# 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/T0353/ # command:# Making conformation for sequence T0353 numbered 1 through 85 Created new target T0353 from T0353.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0353/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t3lA expands to /projects/compbio/data/pdb/1t3l.pdb.gz 1t3lA:# T0353 read from 1t3lA/merged-good-all-a2m # 1t3lA read from 1t3lA/merged-good-all-a2m # adding 1t3lA to template set # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 Number of alignments=1 # 1t3lA read from 1t3lA/merged-good-all-a2m # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 Number of alignments=2 # 1t3lA read from 1t3lA/merged-good-all-a2m # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cthA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2cthA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2cthA/merged-good-all-a2m.gz for input Trying 2cthA/merged-good-all-a2m Error: Couldn't open file 2cthA/merged-good-all-a2m or 2cthA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sgvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sgvA expands to /projects/compbio/data/pdb/1sgv.pdb.gz 1sgvA:# T0353 read from 1sgvA/merged-good-all-a2m # 1sgvA read from 1sgvA/merged-good-all-a2m # adding 1sgvA to template set # found chain 1sgvA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDDKKAIEFAKQWLSSIGE 1sgvA 148 :IRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGV Number of specific fragments extracted= 1 number of extra gaps= 0 total=4 Number of alignments=4 # 1sgvA read from 1sgvA/merged-good-all-a2m # found chain 1sgvA in template set T0353 2 :QIH 1sgvA 149 :RID T0353 5 :VYDTYVKAKDG 1sgvA 153 :FELLAARRRDQ T0353 17 :VMHFDVFTDVRDDKKAIEFAKQWLSSIGEE 1sgvA 164 :LIDIDVEIDCSSGTYIRALARDLGDALGVG Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 Number of alignments=5 # 1sgvA read from 1sgvA/merged-good-all-a2m # found chain 1sgvA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDDKKAIEFAKQWLSSIGEE 1sgvA 148 :IRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVG Number of specific fragments extracted= 1 number of extra gaps= 0 total=8 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a99A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a99A expands to /projects/compbio/data/pdb/1a99.pdb.gz 1a99A:# T0353 read from 1a99A/merged-good-all-a2m # 1a99A read from 1a99A/merged-good-all-a2m # adding 1a99A to template set # found chain 1a99A in template set T0353 12 :AKDGHVMHFDVFT 1a99A 269 :PKEGAMAFFDVFA T0353 25 :DVRDDKKAIEFAKQWLSS 1a99A 285 :DAKNKDEAYQFLNYLLRP T0353 43 :IGE 1a99A 312 :VFY T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Number of alignments=7 # 1a99A read from 1a99A/merged-good-all-a2m # found chain 1a99A in template set T0353 2 :QIHVYD 1a99A 263 :NVSFSI T0353 12 :AKDGHVMHFDVFTDV 1a99A 269 :PKEGAMAFFDVFAMP T0353 27 :RDDKKAIEFAKQWLSS 1a99A 287 :KNKDEAYQFLNYLLRP T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=16 Number of alignments=8 # 1a99A read from 1a99A/merged-good-all-a2m # found chain 1a99A in template set T0353 2 :QIHVY 1a99A 263 :NVSFS T0353 12 :AKDGHVMHFDVFTDVRD 1a99A 269 :PKEGAMAFFDVFAMPAD T0353 29 :DKKAIEFAKQWLSS 1a99A 289 :KDEAYQFLNYLLRP T0353 43 :IGE 1a99A 312 :VFY T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=21 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ffkI/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ffkI expands to /projects/compbio/data/pdb-ca-mod/1ffk.brk_ca_mod.gz 1ffkI:# T0353 read from 1ffkI/merged-good-all-a2m # 1ffkI read from 1ffkI/merged-good-all-a2m # adding 1ffkI to template set # found chain 1ffkI in template set Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAIE 1ffkI 130 :EVILVDRDHPAIKS Number of specific fragments extracted= 4 number of extra gaps= 3 total=25 # 1ffkI read from 1ffkI/merged-good-all-a2m # found chain 1ffkI in template set Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAIE 1ffkI 130 :EVILVDRDHPAIKS Number of specific fragments extracted= 4 number of extra gaps= 3 total=29 # 1ffkI read from 1ffkI/merged-good-all-a2m # found chain 1ffkI in template set Warning: unaligning (T0353)I3 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)M112 Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAI 1ffkI 130 :EVILVDRDHPAIK Number of specific fragments extracted= 4 number of extra gaps= 4 total=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iqtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1iqtA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1iqtA/merged-good-all-a2m.gz for input Trying 1iqtA/merged-good-all-a2m Error: Couldn't open file 1iqtA/merged-good-all-a2m or 1iqtA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nrfA expands to /projects/compbio/data/pdb/1nrf.pdb.gz 1nrfA:# T0353 read from 1nrfA/merged-good-all-a2m # 1nrfA read from 1nrfA/merged-good-all-a2m # adding 1nrfA to template set # found chain 1nrfA in template set T0353 3 :IHVYDTYVKAKD 1nrfA 551 :AGWFIGYVETAD T0353 16 :HVMHFDVFTDVRDD 1nrfA 563 :NTFFFAVHIQGEKR T0353 30 :KKAIEFAKQWLSSIGE 1nrfA 580 :SSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 Number of alignments=10 # 1nrfA read from 1nrfA/merged-good-all-a2m # found chain 1nrfA in template set T0353 4 :HVYDTYVKAKD 1nrfA 552 :GWFIGYVETAD T0353 16 :HVMHFDVFTDVRDD 1nrfA 563 :NTFFFAVHIQGEKR T0353 30 :KKAIEFAKQWLSSIGE 1nrfA 580 :SSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Number of alignments=11 # 1nrfA read from 1nrfA/merged-good-all-a2m # found chain 1nrfA in template set T0353 5 :VYDTYVKAKDGHVMH 1nrfA 553 :WFIGYVETADNTFFF T0353 20 :FDVFTDVRD 1nrfA 569 :VHIQGEKRA T0353 29 :DKKAIEFAKQWLSSIGE 1nrfA 579 :GSSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1j0oA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1j0oA/merged-good-all-a2m.gz for input Trying 1j0oA/merged-good-all-a2m Error: Couldn't open file 1j0oA/merged-good-all-a2m or 1j0oA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8qA expands to /projects/compbio/data/pdb/1y8q.pdb.gz 1y8qA:# T0353 read from 1y8qA/merged-good-all-a2m # 1y8qA read from 1y8qA/merged-good-all-a2m # adding 1y8qA to template set # found chain 1y8qA in template set T0353 29 :DKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 266 :SELLLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAIK 1y8qA 298 :EMAPVCAVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=44 Number of alignments=13 # 1y8qA read from 1y8qA/merged-good-all-a2m # found chain 1y8qA in template set T0353 28 :DDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 265 :DSELLLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAIK 1y8qA 298 :EMAPVCAVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=46 Number of alignments=14 # 1y8qA read from 1y8qA/merged-good-all-a2m # found chain 1y8qA in template set T0353 24 :TDVRDDKK 1y8qA 257 :PSSDTYEE T0353 32 :AIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 269 :LLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAI 1y8qA 298 :EMAPVCAVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1wr5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1wr5A/merged-good-all-a2m.gz for input Trying 1wr5A/merged-good-all-a2m Error: Couldn't open file 1wr5A/merged-good-all-a2m or 1wr5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2mtaC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2mtaC/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2mtaC/merged-good-all-a2m.gz for input Trying 2mtaC/merged-good-all-a2m Error: Couldn't open file 2mtaC/merged-good-all-a2m or 2mtaC/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1is8K/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1is8K