# 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/T0372/
# command:# Making conformation for sequence T0372 numbered 1 through 305
Created new target T0372 from T0372.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0372/
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0372/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0372/decoys/
# ReadConformPDB reading from PDB file T0372.chimera.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 302
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file ../dimer/decoys/T0372.model1_renum.pdb.gz looking for chain 'A' model 1
# Found a chain break before 267
# copying to AlignedFragments data structure
# naming current conformation dimer//model1_renum
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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
# Found a chain break before 259
# 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 277
# 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 303
# 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 300
# 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 301
# 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 303
# 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 301
# 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 279
# 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 302
# 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 303
# 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 213
# 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 298
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 299
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# Found a chain break before 299
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# Found a chain break before 300
# 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 T0372 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
# Found a chain break before 300
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 300
# 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 T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 294
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# Found a chain break before 299
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 300
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# Found a chain break before 300
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 252
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1
# Found a chain break before 274
# 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 226
# 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 266
# 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 259
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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
# WARNING: incomplete conformation T0372 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 T0372 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
# WARNING: incomplete conformation T0372 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 T0372 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
# WARNING: incomplete conformation T0372 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
# WARNING: incomplete conformation T0372 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 T0372 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
Skipped atom 482, because occupancy 1 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 484, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 574, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 576, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 938, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 940, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 942, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 944, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
# WARNING: incomplete conformation T0372 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 T0372 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 292
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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
# Found a chain break before 275
# 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 283
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 209
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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 T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 303
# 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 300
# 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 300
# 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 300
# 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 304
# 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 283
# 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 286
# 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 270
# 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 270
# 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 255
# 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 231
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 298
# 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 T0372 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 T0372 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
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 256
# 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 256
# 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 239
# 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 267
# 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 158
# 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 35
# 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 266
# 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 288
# 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 226
# 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 158
# 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 294
# 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 292
# 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 296
# 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 304
# 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 303
# 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 303
# 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 296
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS4
# ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1
# Found a chain break before 304
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS5
# ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1
# Found a chain break before 243
# 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
# Found a chain break before 289
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS1
# ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1
# Found a chain break before 287
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS2
# ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1
# Found a chain break before 300
# copying to AlignedFragments data structure
# naming current conformation POMYSL_TS3
# ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1
WARNING: atom 1 has residue number 5  < previous residue 291  in servers/POMYSL_TS4.pdb.gz
# WARNING: incomplete conformation T0372 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: atom 1 has residue number 98  < previous residue 305  in servers/POMYSL_TS5.pdb.gz
# WARNING: incomplete conformation T0372 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
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# Found a chain break before 268
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# Found a chain break before 298
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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
# Found a chain break before 284
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# Found a chain break before 299
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS5
# ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 can't currently be optimized by undertaker
# naming current conformation Phyre-2_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1
# Found a chain break before 288
# 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
# Found a chain break before 302
# 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
# Found a chain break before 301
# 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
# Found a chain break before 302
# 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 284
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# Found a chain break before 298
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# 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 152
# 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 294
# 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
# Found a chain break before 289
# 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
# Found a chain break before 213
# 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 258
# 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 232
# 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 301
# 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 301
# 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 298
# 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 294
# 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 241
# 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 213
# 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 213
# 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 250
# 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 192
# 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 288
# 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 260
# 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 287
# 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 112
# 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 283
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)M1.CA and (T0372)M1.CB only 0.000 apart, marking (T0372)M1.CB as missing
WARNING: atoms too close: (T0372)F4.CA and (T0372)F4.CB only 0.000 apart, marking (T0372)F4.CB as missing
WARNING: atoms too close: (T0372)I7.CA and (T0372)I7.CB only 0.000 apart, marking (T0372)I7.CB as missing
WARNING: atoms too close: (T0372)T16.CA and (T0372)T16.CB only 0.000 apart, marking (T0372)T16.CB as missing
WARNING: atoms too close: (T0372)M20.CA and (T0372)M20.CB only 0.000 apart, marking (T0372)M20.CB as missing
WARNING: atoms too close: (T0372)C35.CA and (T0372)C35.CB only 0.000 apart, marking (T0372)C35.CB as missing
WARNING: atoms too close: (T0372)Y41.CA and (T0372)Y41.CB only 0.000 apart, marking (T0372)Y41.CB as missing
WARNING: atoms too close: (T0372)I48.CA and (T0372)I48.CB only 0.000 apart, marking (T0372)I48.CB as missing
WARNING: atoms too close: (T0372)D49.CA and (T0372)D49.CB only 0.000 apart, marking (T0372)D49.CB as missing
WARNING: atoms too close: (T0372)F56.CA and (T0372)F56.CB only 0.000 apart, marking (T0372)F56.CB as missing
WARNING: atoms too close: (T0372)W57.CA and (T0372)W57.CB only 0.000 apart, marking (T0372)W57.CB as missing
WARNING: atoms too close: (T0372)N90.CA and (T0372)N90.CB only 0.000 apart, marking (T0372)N90.CB as missing
WARNING: atoms too close: (T0372)F91.CA and (T0372)F91.CB only 0.000 apart, marking (T0372)F91.CB as missing
WARNING: atoms too close: (T0372)C92.CA and (T0372)C92.CB only 0.000 apart, marking (T0372)C92.CB as missing
WARNING: atoms too close: (T0372)M93.CA and (T0372)M93.CB only 0.000 apart, marking (T0372)M93.CB as missing
WARNING: atoms too close: (T0372)C97.CA and (T0372)C97.CB only 0.000 apart, marking (T0372)C97.CB as missing
WARNING: atoms too close: (T0372)E105.CA and (T0372)E105.CB only 0.000 apart, marking (T0372)E105.CB as missing
WARNING: atoms too close: (T0372)P109.CA and (T0372)P109.CB only 0.000 apart, marking (T0372)P109.CB as missing
WARNING: atoms too close: (T0372)Y120.CA and (T0372)Y120.CB only 0.000 apart, marking (T0372)Y120.CB as missing
WARNING: atoms too close: (T0372)L130.CA and (T0372)L130.CB only 0.000 apart, marking (T0372)L130.CB as missing
WARNING: atoms too close: (T0372)L133.CA and (T0372)L133.CB only 0.000 apart, marking (T0372)L133.CB as missing
WARNING: atoms too close: (T0372)H144.CA and (T0372)H144.CB only 0.000 apart, marking (T0372)H144.CB as missing
WARNING: atoms too close: (T0372)R147.CA and (T0372)R147.CB only 0.000 apart, marking (T0372)R147.CB as missing
WARNING: atoms too close: (T0372)Y152.CA and (T0372)Y152.CB only 0.000 apart, marking (T0372)Y152.CB as missing
WARNING: atoms too close: (T0372)Y157.CA and (T0372)Y157.CB only 0.000 apart, marking (T0372)Y157.CB as missing
WARNING: atoms too close: (T0372)D163.CA and (T0372)D163.CB only 0.000 apart, marking (T0372)D163.CB as missing
WARNING: atoms too close: (T0372)C168.CA and (T0372)C168.CB only 0.000 apart, marking (T0372)C168.CB as missing
WARNING: atoms too close: (T0372)L171.CA and (T0372)L171.CB only 0.000 apart, marking (T0372)L171.CB as missing
WARNING: atoms too close: (T0372)A173.CA and (T0372)A173.CB only 0.000 apart, marking (T0372)A173.CB as missing
WARNING: atoms too close: (T0372)V178.CA and (T0372)V178.CB only 0.000 apart, marking (T0372)V178.CB as missing
WARNING: atoms too close: (T0372)N179.CA and (T0372)N179.CB only 0.000 apart, marking (T0372)N179.CB as missing
WARNING: atoms too close: (T0372)R192.CA and (T0372)R192.CB only 0.000 apart, marking (T0372)R192.CB as missing
WARNING: atoms too close: (T0372)I195.CA and (T0372)I195.CB only 0.000 apart, marking (T0372)I195.CB as missing
WARNING: atoms too close: (T0372)L198.CA and (T0372)L198.CB only 0.000 apart, marking (T0372)L198.CB as missing
WARNING: atoms too close: (T0372)N200.CA and (T0372)N200.CB only 0.000 apart, marking (T0372)N200.CB as missing
WARNING: atoms too close: (T0372)F201.CA and (T0372)F201.CB only 0.000 apart, marking (T0372)F201.CB as missing
WARNING: atoms too close: (T0372)A203.CA and (T0372)A203.CB only 0.000 apart, marking (T0372)A203.CB as missing
WARNING: atoms too close: (T0372)L206.CA and (T0372)L206.CB only 0.000 apart, marking (T0372)L206.CB as missing
WARNING: atoms too close: (T0372)L211.CA and (T0372)L211.CB only 0.000 apart, marking (T0372)L211.CB as missing
WARNING: atoms too close: (T0372)I217.CA and (T0372)I217.CB only 0.000 apart, marking (T0372)I217.CB as missing
WARNING: atoms too close: (T0372)F220.CA and (T0372)F220.CB only 0.000 apart, marking (T0372)F220.CB as missing
WARNING: atoms too close: (T0372)V233.CA and (T0372)V233.CB only 0.000 apart, marking (T0372)V233.CB as missing
WARNING: atoms too close: (T0372)T240.CA and (T0372)T240.CB only 0.000 apart, marking (T0372)T240.CB as missing
WARNING: atoms too close: (T0372)Y246.CA and (T0372)Y246.CB only 0.000 apart, marking (T0372)Y246.CB as missing
WARNING: atoms too close: (T0372)A247.CA and (T0372)A247.CB only 0.000 apart, marking (T0372)A247.CB as missing
WARNING: atoms too close: (T0372)Y251.CA and (T0372)Y251.CB only 0.000 apart, marking (T0372)Y251.CB as missing
WARNING: atoms too close: (T0372)N255.CA and (T0372)N255.CB only 0.000 apart, marking (T0372)N255.CB as missing
WARNING: atoms too close: (T0372)P258.CA and (T0372)P258.CB only 0.000 apart, marking (T0372)P258.CB as missing
WARNING: atoms too close: (T0372)R266.CA and (T0372)R266.CB only 0.000 apart, marking (T0372)R266.CB as missing
WARNING: atoms too close: (T0372)I272.CA and (T0372)I272.CB only 0.000 apart, marking (T0372)I272.CB as missing
WARNING: atoms too close: (T0372)L280.CA and (T0372)L280.CB only 0.000 apart, marking (T0372)L280.CB as missing
WARNING: atoms too close: (T0372)T286.CA and (T0372)T286.CB only 0.000 apart, marking (T0372)T286.CB as missing
WARNING: atoms too close: (T0372)Y291.CA and (T0372)Y291.CB only 0.000 apart, marking (T0372)Y291.CB as missing
WARNING: atoms too close: (T0372)K296.CA and (T0372)K296.CB only 0.000 apart, marking (T0372)K296.CB as missing
WARNING: atoms too close: (T0372)M300.CA and (T0372)M300.CB only 0.000 apart, marking (T0372)M300.CB as missing
WARNING: atoms too close: (T0372)V303.CA and (T0372)V303.CB only 0.000 apart, marking (T0372)V303.CB as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)I2.CA and (T0372)I2.CB only 0.000 apart, marking (T0372)I2.CB as missing
WARNING: atoms too close: (T0372)I7.CA and (T0372)I7.CB only 0.000 apart, marking (T0372)I7.CB as missing
WARNING: atoms too close: (T0372)T16.CA and (T0372)T16.CB only 0.000 apart, marking (T0372)T16.CB as missing
WARNING: atoms too close: (T0372)S22.CA and (T0372)S22.CB only 0.000 apart, marking (T0372)S22.CB as missing
WARNING: atoms too close: (T0372)N26.CA and (T0372)N26.CB only 0.000 apart, marking (T0372)N26.CB as missing
WARNING: atoms too close: (T0372)C35.CA and (T0372)C35.CB only 0.000 apart, marking (T0372)C35.CB as missing
