# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0330/ # command:# Making conformation for sequence T0330 numbered 1 through 233 Created new target T0330 from T0330.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0330/ # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0330/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 215 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 862, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 864, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 866, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 868, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 870, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 872, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 874, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 876, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 215 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 206 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 214 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 215 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 2 < previous residue 233 in servers/POMYSL_TS3.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 204 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 205 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 110, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 112, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 432, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 592, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 594, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 596, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 886, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 888, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 890, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 215 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 498, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 500, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 231 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Metaserver mode NUMB_ALIGNS: 272 Adding 7774 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 235.0000 Optimizing... Probability sum: -379.7826, CN propb: -379.7826 weights: 0.3596 constraints: 604 # command:Found ConstraintSet # PrintContacts align.constraints_meta01 Number of constraints in align.constraints 604 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta01 Number of constraints in align.constraints.bonus 604 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta01 Number of constraints in rejected.constraints 7170 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta01 Number of constraints in rejected.constraints.bonus 7170 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta01 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta01 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta01 Number of constraints in all.constraints 7774 # command: