command executed: rosetta.gcc da 1ubq _ -s 1ubq_faidl.pdb -design -mvbb -nstruct 3
[STR  OPT]Default value for [-paths] paths.txt.
[T/F  OPT]Default FALSE value for [-version]
[T/F  OPT]Default FALSE value for [-score]
[T/F  OPT]Default FALSE value for [-abinitio]
[T/F  OPT]Default FALSE value for [-refine]
[T/F  OPT]Default FALSE value for [-assemble]
[T/F  OPT]Default FALSE value for [-idealize]
[T/F  OPT]Default FALSE value for [-relax]
[T/F  OPT]New TRUE value for [-design]
[T/F  OPT]Default FALSE value for [-onlypack]
[T/F  OPT]Default FALSE value for [-fixbb]
[T/F  OPT]Default FALSE value for [-mcmin_trials]
[T/F  OPT]Default FALSE value for [-design_loops_dock]
[T/F  OPT]Default FALSE value for [-mut_list]
[T/F  OPT]Default FALSE value for [-rotamerize]
[T/F  OPT]Default FALSE value for [-rot_opt]
[T/F  OPT]Default FALSE value for [-design_trials]
[T/F  OPT]New TRUE value for [-mvbb]
[T/F  OPT]Default FALSE value for [-fixseq]
[T/F  OPT]Default FALSE value for [-tail]
[T/F  OPT]Default FALSE value for [-design_inter]
[T/F  OPT]Default FALSE value for [-alter_spec]
[T/F  OPT]Default FALSE value for [-design_in_pieces]
[T/F  OPT]Default FALSE value for [-dna_interface]
[T/F  OPT]Default FALSE value for [-analyze_dna_interface]
[T/F  OPT]Default FALSE value for [-force_basepair_muts]
[T/F  OPT]Default FALSE value for [-natrot]
[T/F  OPT]Default FALSE value for [-optE]
[T/F  OPT]Default FALSE value for [-optE_ctsa]
[T/F  OPT]Default FALSE value for [-optE_inter]
[T/F  OPT]Default FALSE value for [-optE_ctsa]
[T/F  OPT]Default FALSE value for [-optE_inter]
[STR  OPT]Default value for [-Eout] default.
[STR  OPT]Default value for [-sqc] none.
[STR  OPT]Default value for [-pdbout] des.
[INT  OPT]Default value for [-ndruns]  1
[INT  OPT]Default value for [-begin]  0
[INT  OPT]Default value for [-end]  0
[STR  OPT]Default value for [-alter_spec_mutlist] mutlist.
[STR  OPT]Default value for [-point_mut_energies] none.
[STR  OPT]Default value for [-mut_mut_energies] none.
[STR  OPT]Default value for [-design_mutlist] none.
[T/F  OPT]Default FALSE value for [-safety]
[T/F  OPT]Default FALSE value for [-design_dock]
[T/F  OPT]Default FALSE value for [-favor_native_residue]
Rosetta mode: design    
[T/F  OPT]Default FALSE value for [-chain]
[T/F  OPT]Default FALSE value for [-protein]
[T/F  OPT]Default FALSE value for [-series]
series_code = da :: protein_name is 1ubq:: chain_id is _.
[INT  OPT]New value for [-nstruct]  3
[T/F  OPT]Default FALSE value for [-read_all_chains]
[T/F  OPT]Default FALSE value for [-repack]
[T/F  OPT]Default FALSE value for [-overwrite]
[T/F  OPT]Default FALSE value for [-silent_input]
[T/F  OPT]Default FALSE value for [-timer]
[T/F  OPT]Default FALSE value for [-status]
[T/F  OPT]Default FALSE value for [-ise_movie]
[T/F  OPT]Default FALSE value for [-output_all]
[T/F  OPT]Default FALSE value for [-skip_missing_residues]
[T/F  OPT]Default FALSE value for [-use_input_sc]
[STR  OPT]Default value for [-cst] cst.
[STR  OPT]Default value for [-dpl] dpl.
[STR  OPT]Default value for [-resfile] none.