WARNING: atoms too close: (T0372)Y41.CA and (T0372)Y41.CB only 0.000 apart, marking (T0372)Y41.CB as missing
WARNING: atoms too close: (T0372)Q44.CA and (T0372)Q44.CB only 0.000 apart, marking (T0372)Q44.CB as missing
WARNING: atoms too close: (T0372)Y64.CA and (T0372)Y64.CB only 0.000 apart, marking (T0372)Y64.CB as missing
WARNING: atoms too close: (T0372)V76.CA and (T0372)V76.CB only 0.000 apart, marking (T0372)V76.CB as missing
WARNING: atoms too close: (T0372)R78.CA and (T0372)R78.CB only 0.000 apart, marking (T0372)R78.CB as missing
WARNING: atoms too close: (T0372)L104.CA and (T0372)L104.CB only 0.000 apart, marking (T0372)L104.CB as missing
WARNING: atoms too close: (T0372)E105.CA and (T0372)E105.CB only 0.000 apart, marking (T0372)E105.CB as missing
WARNING: atoms too close: (T0372)E110.CA and (T0372)E110.CB only 0.000 apart, marking (T0372)E110.CB as missing
WARNING: atoms too close: (T0372)Y120.CA and (T0372)Y120.CB only 0.000 apart, marking (T0372)Y120.CB as missing
WARNING: atoms too close: (T0372)T132.CA and (T0372)T132.CB only 0.000 apart, marking (T0372)T132.CB as missing
WARNING: atoms too close: (T0372)L133.CA and (T0372)L133.CB only 0.000 apart, marking (T0372)L133.CB as missing
WARNING: atoms too close: (T0372)N146.CA and (T0372)N146.CB only 0.000 apart, marking (T0372)N146.CB as missing
WARNING: atoms too close: (T0372)Y157.CA and (T0372)Y157.CB only 0.000 apart, marking (T0372)Y157.CB as missing
WARNING: atoms too close: (T0372)R164.CA and (T0372)R164.CB only 0.000 apart, marking (T0372)R164.CB as missing
WARNING: atoms too close: (T0372)L171.CA and (T0372)L171.CB only 0.000 apart, marking (T0372)L171.CB as missing
WARNING: atoms too close: (T0372)Q183.CA and (T0372)Q183.CB only 0.000 apart, marking (T0372)Q183.CB as missing
WARNING: atoms too close: (T0372)Q184.CA and (T0372)Q184.CB only 0.000 apart, marking (T0372)Q184.CB as missing
WARNING: atoms too close: (T0372)L194.CA and (T0372)L194.CB only 0.000 apart, marking (T0372)L194.CB as missing
WARNING: atoms too close: (T0372)I195.CA and (T0372)I195.CB only 0.000 apart, marking (T0372)I195.CB as missing
WARNING: atoms too close: (T0372)A203.CA and (T0372)A203.CB only 0.000 apart, marking (T0372)A203.CB as missing
WARNING: atoms too close: (T0372)L204.CA and (T0372)L204.CB only 0.000 apart, marking (T0372)L204.CB as missing
WARNING: atoms too close: (T0372)F220.CA and (T0372)F220.CB only 0.000 apart, marking (T0372)F220.CB as missing
WARNING: atoms too close: (T0372)H228.CA and (T0372)H228.CB only 0.000 apart, marking (T0372)H228.CB as missing
WARNING: atoms too close: (T0372)T240.CA and (T0372)T240.CB only 0.000 apart, marking (T0372)T240.CB as missing
WARNING: atoms too close: (T0372)Y246.CA and (T0372)Y246.CB only 0.000 apart, marking (T0372)Y246.CB as missing
WARNING: atoms too close: (T0372)A247.CA and (T0372)A247.CB only 0.000 apart, marking (T0372)A247.CB as missing
WARNING: atoms too close: (T0372)F253.CA and (T0372)F253.CB only 0.000 apart, marking (T0372)F253.CB as missing
WARNING: atoms too close: (T0372)A254.CA and (T0372)A254.CB only 0.000 apart, marking (T0372)A254.CB as missing
WARNING: atoms too close: (T0372)E259.CA and (T0372)E259.CB only 0.000 apart, marking (T0372)E259.CB as missing
WARNING: atoms too close: (T0372)I272.CA and (T0372)I272.CB only 0.000 apart, marking (T0372)I272.CB as missing
WARNING: atoms too close: (T0372)L275.CA and (T0372)L275.CB only 0.000 apart, marking (T0372)L275.CB as missing
WARNING: atoms too close: (T0372)S281.CA and (T0372)S281.CB only 0.000 apart, marking (T0372)S281.CB as missing
WARNING: atoms too close: (T0372)Q283.CA and (T0372)Q283.CB only 0.000 apart, marking (T0372)Q283.CB as missing
WARNING: atoms too close: (T0372)T286.CA and (T0372)T286.CB only 0.000 apart, marking (T0372)T286.CB as missing
WARNING: atoms too close: (T0372)H298.CA and (T0372)H298.CB only 0.000 apart, marking (T0372)H298.CB as missing
WARNING: atoms too close: (T0372)D301.CA and (T0372)D301.CB only 0.000 apart, marking (T0372)D301.CB as missing
WARNING: atoms too close: (T0372)V303.CA and (T0372)V303.CB only 0.000 apart, marking (T0372)V303.CB as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)I2.CA and (T0372)I2.CB only 0.000 apart, marking (T0372)I2.CB as missing
WARNING: atoms too close: (T0372)F4.CA and (T0372)F4.CB only 0.000 apart, marking (T0372)F4.CB as missing
WARNING: atoms too close: (T0372)I7.CA and (T0372)I7.CB only 0.000 apart, marking (T0372)I7.CB as missing
WARNING: atoms too close: (T0372)T16.CA and (T0372)T16.CB only 0.000 apart, marking (T0372)T16.CB as missing
WARNING: atoms too close: (T0372)S22.CA and (T0372)S22.CB only 0.000 apart, marking (T0372)S22.CB as missing
WARNING: atoms too close: (T0372)D28.CA and (T0372)D28.CB only 0.000 apart, marking (T0372)D28.CB as missing
WARNING: atoms too close: (T0372)C35.CA and (T0372)C35.CB only 0.000 apart, marking (T0372)C35.CB as missing
WARNING: atoms too close: (T0372)Y41.CA and (T0372)Y41.CB only 0.000 apart, marking (T0372)Y41.CB as missing
WARNING: atoms too close: (T0372)F45.CA and (T0372)F45.CB only 0.000 apart, marking (T0372)F45.CB as missing
WARNING: atoms too close: (T0372)K55.CA and (T0372)K55.CB only 0.000 apart, marking (T0372)K55.CB as missing
WARNING: atoms too close: (T0372)F56.CA and (T0372)F56.CB only 0.000 apart, marking (T0372)F56.CB as missing
WARNING: atoms too close: (T0372)M66.CA and (T0372)M66.CB only 0.000 apart, marking (T0372)M66.CB as missing
WARNING: atoms too close: (T0372)R78.CA and (T0372)R78.CB only 0.000 apart, marking (T0372)R78.CB as missing
