# 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/T0376/
# command:# Making conformation for sequence T0376 numbered 1 through 321
Created new target T0376 from T0376.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0376/
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0376/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0376/decoys/
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 280
# 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 252
# 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 291
# 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 272
# 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 272
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# Found a chain break before 316
# 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 320
# 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 286
# 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 274
# 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 274
# 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 320
# 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 320
# 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 313
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# Found a chain break before 291
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 315
# 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 T0376 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 T0376 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 T0376 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 T0376 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 303
# 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 320
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# Found a chain break before 313
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 310
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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
# Found a chain break before 299
# 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 275
# 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 281
# 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 281
# 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 281
# 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 T0376 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 97, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 99, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 333, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 335, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 433, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 435, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 645, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 646, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 647, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 648, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 733, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 735, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 773, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 775, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 881, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 882, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 883, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 884, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
# WARNING: incomplete conformation T0376 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
Skipped atom 986, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 988, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 990, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
Skipped atom 992, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz
# WARNING: incomplete conformation T0376 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 886, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 888, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 890, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
Skipped atom 892, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 986, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 988, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 990, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 992, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0376 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
Skipped atom 882, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 884, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 886, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
Skipped atom 888, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz
# WARNING: incomplete conformation T0376 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 97, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 99, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 333, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 335, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 433, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 435, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 645, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 646, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 647, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 648, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 733, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 734, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 735, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 736, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 773, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 775, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 881, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 882, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 883, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 884, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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 151
# 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 224
# 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 272
# 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 286
# 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 256
# 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 T0376 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 T0376 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 T0376 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 303
# 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 T0376 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 T0376 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 T0376 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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 T0376 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 319
# 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 312
# 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 320
# 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 313
# 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 310
# 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 310
# 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 307
# 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 311
# 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 284
# 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 281
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 260
# 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 260
# 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 281
# 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 260
# 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 301
# 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 190
# 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 274
# 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 281
# 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 301
# 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 310
# 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 241
# 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 190
# 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 310
# 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 317
# 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 320
# 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 320
# 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 319
# 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 319
# 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 300
# copying to AlignedFragments data structure
# naming current conformation NN_PUT_lab_TS1
# 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 T0376 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
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# Found a chain break before 128
# 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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
# Found a chain break before 319
# 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
# Found a chain break before 318
# 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 319
# 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 282
# 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 319
# 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
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 209
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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