[T/F  OPT]Default FALSE value for [-auto_resfile]
[T/F  OPT]Default FALSE value for [-chain_inc]
[T/F  OPT]Default FALSE value for [-full_filename]
[T/F  OPT]Default FALSE value for [-loops]
[T/F  OPT]Default FALSE value for [-taboo]
[T/F  OPT]Default FALSE value for [-ex1]
[T/F  OPT]Default FALSE value for [-ex2]
[T/F  OPT]Default FALSE value for [-ex3]
[T/F  OPT]Default FALSE value for [-ex4]
[T/F  OPT]Default FALSE value for [-ex1aro]
[T/F  OPT]Default FALSE value for [-ex1aro_half]
[T/F  OPT]Default FALSE value for [-ex2aro_only]
[INT  OPT]Default value for [-extrachi_cutoff]  18
[T/F  OPT]Default FALSE value for [-exdb]
[T/F  OPT]Default FALSE value for [-use_electrostatic_repulsion]
[T/F  OPT]Default FALSE value for [-explicit_h2o]
[T/F  OPT]Default FALSE value for [-try_both_his_tautomers]
[T/F  OPT]Default FALSE value for [-minimize_rot]
[T/F  OPT]Default FALSE value for [-read_hetero_h2o]
[T/F  OPT]Default FALSE value for [-Wint_score_only]
[T/F  OPT]Default FALSE value for [-Wint_repack_only]
Weights for packing and scoring: using interface weight for scoring is set to be  F
 and using old packer weight for repacking is set to be  F
[T/F  OPT]Default FALSE value for [-scorefxn]
default centroid scorefxn:  4
default fullatom scorefxn:  12
[INT  OPT]Default value for [-run_level]  0
[T/F  OPT]Default FALSE value for [-silent]
[T/F  OPT]Default FALSE value for [-verbose]
[T/F  OPT]Default FALSE value for [-gush]
[T/F  OPT]Default FALSE value for [-yap]
[T/F  OPT]Default FALSE value for [-chat]
[T/F  OPT]Default FALSE value for [-inform]
[T/F  OPT]Default FALSE value for [-quiet]
run level:  0
[T/F  OPT]Default FALSE value for [-benchmark]
[T/F  OPT]Default FALSE value for [-debug]
[STR  OPT]New value for [-s] 1ubq_faidl.pdb.
Starting structure: 1ubq_faidl
Reading ../../rosetta_database/Rama_smooth_dyn.dat_ss_6.4
Reading ../../rosetta_database/phi.theta.36.HS.resmooth
Reading ../../rosetta_database/phi.theta.36.SS.resmooth
[STR  OPT]Default value for [-atom_vdw_set] default.
[T/F  OPT]Default FALSE value for [-IUPAC]
Atom_mode set to all       
Reading ../../rosetta_database/paircutoffs
[T/F  OPT]Default FALSE value for [-decoystats]
set_decoystats_flag: from,to F F
[T/F  OPT]Default FALSE value for [-jumping]
Searching for dat file: ./1ubq.dat
Searching for dat file: ./1ubq.dat
WARNING!! .dat file not found!
Looking for fasta file: ./1ubq_.fasta
[T/F  OPT]Default FALSE value for [-find_disulf]
[T/F  OPT]Default FALSE value for [-fix_disulf]
[T/F  OPT]Default FALSE value for [-barcode_mode]
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: CONSTRAINT FILE NOT FOUND
Searched for: ./1ubq_.cst
Running without distance constraints
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
WARNING: DIPOLAR CONSTRAINT FILE NOT FOUND
 Searched for: ./1ubq_.dpl
 Dipolar constraints will not be used
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
fragment file: ./ab1ubq_03_05.200_v1_3
Total Residue 76
frag size: 3    frags/residue: 200
fragment file: ./ab1ubq_09_05.200_v1_3
Total Residue 76
frag size: 9    frags/residue: 200
generating 1mer library from 3mer library
[T/F  OPT]Default FALSE value for [-ssblocks]
[T/F  OPT]Default FALSE value for [-check_homs]
calculating fragment_diversity...
disabling all filters
Looking for psipred file: ./1ubq_.psipred_ss2
Looking for psipred file: ./1ubq_.psipred_ss2
Looking for psipred file: ./1ubq_.jones
Looking for psipred file: ./1ubq_.psipred
Looking for psipred file: ./1ubq_.jones
Looking for psipred file: ./1ubq_.psipred
WARNING :: Unable to find psipred file!
[REAL OPT]Default value for [-co]  -1
[REAL OPT]Default value for [-rms]  -1
Searching for pdb...: ./1ubq.pdb
initializing full atom functions
[T/F  OPT]Default FALSE value for [-soft_rep]
[T/F  OPT]Default FALSE value for [-gen_born]
[STR  OPT]Default value for [-fa_lj_rep_slope] highres.