WARNING: atoms too close: (T0372)D83.CA and (T0372)D83.CB only 0.000 apart, marking (T0372)D83.CB as missing
WARNING: atoms too close: (T0372)A84.CA and (T0372)A84.CB only 0.000 apart, marking (T0372)A84.CB as missing
WARNING: atoms too close: (T0372)C92.CA and (T0372)C92.CB only 0.000 apart, marking (T0372)C92.CB as missing
WARNING: atoms too close: (T0372)L108.CA and (T0372)L108.CB only 0.000 apart, marking (T0372)L108.CB as missing
WARNING: atoms too close: (T0372)E110.CA and (T0372)E110.CB only 0.000 apart, marking (T0372)E110.CB as missing
WARNING: atoms too close: (T0372)I113.CA and (T0372)I113.CB only 0.000 apart, marking (T0372)I113.CB as missing
WARNING: atoms too close: (T0372)E116.CA and (T0372)E116.CB only 0.000 apart, marking (T0372)E116.CB as missing
WARNING: atoms too close: (T0372)Y120.CA and (T0372)Y120.CB only 0.000 apart, marking (T0372)Y120.CB as missing
WARNING: atoms too close: (T0372)N146.CA and (T0372)N146.CB only 0.000 apart, marking (T0372)N146.CB as missing
WARNING: atoms too close: (T0372)Q166.CA and (T0372)Q166.CB only 0.000 apart, marking (T0372)Q166.CB as missing
WARNING: atoms too close: (T0372)W175.CA and (T0372)W175.CB only 0.000 apart, marking (T0372)W175.CB as missing
WARNING: atoms too close: (T0372)V178.CA and (T0372)V178.CB only 0.000 apart, marking (T0372)V178.CB as missing
WARNING: atoms too close: (T0372)Q184.CA and (T0372)Q184.CB only 0.000 apart, marking (T0372)Q184.CB as missing
WARNING: atoms too close: (T0372)L194.CA and (T0372)L194.CB only 0.000 apart, marking (T0372)L194.CB as missing
WARNING: atoms too close: (T0372)L198.CA and (T0372)L198.CB only 0.000 apart, marking (T0372)L198.CB as missing
WARNING: atoms too close: (T0372)N200.CA and (T0372)N200.CB only 0.000 apart, marking (T0372)N200.CB as missing
WARNING: atoms too close: (T0372)F201.CA and (T0372)F201.CB only 0.000 apart, marking (T0372)F201.CB as missing
WARNING: atoms too close: (T0372)L211.CA and (T0372)L211.CB only 0.000 apart, marking (T0372)L211.CB as missing
WARNING: atoms too close: (T0372)N214.CA and (T0372)N214.CB only 0.000 apart, marking (T0372)N214.CB as missing
WARNING: atoms too close: (T0372)K216.CA and (T0372)K216.CB only 0.000 apart, marking (T0372)K216.CB as missing
WARNING: atoms too close: (T0372)V218.CA and (T0372)V218.CB only 0.000 apart, marking (T0372)V218.CB as missing
WARNING: atoms too close: (T0372)T230.CA and (T0372)T230.CB only 0.000 apart, marking (T0372)T230.CB as missing
WARNING: atoms too close: (T0372)V235.CA and (T0372)V235.CB only 0.000 apart, marking (T0372)V235.CB as missing
WARNING: atoms too close: (T0372)K237.CA and (T0372)K237.CB only 0.000 apart, marking (T0372)K237.CB as missing
WARNING: atoms too close: (T0372)S241.CA and (T0372)S241.CB only 0.000 apart, marking (T0372)S241.CB as missing
WARNING: atoms too close: (T0372)D243.CA and (T0372)D243.CB only 0.000 apart, marking (T0372)D243.CB as missing
WARNING: atoms too close: (T0372)Y246.CA and (T0372)Y246.CB only 0.000 apart, marking (T0372)Y246.CB as missing
WARNING: atoms too close: (T0372)E252.CA and (T0372)E252.CB only 0.000 apart, marking (T0372)E252.CB as missing
WARNING: atoms too close: (T0372)Y263.CA and (T0372)Y263.CB only 0.000 apart, marking (T0372)Y263.CB as missing
WARNING: atoms too close: (T0372)E267.CA and (T0372)E267.CB only 0.000 apart, marking (T0372)E267.CB as missing
WARNING: atoms too close: (T0372)I272.CA and (T0372)I272.CB only 0.000 apart, marking (T0372)I272.CB as missing
WARNING: atoms too close: (T0372)L280.CA and (T0372)L280.CB only 0.000 apart, marking (T0372)L280.CB as missing
WARNING: atoms too close: (T0372)Q283.CA and (T0372)Q283.CB only 0.000 apart, marking (T0372)Q283.CB as missing
WARNING: atoms too close: (T0372)P284.CA and (T0372)P284.CB only 0.000 apart, marking (T0372)P284.CB as missing
WARNING: atoms too close: (T0372)E289.CA and (T0372)E289.CB only 0.000 apart, marking (T0372)E289.CB as missing
WARNING: atoms too close: (T0372)P299.CA and (T0372)P299.CB only 0.000 apart, marking (T0372)P299.CB as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)I2.CA and (T0372)I2.CB only 0.000 apart, marking (T0372)I2.CB as missing
WARNING: atoms too close: (T0372)P3.CA and (T0372)P3.CB only 0.000 apart, marking (T0372)P3.CB as missing
WARNING: atoms too close: (T0372)F18.CA and (T0372)F18.CB only 0.000 apart, marking (T0372)F18.CB as missing
WARNING: atoms too close: (T0372)K21.CA and (T0372)K21.CB only 0.000 apart, marking (T0372)K21.CB as missing
WARNING: atoms too close: (T0372)S22.CA and (T0372)S22.CB only 0.000 apart, marking (T0372)S22.CB as missing
WARNING: atoms too close: (T0372)N26.CA and (T0372)N26.CB only 0.000 apart, marking (T0372)N26.CB as missing
WARNING: atoms too close: (T0372)S30.CA and (T0372)S30.CB only 0.000 apart, marking (T0372)S30.CB as missing
WARNING: atoms too close: (T0372)L40.CA and (T0372)L40.CB only 0.000 apart, marking (T0372)L40.CB as missing
WARNING: atoms too close: (T0372)D42.CA and (T0372)D42.CB only 0.000 apart, marking (T0372)D42.CB as missing
WARNING: atoms too close: (T0372)Q44.CA and (T0372)Q44.CB only 0.000 apart, marking (T0372)Q44.CB as missing
WARNING: atoms too close: (T0372)D49.CA and (T0372)D49.CB only 0.000 apart, marking (T0372)D49.CB as missing
WARNING: atoms too close: (T0372)D50.CA and (T0372)D50.CB only 0.000 apart, marking (T0372)D50.CB as missing
WARNING: atoms too close: (T0372)W57.CA and (T0372)W57.CB only 0.000 apart, marking (T0372)W57.CB as missing
WARNING: atoms too close: (T0372)A58.CA and (T0372)A58.CB only 0.000 apart, marking (T0372)A58.CB as missing