# WARNING: incomplete conformation T0376 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 251
# 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 281
# 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 281
# 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 306
# 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 277
# 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 280
# 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 320
# 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 311
# 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 305
# 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 314
# 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 315
# 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 215
# 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 260
# 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 301
# 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 260
# 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 281
# 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 251
# 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 282
# 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 209
# 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 209
# 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 276
# 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 274
# 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 280
# 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 281
# 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 281
# 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 281
# 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
Skipped atom 890, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 892, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 894, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 896, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 T0376 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 T0376 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
# WARNING: incomplete conformation T0376 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
Skipped atom 1095, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz
# WARNING: incomplete conformation T0376 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
# WARNING: incomplete conformation T0376 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
Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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 284
# 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 T0376 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 T0376 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 T0376 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 T0376 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 280
# 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 274
# 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 215
# 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 215
# 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 260
# 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 274
# 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 280
# 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 260
# 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 215
# 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 281
# 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 300
# 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 280
# 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 272
# 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 215
# 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 260
# 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 can't currently be optimized by undertaker
# 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 T0376 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 T0376 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 T0376 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
# WARNING: incomplete conformation T0376 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 T0376 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 314
# 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 310
# 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 311
# 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 319
# 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 305
# 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
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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
Skipped atom 986, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 988, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 990, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
Skipped atom 992, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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
Skipped atom 882, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 884, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 886, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 888, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 227
# 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 303
# 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 227
# 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 227
# 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 227
# 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 318
# 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 320
# 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
WARNING: atoms too close: (T0376)M189.O and (T0376)I190.N only 0.000 apart, marking (T0376)I190.N as missing
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# 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 318
# 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 318
# 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 T0376 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 T0376 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 T0376 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 T0376 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 T0376 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
# Found a chain break before 134
# 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 136
# 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
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0376 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 T0376 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 T0376 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 T0376 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: atom 1 has residue number 5  < previous residue 256  in servers/nFOLD_TS4.pdb.gz
# WARNING: incomplete conformation T0376 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 T0376 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: (T0376)I5.N and (T0376)A119.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)A119.CA only 0.000 apart, marking (T0376)A119.CA as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)A119.CB only 0.000 apart, marking (T0376)A119.CB as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)A119.O only 0.000 apart, marking (T0376)A119.O as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)A119.C only 0.000 apart, marking (T0376)A119.C as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)A127.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)A127.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)A127.CA only 0.000 apart, marking (T0376)A127.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)A127.CA only 0.000 apart, marking (T0376)A127.CA as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)A127.CB only 0.000 apart, marking (T0376)A127.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)A127.CB only 0.000 apart, marking (T0376)A127.CB as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)A127.O only 0.000 apart, marking (T0376)A127.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)A127.O only 0.000 apart, marking (T0376)A127.O as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)A127.C only 0.000 apart, marking (T0376)A127.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)A127.C only 0.000 apart, marking (T0376)A127.C as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)P169.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)P169.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)P169.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)P169.CA only 0.000 apart, marking (T0376)P169.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)P169.CA only 0.000 apart, marking (T0376)P169.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)P169.CA only 0.000 apart, marking (T0376)P169.CA as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)P169.CB only 0.000 apart, marking (T0376)P169.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)P169.CB only 0.000 apart, marking (T0376)P169.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)P169.CB only 0.000 apart, marking (T0376)P169.CB as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)P169.O only 0.000 apart, marking (T0376)P169.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)P169.O only 0.000 apart, marking (T0376)P169.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)P169.O only 0.000 apart, marking (T0376)P169.O as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)P169.C only 0.000 apart, marking (T0376)P169.