expands to /projects/compbio/data/pdb/1is8.pdb.gz 1is8K:# T0353 read from 1is8K/merged-good-all-a2m # 1is8K read from 1is8K/merged-good-all-a2m # adding 1is8K to template set # found chain 1is8K in template set T0353 2 :QIHVY 1is8K 3 :YLLIS T0353 8 :TYVKAKDGHVM 1is8K 8 :TQIRMEVGPTM T0353 23 :FTDVRDDKKAIE 1is8K 19 :VGDEHSDPELMQ T0353 42 :SIG 1is8K 31 :QLG T0353 45 :EEGAT 1is8K 39 :VLGNN T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEGCN 1is8K 49 :VNDPPRIVLDKLECRGFRVLSMTGVG Number of specific fragments extracted= 6 number of extra gaps= 0 total=55 Number of alignments=16 # 1is8K read from 1is8K/merged-good-all-a2m # found chain 1is8K in template set T0353 2 :QIHVYDT 1is8K 3 :YLLISTQ T0353 10 :VKAKDGHV 1is8K 10 :IRMEVGPT T0353 22 :VFTDVRDDKKAIE 1is8K 18 :MVGDEHSDPELMQ T0353 42 :SIG 1is8K 31 :QLG T0353 45 :EEGAT 1is8K 39 :VLGNN T0353 59 :HSQKAPDEVIEAIKQNGYFIYKMEGC 1is8K 48 :YVNDPPRIVLDKLECRGFRVLSMTGV Number of specific fragments extracted= 6 number of extra gaps= 0 total=61 Number of alignments=17 # 1is8K read from 1is8K/merged-good-all-a2m # found chain 1is8K in template set T0353 5 :VYDTYVKAKDGHVM 1is8K 5 :LISTQIRMEVGPTM T0353 23 :FTDVRDDKKA 1is8K 19 :VGDEHSDPEL T0353 40 :LSSIGEEGA 1is8K 29 :MQQLGASKR T0353 51 :TSEECRF 1is8K 38 :RVLGNNF T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEG 1is8K 49 :VNDPPRIVLDKLECRGFRVLSMTG Number of specific fragments extracted= 5 number of extra gaps= 0 total=66 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1es6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1es6A/merged-good-all-a2m.gz for input Trying 1es6A/merged-good-all-a2m Error: Couldn't open file 1es6A/merged-good-all-a2m or 1es6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 155c/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 155c expands to /projects/compbio/data/pdb/155c.pdb.gz 155c:Warning: there is no chain 155c will retry with 155cA Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X # T0353 read from 155c/merged-good-all-a2m # 155c read from 155c/merged-good-all-a2m # adding 155c to template set # found chain 155c in template set Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 T0353 27 :RDDKKAIEFAKQW 155c 105 :KNQADVVAFLAQD T0353 47 :GATV 155c 118 :DPDA Number of specific fragments extracted= 2 number of extra gaps= 1 total=68 # 155c read from 155c/merged-good-all-a2m # found chain 155c in template set Warning: unaligning (T0353)E45 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)E46 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)G47 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 Warning: unaligning (T0353)A48 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X125 Warning: unaligning (T0353)T49 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X126 Warning: unaligning (T0353)V50 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X127 Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X128 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X129 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X130 Warning: unaligning (T0353)E54 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X131 Warning: unaligning (T0353)C55 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X132 T0353 26 :VRDDKKAIEFAKQW 155c 104 :GKNQADVVAFLAQD T0353 42 :S 155c 120 :D T0353 44 :G 155c 121 :A Number of specific fragments extracted= 3 number of extra gaps= 1 total=71 Number of alignments=19 # 155c read from 155c/merged-good-all-a2m # found chain 155c in template set Warning: unaligning (T0353)E45 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)E46 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)G47 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 Warning: unaligning (T0353)A48 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X125 Warning: unaligning (T0353)T49 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X126 Warning: unaligning (T0353)V50 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X127 Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X128 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X129 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X130 Warning: unaligning (T0353)E54 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X131 Warning: unaligning (T0353)C55 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X132 Warning: unaligning (T0353)R56 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X133 T0353 26 :VRDDKKAIEFAKQW 155c 104 :GKNQADVVAFLAQD T0353 44 :G 155c 121 :A Number of specific fragments extracted= 2 number of extra gaps= 1 total=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1udzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0353 read from 1udzA/merged-good-all-a2m # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 25 :DVRDDKKAIEFAKQW 1udzA 321 :APAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=75 Number of alignments=20 # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 25 :DVRDDKKAIEFAKQW 1udzA 321 :APAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=77 Number of alignments=21 # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 9 :YVKAKDGHVMH 1udzA 308 :YVSQEDGTGIV T0353 23 :FTDVRDDKKAIEFAKQW 1udzA 319 :HQAPAFGAEDLETARVY T0353 45 :EEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 344 :DEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=80 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cybA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cybA expands to /projects/compbio/data/pdb/2cyb.pdb.gz 2cybA:# T0353 read from 2cybA/merged-good-all-a2m # 2cybA read from 2cybA/merged-good-all-a2m # adding 2cybA to template set # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGY T0353 46 :EGATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 211 :DGQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=82 Number of alignments=23 # 2cybA read from 2cybA/merged-good-all-a2m # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGY T0353 46 :EGATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 211 :DGQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=84 Number of alignments=24 # 2cybA read from 2cybA/merged-good-all-a2m # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGEE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGYS T0353 47 :GATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 212 :GQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=86 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cdv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2cdv/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2cdv/merged-good-all-a2m.gz for input Trying 2cdv/merged-good-all-a2m Error: Couldn't open file 2cdv/merged-good-all-a2m or 2cdv/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y9kA expands to /projects/compbio/data/pdb/1y9k.pdb.gz 1y9kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1099, because occupancy 0.5 <= existing 0.500 in 1y9kA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1y9kA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0353 read from 1y9kA/merged-good-all-a2m # 1y9kA read from 1y9kA/merged-good-all-a2m # adding 1y9kA to template set # found chain 1y9kA in template set T0353 7 :DTYVKAKDGHVMHFDVFTDVRDD 1y9kA 36 :LTYVAKQGGSVIGVYVLLETRPK T0353 30 :KKAIEFAKQWLSSIGEE 1y9kA 78 :KKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKMEG 1y9kA 102 :NSSVSQLALYQKCGFRIFSIDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=89 Number of alignments=26 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set T0353 8 :TYVKAKDGHVMHFDVFTDVRDD 1y9kA 37 :TYVAKQGGSVIGVYVLLETRPK