WARNING: atoms too close: (T0372)V68.CA and (T0372)V68.CB only 0.000 apart, marking (T0372)V68.CB as missing
WARNING: atoms too close: (T0372)V76.CA and (T0372)V76.CB only 0.000 apart, marking (T0372)V76.CB as missing
WARNING: atoms too close: (T0372)D83.CA and (T0372)D83.CB only 0.000 apart, marking (T0372)D83.CB as missing
WARNING: atoms too close: (T0372)N90.CA and (T0372)N90.CB only 0.000 apart, marking (T0372)N90.CB as missing
WARNING: atoms too close: (T0372)L104.CA and (T0372)L104.CB only 0.000 apart, marking (T0372)L104.CB as missing
WARNING: atoms too close: (T0372)R111.CA and (T0372)R111.CB only 0.000 apart, marking (T0372)R111.CB as missing
WARNING: atoms too close: (T0372)L126.CA and (T0372)L126.CB only 0.000 apart, marking (T0372)L126.CB as missing
WARNING: atoms too close: (T0372)A131.CA and (T0372)A131.CB only 0.000 apart, marking (T0372)A131.CB as missing
WARNING: atoms too close: (T0372)R142.CA and (T0372)R142.CB only 0.000 apart, marking (T0372)R142.CB as missing
WARNING: atoms too close: (T0372)H144.CA and (T0372)H144.CB only 0.000 apart, marking (T0372)H144.CB as missing
WARNING: atoms too close: (T0372)I145.CA and (T0372)I145.CB only 0.000 apart, marking (T0372)I145.CB as missing
WARNING: atoms too close: (T0372)N146.CA and (T0372)N146.CB only 0.000 apart, marking (T0372)N146.CB as missing
WARNING: atoms too close: (T0372)R164.CA and (T0372)R164.CB only 0.000 apart, marking (T0372)R164.CB as missing
WARNING: atoms too close: (T0372)Q166.CA and (T0372)Q166.CB only 0.000 apart, marking (T0372)Q166.CB as missing
WARNING: atoms too close: (T0372)C168.CA and (T0372)C168.CB only 0.000 apart, marking (T0372)C168.CB as missing
WARNING: atoms too close: (T0372)N189.CA and (T0372)N189.CB only 0.000 apart, marking (T0372)N189.CB as missing
WARNING: atoms too close: (T0372)A193.CA and (T0372)A193.CB only 0.000 apart, marking (T0372)A193.CB as missing
WARNING: atoms too close: (T0372)L194.CA and (T0372)L194.CB only 0.000 apart, marking (T0372)L194.CB as missing
WARNING: atoms too close: (T0372)Y196.CA and (T0372)Y196.CB only 0.000 apart, marking (T0372)Y196.CB as missing
WARNING: atoms too close: (T0372)F201.CA and (T0372)F201.CB only 0.000 apart, marking (T0372)F201.CB as missing
WARNING: atoms too close: (T0372)L206.CA and (T0372)L206.CB only 0.000 apart, marking (T0372)L206.CB as missing
WARNING: atoms too close: (T0372)K216.CA and (T0372)K216.CB only 0.000 apart, marking (T0372)K216.CB as missing
WARNING: atoms too close: (T0372)F220.CA and (T0372)F220.CB only 0.000 apart, marking (T0372)F220.CB as missing
WARNING: atoms too close: (T0372)H228.CA and (T0372)H228.CB only 0.000 apart, marking (T0372)H228.CB as missing
WARNING: atoms too close: (T0372)T240.CA and (T0372)T240.CB only 0.000 apart, marking (T0372)T240.CB as missing
WARNING: atoms too close: (T0372)I242.CA and (T0372)I242.CB only 0.000 apart, marking (T0372)I242.CB as missing
WARNING: atoms too close: (T0372)K277.CA and (T0372)K277.CB only 0.000 apart, marking (T0372)K277.CB as missing
WARNING: atoms too close: (T0372)A278.CA and (T0372)A278.CB only 0.000 apart, marking (T0372)A278.CB as missing
WARNING: atoms too close: (T0372)Y282.CA and (T0372)Y282.CB only 0.000 apart, marking (T0372)Y282.CB as missing
WARNING: atoms too close: (T0372)Q283.CA and (T0372)Q283.CB only 0.000 apart, marking (T0372)Q283.CB as missing
WARNING: atoms too close: (T0372)P284.CA and (T0372)P284.CB only 0.000 apart, marking (T0372)P284.CB as missing
WARNING: atoms too close: (T0372)Y291.CA and (T0372)Y291.CB only 0.000 apart, marking (T0372)Y291.CB as missing
WARNING: atoms too close: (T0372)A293.CA and (T0372)A293.CB only 0.000 apart, marking (T0372)A293.CB as missing
WARNING: atoms too close: (T0372)R304.CA and (T0372)R304.CB only 0.000 apart, marking (T0372)R304.CB as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)M1.CA and (T0372)M1.CB only 0.000 apart, marking (T0372)M1.CB as missing
WARNING: atoms too close: (T0372)F4.CA and (T0372)F4.CB only 0.000 apart, marking (T0372)F4.CB as missing
WARNING: atoms too close: (T0372)R12.CA and (T0372)R12.CB only 0.000 apart, marking (T0372)R12.CB as missing
WARNING: atoms too close: (T0372)N26.CA and (T0372)N26.CB only 0.000 apart, marking (T0372)N26.CB as missing
WARNING: atoms too close: (T0372)N33.CA and (T0372)N33.CB only 0.000 apart, marking (T0372)N33.CB as missing
WARNING: atoms too close: (T0372)A46.CA and (T0372)A46.CB only 0.000 apart, marking (T0372)A46.CB as missing
WARNING: atoms too close: (T0372)F54.CA and (T0372)F54.CB only 0.000 apart, marking (T0372)F54.CB as missing
WARNING: atoms too close: (T0372)A58.CA and (T0372)A58.CB only 0.000 apart, marking (T0372)A58.CB as missing
WARNING: atoms too close: (T0372)N70.CA and (T0372)N70.CB only 0.000 apart, marking (T0372)N70.CB as missing
WARNING: atoms too close: (T0372)K88.CA and (T0372)K88.CB only 0.000 apart, marking (T0372)K88.CB as missing
WARNING: atoms too close: (T0372)F91.CA and (T0372)F91.CB only 0.000 apart, marking (T0372)F91.CB as missing
WARNING: atoms too close: (T0372)S98.CA and (T0372)S98.CB only 0.000 apart, marking (T0372)S98.CB as missing
WARNING: atoms too close: (T0372)N99.CA and (T0372)N99.CB only 0.000 apart, marking (T0372)N99.CB as missing
WARNING: atoms too close: (T0372)R101.CA and (T0372)R101.CB only 0.000 apart, marking (T0372)R101.CB as missing
WARNING: atoms too close: (T0372)D122.CA and (T0372)D122.CB only 0.000 apart, marking (T0372)D122.CB as missing
WARNING: atoms too close: (T0372)L126.CA and (T0372)L126.CB only 0.000 apart, marking (T0372)L126.CB as missing