Reading ../../rosetta_database/bbdep02.May.sortlib
Reading ../../rosetta_database/plane_data_table_1015.dat
Reading ../../rosetta_database/pdbpairstats_fine
Reading ../../rosetta_database/Paa
Reading ../../rosetta_database/Paa_n
Reading ../../rosetta_database/Paa_pp
generating Etable...
Starting energy table calculation
Energy table parameter set: polh_aroh  Revision: 1.5 Date: 2004/10/06 17:24:51
Finished calculating energy tables.
Reading ../../rosetta_database/avgE_from_pdb
Filling missing atoms
optimizing missing atoms
optimizing hydrogen positions
[T/F  OPT]Default FALSE value for [-constant_seed]
[INT  OPT]Default value for [-seed_offset]  0
# =====================================
# random seed: 1011861
# =====================================
Looking for dssp file: ./1ubq.dssp
dssp file not found
Looking for secondary structure assignment file: ./1ubq_.ssa
ssa file not found
calculating secondary structure from torsion angles
Reading ../../rosetta_database/SASA-masks.dat
Reading ../../rosetta_database/SASA-angles.dat
========================================
Reading ../../rosetta_database/sasa_offsets.txt
Constraints Scores
viol stage res1  atom1 res2  atom2    dist    upper    delta    aa1   aa2   score
 Constraints: 0 Scores Total   0
[STR  OPT]Default value for [-scorefile] da1ubq.
score file: ./da1ubq
[T/F  OPT]Default FALSE value for [-repeatin]
[T/F  OPT]Default FALSE value for [-repeatout]
reading starting structure: ./1ubq_faidl.pdb
Filling missing atoms
optimizing missing atoms
optimizing hydrogen positions
secondary structure defined, not reading dssp file
[T/F  OPT]Default FALSE value for [-regions]
[T/F  OPT]Default FALSE value for [-use_input_bond]
[T/F  OPT]Default FALSE value for [-knot_filter]
Constraints Scores
viol stage res1  atom1 res2  atom2    dist    upper    delta    aa1   aa2   score
 Constraints: 0 Scores Total   0
NEXT STRUCTURE: ./da1ubq_faidl_0001.pdb
[T/F  OPT]Default FALSE value for [-movie]
[T/F  OPT]Default FALSE value for [-trajectory]

Start of design structure

Looking for refinement input file: ./1ubq_.refine
unable to find refine input file
using default values
initializing full atom coordinates
-----------------------------------------------------
-----------------------------------------------------
linmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-2     0      55.16     55.16  0.00  0.35   -251.59    36.40
seq -2MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  1
designing with this many rotamers  9665
seq -1EYVFVKTTNGNVYRFHSYKSDKIEKVKRKIKDQAGIDANKIILVFNNLVLVDNHTLSYYNITKGATMLEFIYLFGG  0.407894731
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-1     0    -153.34   -153.34  0.00  0.35   -248.09    24.39
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     0    -158.33   -158.33  0.11  0.31   -244.50    21.67
pre-computing chuck/gunn move set for frag length 3
pre-computing chuck/gunn move set for frag length 1
 1     4    -146.80   -158.59  0.37  0.35   -229.37    17.07
 2     4    -145.45   -158.59  0.38  0.35   -232.04    20.13
 3     4    -149.38   -158.59  0.39  0.35   -234.74    20.31
 4     4    -142.28   -158.59  0.41  0.35   -232.53    21.77
 5     4    -138.81   -158.59  0.52  0.35   -231.47    22.18
designing with this many rotamers  9789
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -146.518875 -146.518875
seq 6KWTYVRTLNGYVLLLYTLENDKVEKVWRLIARILGISISLIIEVYNGLVAFPNRKMSDFGITKGAYVWITLLLDGG  0.276315778
 6     4    -146.52   -158.59  0.64  0.35   -220.79    17.82
 7     4    -142.55   -158.59  0.68  0.35   -221.25    20.79
 8     4    -144.73   -158.59  0.62  0.35   -223.44    20.46
 9     4    -143.84   -158.59  0.65  0.35   -223.92    22.32
10     4    -140.44   -158.59  0.69  0.35   -218.53    18.80
11     4    -139.11   -158.59  0.73  0.35   -219.06    19.65
