts= 0.3878;  energy_drop/trial=   0.00103
protocols.abinitio: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 vdw                          1.000       0.000       0.000
 cenpack                      0.500     -18.416      -9.208
 pair                         1.000      -4.176      -4.176
 env                          1.000     -22.501     -22.501
 cbeta                        0.250      23.131       5.783
 hs_pair                      1.000       0.000       0.000
 ss_pair                      1.000       0.000       0.000
 sheet                        1.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                      -30.103

===================================================================
   Stage 4                                                         
   Folding with score3 for 40000
protocols.moves.MonteCarlo: ClassicFragmentM trials=  40000;  accepts= 0.2631;  energy_drop/trial=   0.00140
protocols.moves.MonteCarlo: SmoothFragmentMo trials=  80000;  accepts= 0.2988;  energy_drop/trial=   0.00116
protocols.abinitio: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 vdw                          1.000       0.515       0.515
 cenpack                      1.000     -24.995     -24.995
 pair                         1.000      -4.497      -4.497
 env                          1.000     -19.582     -19.582
 cbeta                        1.000      22.769      22.769
 rg                           1.500      15.096      22.644
 hs_pair                      1.000       0.000       0.000
 ss_pair                      1.000       0.000       0.000
 rsigma                       1.000       0.000       0.000
 sheet                        1.000       0.000       0.000
---------------------------------------------------
 Total weighted score:                       -3.147

===================================================================
   Finished Abinitio                                                 

protocols.filters.AbinitioBaseFilter: apply filter: RGFilter
protocols.filters.AbinitioBaseFilter: apply filter: Contact-Order Filter
protocols.filters.AbinitioBaseFilter: apply filter: SheetFilter
protocols.abinitio.AbrelaxApplication:  passed all filters 
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1093 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 845356 bytes
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.relax.FastRelax: ================== Using default script ==================
core.pack.task: Packer task: initialize from command line() 
protocols.relax.FastRelax: CMD: repeat  72.0617  0  0  0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1270 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 1004756 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -281.658  1.17642  1.17642  0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1167 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 896816 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -240.401  2.31525  2.31525  0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1139 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 815752 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -223.363  2.61765  2.61765  0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1120 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 783420 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -240.274  3.43774  3.43774  0.44
protocols.relax.FastRelax: MRP: 0  -240.274  -240.274  3.43774  3.43774  
protocols.relax.FastRelax: CMD: accept_to_best  -240.274  3.43774  3.43774  0.44
protocols.relax.FastRelax: CMD: endrepeat  -240.274  3.43774  3.43774  0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1319 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 1057648 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -327.979  3.17596  3.17596  0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1173 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 910512 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -281.927  3.69218  3.69218  0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1147 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 828976 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -259.218  3.67522  3.67522  0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1148 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 814096 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -250.613  4.04484  4.04484  0.44
protocols.relax.FastRelax: MRP: 1  -250.613  -250.613  4.04484  4.04484  
protocols.relax.FastRelax: CMD: accept_to_best  -250.613  4.04484  4.04484  0.44
protocols.relax.FastRelax: CMD: endrepeat  -250.613  4.04484  4.04484  0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1342 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 1084188 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -330.533  3.4605  3.4605  0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1186 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 905240 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -286.036  3.96093  3.96093  0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1176 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 864736 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -265.659  4.05099  4.05099  0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1160 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 829344 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -255.63  3.87089  3.87089  0.44
protocols.relax.FastRelax: MRP: 2  -255.63  -255.63  3.87089  3.87089  
protocols.relax.FastRelax: CMD: accept_to_best  -255.63  3.87089  3.87089  0.44
protocols.relax.FastRelax: CMD: endrepeat  -255.63  3.87089  3.87089  0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1343 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 1117224 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -327.302  3.91581  3.91581  0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1192 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 905160 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -293.967  3.89599  3.89599  0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1170 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 860040 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -273.322  4.00523  4.00523  0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1150 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 819180 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -258.208  3.56834  3.56834  0.44
protocols.relax.FastRelax: MRP: 3  -258.208  -258.208  3.56834  3.56834  
protocols.relax.FastRelax: CMD: accept_to_best  -258.208  3.56834  3.56834  0.44
protocols.relax.FastRelax: CMD: endrepeat  -258.208  3.56834  3.56834  0.44
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1367 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 1145788 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -336.332  3.62396  3.62396  0.0088
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1207 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 931996 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -299.038  3.55535  3.55535  0.11
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1165 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 861716 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -279.293  3.71527  3.71527  0.242
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 1151 rotamers at 117 positions.
core.pack.pack_rotamers: IG: 832672 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min  -265.246  3.58111  3.58111  0.44
protocols.relax.FastRelax: MRP: 4  -265.246  -265.246  3.58111  3.58111  
protocols.relax.FastRelax: CMD: accept_to_best  -265.246  3.58111  3.58111  0.44
protocols.relax.FastRelax: CMD: endrepeat  -265.246  3.58111  3.58111  0.44
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.abinitio.AbrelaxApplication: Finished _0001 in 470 seconds.
protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: Deleting checkpoints of Abrelax
protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: Deleting checkpoints of Abrelax