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)P169.C only 0.000 apart, marking (T0376)P169.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)P169.C only 0.000 apart, marking (T0376)P169.C as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)A170.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)A170.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)A170.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)A170.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)A170.CA only 0.000 apart, marking (T0376)A170.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)A170.CA only 0.000 apart, marking (T0376)A170.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)A170.CA only 0.000 apart, marking (T0376)A170.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)A170.CA only 0.000 apart, marking (T0376)A170.CA as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)A170.CB only 0.000 apart, marking (T0376)A170.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)A170.CB only 0.000 apart, marking (T0376)A170.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)A170.CB only 0.000 apart, marking (T0376)A170.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)A170.CB only 0.000 apart, marking (T0376)A170.CB as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)A170.O only 0.000 apart, marking (T0376)A170.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)A170.O only 0.000 apart, marking (T0376)A170.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)A170.O only 0.000 apart, marking (T0376)A170.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)A170.O only 0.000 apart, marking (T0376)A170.O as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)A170.C only 0.000 apart, marking (T0376)A170.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)A170.C only 0.000 apart, marking (T0376)A170.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)A170.C only 0.000 apart, marking (T0376)A170.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)A170.C only 0.000 apart, marking (T0376)A170.C as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)G199.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)G199.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)G199.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)G199.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)G199.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)G199.CA only 0.000 apart, marking (T0376)G199.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)G199.CA only 0.000 apart, marking (T0376)G199.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)G199.CA only 0.000 apart, marking (T0376)G199.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)G199.CA only 0.000 apart, marking (T0376)G199.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)G199.CA only 0.000 apart, marking (T0376)G199.CA as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)G199.O only 0.000 apart, marking (T0376)G199.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)G199.O only 0.000 apart, marking (T0376)G199.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)G199.O only 0.000 apart, marking (T0376)G199.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)G199.O only 0.000 apart, marking (T0376)G199.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)G199.O only 0.000 apart, marking (T0376)G199.O as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)G199.C only 0.000 apart, marking (T0376)G199.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)G199.C only 0.000 apart, marking (T0376)G199.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)G199.C only 0.000 apart, marking (T0376)G199.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)G199.C only 0.000 apart, marking (T0376)G199.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)G199.C only 0.000 apart, marking (T0376)G199.C as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)L251.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)L251.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)L251.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)L251.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)L251.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)L251.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)L251.CA only 0.000 apart, marking (T0376)L251.CA as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)L251.CB only 0.000 apart, marking (T0376)L251.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)L251.CB only 0.000 apart, marking (T0376)L251.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)L251.CB only 0.000 apart, marking (T0376)L251.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)L251.CB only 0.000 apart, marking (T0376)L251.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)L251.CB only 0.000 apart, marking (T0376)L251.CB as missing
WARNING: atoms too close: (T0376)I5.CG1 and (T0376)L251.CG only 0.000 apart, marking (T0376)L251.CG as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)L251.O only 0.000 apart, marking (T0376)L251.O as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)L251.C only 0.000 apart, marking (T0376)L251.C as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)S252.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)S252.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)S252.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)S252.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)S252.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)S252.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)S252.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)S252.CA only 0.000 apart, marking (T0376)S252.CA as missing
WARNING: atoms too close: (T0376)L251.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)S252.CB only 0.000 apart, marking (T0376)S252.CB as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)S252.O only 0.000 apart, marking (T0376)S252.O as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)S252.C only 0.000 apart, marking (T0376)S252.C as missing
WARNING: atoms too close: (T0376)S252.N and (T0376)S253.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)S253.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)S253.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)S253.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)S253.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)S253.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)S253.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)S253.N only 0.000 apart, marking (T0376)S253.N as missing
WARNING: atoms too close: (T0376)S252.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)S253.CA only 0.000 apart, marking (T0376)S253.CA as missing
WARNING: atoms too close: (T0376)S252.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)L251.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)S253.CB only 0.000 apart, marking (T0376)S253.CB as missing
WARNING: atoms too close: (T0376)S252.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)S253.O only 0.000 apart, marking (T0376)S253.O as missing
WARNING: atoms too close: (T0376)S252.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)S253.C only 0.000 apart, marking (T0376)S253.C as missing
WARNING: atoms too close: (T0376)S253.N and (T0376)F254.N only 0.000 apart, marking (T0376)S253.N as missing
WARNING: atoms too close: (T0376)S252.N and (T0376)F254.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)F254.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)F254.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)F254.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)F254.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)F254.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)F254.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)F254.N only 0.000 apart, marking (T0376)F254.N as missing
WARNING: atoms too close: (T0376)S253.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)S252.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)F254.CA only 0.000 apart, marking (T0376)F254.CA as missing
WARNING: atoms too close: (T0376)S253.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)S252.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)L251.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)F254.CB only 0.000 apart, marking (T0376)F254.CB as missing
WARNING: atoms too close: (T0376)L251.CG and (T0376)F254.CG only 0.000 apart, marking (T0376)F254.CG as missing
WARNING: atoms too close: (T0376)I5.CG1 and (T0376)F254.CG only 0.000 apart, marking (T0376)F254.CG as missing
WARNING: atoms too close: (T0376)S253.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)S252.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)F254.O only 0.000 apart, marking (T0376)F254.O as missing
WARNING: atoms too close: (T0376)S253.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)S252.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)F254.C only 0.000 apart, marking (T0376)F254.C as missing
WARNING: atoms too close: (T0376)F254.N and (T0376)G272.N only 0.000 apart, marking (T0376)F254.N as missing
WARNING: atoms too close: (T0376)S253.N and (T0376)G272.N only 0.000 apart, marking (T0376)S253.N as missing
WARNING: atoms too close: (T0376)S252.N and (T0376)G272.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)G272.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)G272.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)G272.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)G272.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)G272.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)G272.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)G272.N only 0.000 apart, marking (T0376)G272.N as missing
WARNING: atoms too close: (T0376)F254.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)S253.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)S252.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)G272.CA only 0.000 apart, marking (T0376)G272.CA as missing
WARNING: atoms too close: (T0376)F254.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)S253.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)S252.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)G272.O only 0.000 apart, marking (T0376)G272.O as missing
WARNING: atoms too close: (T0376)F254.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)S253.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)S252.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)G272.C only 0.000 apart, marking (T0376)G272.C as missing
WARNING: atoms too close: (T0376)G272.N and (T0376)D273.N only 0.000 apart, marking (T0376)G272.N as missing
WARNING: atoms too close: (T0376)F254.N and (T0376)D273.N only 0.000 apart, marking (T0376)F254.N as missing
WARNING: atoms too close: (T0376)S253.N and (T0376)D273.N only 0.000 apart, marking (T0376)S253.N as missing
WARNING: atoms too close: (T0376)S252.N and (T0376)D273.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)D273.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)D273.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)D273.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)D273.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)D273.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)D273.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)D273.N only 0.000 apart, marking (T0376)D273.N as missing
WARNING: atoms too close: (T0376)G272.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)F254.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)S253.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)S252.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)D273.CA only 0.000 apart, marking (T0376)D273.CA as missing
WARNING: atoms too close: (T0376)F254.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)S253.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)S252.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)L251.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)D273.CB only 0.000 apart, marking (T0376)D273.CB as missing
WARNING: atoms too close: (T0376)F254.CG and (T0376)D273.CG only 0.000 apart, marking (T0376)D273.CG as missing
WARNING: atoms too close: (T0376)L251.CG and (T0376)D273.CG only 0.000 apart, marking (T0376)D273.CG as missing
WARNING: atoms too close: (T0376)I5.CG1 and (T0376)D273.CG only 0.000 apart, marking (T0376)D273.CG as missing
WARNING: atoms too close: (T0376)G272.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)F254.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)S253.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)S252.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)D273.O only 0.000 apart, marking (T0376)D273.O as missing
WARNING: atoms too close: (T0376)G272.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)F254.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)S253.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)S252.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)D273.C only 0.000 apart, marking (T0376)D273.C as missing
WARNING: atoms too close: (T0376)D273.N and (T0376)E282.N only 0.000 apart, marking (T0376)D273.N as missing
WARNING: atoms too close: (T0376)G272.N and (T0376)E282.N only 0.000 apart, marking (T0376)G272.N as missing
WARNING: atoms too close: (T0376)F254.N and (T0376)E282.N only 0.000 apart, marking (T0376)F254.N as missing
WARNING: atoms too close: (T0376)S253.N and (T0376)E282.N only 0.000 apart, marking (T0376)S253.N as missing
WARNING: atoms too close: (T0376)S252.N and (T0376)E282.N only 0.000 apart, marking (T0376)S252.N as missing
WARNING: atoms too close: (T0376)L251.N and (T0376)E282.N only 0.000 apart, marking (T0376)L251.N as missing
WARNING: atoms too close: (T0376)G199.N and (T0376)E282.N only 0.000 apart, marking (T0376)G199.N as missing
WARNING: atoms too close: (T0376)A170.N and (T0376)E282.N only 0.000 apart, marking (T0376)A170.N as missing
WARNING: atoms too close: (T0376)P169.N and (T0376)E282.N only 0.000 apart, marking (T0376)P169.N as missing
WARNING: atoms too close: (T0376)A127.N and (T0376)E282.N only 0.000 apart, marking (T0376)A127.N as missing
WARNING: atoms too close: (T0376)A119.N and (T0376)E282.N only 0.000 apart, marking (T0376)A119.N as missing
WARNING: atoms too close: (T0376)I5.N and (T0376)E282.N only 0.000 apart, marking (T0376)E282.N as missing
WARNING: atoms too close: (T0376)D273.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)G272.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)F254.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)S253.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)S252.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)L251.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)G199.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)A170.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)P169.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)A127.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)A119.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)I5.CA and (T0376)E282.CA only 0.000 apart, marking (T0376)E282.CA as missing
WARNING: atoms too close: (T0376)D273.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)F254.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)S253.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)S252.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)L251.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)A170.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)P169.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)A127.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)A119.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)I5.CB and (T0376)E282.CB only 0.000 apart, marking (T0376)E282.CB as missing
WARNING: atoms too close: (T0376)D273.CG and (T0376)E282.CG only 0.000 apart, marking (T0376)E282.CG as missing
WARNING: atoms too close: (T0376)F254.CG and (T0376)E282.CG only 0.000 apart, marking (T0376)E282.CG as missing
WARNING: atoms too close: (T0376)L251.CG and (T0376)E282.CG only 0.000 apart, marking (T0376)E282.CG as missing
WARNING: atoms too close: (T0376)I5.CG1 and (T0376)E282.CG only 0.000 apart, marking (T0376)E282.CG as missing
WARNING: atoms too close: (T0376)D273.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)G272.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)F254.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)S253.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)S252.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)L251.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)G199.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)A170.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)P169.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)A127.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)A119.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)I5.O and (T0376)E282.O only 0.000 apart, marking (T0376)E282.O as missing
WARNING: atoms too close: (T0376)D273.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)G272.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)F254.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)S253.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)S252.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)L251.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)G199.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)A170.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)P169.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)A127.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)A119.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
WARNING: atoms too close: (T0376)I5.C and (T0376)E282.C only 0.000 apart, marking (T0376)E282.C as missing
# WARNING: incomplete conformation T0376 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
# WARNING: incomplete conformation T0376 can't currently be optimized by undertaker
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 257
Adding 11518 constraints to all.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all.constraints
maxweight: 232.0000
Optimizing...
 Probability sum: -549.4636, CN propb: -549.4636 weights: 0.3059 constraints: 1383
# command:Found ConstraintSet
# PrintContacts align.constraints_meta01
Number of constraints in align.constraints 1383
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta01
Number of constraints in align.constraints.bonus 1383
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta01
Number of constraints in rejected.constraints 10135
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta01
Number of constraints in rejected.constraints.bonus 10135
# 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 11518
# command: