qgem@xtalsun1:~$ setup rosetta Setting up environment for rosetta ... qgem@xtalsun1:~$ /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/source/bin/enzyme_design.linuxgccrelease -s /home/qgem/Documents/dockedDomain2.pdb -resfile /home/qgem/Documents/positions.resfile -enzdes:cst_opt -enzdes:cst_design -enzdes:design_min_cycles 3 -enzdes:cst_min -packing:ex1 -packing:ex2 -packing:use_input_sc -packing:linmem_ig 10 -out::overwrite -out:path:all /home/qgem/Documents/pdbs -out:path:score /home/qgem/Documents/pdbs -o /home/qgem/Documents/output core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/source/bin/enzyme_design.linuxgccrelease -s /home/qgem/Documents/dockedDomain2.pdb -resfile /home/qgem/Documents/positions.resfile -enzdes:cst_opt -enzdes:cst_design -enzdes:design_min_cycles 3 -enzdes:cst_min -packing:ex1 -packing:ex2 -packing:use_input_sc -packing:linmem_ig 10 -out::overwrite -out:path:all /home/qgem/Documents/pdbs -out:path:score /home/qgem/Documents/pdbs -o /home/qgem/Documents/output core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-844235202 seed_offset=0 real_seed=-844235202 core.init.random: RandomGenerator:init: Normal mode, seed=-844235202 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database 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/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/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/rama/Rama_smooth_dyn.dat_ss_6.4 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. core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 785 residue types basic.io.database: Database file opened: scoring/score_functions/envsmooth/envdata.txt basic.io.database: Database file opened: scoring/score_functions/carbon_hbond/ch_o_bond_potential.dat basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/pos_charge_repulsion basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/neg_charge_repulsion core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy: Added 6480 AtomPairFuncList lists protocols.jobdist.JobDistributors: Looking for an available job: 1 1 /home/qgem/Documents/dockedDomain2.pdb 1 apps.public.enzdes.enzyme_design: Starting dockedDomain2_0001 ... core.io.pdb.file_data: PDB reader is ignoring atom N in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom CA in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom C in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom O in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom CB in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom CG in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom CD1 in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom CD2 in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom OXT in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom H in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom H1 in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pdb.file_data: PDB reader is ignoring atom H2 in residue 1 X. Pass flag -ignore_zero_occupancy false to change this behavior core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 18 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 47 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 106 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 106 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 106 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 106 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 109 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 109 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 109 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 109 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 110 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 111 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 111 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 111 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 111 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 117 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 117 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 117 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 120 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 122 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 122 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 122 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 128 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 128 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 128 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 128 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue ILE 134 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue ILE 134 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 134 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 135 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 136 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 136 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 136 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue ILE 137 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue ILE 137 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 137 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 138 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASN 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 148 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 148 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 148 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 148 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 149 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 149 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 149 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue ILE 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue ILE 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 151 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 152 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 152 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 152 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 152 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue ILE 153 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue ILE 153 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 153 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 164 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 202 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 202 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 202 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 235 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 235 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 235 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 243 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 243 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 269 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 269 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 269 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 294 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 294 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 295 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 295 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 295 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 318 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 318 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 319 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 319 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 319 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 319 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR 320 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR 320 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 413 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 413 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 413 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 413 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 415 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 418 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 443 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 447 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 447 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 447 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 447 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 459 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 459 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 459 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 459 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 464 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 464 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 464 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 500 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 500 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ASP 506 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 506 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 506 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PHE:CtermProteinFull 509 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 18 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 47 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 106 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 109 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 110 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 111 because of missing atom number 8 atom name NE core.pack.pack_missing_sidechains: packing residue number 117 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 120 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 122 because of missing atom number 9 atom name CZ core.pack.pack_missing_sidechains: packing residue number 128 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 134 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 135 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 136 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 137 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 138 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 148 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 149 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 151 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 152 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 153 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 164 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 202 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 235 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 243 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 269 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 294 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 295 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 318 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 319 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 320 because of missing atom number 6 atom name OG1 core.pack.pack_missing_sidechains: packing residue number 413 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 415 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 418 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 443 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 447 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 459 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 464 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 500 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 506 because of missing atom number 6 atom name CG core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin core.pack.dunbrack: cannot find binary dunbrack library under name /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin core.pack.dunbrack: Reading Dunbrack Libraries core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/cys.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/ile.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/lys.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/leu.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/met.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/pro.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/arg.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/ser.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/thr.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/val.bbdep.rotamers.lib core.pack.dunbrack: In SingleResidueDunbrackLibraryOP RotamerLibrary::create_rotameric_dunlib Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asp.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asp.bbind.chi2.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/glu.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/glu.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/glu.bbind.chi3.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/phe.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/phe.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/phe.bbind.chi2.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/his.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/his.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/his.bbind.chi2.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asn.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asn.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/asn.bbind.chi2.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/gln.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/gln.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/gln.bbind.chi3.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/trp.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/trp.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/trp.bbind.chi2.Definitions.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/tyr.bbdep.rotamers.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/tyr.bbdep.densities.lib core.pack.dunbrack: Reading /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/rotamer/ExtendedOpt1-5/tyr.bbind.chi2.Definitions.lib core.pack.dunbrack: Finished reading Dunbrack Libraries core.pack.dunbrack: Dunbrack 2010 library took 44.6 seconds to load from ASCII core.pack.dunbrack: Memory usage: core.pack.dunbrack: CYS with 188112 bytes core.pack.dunbrack: ILE with 655104 bytes core.pack.dunbrack: LYS with 6819072 bytes core.pack.dunbrack: LEU with 655104 bytes core.pack.dunbrack: MET with 2242800 bytes core.pack.dunbrack: PRO with 167400 bytes core.pack.dunbrack: ARG with 7005840 bytes core.pack.dunbrack: SER with 188112 bytes core.pack.dunbrack: THR with 188112 bytes core.pack.dunbrack: VAL with 188112 bytes core.pack.dunbrack: ASP with 10268496 bytes core.pack.dunbrack: GLU with 30987160 bytes core.pack.dunbrack: PHE with 10268496 bytes core.pack.dunbrack: HIS with 11201904 bytes core.pack.dunbrack: ASN with 11201904 bytes core.pack.dunbrack: GLN with 33787384 bytes core.pack.dunbrack: TRP with 11201904 bytes core.pack.dunbrack: TYR with 10268496 bytes core.pack.dunbrack: Total memory on Dunbrack Libraries: 147483512 bytes. Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin Warning: Unable to locate database file rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin core.pack.dunbrack: Random tempname will be: /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/Rdun10_binary core.pack.dunbrack: Opening file /software/rosetta/rosetta_bin_linux_2015.12.57698_bundle/main/database/Rdun10_binary for output. core.pack.dunbrack: Unable to open temporary file in rosetta database for writing the binary version of the Dunbrack '10 library. core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.pack_rotamers: built 561 rotamers at 40 positions. core.pack.pack_rotamers: IG: 200680 bytes protocols.enzdes.EnzdesFixBBProtocol: starting apply function... protocols.enzdes.EnzdesFixBBProtocol: Done setting up the task and constraints... core.pack.task: Packer task: initialize from command line() protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: /home/qgem/Documents/positions.resfile protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: 215, 218, 257, 278, 280, 301, 309, 310, protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 214, 215, 218, 257, 278, 280, 301, 309, 310, 496, protocols.enzdes.EnzdesFixBBProtocol: starting cst_opt minimization... protocols.enzdes.EnzdesFixBBProtocol: done cst_opt minimization. core.pack.task: Packer task: initialize from command line() protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: /home/qgem/Documents/positions.resfile protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: 215, 218, 257, 278, 280, 301, 309, 310, protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 214, 215, 218, 257, 278, 280, 301, 309, 310, 496, protocols.enzdes.EnzdesFixBBProtocol: starting cst_design, 3 cycles of design/minimization ... core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.pack_rotamers: built 8463 rotamers at 10 positions. core.pack.pack_rotamers: IG: 923241 bytes core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.pack_rotamers: built 8466 rotamers at 10 positions. core.pack.pack_rotamers: IG: 923541 bytes core.pack.task: Packer task: initialize from command line() core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.pack_rotamers: built 8465 rotamers at 10 positions. core.pack.pack_rotamers: IG: 923441 bytes core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: /home/qgem/Documents/positions.resfile protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 214, 215, 218, 257, 278, 280, 301, 309, 310, 496, protocols.enzdes.AddorRemoveCsts: Warning: apply function of enzdes constraints mover called even though no cstfile has been specified on the commandline, in the tag, or programmatically. This function will have no effect. protocols.enzdes.AddorRemoveCsts: Warning: apply function of enzdes constraints mover called even though no cstfile has been specified on the commandline, in the tag, or programmatically. This function will have no effect. protocols.enzdes.AddorRemoveCsts: Warning: apply function of enzdes constraints mover called even though no cstfile has been specified on the commandline, in the tag, or programmatically. This function will have no effect. core.pack.task: Packer task: initialize from command line() protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: /home/qgem/Documents/positions.resfile protocols.enzdes.EnzdesTaskOperations: Final Design Shell Residues: protocols.enzdes.EnzdesTaskOperations: Final Repack Shell Residues: 214, 215, 218, 257, 278, 280, 301, 309, 310, 496, protocols.enzdes.EnzdesFixBBProtocol: Starting after design unconstrained repack/minimization... core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.pack_rotamers: built 592 rotamers at 10 positions. core.pack.pack_rotamers: IG: 114741 bytes protocols.enzdes.AddorRemoveCsts: Warning: apply function of enzdes constraints mover called even though no cstfile has been specified on the commandline, in the tag, or programmatically. This function will have no effect. protocols.enzdes.EnzdesFixBBProtocol: Finished after design unconstrained repack/minimization... basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/average_hASA_by_res_and_neighbor.txt basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/surface_score.txt basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/hpatch_score.txt apps.public.enzdes.enzyme_design: Finished dockedDomain2_0001 in 155 seconds. apps.public.enzdes.enzyme_design: Finished all 1 structures in 159 seconds.