Found rosetta database at: /usr/lib/python3.6/site-packages/pyrosetta-2018.7+release.5ea0761-py3.6-linux-x86_64.egg/pyrosetta/database; using it.... PyRosetta-4 2017 [Rosetta PyRosetta4.Release.python36.ubuntu 2018.07+release.5ea07615ea0761986ab916a646771656ceb20339ab6cd10 2018-02-16T11:56:02] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r170 2018.07+release.5ea0761 5ea0761986ab916a646771656ceb20339ab6cd10 http://www.pyrosetta.org 2018-02-16T11:56:02 core.init: command: PyRosetta -ex1 -ex2aro -database /usr/lib/python3.6/site-packages/pyrosetta-2018.7+release.5ea0761-py3.6-linux-x86_64.egg/pyrosetta/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=395893745 seed_offset=0 real_seed=395893745 core.init.random: RandomGenerator:init: Normal mode, seed=395893745 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 600 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.65283 seconds. core.import_pose.import_pose: File 'test.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 71 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 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: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop protocols.relax.FastRelax: ================== Using default script ================== ++++++++++++++++++++++++++++++ PDB file name: test.pdb Total residues:71 Sequence: ITIDALGQVCPIPVIRAKKALAELGEAGGVVTVLVDNDISRQNLQKAEGGYQSEYLEKDNGVIEVTIVAGE Fold tree: FOLD_TREE EDGE 1 71 -1 ++++++++++++++++++++++++++++++ protocols.simple_moves.GenericMonteCarloMover: No task inputted protocols.simple_moves.GenericMonteCarloMover: The number of trials for this run is: 1 protocols.simple_moves.GenericMonteCarloMover: Initialization done protocols.simple_moves.GenericMonteCarloMover: Trial number: 1 protocols.denovo_design.movers.FastDesign: #Packer_Task protocols.denovo_design.movers.FastDesign: protocols.denovo_design.movers.FastDesign: resid pack? design? allowed_aas protocols.denovo_design.movers.FastDesign: 1 TRUE FALSE ILE:NtermProteinFull protocols.denovo_design.movers.FastDesign: 2 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 3 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 4 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 5 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 6 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 7 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 8 TRUE FALSE GLN protocols.denovo_design.movers.FastDesign: 9 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 10 TRUE FALSE CYS protocols.denovo_design.movers.FastDesign: 11 TRUE FALSE PRO protocols.denovo_design.movers.FastDesign: 12 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 13 TRUE FALSE PRO protocols.denovo_design.movers.FastDesign: 14 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 15 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 16 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 17 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 18 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 19 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 20 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 21 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 22 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 23 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 24 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 25 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 26 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 27 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 28 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 29 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 30 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 31 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 32 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 33 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 34 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 35 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 36 TRUE FALSE ASP protocols.denovo_design.movers.FastDesign: 37 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 38 TRUE FALSE ASP protocols.denovo_design.movers.FastDesign: 39 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 40 TRUE FALSE SER protocols.denovo_design.movers.FastDesign: 41 TRUE FALSE ARG protocols.denovo_design.movers.FastDesign: 42 TRUE FALSE GLN protocols.denovo_design.movers.FastDesign: 43 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 44 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 45 TRUE FALSE GLN protocols.denovo_design.movers.FastDesign: 46 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 47 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 48 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 49 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 50 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 51 TRUE FALSE TYR protocols.denovo_design.movers.FastDesign: 52 TRUE FALSE GLN protocols.denovo_design.movers.FastDesign: 53 TRUE FALSE SER protocols.denovo_design.movers.FastDesign: 54 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 55 TRUE FALSE TYR protocols.denovo_design.movers.FastDesign: 56 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 57 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 58 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 59 TRUE FALSE ASP protocols.denovo_design.movers.FastDesign: 60 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 61 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 62 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 63 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 64 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 65 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 66 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 67 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 68 TRUE FALSE VAL protocols.denovo_design.movers.FastDesign: 69 TRUE FALSE ALA protocols.denovo_design.movers.FastDesign: 70 TRUE FALSE GLY protocols.denovo_design.movers.FastDesign: 71 TRUE FALSE GLU:CtermProteinFull basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /usr/lib/python3.6/site-packages/pyrosetta-2018.7+release.5ea0761-py3.6-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/usr/lib/python3.6/site-packages/pyrosetta-2018.7+release.5ea0761-py3.6-linux-x86_64.