WARNING: atoms too close: (T0372)T132.CA and (T0372)T132.CB only 0.000 apart, marking (T0372)T132.CB as missing
WARNING: atoms too close: (T0372)R142.CA and (T0372)R142.CB only 0.000 apart, marking (T0372)R142.CB as missing
WARNING: atoms too close: (T0372)Y157.CA and (T0372)Y157.CB only 0.000 apart, marking (T0372)Y157.CB as missing
WARNING: atoms too close: (T0372)P162.CA and (T0372)P162.CB only 0.000 apart, marking (T0372)P162.CB as missing
WARNING: atoms too close: (T0372)Q166.CA and (T0372)Q166.CB only 0.000 apart, marking (T0372)Q166.CB as missing
WARNING: atoms too close: (T0372)D170.CA and (T0372)D170.CB only 0.000 apart, marking (T0372)D170.CB as missing
WARNING: atoms too close: (T0372)Q183.CA and (T0372)Q183.CB only 0.000 apart, marking (T0372)Q183.CB as missing
WARNING: atoms too close: (T0372)Q184.CA and (T0372)Q184.CB only 0.000 apart, marking (T0372)Q184.CB as missing
WARNING: atoms too close: (T0372)A197.CA and (T0372)A197.CB only 0.000 apart, marking (T0372)A197.CB as missing
WARNING: atoms too close: (T0372)H199.CA and (T0372)H199.CB only 0.000 apart, marking (T0372)H199.CB as missing
WARNING: atoms too close: (T0372)F201.CA and (T0372)F201.CB only 0.000 apart, marking (T0372)F201.CB as missing
WARNING: atoms too close: (T0372)A203.CA and (T0372)A203.CB only 0.000 apart, marking (T0372)A203.CB as missing
WARNING: atoms too close: (T0372)F220.CA and (T0372)F220.CB only 0.000 apart, marking (T0372)F220.CB as missing
WARNING: atoms too close: (T0372)T221.CA and (T0372)T221.CB only 0.000 apart, marking (T0372)T221.CB as missing
WARNING: atoms too close: (T0372)A238.CA and (T0372)A238.CB only 0.000 apart, marking (T0372)A238.CB as missing
WARNING: atoms too close: (T0372)A247.CA and (T0372)A247.CB only 0.000 apart, marking (T0372)A247.CB as missing
WARNING: atoms too close: (T0372)Q260.CA and (T0372)Q260.CB only 0.000 apart, marking (T0372)Q260.CB as missing
WARNING: atoms too close: (T0372)I262.CA and (T0372)I262.CB only 0.000 apart, marking (T0372)I262.CB as missing
WARNING: atoms too close: (T0372)N265.CA and (T0372)N265.CB only 0.000 apart, marking (T0372)N265.CB as missing
WARNING: atoms too close: (T0372)L275.CA and (T0372)L275.CB only 0.000 apart, marking (T0372)L275.CB as missing
WARNING: atoms too close: (T0372)T286.CA and (T0372)T286.CB only 0.000 apart, marking (T0372)T286.CB as missing
WARNING: atoms too close: (T0372)L288.CA and (T0372)L288.CB only 0.000 apart, marking (T0372)L288.CB as missing
WARNING: atoms too close: (T0372)C294.CA and (T0372)C294.CB only 0.000 apart, marking (T0372)C294.CB as missing
WARNING: atoms too close: (T0372)M300.CA and (T0372)M300.CB only 0.000 apart, marking (T0372)M300.CB as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# 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 T0372 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
# WARNING: incomplete conformation T0372 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 T0372 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
# WARNING: incomplete conformation T0372 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
# WARNING: incomplete conformation T0372 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 55, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
Skipped atom 461, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 302
# 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 T0372 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 T0372 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 T0372 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 T0372 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 289
# 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 213
# 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 206
# 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 252
# 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 229
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 213
# 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 286
# 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 259
# copying to AlignedFragments data structure
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# Found a chain break before 179
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# Found a chain break before 243
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# Found a chain break before 213
# 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 284
# 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 227
# 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 280
# 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 T0372 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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
# WARNING: incomplete conformation T0372 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 T0372 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 178, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz
# WARNING: incomplete conformation T0372 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 T0372 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 298
# 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 302
# 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 295
# 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 299
# 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 299
# 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 303
# 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 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 T0372 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 290
# 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 294
# 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 218
# 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 300
# 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 301
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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 T0372 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
