core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.mac.release-260 r260 2020.28+release.8ecab77aa50 8ecab77aa50ac1301efe53641e07e09ac91fee3b https://www.rosettacommons.org 2020-07-19T19:33:40.565968 core.init: command: /Users/yarovoylab/local/rosetta_bin_mac_2020.28.61328_bundle/main/source/bin/rosetta_scripts.static.macosclangrelease -database /Users/yarovoylab/local/rosetta_bin_mac_2020.28.61328_bundle/main/database -score:weights ref2015.wts -parser:protocol ./RMSD_helices.xml -in:file:fullatom -in:file:s ./c.0.0.pdb -in:file:native ./6n4r_rmsd_template.pdb -out:pdb -out:file:scorefile rmsd_SCN2a_MP.sc -packing:pack_missing_sidechains 1 basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-170834563 seed_offset=0 real_seed=-170834563 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-170834563 RG_type=mt19937 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed ./c.0.0.pdb nstruct index 1 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 981 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.838509 seconds. core.import_pose.import_pose: File './6n4r_rmsd_template.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO:CtermProteinFull 105 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB ./c.0.0.pdb core.import_pose.import_pose: File './c.0.0.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MEM' from the PDB components dictionary for residue type 'pdb_MEM' protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=./RMSD_helices.xml protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: protocols.rosetta_scripts.RosettaScriptsParser: Loading native resource as native_pose to the datamap core.import_pose.import_pose: File './6n4r_rmsd_template.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO:CtermProteinFull 105 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015.wts 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 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/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt 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 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.jd2.parser.ScoreFunctionLoader: defined score function "ref2015" with weights "ref2015" core.pose.ref_pose: Loading PDB: 6n4r_rmsd_template protocols.protein_interface_design.filters.RmsdFilter: RMSD filter with superimpose=0 and threshold=99 protocols.protein_interface_design.filters.RmsdFilter: superimpose_on_all set to true. Any spans defined will be used only to measure RMSd but the pose will be supreimposed on the reference pose through all residues selected residues protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "RMSD" of type Rmsd protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "RMSD" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy ./c.0.0.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER RMSD======================= protocols.protein_interface_design.filters.RmsdFilter: template segments to align and calculate RMSD on: [] query segments to align and calculate RMSD on: [] protocols.protein_interface_design.filters.RmsdFilter: Found 0 residues to calculate RMSD over protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/protocols/protein_interface_design/filters/RmsdFilter.cc:217 [ ERROR ] UtilityExitException ERROR: Assertion `template_segm.size() > 10` failed. MSG:there must be more that 10 residues to calculate RMSD over protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job c.0.0_0001 protocols.jd2.JobDistributor: [ WARNING ] c.0.0_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 8 seconds