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.161463 seconds to load from binary protocols.relax.FastRelax: CMD: repeat 104.809 0 0 0.55 core.pack.pack_rotamers: built 2240 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5707632 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -141.479 0 0 0.011 core.pack.pack_rotamers: built 2138 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5134968 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -106.991 0 0 0.1375 core.pack.pack_rotamers: built 2058 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4828820 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -75.4301 0 0 0.3025 core.pack.pack_rotamers: built 2035 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4746440 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -71.5114 0 0 0.55 protocols.relax.FastRelax: MRP: 0 -71.5114 -71.5114 0 0 protocols.relax.FastRelax: CMD: accept_to_best -71.5114 0 0 0.55 protocols.relax.FastRelax: CMD: endrepeat -71.5114 0 0 0.55 core.pack.pack_rotamers: built 2240 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5697836 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -143.361 0 0 0.011 core.pack.pack_rotamers: built 2138 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5134584 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -112.469 0 0 0.1375 core.pack.pack_rotamers: built 2058 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4828820 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -81.588 0 0 0.3025 core.pack.pack_rotamers: built 2035 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4746472 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -70.9818 0 0 0.55 protocols.relax.FastRelax: MRP: 1 -70.9818 -71.5114 0 0 protocols.relax.FastRelax: CMD: accept_to_best -70.9818 0 0 0.55 protocols.relax.FastRelax: CMD: endrepeat -70.9818 0 0 0.55 core.pack.pack_rotamers: built 2239 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5693736 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -145.397 0 0 0.011 core.pack.pack_rotamers: built 2138 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5134968 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -112.273 0 0 0.1375 core.pack.pack_rotamers: built 2058 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4828844 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -81.5351 0 0 0.3025 core.pack.pack_rotamers: built 2035 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4746440 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -71.517 0 0 0.55 protocols.relax.FastRelax: MRP: 2 -71.517 -71.517 0 0 protocols.relax.FastRelax: CMD: accept_to_best -71.517 0 0 0.55 protocols.relax.FastRelax: CMD: endrepeat -71.517 0 0 0.55 core.pack.pack_rotamers: built 2240 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5697836 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -145.398 0 0 0.011 core.pack.pack_rotamers: built 2138 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5134968 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -112.476 0 0 0.1375 core.pack.pack_rotamers: built 2058 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4828820 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -81.597 0 0 0.3025 core.pack.pack_rotamers: built 2035 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4746472 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -69.8006 0 0 0.55 protocols.relax.FastRelax: MRP: 3 -69.8006 -71.517 0 0 protocols.relax.FastRelax: CMD: accept_to_best -69.8006 0 0 0.55 protocols.relax.FastRelax: CMD: endrepeat -69.8006 0 0 0.55 core.pack.pack_rotamers: built 2239 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5693736 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -142.621 0 0 0.011 core.pack.pack_rotamers: built 2138 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 5134536 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -111.9 0 0 0.1375 core.pack.pack_rotamers: built 2058 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4828820 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -80.5477 0 0 0.3025 core.pack.pack_rotamers: built 2035 rotamers at 71 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 4746464 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -69.803 0 0 0.55 protocols.relax.FastRelax: MRP: 4 -69.803 -71.517 0 0 protocols.relax.FastRelax: CMD: accept_to_best -69.803 0 0 0.55 protocols.relax.FastRelax: CMD: endrepeat -69.803 0 0 0.55 protocols::checkpoint: Deleting checkpoints of FastRelax protocols.denovo_design.movers.FastDesign: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -342.292 -342.292 fa_rep 0.550 83.597 45.978 fa_sol 1.000 206.982 206.982 fa_intra_rep 0.005 213.891 1.069 fa_intra_sol_xover4 1.000 13.151 13.151 lk_ball_wtd 1.000 -5.807 -5.807 fa_elec 1.000 -102.685 -102.685 pro_close 1.250 0.950 1.187 hbond_sr_bb 1.000 -22.396 -22.396 hbond_lr_bb 1.000 -19.969 -19.969 hbond_bb_sc 1.000 -3.162 -3.162 hbond_sc 1.000 -8.430 -8.430 dslf_fa13 1.250 0.000 0.000 omega 0.400 116.898 46.759 fa_dun 0.700 112.606 78.824 p_aa_pp 0.600 -23.945 -14.367 yhh_planarity 0.625 0.006 0.004 ref 1.000 29.182 29.182 rama_prepro 0.450 54.341 24.453 --------------------------------------------------- Total weighted score: -71.517 protocols.simple_moves.GenericMonteCarloMover: MC stopping condition met at trial 1 because maximum number of accepted moves was achieved protocols.simple_moves.GenericMonteCarloMover: Higher score sampled: trial= 0, score(current/last_accepted/best)= 0.000/-99999999.990/-99999999.990 protocols.simple_moves.GenericMonteCarloMover: mover= FastDesign Score_eval= trials= 0 NO ACCEPTS. protocols.simple_moves.GenericMonteCarloMover: Number of rejections per filter: 0 protocols.simple_moves.GenericMonteCarloMover: Finished MC. Out of 1 0 accepted and 0 rejected. ++++++++++++++++++++++++++++++ Total residues:0 Sequence: Fold tree: FOLD_TREE ++++++++++++++++++++++++++++++ protocols::checkpoint: Deleting checkpoints of FastRelax