designing with this many rotamers  9635
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -151.2444 -151.2444
seq 12KWTYVTTLNGLVFLFFSFPSDKTEQDAEKVARRMGIAKNLALFFYNGYLRFPNRKQEDFGITQGAFVTLKLLVDGG  0.25
12     4    -151.24   -158.59  0.83  0.35   -223.92    12.73
13     4    -144.47   -158.59  0.92  0.35   -216.08    12.89
14     4    -142.37   -158.59  0.83  0.35   -217.00    15.57
15     4    -142.86   -158.59  0.85  0.35   -218.34    16.41
16     4    -139.48   -158.59  0.86  0.35   -215.65    18.07
17     4    -138.06   -158.59  0.85  0.35   -212.76    15.42
designing with this many rotamers  9641
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -146.623947 -146.623947
seq 18IWNYVLTTTGLMFVFFSFPTDKVEKDARIIARILGISESLIVIVWNGYVAYQNRKMADFGITEGAFRWIYIVVDGG  0.210526317
18     4    -146.62   -158.59  0.87  0.35   -220.99    15.24
19     4    -142.65   -158.59  0.90  0.35   -224.98    22.30
20     4    -147.16   -158.59  1.03  0.35   -223.65    16.15
21     4    -141.90   -158.59  1.06  0.35   -220.79    19.23
22     4    -136.28   -158.59  0.91  0.35   -220.84    21.60
23     4    -136.13   -158.59  0.97  0.35   -219.12    18.58
designing with this many rotamers  9854
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -145.565536 -145.565536
seq 24SWMYVMTLNGKVYVYYSTSDDKVERIKRIIERILGISSSLIFIFWNGMELQENNKEADYGITQGAFMYMIILKVGG  0.236842111
24     4    -145.57   -158.59  0.95  0.35   -224.70    15.89
25     4    -150.40   -158.59  0.91  0.35   -229.96    18.76
unknown                        trials: 125 accepts: 125 %: 100
shearmin                       trials: 500 accepts: 212 %: 42.4
smallmin                       trials: 500 accepts: 125 %: 25
wobblemin                      trials: 500 accepts: 37 %: 7.4
crankmin                       trials: 500 accepts: 23 %: 4.6
-----------------------------------------------------
-----------------------------------------------------
dfpmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     4    -158.59   -158.59  0.24  0.35   -238.50    17.52
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     4    -159.01   -159.01  0.23  0.34   -237.63    16.66
 1     7    -158.85   -162.51  0.28  0.32   -237.10    16.20
 2     7    -158.21   -162.51  0.38  0.32   -235.50    15.41
 3     7    -154.67   -162.51  0.41  0.32   -230.35    15.13
 4     7    -150.84   -162.51  0.39  0.32   -238.31    19.39
 5     7    -147.63   -162.51  0.49  0.32   -237.48    21.67
designing with this many rotamers  9555
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -156.316071 -156.316071
seq 6EFVYVVTLNGLTFTFRSSKTDFVKKIKEKIKKQAGIDKDKIALYYNGVKLYAWRKAEDFNITKGAVMLEVVIVPGG  0.315789461
 6     7    -156.32   -162.51  0.52  0.32   -232.01    15.88
 7     7    -157.83   -162.51  0.50  0.32   -233.28    15.41
 8     7    -155.19   -162.51  0.58  0.32   -234.98    17.95
 9     7    -157.48   -162.51  0.52  0.32   -233.36    16.67
10     7    -154.26   -162.51  0.54  0.32   -232.88    19.89
11     7    -156.14   -162.51  0.53  0.32   -234.67    18.25
designing with this many rotamers  9479
monte carlo id for design run 0
rotamers_exist flag 1
score vs  best_score -151.23082 -152.567688
seq 12EFVYVVTLNGLTFTFRSSKTDFVKKIKEKIKKQAGIDKDKIALYYNGVKLYAWRKAEDFNITKGAVMLEVVIVPGG  0.315789461
12     7    -152.57   -162.51  0.57  0.32   -237.59    20.80
13     7    -154.18   -162.51  0.56  0.32   -236.49    19.14
14     7    -155.68   -162.51  0.54  0.32   -234.74    18.62
15     7    -152.73   -162.51  0.57  0.32   -231.96    18.80
16     7    -150.25   -162.51  0.51  0.32   -232.21    22.77
17     7    -151.49   -162.51  0.47  0.32   -232.91    19.66
designing with this many rotamers  9547
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -159.86853 -159.86853
seq 18KYIYTVTSDGLRYRLYSSEDDFVARLKELIKRTAGIDASKIVLVYNGLVLLSNKKLSDYNVTKGAVIYVLVVVPGG  0.263157904
18     7    -159.87   -162.51  0.43  0.32   -230.94    20.10
19     7    -160.04   -162.51  0.40  0.32   -230.16    18.64
20     7    -156.29   -162.51  0.53  0.32   -228.08    20.93
21     7    -156.34   -162.51  0.59  0.32   -229.46    20.80
22     7    -155.05   -162.51  0.60  0.32   -226.78    20.43
23     7    -153.61   -162.51  0.64  0.32   -222.76    18.80
designing with this many rotamers  9403
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -159.679901 -159.679901
seq 24EFIFIVQSNGQSFRLYSSSSDPVKKLKEIIKKVAGVDANKILLWYNGLLLYETRYLSDFNVTKGAFIYVLIYVDGG  0.263157904
24     7    -159.68   -162.51  0.61  0.32   -232.92    19.96
25     7    -157.90   -162.51  0.60  0.32   -230.98    19.28
unknown                        trials: 104 accepts: 98 %: 94.2308
smallmin                       trials: 500 accepts: 323 %: 64.6
shearmin                       trials: 500 accepts: 227 %: 45.4
wobblemin                      trials: 500 accepts: 71 %: 14.2
crankmin                       trials: 500 accepts: 10 %: 2
NEXT STRUCTURE: ./da1ubq_faidl_0002.pdb

Start of design structure

Looking for refinement input file: ./1ubq_.refine
unable to find refine input file
using default values
initializing full atom coordinates
-----------------------------------------------------
-----------------------------------------------------
linmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-2     0      55.16     55.16  0.00  0.35   -251.59    36.40
seq -2MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  1
designing with this many rotamers  9665
seq -1EKIFAKTTNGNVYTFVSYKSDTGQRVKNKIKDQAGIDANKIIIVFNNLVVVDNHTLSYYNITKGATILVFIYLFGG  0.381578952
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-1     0    -148.51   -148.51  0.00  0.35   -232.33    22.26
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     0    -153.57   -153.57  0.11  0.31   -229.51    19.88
 1     1    -145.26   -155.14  0.29  0.31   -221.64    21.80
 2     1    -145.05   -155.14  0.43  0.31   -217.41    19.09
 3     1    -140.03   -155.14  0.44  0.31   -217.84    23.58
 4     1    -133.20   -155.14  0.49  0.31   -208.20    19.36
 5     1    -143.06   -155.14  0.42  0.31   -217.53    20.34
designing with this many rotamers  9601
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -154.452774 -154.452774
seq 6KWHYAKTTNGLIFRLYSLESDYTEKVKRLIKKYAGIEASKILLVYNGMLMYEWRTESDYNITKGAVLLIYLYYFGG  0.342105269
 6     1    -154.45   -155.14  0.46  0.31   -234.93    14.29
 7     1    -151.45   -155.14  0.56  0.31   -237.50    19.56
 8     1    -151.30   -155.14  0.57  0.31   -238.16    18.47
 9     1    -151.37   -155.14  0.57  0.31   -237.89    18.86
10     1    -150.16   -155.14  0.48  0.31   -232.94    16.16
11     1    -147.69   -155.14  0.57  0.31   -237.33    21.74
designing with this many rotamers  9573
monte carlo id for design run 3
rotamers_exist flag 1
score vs  best_score -156.570511 -156.570511
seq 12LWHFVITLNGLTFLFLSYSSDSAEDVRRLIKKLAGVEADKILIFTNGMLMQRNKTESDFNLTKGAFLLMVLFLFGG  0.328947365
12     2    -156.57   -156.57  0.56  0.54   -227.66    17.14
13     2    -149.23   -156.57  0.62  0.54   -226.88    20.29
14     2    -149.19   -156.57  0.58  0.54   -227.33    18.73
15     2    -144.65   -156.57  0.70  0.54   -222.28    16.88
16     2    -142.07   -156.57  0.79  0.54   -223.50    21.49
17     2    -137.57   -156.57  0.93  0.54   -225.47    25.01
designing with this many rotamers  9554
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -149.590927 -149.590927
seq 18LWLYTITLLGYMLLLLVEPTHPAKFIKEQLKKLLGIDVKKILLVVNGLVMYETRTAADFNLTKGAFILIYLYFFGG  0.263157904
18     2    -149.59   -156.57  0.96  0.54   -221.82    18.34
19     2    -150.34   -156.57  0.80  0.54   -222.30    18.73
20     2    -148.15   -156.57  0.83  0.54   -221.83    19.25
21     2    -146.61   -156.57  0.75  0.54   -222.72    21.04
22     2    -144.09   -156.57  0.88  0.54   -219.97    20.50
23     2    -147.06   -156.57  0.83  0.54   -221.37    22.01
designing with this many rotamers  9669
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -150.632797 -150.632797
seq 24TFHYFIDLNGNTFLQLSSSSRPAEFNKRELKKEMGVDVKKIREFVNGLEMFKTRTESDFNLTKGAFVFLFIYLFGG  0.25
24     2    -150.63   -156.57  0.79  0.54   -235.99    14.81
25     2    -146.99   -156.57  0.75  0.54   -235.03    18.10
unknown                        trials: 125 accepts: 119 %: 95.2
shearmin                       trials: 500 accepts: 214 %: 42.8
smallmin                       trials: 500 accepts: 122 %: 24.4
wobblemin                      trials: 500 accepts: 43 %: 8.6
crankmin                       trials: 500 accepts: 16 %: 3.2
-----------------------------------------------------
-----------------------------------------------------
dfpmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     2    -156.57   -156.57  0.56  0.54   -227.66    17.14
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     2    -159.65   -159.65  0.55  0.54   -231.35    18.01
 1     8    -159.38   -162.52  0.48  0.52   -231.18    17.87
 2     8    -159.91   -162.52  0.48  0.52   -229.26    17.00
 3     8    -154.00   -162.52  0.52  0.52   -228.53    20.28
 4     8    -153.50   -162.52  0.48  0.52   -227.57    20.75
 5     8    -156.86   -162.52  0.46  0.52   -230.61    20.76
designing with this many rotamers  9548
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -159.989883 -159.989883
seq 6KYYWVITQNGLTLLLLAYESDYTEKLKRLIKKFAGVEARKILIWYNGLLTLKNLTLSDFNATKGAFFEMRLYLFGG  0.289473683
 6     8    -159.99   -162.52  0.48  0.52   -233.28    17.46
 7     8    -159.17   -162.52  0.54  0.52   -230.91    14.64
 8     8    -158.20   -162.52  0.60  0.52   -232.21    17.10
 9     8    -155.89   -162.52  0.58  0.52   -230.70    15.80
10     8    -153.93   -162.52  0.63  0.52   -229.77    17.62
11     8    -150.74   -162.52  0.68  0.52   -227.81    15.52
designing with this many rotamers  9565
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -158.896255 -158.896255
seq 12PWYWVITQNGKTLLLFALLSDYAERLKRLIKKYQGLDTDKLLIWYRGLLMEKTKTISDFNATQGAFFLLRLYTYGG  0.302631587
12     8    -158.90   -162.52  0.66  0.52   -232.46    16.33
13    10    -161.93   -163.52  0.64  0.66   -237.72    18.53
14    10    -160.07   -163.52  0.69  0.66   -238.60    20.88
15    10    -161.15   -163.52  0.67  0.66   -236.64    18.69
16    10    -161.76   -163.52  0.65  0.66   -236.08    18.28
17    10    -158.15   -163.52  0.67  0.66   -236.38    19.53
designing with this many rotamers  9572
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -160.816071 -160.816071
seq 18LWYYHITLNGNVVLVYAYLSDKAERVKRALKKYLGLPTDMLIIIFQGLVMEKNKKISDFNATQGAFFLIVLFFYGG  0.289473683
18    10    -160.82   -163.52  0.65  0.66   -230.11    17.20
19    10    -158.99   -163.52  0.72  0.66   -231.42    19.91
20    10    -157.02   -163.52  0.67  0.66   -230.34    20.32
21    10    -155.52   -163.52  0.73  0.66   -228.22    20.36
22    10    -156.61   -163.52  0.75  0.66   -225.92    18.08
23    10    -154.84   -163.52  0.69  0.66   -229.28    19.98
designing with this many rotamers  9414
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -158.052322 -158.052322
seq 24LWFYALTRNGQILLIYAYLSDKASRFKKALKYYLGVPENWLITVFRGLVMLDDLKISDFNATQGALFLIIFDVDGG  0.197368428
24    10    -158.05   -163.52  0.71  0.66   -228.62    17.55
25    10    -159.04   -163.52  0.80  0.66   -231.30    19.88
unknown                        trials: 104 accepts: 101 %: 97.1154
smallmin                       trials: 500 accepts: 303 %: 60.6
shearmin                       trials: 500 accepts: 202 %: 40.4
wobblemin                      trials: 500 accepts: 31 %: 6.2
crankmin                       trials: 500 accepts: 6 %: 1.2
NEXT STRUCTURE: ./da1ubq_faidl_0003.pdb

Start of design structure

Looking for refinement input file: ./1ubq_.refine
unable to find refine input file
using default values
initializing full atom coordinates
-----------------------------------------------------
-----------------------------------------------------
linmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-2     0      55.16     55.16  0.00  0.35   -251.59    36.40
seq -2MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  1
designing with this many rotamers  9665
seq -1EKVFVLSTNGQMQTQVSTKSDKIEKVKRKLKDTDGVEARKILLVFNNLKLVDNHTLSYYNITKGATMLRFLIYFGG  0.368421048
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
-1     0    -151.72   -151.72  0.00  0.35   -244.41    22.39
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     0    -155.99   -155.99  0.09  0.32   -241.31    20.30
 1     0    -143.95   -155.99  0.43  0.32   -220.58    15.72
 2     0    -131.37   -155.99  0.53  0.32   -224.93    24.23
 3     0    -129.37   -155.99  0.58  0.32   -219.45    20.06
 4     0    -129.97   -155.99  0.62  0.32   -219.44    20.50
 5     0    -133.22   -155.99  0.69  0.32   -223.24    23.57
designing with this many rotamers  9717
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -143.903656 -143.903656
seq 6LPFLIKGTNGLIYTVWSTKSDPVEKDKRDMKDLFGIEARKVFLFFNGLRELDNKKNEDYNKTAGSMMLVFIYLFGG  0.276315778
 6     0    -143.90   -155.99  0.79  0.32   -220.89    17.24
 7     0    -132.22   -155.99  0.82  0.32   -217.49    21.68
 8     0    -128.18   -155.99  0.90  0.32   -219.83    25.18
 9     0    -132.11   -155.99  0.85  0.32   -221.09    24.67
10     0    -135.28   -155.99  0.87  0.32   -218.38    21.09
11     0    -135.63   -155.99  0.88  0.32   -220.32    22.65
designing with this many rotamers  9573
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -141.043396 -141.043396
seq 12ELFYLKTLNGLVYVWKGQRNDAVKLEKLRIKQVMGIDANKIYLFFNNLRLQDDHTNAYYNITKGDMMLIVIFQYGG  0.276315778
12     0    -141.04   -155.99  1.05  0.32   -232.63    18.61
13     0    -141.83   -155.99  1.22  0.32   -230.54    17.42
14     0    -141.47   -155.99  1.02  0.32   -235.09    21.15
15     0    -136.33   -155.99  1.00  0.32   -233.76    22.76
16     0    -134.71   -155.99  0.96  0.32   -231.23    21.84
17     0    -132.95   -155.99  1.03  0.32   -228.67    20.37
designing with this many rotamers  9458
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -144.748917 -144.748917
seq 18YKFYLKTTNGLIFVWLGTYTRPAERFKRIIKQQQGIQKDQIYLVLNGLVLQDNKTNADFNITKGATMLIYVYLPGG  0.302631587
18     0    -144.75   -155.99  0.89  0.32   -230.11    23.36
19     0    -139.86   -155.99  1.17  0.32   -221.26    18.48
20     0    -139.51   -155.99  1.05  0.32   -226.33    24.20
21     0    -135.63   -155.99  1.14  0.32   -218.14    19.79
22     0    -139.06   -155.99  1.09  0.32   -222.82    22.92
23     0    -136.43   -155.99  1.07  0.32   -218.80    21.93
designing with this many rotamers  9572
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -143.711411 -143.711411
seq 24FKFYVKTLNGLVFTWLGTYSRPWERFKEIIKQQQGIDKEKITIVYRGMVALDTLTNQYFGVTKGAVTLVYSSTKGG  0.236842111
24     0    -143.71   -155.99  1.16  0.32   -214.67    17.57
25     0    -144.94   -155.99  1.11  0.32   -218.63    18.27
unknown                        trials: 125 accepts: 121 %: 96.8
shearmin                       trials: 500 accepts: 183 %: 36.6
smallmin                       trials: 500 accepts: 139 %: 27.8
wobblemin                      trials: 500 accepts: 43 %: 8.6
crankmin                       trials: 500 accepts: 15 %: 3
-----------------------------------------------------
-----------------------------------------------------
dfpmin moves...
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     0    -155.99   -155.99  0.09  0.32   -241.31    20.30
jk nlowacc   score    low_sc st_rms   low_rms    atr    rep
 0     0    -158.80   -158.80  0.13  0.30   -239.03    17.85
 1     2    -159.63   -160.16  0.24  0.31   -237.09    16.96
 2     2    -158.67   -160.16  0.36  0.31   -234.24    16.69
 3     2    -146.18   -160.16  0.42  0.31   -229.80    18.77
 4     2    -146.80   -160.16  0.54  0.31   -223.97    15.70
 5     2    -146.00   -160.16  0.54  0.31   -226.65    17.84
designing with this many rotamers  9511
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -155.056091 -155.056091
seq 6EWSYVVTTNGQVVRVKADSSKKVEDVKRMLKQQLGIEANRILLVYNGLYLLDTAKMSDYNITKGAVTYQYLLFVGG  0.289473683
 6     2    -155.06   -160.16  0.49  0.31   -219.82    14.39
 7     2    -155.22   -160.16  0.49  0.31   -220.04    14.42
 8     2    -153.67   -160.16  0.52  0.31   -221.77    14.26
 9     2    -152.64   -160.16  0.74  0.31   -217.98    13.81
10     2    -147.78   -160.16  0.78  0.31   -217.18    14.23
11     2    -145.35   -160.16  0.77  0.31   -215.60    13.10
designing with this many rotamers  9631
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -152.874039 -152.874039
seq 12EWSFIVTTNGQVIRVKSSSSDKVERLKAQLKQTTGLEANRILLVYNGLRLYDNRKMSDFNITKGAVILMFLYFIGG  0.302631587
12     2    -152.87   -160.16  0.72  0.31   -219.91    16.17
13     2    -154.52   -160.16  0.71  0.31   -217.55    13.92
14     2    -157.61   -160.16  0.60  0.31   -220.39    13.37
15     2    -155.46   -160.16  0.67  0.31   -219.44    14.94
16     2    -154.14   -160.16  0.78  0.31   -219.32    14.97
17     2    -156.88   -160.16  0.81  0.31   -219.15    11.82
designing with this many rotamers  9492
monte carlo id for design run 2
rotamers_exist flag 0
score vs  best_score -157.992462 -157.992462
seq 18KKSKFLFTEGKVLVLVSDSSKKVKEVKELIAKLQGARSDKLLFVYNGLYLYEERKESDFNITKGAVVLVYFLPIGG  0.25
18     2    -157.99   -160.16  0.61  0.31   -216.22    14.08
19     2    -155.15   -160.16  0.65  0.31   -219.42    18.05
20     2    -155.52   -160.16  0.69  0.31   -218.46    16.37
21     2    -157.20   -160.16  0.65  0.31   -220.01    16.73
22     2    -153.40   -160.16  0.65  0.31   -219.86    16.50
23     2    -149.26   -160.16  0.64  0.31   -217.77    17.63
designing with this many rotamers  9536
monte carlo id for design run 2
rotamers_exist flag 1
score vs  best_score -154.921158 -154.921158
seq 24NLAKFLSTNGKVLVLDADSDKKVEEVLKLIKRLQGLDADKILLKFNGLWLVKNRKMSDFNITKGAVILMFILEIGG  0.263157904
24     2    -154.92   -160.16  0.68  0.31   -213.54    12.39
25     5    -159.68   -162.42  0.78  0.83   -217.27    11.06
unknown                        trials: 104 accepts: 104 %: 100
smallmin                       trials: 500 accepts: 330 %: 66
shearmin                       trials: 500 accepts: 217 %: 43.4
wobblemin                      trials: 500 accepts: 72 %: 14.4
crankmin                       trials: 500 accepts: 19 %: 3.8
======================================================
DONE ::     1 starting structures built         3 (nstruct) times
This process generated      3 decoys from       3 attempts
                            0 starting pdbs were skipped
======================================================