T0353 30 :KKAIEFAKQWLSSIGEE 1y9kA 78 :KKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKMEG 1y9kA 102 :NSSVSQLALYQKCGFRIFSIDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=92 Number of alignments=27 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set T0353 3 :IHVYDTYVKAKDGHVMHFDVFTDVRD 1y9kA 46 :VIGVYVLLETRPKTMEIMNIAVAEHL T0353 29 :DKKAIEFAKQWLSSIGEE 1y9kA 77 :GKKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKME 1y9kA 102 :NSSVSQLALYQKCGFRIFSID Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2drpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2drpA expands to /projects/compbio/data/pdb/2drp.pdb.gz 2drpA:# T0353 read from 2drpA/merged-good-all-a2m # 2drpA read from 2drpA/merged-good-all-a2m # adding 2drpA to template set # found chain 2drpA in template set T0353 9 :YVKAKDGH 2drpA 111 :YRCKVCSR T0353 25 :DVRDDKKAIE 2drpA 119 :VYTHISNFCR T0353 39 :WLSSIGE 2drpA 129 :HYVTSHK T0353 48 :ATVTSEECRFCHSQ 2drpA 136 :RNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIK 2drpA 151 :TRKDNMTAHVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=100 Number of alignments=29 # 2drpA read from 2drpA/merged-good-all-a2m # found chain 2drpA in template set T0353 14 :DGH 2drpA 116 :CSR T0353 25 :DVRDDKKAIEF 2drpA 119 :VYTHISNFCRH T0353 40 :LSSIG 2drpA 130 :YVTSH T0353 47 :GATVTSEECRFCHSQ 2drpA 135 :KRNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIKQ 2drpA 151 :TRKDNMTAHVKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=105 Number of alignments=30 # 2drpA read from 2drpA/merged-good-all-a2m # found chain 2drpA in template set T0353 27 :RDDKKAIEF 2drpA 121 :THISNFCRH T0353 40 :LSSI 2drpA 130 :YVTS T0353 46 :EGATVTSEECRFCHSQ 2drpA 134 :HKRNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIK 2drpA 151 :TRKDNMTAHVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=109 Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mdvA expands to /projects/compbio/data/pdb/1mdv.pdb.gz 1mdvA:# T0353 read from 1mdvA/merged-good-all-a2m # 1mdvA read from 1mdvA/merged-good-all-a2m # adding 1mdvA to template set # found chain 1mdvA in template set T0353 49 :TVTSEECRFCHSQKA 1mdvA 73 :NTKFKSCVGCHVEVA T0353 64 :PDEVIE 1mdvA 90 :DAAKKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=111 Number of alignments=32 # 1mdvA read from 1mdvA/merged-good-all-a2m # found chain 1mdvA in template set T0353 49 :TVTSEECRFCHSQ 1mdvA 73 :NTKFKSCVGCHVE Number of specific fragments extracted= 1 number of extra gaps= 0 total=112 # 1mdvA read from 1mdvA/merged-good-all-a2m # found chain 1mdvA in template set T0353 48 :ATVTSEECRFCHSQKA 1mdvA 72 :KNTKFKSCVGCHVEVA T0353 64 :PDEVIE 1mdvA 90 :DAAKKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=114 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2faoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2faoA expands to /projects/compbio/data/pdb/2fao.pdb.gz 2faoA:# T0353 read from 2faoA/merged-good-all-a2m # 2faoA read from 2faoA/merged-good-all-a2m # adding 2faoA to template set # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDV 2faoA 700 :FLKTSGGKGMHLLVPLER T0353 27 :RDDKKAIEFAKQWLSSI 2faoA 719 :HGWDEVKDFAQAISQHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=116 Number of alignments=34 # 2faoA read from 2faoA/merged-good-all-a2m # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDV 2faoA 700 :FLKTSGGKGMHLLVPLER T0353 27 :RDDKKAIEFAKQWLSSI 2faoA 719 :HGWDEVKDFAQAISQHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=118 Number of alignments=35 # 2faoA read from 2faoA/merged-good-all-a2m # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDVR 2faoA 700 :FLKTSGGKGMHLLVPLERR T0353 28 :DDKKAIEFAKQWLSSI 2faoA 720 :GWDEVKDFAQAISQHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=120 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a26/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a26 expands to /projects/compbio/data/pdb/1a26.pdb.gz 1a26:Warning: there is no chain 1a26 will retry with 1a26A # T0353 read from 1a26/merged-good-all-a2m # 1a26 read from 1a26/merged-good-all-a2m # adding 1a26 to template set # found chain 1a26 in template set T0353 27 :RDDKKAIEF 1a26 664 :KLAKPIQDL T0353 36 :AKQWLSSIGEEGATVTSEECRFCHSQKA 1a26 682 :MKKAMVEFEIDLQKMPLGKLSKRQIQSA T0353 66 :EVIEAIKQNG 1a26 715 :EVQQAVSDGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=123 Number of alignments=37 # 1a26 read from 1a26/merged-good-all-a2m # found chain 1a26 in template set T0353 29 :DKKAIEFAKQWLSSIGEEGA 1a26 706 :IQSAYSILNEVQQAVSDGGS T0353 52 :SEEC 1a26 726 :ESQI T0353 65 :DEVIEAIKQ 1a26 730 :LDLSNRFYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=126 Number of alignments=38 # 1a26 read from 1a26/merged-good-all-a2m # found chain 1a26 in template set T0353 29 :DKKAIEF 1a26 666 :AKPIQDL T0353 36 :AKQWLSSIGEEGATVTSEECRFCHSQKA 1a26 682 :MKKAMVEFEIDLQKMPLGKLSKRQIQSA T0353 66 :EVIEAIKQNG 1a26 715 :EVQQAVSDGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=129 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a7e/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a7e expands to /projects/compbio/data/pdb/1a7e.pdb.gz 1a7e:Warning: there is no chain 1a7e will retry with 1a7eA # T0353 read from 1a7e/merged-good-all-a2m # 1a7e read from 1a7e/merged-good-all-a2m # adding 1a7e to template set # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=131 Number of alignments=40 # 1a7e read from 1a7e/merged-good-all-a2m # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=133 Number of alignments=41 # 1a7e read from 1a7e/merged-good-all-a2m # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=135 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0hB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t0hB expands to /projects/compbio/data/pdb/1t0h.pdb.gz 1t0hB:# T0353 read from 1t0hB/merged-good-all-a2m # 1t0hB read from 1t0hB/merged-good-all-a2m # adding 1t0hB to template set # found chain 1t0hB in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t0hB 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=136 Number of alignments=43 # 1t0hB read from 1t0hB/merged-good-all-a2m # found chain 1t0hB in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t0hB 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=137 Number of alignments=44 # 1t0hB read from 1t0hB/merged-good-all-a2m # found chain 1t0hB in template set Warning: unaligning (T0353)E46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0hB)R424 T0353 20 :FDVFTDVRDDKK 1t0hB 383 :FDVILDENQLED T0353 32 :AIEFAKQWLSSIGE 1t0hB 399 :LADYLEAYWKATHP Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jg5A expands to /projects/compbio/data/pdb/1jg5.pdb.gz 1jg5A:# T0353 read from 1jg5A/merged-good-all-a2m # 1jg5A read from 1jg5A/merged-good-all-a2m # adding 1jg5A to template set # found chain 1jg5A in template set Warning: unaligning (T0353)V10 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 2 :QIHV 1jg5A 2 :YLLI T0353 7 :DTY 1jg5A 6 :STQ T0353 12 :AKDGHVM 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKKA 1jg5A 18 :VGDEHSDPEL T0353 40 :LSSIG 1jg5A 28 :MQQLG T0353 45 :EEGAT 1jg5A 38 :VLGNN T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEGCN 1jg5A 48 :VNDPPRIVLDKLECRGFRVLSMTGVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=146 Number of alignments=46 # 1jg5A read from 1jg5A/merged-good-all-a2m # found chain 1jg5A in template set Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)A12 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 2 :QIHVY 1jg5A 2 :YLLIS T0353 9 :YV 1jg5A 7 :TQ T0353 13 :KDGHVMH 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKKA 1jg5A 18 :VGDEHSDPEL T0353 40 :LSSIGEEGAT 