core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: relax.linuxgccrelease -linmem_ig 100 -use_input_sc -nstruct 1 -relax:fast -relax:constrain_relax_to_start_coords -scorefile relax.fasc -s pSer.pdb -out:prefix relax core.init: 'RNG device' seed mode, using '/dev/urandom', seed=2476519 seed_offset=0 real_seed=2476519 core.init.random: RandomGenerator:init: Normal mode, seed=2476519 RG_type=mt19937 core.init: Resolved executable path: /home/rz/Software/rosetta_bin_linux_2017.08.59291_bundle/main/source/build/src/release/linux/3.17/64/x86/gcc/4.8/default/relax.default.linuxgccrelease core.init: Looking for database based on location of executable: /home/rz/Software/rosetta_bin_linux_2017.08.59291_bundle/main/database/ core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 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/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 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 basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp protocols.relax.FastRelax: ================== Using default script ================== protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed pSer.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB pSer.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.915307 seconds. core.import_pose.import_pose: File 'pSer.pdb' automatically determined to be of type PDB core.conformation.Conformation: Found disulfide between residues 7 137 core.conformation.Conformation: current variant for 7 CYS core.conformation.Conformation: current variant for 137 CYS core.conformation.Conformation: current variant for 7 CYD core.conformation.Conformation: current variant for 137 CYD core.conformation.Conformation: Found disulfide between residues 25 41 core.conformation.Conformation: current variant for 25 CYS core.conformation.Conformation: current variant for 41 CYS core.conformation.Conformation: current variant for 25 CYD core.conformation.Conformation: current variant for 41 CYD core.conformation.Conformation: Found disulfide between residues 109 210 core.conformation.Conformation: current variant for 109 CYS core.conformation.Conformation: current variant for 210 CYS core.conformation.Conformation: current variant for 109 CYD core.conformation.Conformation: current variant for 210 CYD core.conformation.Conformation: Found disulfide between residues 116 183 core.conformation.Conformation: current variant for 116 CYS core.conformation.Conformation: current variant for 183 CYS core.conformation.Conformation: current variant for 116 CYD core.conformation.Conformation: current variant for 183 CYD core.conformation.Conformation: Found disulfide between residues 148 162 core.conformation.Conformation: current variant for 148 CYS core.conformation.Conformation: current variant for 162 CYS core.conformation.Conformation: current variant for 148 CYD core.conformation.Conformation: current variant for 162 CYD core.conformation.Conformation: Found disulfide between residues 173 197 core.conformation.Conformation: current variant for 173 CYS core.conformation.Conformation: current variant for 197 CYS core.conformation.Conformation: current variant for 173 CYD core.conformation.Conformation: current variant for 197 CYD core.conformation.Conformation: Found disulfide between residues 226 276 core.conformation.Conformation: current variant for 226 CYS core.conformation.Conformation: current variant for 276 CYS core.conformation.Conformation: current variant for 226 CYD core.conformation.Conformation: current variant for 276 CYD core.conformation.Conformation: Found disulfide between residues 235 259 core.conformation.Conformation: current variant for 235 CYS core.conformation.Conformation: current variant for 259 CYS core.conformation.Conformation: current variant for 235 CYD core.conformation.Conformation: current variant for 259 CYD core.conformation.Conformation: Found disulfide between residues 251 272 core.conformation.Conformation: current variant for 251 CYS core.conformation.Conformation: current variant for 272 CYS core.conformation.Conformation: current variant for 251 CYD core.conformation.Conformation: current variant for 272 CYD core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/rz/Software/rosetta_bin_linux_2017.08.59291_bundle/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.199621 seconds to load from binary protocols.relax.FastRelax: CMD: repeat 286.442 0 0 0.55 Segmentation fault (core dumped)