core.init: Mini-Rosetta version 53486 from https://svn.rosettacommons.org/source/trunk/rosetta/rosetta_source core.init: command: /home/rosie/rosie/rosie.back/data/antibody/bin/antibody_model_CDR_H3.static.linuxgccrelease -seed_offset 60 -database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database -s model.pdb -constraints:cst_file ../cter_constraint -scorefile score.sf -multiple_processes_writing_to_one_directory -ex1 -ex2 -antibody::remodel perturb_kic -antibody::snugfit true -antibody::refine refine_kic -antibody::cter_insert false -antibody::flank_residue_min true -antibody::h3_filter true -antibody:constrain_cter -antibody::h3_filter_tolerance 3 -nstruct 100 core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-545733395 seed_offset=60 real_seed=-545733335 core.init.random: RandomGenerator:init: Normal mode, seed=-545733335 RG_type=mt19937 protocols.antibody2.AntibodyModelerProtocol: Setting Up defaults.......... protocols.antibody2.AntibodyModelerProtocol: Start Reading and Setting Options ... protocols.antibody2.AntibodyModelerProtocol: Finish Reading and Setting Options !!! 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/hbonds/standard_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv 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 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 opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.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 basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp 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 opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 protocols.antibody2: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2: /// protocols.antibody2: /// Rosetta 3 Antibody Modeler /// protocols.antibody2: /// /// protocols.antibody2: /// camelid : 0 protocols.antibody2: /// protocols.antibody2: /// ****** model_h3 : 1 protocols.antibody2: /// h3_perturb_type = 'perturb_kic' protocols.antibody2: /// cter_insert = 0 protocols.antibody2: /// h3_filter = 1 protocols.antibody2: /// protocols.antibody2: /// ****** snugfit : 1 protocols.antibody2: /// LH_repulsive_ramp = 1 protocols.antibody2: /// protocols.antibody2: /// ****** refine_h3 : 1 protocols.antibody2: /// h3_refine_type = 'refine_kic' protocols.antibody2: /// h3_filter = 1 protocols.antibody2: /// h3_filter_tolerance = 3 protocols.antibody2: /// protocols.antibody2: //////////////////////////////////////////////////////////////////////////////// protocols.antibody2: protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 1 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 2 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 3 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 4 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 5 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 6 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 7 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 8 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 9 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 10 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 11 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 12 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 13 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 14 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 15 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 16 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 17 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 18 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protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 49 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 50 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 51 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 52 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 53 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 54 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 55 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 56 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 57 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 58 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 59 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 60 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 61 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 62 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 63 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protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 94 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 95 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 96 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 97 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 98 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 99 protocols.jd2.PDBJobInputter: pushing model.pdb nstruct index 100 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB model.pdb Warning: Unable to locate database file chemical/element_sets/fa_standard/element_properties.txt