Branch: rosetta:commits 「revision: №20469」
Test: linux.clang.python310.PyRosetta.unit
SubTest: T400_Refinement
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: T400_Refinement

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+5.HEAD.c9abca8 c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 git@github.com:RosettaCommons/rosetta.git 2024-09-07T17:30:08 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.12 seconds. core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 core.import_pose.import_pose: File '../test/data/test_fragments.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 10 resnum BB CHI NU BRANCH 001 TRUE FALSE FALSE FALSE 002 TRUE FALSE FALSE FALSE 003 TRUE FALSE FALSE FALSE 004 TRUE FALSE FALSE FALSE 005 TRUE FALSE FALSE FALSE 006 TRUE FALSE FALSE FALSE 007 TRUE FALSE FALSE FALSE 008 TRUE FALSE FALSE FALSE 009 TRUE FALSE FALSE FALSE 010 FALSE FALSE FALSE FALSE core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../test/data/test3_fragments core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ../test/data/test9_fragments 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 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: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.19 seconds to load from binary core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 23.6488 23.6488 protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 protocols.moves.MonteCarlo: MC: 1 23.6488 23.6488 23.6488 23.6488 0 0 0 accepted score beat low protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file ope┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+5.HEAD.c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 2024-09-07T17:30:08] retrieved from: git@github.com:RosettaCommons/rosetta.git Refinement ---------------------------------------------- setting up a move map setting all backbone movement to true, and residue 10 to false outputting movemap mover: ClassicFragmentMover, 3mer Creating standard score function with patch and scoring mover: SmallMover Mover name: Small, Mover type: SmallMover, Mover current tag:NoTag Max angle for helices (H): 0 Max angle for strands (E): 5 Max angle for loops (L): 50 Temperature factor (kT): 0.5 Number of moves: 1 mover: ShearMover Mover name: Shear, Mover type: ShearMover, Mover current tag:NoTag Max angle for helices (H): 0 Max angle for strands (E): 50 Max angle for loops (L): 6 Temperature factor (kT): 0.5 Number of moves: 1 mover: MinMover mover: MonteCarlo protocols.moves.MonteCarlo: "Temperature" (kT): 1 Total Trials: 4 Lowest Score: 23.6488 Last Accepted Score: 23.6488 last_accept = 23.6488 mover: SequenceMover mover: TrialMover ned: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth core.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_env_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_cbeta_params.txt basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_rot_pair_ang_params.txt core.scoring.AtomVDW: Openning alternative vdw file: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/chemical/atom_type_sets/centroid_rot//min.txt core.scoring.ScoreFunction: ATOM_VDW set to CENTROID_ROT_MIN protocols.TrialMover: Acceptance rate: 1 protocols.moves.MonteCarlo: MC: 1 22.6785 22.6785 22.6785 22.6785 0 0 0 accepted score beat low protocols.moves.TrialCounter: ClassicFragmentM trials= 1; accepts= 1.0000; energy_drop/trial= -0.97029 protocols.moves.TrialCounter: unk trials= 4; accepts= 0.7500; energy_drop/trial= -0.31820 Finished T400_Refinement in 0:00:09.539645