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
WARNING: atom 557 has residue number 1  < previous residue 267  in servers/mGen-3D_TS1.pdb.gz
WARNING: atom 1094 has residue number 22  < previous residue 305  in servers/mGen-3D_TS1.pdb.gz
# WARNING: incomplete conformation T0372 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 T0372 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 T0372 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 T0372 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 T0372 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: atom 1 has residue number 1  < previous residue 305  in servers/nFOLD_TS5.pdb.gz
# WARNING: incomplete conformation T0372 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: atoms too close: (T0372)C181.N and (T0372)D182.N only 0.000 apart, marking (T0372)D182.N as missing
WARNING: atoms too close: (T0372)C181.CA and (T0372)D182.CA only 0.000 apart, marking (T0372)D182.CA as missing
WARNING: atoms too close: (T0372)C181.O and (T0372)D182.O only 0.000 apart, marking (T0372)D182.O as missing
WARNING: atoms too close: (T0372)C181.C and (T0372)D182.C only 0.000 apart, marking (T0372)D182.C as missing
WARNING: atoms too close: (T0372)D182.N and (T0372)Q183.N only 0.000 apart, marking (T0372)D182.N as missing
WARNING: atoms too close: (T0372)C181.N and (T0372)Q183.N only 0.000 apart, marking (T0372)Q183.N as missing
WARNING: atoms too close: (T0372)D182.CA and (T0372)Q183.CA only 0.000 apart, marking (T0372)Q183.CA as missing
WARNING: atoms too close: (T0372)C181.CA and (T0372)Q183.CA only 0.000 apart, marking (T0372)Q183.CA as missing
WARNING: atoms too close: (T0372)D182.O and (T0372)Q183.O only 0.000 apart, marking (T0372)Q183.O as missing
WARNING: atoms too close: (T0372)C181.O and (T0372)Q183.O only 0.000 apart, marking (T0372)Q183.O as missing
WARNING: atoms too close: (T0372)D182.C and (T0372)Q183.C only 0.000 apart, marking (T0372)Q183.C as missing
WARNING: atoms too close: (T0372)C181.C and (T0372)Q183.C only 0.000 apart, marking (T0372)Q183.C as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1
WARNING: atoms too close: (T0372)D117.N and (T0372)Y155.N only 0.000 apart, marking (T0372)Y155.N as missing
WARNING: atoms too close: (T0372)D117.CA and (T0372)Y155.CA only 0.000 apart, marking (T0372)Y155.CA as missing
WARNING: atoms too close: (T0372)D117.CB and (T0372)Y155.CB only 0.000 apart, marking (T0372)Y155.CB as missing
WARNING: atoms too close: (T0372)D117.CG and (T0372)Y155.CG only 0.000 apart, marking (T0372)Y155.CG as missing
WARNING: atoms too close: (T0372)D117.O and (T0372)Y155.O only 0.000 apart, marking (T0372)Y155.O as missing
WARNING: atoms too close: (T0372)D117.C and (T0372)Y155.C only 0.000 apart, marking (T0372)Y155.C as missing
WARNING: atoms too close: (T0372)Y155.N and (T0372)L171.N only 0.000 apart, marking (T0372)Y155.N as missing
WARNING: atoms too close: (T0372)D117.N and (T0372)L171.N only 0.000 apart, marking (T0372)L171.N as missing
WARNING: atoms too close: (T0372)Y155.CA and (T0372)L171.CA only 0.000 apart, marking (T0372)L171.CA as missing
WARNING: atoms too close: (T0372)D117.CA and (T0372)L171.CA only 0.000 apart, marking (T0372)L171.CA as missing
WARNING: atoms too close: (T0372)Y155.CB and (T0372)L171.CB only 0.000 apart, marking (T0372)L171.CB as missing
WARNING: atoms too close: (T0372)D117.CB and (T0372)L171.CB only 0.000 apart, marking (T0372)L171.CB as missing
WARNING: atoms too close: (T0372)Y155.CG and (T0372)L171.CG only 0.000 apart, marking (T0372)L171.CG as missing
WARNING: atoms too close: (T0372)D117.CG and (T0372)L171.CG only 0.000 apart, marking (T0372)L171.CG as missing
WARNING: atoms too close: (T0372)Y155.O and (T0372)L171.O only 0.000 apart, marking (T0372)L171.O as missing
WARNING: atoms too close: (T0372)D117.O and (T0372)L171.O only 0.000 apart, marking (T0372)L171.O as missing
WARNING: atoms too close: (T0372)Y155.C and (T0372)L171.C only 0.000 apart, marking (T0372)L171.C as missing
WARNING: atoms too close: (T0372)D117.C and (T0372)L171.C only 0.000 apart, marking (T0372)L171.C as missing
# WARNING: incomplete conformation T0372 can't currently be optimized by undertaker
# naming current conformation panther3_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# Found a chain break before 304
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 248
Adding 23101 constraints to all.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all.constraints
maxweight: 142.0000
Optimizing...
 Probability sum: -557.6283, CN propb: -557.6283 weights: 0.2056 constraints: 1147
# command:Found ConstraintSet
# PrintContacts align.constraints_meta01
Number of constraints in align.constraints 1147
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta01
Number of constraints in align.constraints.bonus 1147
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta01
Number of constraints in rejected.constraints 21954
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta01
Number of constraints in rejected.constraints.bonus 21954
# 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 23101
# command: