core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-21T14:46:08.581859 core.init: command: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/minimize.static.linuxgccrelease @minwithcsts_flags -overwrite basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=571696764 seed_offset=0 real_seed=571696764 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=571696764 RG_type=mt19937 core.init: Resolved executable path: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/minimize.static.linuxgccrelease core.init: Looking for database based on location of executable: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/ core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015_cst 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 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 980 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.46 seconds. 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.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed pes.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB pes.pdb core.import_pose.import_pose: File 'pes.pdb' automatically determined to be of type PDB core.io.pdb.HeaderInformation: [ ERROR ] Malformed Compound record found: ' geometry' core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 1 in file pes.pdb. Best match rsd_type: TRP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.conformation.Conformation: [ WARNING ] missing heavyatom: CO on residue TRP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue TRP:MethylatedCtermProteinFull:AcetylatedNtermProteinFull 1 core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 1 atom OY (trying to store temperature in PDBInfo) core.scoring.constraints.util: Constraint choice: cstfile core.scoring.constraints.ConstraintsIO: read constraints from cstfile core.scoring.constraints.ConstraintsIO: Read in 2 constraints 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/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.07 seconds to load from binary core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 7.45058e-09 Deriv= -130863 Finite Diff= 2.11841e+14 core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 8.90234e-09 Deriv= -1.17515e+07 Finite Diff= 1.77295e+14 core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#30 minimize: Score: 0 224721 minimize: FinalScore: 224721 protocols.jd2.JobDistributor: pes_minwithcsts_0001 reported success in 0 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-21T14:46:08.581859 core.init: command: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/score.static.linuxgccrelease -in:file:s pes_minwithcsts_0001.pdb basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1233320424 seed_offset=0 real_seed=-1233320424 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1233320424 RG_type=mt19937 core.init: Resolved executable path: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/score.static.linuxgccrelease core.init: Looking for database based on location of executable: /home/richard/reoz/1-Richard/pnnl/ncaa/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/ Rosetta Tool: score - rescores PDBs and silent files, extracts PDBs from silent files, assembles PDBs into silent files. Usage: PDB input: -in:file:s *.pdb or -in:file:l list_of_pdbs -no_optH Dont change positions of Hydrogen atoms! (default true, specify false if you want optH) Silent input: -in:file:silent silent.out silent input filesname -in:file:tags specify specific tags to be extracted, if left out all will be taken -in:file:fullatom for full atom structures -in:file:binary_silentfile for non-ideal structures (such as from looprelax) -in:file:silent_optH Call optH when reading silent files (useful for HisD/HisE determination) -score_app:linmin Run a quick linmin before scoring Native: -in:file:native native PDB (rms, maxsub and gdtm scores will be calculated) Scorefunction: -score:weights weights weight set or weights file -score:patch patch patch set -score:optH_weights Weights file for optH (default standard.wts w/ sc12 patch) -score:optH_patch Weights patch file for optH -rescore:verbose display score breakdown Output: -out:nooutput don't print PDB structures (default now) -out:output force printing of PDB structures -out:file:silent write silent-out file -out:file:scorefile name write scorefile (default default.sc) -out:prefix myprefix prefix the output structures with a string Examples: score -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb Will rescore all structures in silent.out, in full atom mode and accounting for nonideal structure if present. Additionally it will print a PDB for every structure with -out:output flag