core.init: Rosetta version from core.init: command: pepspec.linuxgccrelease @flags_bestrelaxed_append_test core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1495498123 seed_offset=0 real_seed=-1495498123 core.init.random: RandomGenerator:init: Normal mode, seed=-1495498123 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 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 Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/DonStrength.csv Warning: Unable to locate database file scoring/score_functions/hbonds/sp2_elec_params/AccStrength.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 core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction. 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 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. apps.public.pepspec: Initializing best_relaxed_prepend_test_1 with best_relaxed.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 8523 residue types core.pack.task: Packer task: initialize from command line() apps.public.pepspec: FOLD_TREE EDGE 1 163 -1 JEDGE 1 168 1 CA CB END EDGE 168 171 -1 EDGE 168 164 -1 apps.public.pepspec: core.pack.dunbrack: Dunbrack 2010 library took 0.18 seconds to load from binary core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 12892 rotamers at 163 positions. core.pack.pack_rotamers: IG: 49418620 bytes caught exception [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/util.cc line: 97 ERROR: moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()