1jg5A 28 :MQQLGASKRR T0353 52 :SEECRFC 1jg5A 38 :VLGNNFY T0353 59 :HSQKAPDEVIEAIKQNGYFIYKMEGC 1jg5A 47 :YVNDPPRIVLDKLECRGFRVLSMTGV Number of specific fragments extracted= 7 number of extra gaps= 1 total=153 Number of alignments=47 # 1jg5A read from 1jg5A/merged-good-all-a2m # found chain 1jg5A in template set Warning: unaligning (T0353)V10 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 5 :VYDTY 1jg5A 4 :LISTQ T0353 12 :AKDGHVM 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKK 1jg5A 18 :VGDEHSDPE T0353 39 :WLSSIGEEGA 1jg5A 27 :LMQQLGASKR T0353 51 :TSEECRFCH 1jg5A 37 :RVLGNNFYE T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEG 1jg5A 48 :VNDPPRIVLDKLECRGFRVLSMTG Number of specific fragments extracted= 6 number of extra gaps= 1 total=159 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r3eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r3eA expands to /projects/compbio/data/pdb/1r3e.pdb.gz 1r3eA:# T0353 read from 1r3eA/merged-good-all-a2m # 1r3eA read from 1r3eA/merged-good-all-a2m # adding 1r3eA to template set # found chain 1r3eA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDD 1r3eA 151 :KRVKIFKIWDVNIEGRDVSFRVEVSPGTY T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 49 :TVTSEECR 1r3eA 207 :PHTIEESL T0353 58 :CHSQKAPDEVIEA 1r3eA 215 :NVFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 5 number of extra gaps= 0 total=164 Number of alignments=49 # 1r3eA read from 1r3eA/merged-good-all-a2m # found chain 1r3eA in template set T0353 2 :QIHVYDTYVKAKDGHVMHFDVFTDVRDD 1r3eA 152 :RVKIFKIWDVNIEGRDVSFRVEVSPGTY T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 49 :TVTSEECR 1r3eA 207 :PHTIEESL T0353 58 :CHSQKAPDEVIEA 1r3eA 215 :NVFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 5 number of extra gaps= 0 total=169 Number of alignments=50 # 1r3eA read from 1r3eA/merged-good-all-a2m # found chain 1r3eA in template set T0353 4 :HVYDTYV 1r3eA 157 :KIWDVNI T0353 14 :DGHVMHFDVFTDVR 1r3eA 164 :EGRDVSFRVEVSPG T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 48 :ATVTSEECRF 1r3eA 206 :GPHTIEESLN T0353 59 :HSQKAPDEVIEA 1r3eA 216 :VFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 6 number of extra gaps= 0 total=175 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1wtbA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1wtbA/merged-good-all-a2m.gz for input Trying 1wtbA/merged-good-all-a2m Error: Couldn't open file 1wtbA/merged-good-all-a2m or 1wtbA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wnyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wnyA expands to /projects/compbio/data/pdb/1wny.pdb.gz 1wnyA:# T0353 read from 1wnyA/merged-good-all-a2m # 1wnyA read from 1wnyA/merged-good-all-a2m # adding 1wnyA to template set # found chain 1wnyA in template set T0353 27 :RDDKKAIEFAKQW 1wnyA 323 :AFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFI 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=177 Number of alignments=52 # 1wnyA read from 1wnyA/merged-good-all-a2m # found chain 1wnyA in template set T0353 27 :RDDKKAIEFAKQW 1wnyA 323 :AFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=179 Number of alignments=53 # 1wnyA read from 1wnyA/merged-good-all-a2m # found chain 1wnyA in template set Warning: unaligning (T0353)G83 because last residue in template chain is (1wnyA)S381 T0353 9 :YVKAKDGHVM 1wnyA 308 :YVSQEDGTGI T0353 22 :VFTDVRDDKKAIEFAKQW 1wnyA 318 :VHQAPAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGY 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGL T0353 78 :IYKME 1wnyA 376 :LFKEE Number of specific fragments extracted= 4 number of extra gaps= 0 total=183 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mg2D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1mg2D/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1mg2D/merged-good-all-a2m.gz for input Trying 1mg2D/merged-good-all-a2m Error: Couldn't open file 1mg2D/merged-good-all-a2m or 1mg2D/merged-good-all-a2m.gz for input # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/T0353/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/T0353/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0353/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0353/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0353)T24.CB, (T0353)F35.CB) [> 3.9724 = 6.6206 < 8.6068] w=1.0000 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)F20.CB) [> 4.2156 = 7.0261 < 9.1339] w=0.9939 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)F23.CB) [> 3.7641 = 6.2735 < 8.1555] w=0.9575 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)F20.CB) [> 3.4970 = 5.8283 < 7.5767] w=0.9210 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)H19.CB) [> 4.3074 = 7.1789 < 9.3326] w=0.9195 to align # Constraint # added constraint: constraint((T0353)I68.CB, (T0353)I78.CB) [> 3.9711 = 6.6184 < 8.6040] w=0.9086 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)F35.CB) [> 4.0349 = 6.7249 < 8.7423] w=0.8565 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)T24.CB) [> 3.9625 = 6.6042 < 8.5855] w=0.8086 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)F20.CB) [> 3.5110 = 5.8517 < 7.6072] w=0.7713 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)D25.CB) [> 3.3889 = 5.6481 < 7.3425] w=0.7217 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)D21.CB) [> 2.9136 = 4.8561 < 6.3129] w=0.7191 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)V22.CB) [> 4.0376 = 6.7294 < 8.7481] w=0.7100 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)D21.CB) [> 4.0687 = 6.7812 < 8.8156] w=0.6983 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)V22.CB) [> 4.4467 = 7.4111 < 9.6344] w=0.6469 to align # Constraint # added constraint: constraint((T0353)G44.CA, (T0353)S60.CB) [> 3.8579 = 6.4298 < 8.3587] w=0.6260 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)I43.CB) [> 3.6018 = 6.0030 < 7.8039] w=0.6144 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)T24.CB) [> 4.1431 = 6.9051 < 8.9767] w=0.5927 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)F23.CB) [> 3.2582 = 5.4303 < 7.0594] w=0.5896 to align # Constraint # added constraint: constraint((T0353)A32.CB, (T0353)N74.CB) [> 3.8908 = 6.4847 < 8.4301] w=0.5853 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)A36.CB) [> 3.9114 = 6.5190 < 8.4747] w=0.5731 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)V22.CB) [> 3.6001 = 6.0002 < 7.8002] w=0.5701 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)V22.CB) [> 3.3956 = 5.6593 < 7.3571] w=0.5635 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)A36.CB) [> 3.5487 = 5.9145 < 7.6888] w=0.5631 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)A32.CB) [> 3.6155 = 6.0259 < 7.8336] w=0.5623 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)T24.CB) [> 3.8384 = 6.3974 < 8.3166] w=0.5106 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)D25.CB) [> 3.8922 = 6.4870 < 8.4331] w=0.5081 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)V22.CB) [> 3.7560 = 6.2601 < 8.1381] w=0.5045 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)F23.CB) [> 4.3421 = 7.2369 < 9.4079] w=0.5011 to align # Constraint # added constraint: constraint((T0353)C55.CB, (T0353)V67.CB) [> 3.8418 = 6.4030 < 8.3239] w=0.5007 to align # Constraint # added constraint: constraint((T0353)K11.CB, (T0353)F20.CB) [> 3.3515 = 5.5859 < 7.2617] w=0.4965 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)W39.CB) [> 3.5069 = 5.8449 < 7.5983] w=0.4960 to align # Constraint # added constraint: constraint((T0353)K13.CB, (T0353)A63.CB) [> 3.7187 = 6.1978 < 8.0571] w=0.4803 to align # Constraint # added constraint: constraint((T0353)G15.CA, (T0353)P64.CB) [> 4.2839 = 7.1398 < 9.2817] w=0.4803 to align # Constraint # added constraint: constraint((T0353)H16.CB, (T0353)Q61.CB) [> 3.2008 = 5.3346 < 6.9350] w=0.4803 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)S60.CB) [> 3.2777 = 5.4628 < 7.1017] w=0.4803 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)V67.CB) [> 3.7666 = 6.2777 < 8.1610] w=0.4803 to align # Constraint # added constraint: constraint((T0353)I43.CB, (T0353)S60.CB) [> 3.6227 = 6.0378 < 7.8492] w=0.4803 to align # Constraint # added constraint: constraint((T0353)I43.CB, (T0353)A70.CB) [> 3.7692 = 6.2821 < 8.1667] w=0.4803 to align # Constraint # added constraint: constraint((T0353)I43.CB, (T0353)I71.CB) [> 4.7308 = 7.8847 < 10.2501] w=0.4803 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)M18.CB) [> 4.3534 = 7.2557 < 9.4324] w=0.4606 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)L40.CB) [> 3.9574 = 6.5956 < 8.5743] w=0.4570 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)T24.CB) [> 4.0207 = 6.7012 < 8.7116] w=0.4439 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)D25.CB) [> 4.0094 = 6.6823 < 8.6870] w=0.4299 to align # Constraint # added constraint: constraint((T0353)T24.CB, (T0353)A36.CB) [> 3.7608 = 6.2680 < 8.1484] w=0.4298 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)F23.CB) [> 3.0758 = 5.1263 < 6.6642] w=0.4243 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)H19.CB) [> 3.4131 = 5.6885 < 7.3951] w=0.4236 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)M18.CB) [> 3.5858 = 5.9763 < 7.7692] w=0.4236 to align # Constraint # added constraint: constraint((T0353)K37.CB, (T0353)G47.CA) [> 3.8672 = 6.4454 < 8.3790] w=0.4114 to align # Constraint # added constraint: constraint((T0353)L40.CB, (T0353)V50.CB) [> 4.3809 = 7.3015 < 9.4919] w=0.4114 to align # Constraint # added constraint: constraint((T0353)C58.CB, (T0353)V67.CB) [> 3.7573 = 6.2621 < 8.1408] w=0.4103 to align # Constraint # added constraint: constraint((T0353)A12.CB, (T0353)A63.CB) [> 4.3443 = 7.2404 < 9.4125] w=0.3989 to align # Constraint # added constraint: constraint((T0353)V17.CB, (T0353)K62.CB) [> 3.4719 = 5.7866 < 7.5225] w=0.3989 to align # Constraint # added constraint: constraint((T0353)V17.CB, (T0353)A63.CB) [> 4.0517 = 6.7527 < 8.7786] w=0.3989 to align # Constraint # added constraint: constraint((T0353)V17.CB, (T0353)V67.CB) [> 2.9966 = 4.9944 < 6.4927] w=0.3989 to align # Constraint # added constraint: constraint((T0353)K11.CB, (T0353)D21.CB) [> 4.4883 = 7.4804 < 9.7246] w=0.3670 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)D21.CB) [> 2.8826 = 4.8044 < 6.2457] w=0.3624 to align # Constraint # added constraint: constraint((T0353)D21.CB, (T0353)W39.CB) [> 4.5541 = 7.5901 < 9.8672] w=0.3612 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)F20.CB) [> 4.1351 = 6.8919 < 8.9594] w=0.3474 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)D21.CB) [> 3.4539 = 5.7565 < 7.4834] w=0.3470 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)H19.CB) [> 4.2553 = 7.0922 < 9.2199] w=0.3422 to align # Constraint # added constraint: constraint((T0353)T24.CB, (T0353)L40.CB) [> 3.3624 = 5.6041 < 7.2853] w=0.3230 to align # Constraint # added constraint: constraint((T0353)D29.CB, (T0353)L40.CB) [> 3.9664 = 6.6106 < 8.5938] w=0.3230 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)I71.CB) [> 4.1352 = 6.8920 < 8.9595] w=0.3202 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)Y76.CB) [> 3.3722 = 5.6204 < 7.3065] w=0.3202 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)M18.CB) [> 3.8692 = 6.4487 < 8.3833] w=0.3202 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)V67.CB) [> 3.5566 = 5.9277 < 7.7061] w=0.3202 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)I68.CB) [> 4.7103 = 7.8505 < 10.2056] w=0.3202 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)I71.CB) [> 4.5880 = 7.6467 < 9.9407] w=0.3202 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)M18.CB) [> 3.6102 = 6.0170 < 7.8221] w=0.3202 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)V17.CB) [> 3.8811 = 6.4685 < 8.4090] w=0.3202 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)V17.CB) [> 2.8906 = 4.8177 < 6.2630] w=0.3202 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)A63.CB) [> 4.4226 = 7.3710 < 9.5822] w=0.3202 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)P64.CB) [> 2.7762 = 4.6270 < 6.0152] w=0.3202 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)V17.CB) [> 3.8024 = 6.3373 < 8.2384] w=0.3175 to align # Constraint # added constraint: constraint((T0353)E54.CB, (T0353)V67.CB) [> 4.1888 = 6.9814 < 9.0758] w=0.2949 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)V22.CB) [> 4.5617 = 7.6028 < 9.8836] w=0.2865 to align # Constraint # added constraint: constraint((T0353)C55.CB, (T0353)E66.CB) [> 4.2575 = 7.0959 < 9.2247] w=0.2842 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)V26.CB) [> 3.6503 = 6.0839 < 7.9091] w=0.2840 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)D21.CB) [> 4.2546 = 7.0909 < 9.2182] w=0.2752 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)D21.CB) [> 3.9732 = 6.6220 < 8.6086] w=0.2748 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)A32.CB) [> 3.0128 = 5.0213 < 6.5277] w=0.2693 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)A32.CB) [> 3.4252 = 5.7087 < 7.4212] w=0.2693 to align # Constraint # added constraint: constraint((T0353)D21.CB, (T0353)A36.CB) [> 4.0032 = 6.6719 < 8.6735] w=0.2689 to align # Constraint # added constraint: constraint((T0353)A32.CB, (T0353)E54.CB) [> 4.6350 = 7.7250 < 10.0424] w=0.2546 to align # Constraint # added constraint: constraint((T0353)A32.CB, (T0353)C55.CB) [> 3.0057 = 5.0095 < 6.5123] w=0.2546 to align # Constraint # added constraint: constraint((T0353)A32.CB, (T0353)C58.CB) [> 4.5742 = 7.6237 < 9.9108] w=0.2546 to align # Constraint # added constraint: constraint((T0353)I33.CB, (T0353)C55.CB) [> 3.7818 = 6.3030 < 8.1939] w=0.2546 to align # Constraint # added constraint: constraint((T0353)A36.CB, (T0353)G47.CA) [> 3.6879 = 6.1465 < 7.9904] w=0.2546 to align # Constraint # added constraint: constraint((T0353)A36.CB, (T0353)V50.CB) [> 3.4927 = 5.8212 < 7.5676] w=0.2546 to align # Constraint # added constraint: constraint((T0353)A36.CB, (T0353)E54.CB) [> 4.5795 = 7.6326 < 9.9224] w=0.2546 to align # Constraint # added constraint: constraint((T0353)T24.CB, (T0353)H59.CB) [> 3.8521 = 6.4201 < 8.3462] w=0.2450 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)M18.CB) [> 2.7212 = 4.5353 < 5.8959] w=0.2415 to align # Constraint # added constraint: constraint((T0353)D25.CB, (T0353)F57.CB) [> 4.2103 = 7.0172 < 9.1224] w=0.2415 to align # Constraint # added constraint: constraint((T0353)V26.CB, (T0353)F57.CB) [> 3.7311 = 6.2185 < 8.0841] w=0.2415 to align # Constraint # added constraint: constraint((T0353)M18.CB, (T0353)S60.CB) [> 4.1809 = 6.9681 < 9.0585] w=0.2388 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)F23.CB) [> 4.5866 = 7.6444 < 9.9377] w=0.2303 to align # Constraint # added constraint: constraint((T0353)C58.CB, (T0353)I71.CB) [> 4.7603 = 7.9338 < 10.3139] w=0.2239 to align # Constraint # added constraint: constraint((T0353)C58.CB, (T0353)A70.CB) [> 3.5734 = 5.9557 < 7.7424] w=0.2239 to align # Constraint # added constraint: constraint((T0353)M18.CB, (T0353)W39.CB) [> 4.7982 = 7.9970 < 10.3962] w=0.2187 to align # Constraint # added constraint: constraint((T0353)R56.CB, (T0353)E66.CB) [> 4.2912 = 7.1520 < 9.2976] w=0.2187 to align # Constraint # added constraint: constraint((T0353)R56.CB, (T0353)A70.CB) [> 2.8517 = 4.7528 < 6.1787] w=0.2187 to align # Constraint # added constraint: constraint((T0353)V67.CB, (T0353)I78.CB) [> 4.3929 = 7.3214 < 9.5179] w=0.2187 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)F23.CB) [> 4.3903 = 7.3171 < 9.5123] w=0.2180 to align # Constraint # added constraint: constraint((T0353)M1.CB, (T0353)R27.CB) [> 3.3722 = 5.6203 < 7.3064] w=0.2173 to align # Constraint # added constraint: constraint((T0353)Q2.CB, (T0353)V26.CB) [> 3.8476 = 6.4127 < 8.3365] w=0.2166 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)F35.CB) [> 3.7896 = 6.3159 < 8.2107] w=0.2166 to align # Constraint # added constraint: constraint((T0353)S41.CB, (T0353)V50.CB) [> 4.4265 = 7.3775 < 9.5907] w=0.2165 to align # Constraint # added constraint: constraint((T0353)F57.CB, (T0353)I71.CB) [> 4.0092 = 6.6820 < 8.6865] w=0.2165 to align # Constraint # added constraint: constraint((T0353)F20.CB, (T0353)C55.CB) [> 4.5080 = 7.5133 < 9.7673] w=0.2152 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)T24.CB) [> 4.6438 = 7.7396 < 10.0615] w=0.2114 to align # Constraint # added constraint: constraint((T0353)D21.CB, (T0353)F35.CB) [> 4.5235 = 7.5392 < 9.8009] w=0.2083 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)F23.CB) [> 3.8045 = 6.3408 < 8.2430] w=0.2078 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)H19.CB) [> 4.1047 = 6.8412 < 8.8936] w=0.2074 to align # Constraint # added constraint: constraint((T0353)K11.CB, (T0353)A32.CB) [> 3.5347 = 5.8911 < 7.6584] w=0.2062 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)A32.CB) [> 3.8762 = 6.4603 < 8.3983] w=0.2062 to align # Constraint # added constraint: constraint((T0353)V50.CB, (T0353)A63.CB) [> 3.0394 = 5.0657 < 6.5855] w=0.2058 to align # Constraint # added constraint: constraint((T0353)V50.CB, (T0353)S60.CB) [> 3.9539 = 6.5898 < 8.5668] w=0.2058 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)A36.CB) [> 2.9191 = 4.8652 < 6.3248] w=0.2023 to align # Constraint # added constraint: constraint((T0353)T8.CB, (T0353)A36.CB) [> 4.4537 = 7.4228 < 9.6496] w=0.2023 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)L40.CB) [> 4.1372 = 6.8953 < 8.9638] w=0.2023 to align # Constraint # added constraint: constraint((T0353)F20.CB, (T0353)A36.CB) [> 3.2048 = 5.3413 < 6.9436] w=0.2023 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)I33.CB) [> 4.4887 = 7.4811 < 9.7255] w=0.2019 to align # Constraint # added constraint: constraint((T0353)F20.CB, (T0353)A32.CB) [> 3.9936 = 6.6561 < 8.6529] w=0.2015 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)A36.CB) [> 4.2273 = 7.0454 < 9.1590] w=0.2011 to align # Constraint # added constraint: constraint((T0353)Y9.CB, (T0353)W39.CB) [> 4.0396 = 6.7327 < 8.7525] w=0.2011 to align # Constraint # added constraint: constraint((T0353)K37.CB, (T0353)N74.CB) [> 4.5250 = 7.5416 < 9.8041] w=0.2011 to align # Constraint # added constraint: constraint((T0353)I68.CB, (T0353)K80.CB) [> 4.6384 = 7.7307 < 10.0499] w=0.1888 to align # Constraint # added constraint: constraint((T0353)S42.CB, (T0353)F57.CB) [> 4.3905 = 7.3174 < 9.5126] w=0.1864 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)I71.CB) [> 4.6102 = 7.6837 < 9.9889] w=0.1601 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)H16.CB) [> 3.7157 = 6.1928 < 8.0506] w=0.1504 to align # Constraint # added constraint: constraint((T0353)I3.CB, (T0353)D28.CB) [> 2.6335 = 4.3892 < 5.7060] w=0.1458 to align # Constraint # added constraint: constraint((T0353)M1.CB, (T0353)V26.CB) [> 4.0217 = 6.7028 < 8.7137] w=0.1444 to align # Constraint # added constraint: constraint((T0353)M1.CB, (T0353)K31.CB) [> 3.3356 = 5.5594 < 7.2272] w=0.1444 to align # Constraint # added constraint: constraint((T0353)H16.CB, (T0353)A32.CB) [> 4.7263 = 7.8771 < 10.2402] w=0.1443 to align # Constraint # added constraint: constraint((T0353)G15.CA, (T0353)D25.CB) [> 4.0545 = 6.7575 < 8.7848] w=0.1443 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)F20.CB) [> 3.5291 = 5.8818 < 7.6464] w=0.1403 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)F20.CB) [> 3.8167 = 6.3611 < 8.2695] w=0.1403 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)A32.CB) [> 2.0816 = 3.4694 < 4.5102] w=0.1349 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)I33.CB) [> 4.7255 = 7.8759 < 10.2387] w=0.1349 to align # Constraint # added constraint: constraint((T0353)M18.CB, (T0353)L40.CB) [> 4.7267 = 7.8778 < 10.2411] w=0.1349 to align # Constraint # added constraint: constraint((T0353)F23.CB, (T0353)A32.CB) [> 4.1441 = 6.9069 < 8.9790] w=0.1349 to align # Constraint # added constraint: constraint((T0353)H19.CB, (T0353)A36.CB) [> 3.4538 = 5.7563 < 7.4832] w=0.1344 to align # Constraint # added constraint: constraint((T0353)H19.CB, (T0353)A32.CB) [> 3.1231 = 5.2052 < 6.7667] w=0.1340 to align # Constraint # added constraint: constraint((T0353)T24.CB, (T0353)C58.CB) [> 3.9296 = 6.5493 < 8.5141] w=0.0849 to align # Constraint # added constraint: constraint((T0353)V5.CB, (T0353)H19.CB) [> 3.6115 = 6.0191 < 7.8249] w=0.0814 to align # Constraint # added constraint: constraint((T0353)Y6.CB, (T0353)H19.CB) [> 2.8694 = 4.7823 < 6.2170] w=0.0814 to align # Constraint # added constraint: constraint((T0353)H19.CB, (T0353)H59.CB) [> 3.2377 = 5.3962 < 7.0151] w=0.0814 to align # Constraint # added constraint: constraint((T0353)H4.CB, (T0353)M18.CB) [> 4.7433 = 7.9054 < 10.2771] w=0.0787 to align # Constraint # added constraint: constraint((T0353)V22.CB, (T0353)H59.CB) [> 3.3997 = 5.6663 < 7.3661] w=0.0787 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)D25.CB) [> 2.8674 = 4.7790 < 6.2127] w=0.0722 to align # Constraint # added constraint: constraint((T0353)F20.CB, (T0353)W39.CB) [> 4.6069 = 7.6781 < 9.9815] w=0.0674 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)A32.CB) [> 3.0296 = 5.0494 < 6.5642] w=0.0670 to align # Constraint # added constraint: constraint((T0353)D7.CB, (T0353)A36.CB) [> 3.2155 = 5.3591 < 6.9668] w=0.0670 to align # Constraint # added constraint: constraint((T0353)H19.CB, (T0353)I33.CB) [> 4.6757 = 7.7928 < 10.1307] w=0.0670 to align # Constraint # added constraint: constraint((T0353)V10.CB, (T0353)V22.CB) [> 3.1755 = 5.2925 < 6.8803] w=0.0085 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0353/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # 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 T0353 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 T0353 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 # Found a chain break before 82 # copying to AlignedFragments data structure # 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 51 # 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 78 # 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 76 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # 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 # 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 84 # 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 84 # 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 84 # 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 84 # 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 83 # 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 74 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 83 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 80 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # 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 68 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 52 # 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 55 # 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 42 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 62 # 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 36 # 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 78 # 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 15 # 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 84 # 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 80 # 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 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 90, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 92, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 Skipped atom 21, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 23, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 61, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 63, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 229, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 231, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz # WARNING: incomplete conformation T0353 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 T0353 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 77 # 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 83 # 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 72 # 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 84 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # 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 74 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 73 # 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 62 # 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 62 # 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # 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 # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # 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 75 # 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 # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # 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 61 # 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 49 # 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 25 # 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 21 # 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 84 # 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 84 # 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 84 # 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 81 # 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 84 # 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 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # 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 # Found a chain break before 78 # copying to AlignedFragments data structure # 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 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # 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 82 # 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 18 # 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 49 # 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 T0353 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 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 48 # 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 22 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 58 # 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 15 # 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 9 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # 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 79 # 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 48 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 75 # 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 T0353 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 T0353 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 T0353 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 T0353 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 62 # 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 55 # 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 47 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # 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 62 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 75 # 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 50 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 53 # 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 54 # 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 T0353 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 T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0353 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: atoms too close: (T0353)R56.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)F57.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing # WARNING: incomplete conformation T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 T0353 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 79 # 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 84 # 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 78 # 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 76 # 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 83 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # 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 52 # 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 21 # 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 61 # 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 # 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 81 # 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 WARNING: atoms too close: (T0353)M81.O and (T0353)E82.N only 0.000 apart, marking (T0353)E82.N as missing # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 82 # 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 82 # 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 82 # 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 T0353 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 T0353 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 T0353 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 T0353 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 # Found a chain break before 61 # copying to AlignedFragments data structure # 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 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # 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 T0353 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 T0353 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 T0353 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 T0353 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 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 T0353 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: (T0353)H16.N and (T0353)V17.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)V17.CA only 0.000 apart, marking (T0353)V17.CA as missing WARNING: atoms too close: (T0353)H16.O and (T0353)V17.O only 0.000 apart, marking (T0353)V17.O as missing WARNING: atoms too close: (T0353)H16.C and (T0353)V17.C only 0.000 apart, marking (T0353)V17.C as missing WARNING: atoms too close: (T0353)V17.N and (T0353)M18.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)M18.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)M18.CA only 0.000 apart, marking (T0353)M18.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)M18.CA only 0.000 apart, marking (T0353)M18.CA as missing WARNING: atoms too close: (T0353)V17.O and (T0353)M18.O only 0.000 apart, marking (T0353)M18.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)M18.O only 0.000 apart, marking (T0353)M18.O as missing WARNING: atoms too close: (T0353)V17.C and (T0353)M18.C only 0.000 apart, marking (T0353)M18.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)M18.C only 0.000 apart, marking (T0353)M18.C as missing WARNING: atoms too close: (T0353)M18.N and (T0353)V22.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)V22.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)V22.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)V22.CA only 0.000 apart, marking (T0353)V22.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)V22.CA only 0.000 apart, marking (T0353)V22.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)V22.CA only 0.000 apart, marking (T0353)V22.CA as missing WARNING: atoms too close: (T0353)M18.O and (T0353)V22.O only 0.000 apart, marking (T0353)V22.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)V22.O only 0.000 apart, marking (T0353)V22.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)V22.O only 0.000 apart, marking (T0353)V22.O as missing WARNING: atoms too close: (T0353)M18.C and (T0353)V22.C only 0.000 apart, marking (T0353)V22.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)V22.C only 0.000 apart, marking (T0353)V22.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)V22.C only 0.000 apart, marking (T0353)V22.C as missing WARNING: atoms too close: (T0353)V22.N and (T0353)G44.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)G44.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)G44.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)G44.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)G44.CA only 0.000 apart, marking (T0353)G44.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)G44.CA only 0.000 apart, marking (T0353)G44.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)G44.CA only 0.000 apart, marking (T0353)G44.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)G44.CA only 0.000 apart, marking (T0353)G44.CA as missing WARNING: atoms too close: (T0353)V22.O and (T0353)G44.O only 0.000 apart, marking (T0353)G44.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)G44.O only 0.000 apart, marking (T0353)G44.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)G44.O only 0.000 apart, marking (T0353)G44.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)G44.O only 0.000 apart, marking (T0353)G44.O as missing WARNING: atoms too close: (T0353)V22.C and (T0353)G44.C only 0.000 apart, marking (T0353)G44.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)G44.C only 0.000 apart, marking (T0353)G44.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)G44.C only 0.000 apart, marking (T0353)G44.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)G44.C only 0.000 apart, marking (T0353)G44.C as missing WARNING: atoms too close: (T0353)G44.N and (T0353)C58.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)C58.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)C58.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)C58.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)C58.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)C58.CA only 0.000 apart, marking (T0353)C58.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)C58.CA only 0.000 apart, marking (T0353)C58.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)C58.CA only 0.000 apart, marking (T0353)C58.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)C58.CA only 0.000 apart, marking (T0353)C58.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)C58.CA only 0.000 apart, marking (T0353)C58.CA as missing WARNING: atoms too close: (T0353)G44.O and (T0353)C58.O only 0.000 apart, marking (T0353)C58.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)C58.O only 0.000 apart, marking (T0353)C58.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)C58.O only 0.000 apart, marking (T0353)C58.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)C58.O only 0.000 apart, marking (T0353)C58.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)C58.O only 0.000 apart, marking (T0353)C58.O as missing WARNING: atoms too close: (T0353)G44.C and (T0353)C58.C only 0.000 apart, marking (T0353)C58.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)C58.C only 0.000 apart, marking (T0353)C58.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)C58.C only 0.000 apart, marking (T0353)C58.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)C58.C only 0.000 apart, marking (T0353)C58.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)C58.C only 0.000 apart, marking (T0353)C58.C as missing WARNING: atoms too close: (T0353)C58.N and (T0353)H59.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.N and (T0353)H59.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)H59.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)H59.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)H59.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)H59.N only 0.000 apart, marking (T0353)H59.N as missing WARNING: atoms too close: (T0353)C58.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)H59.CA only 0.000 apart, marking (T0353)H59.CA as missing WARNING: atoms too close: (T0353)C58.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)G44.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)H59.O only 0.000 apart, marking (T0353)H59.O as missing WARNING: atoms too close: (T0353)C58.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)G44.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)H59.C only 0.000 apart, marking (T0353)H59.C as missing WARNING: atoms too close: (T0353)H59.N and (T0353)S60.N only 0.000 apart, marking (T0353)H59.N as missing WARNING: atoms too close: (T0353)C58.N and (T0353)S60.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.N and (T0353)S60.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)S60.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)S60.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)S60.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)S60.N only 0.000 apart, marking (T0353)S60.N as missing WARNING: atoms too close: (T0353)H59.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)C58.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)S60.CA only 0.000 apart, marking (T0353)S60.CA as missing WARNING: atoms too close: (T0353)H59.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)C58.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)G44.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)S60.O only 0.000 apart, marking (T0353)S60.O as missing WARNING: atoms too close: (T0353)H59.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)C58.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)G44.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)S60.C only 0.000 apart, marking (T0353)S60.C as missing WARNING: atoms too close: (T0353)S60.N and (T0353)Q61.N only 0.000 apart, marking (T0353)S60.N as missing WARNING: atoms too close: (T0353)H59.N and (T0353)Q61.N only 0.000 apart, marking (T0353)H59.N as missing WARNING: atoms too close: (T0353)C58.N and (T0353)Q61.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.N and (T0353)Q61.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)Q61.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)Q61.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)Q61.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)Q61.N only 0.000 apart, marking (T0353)Q61.N as missing WARNING: atoms too close: (T0353)S60.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)H59.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)C58.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)Q61.CA only 0.000 apart, marking (T0353)Q61.CA as missing WARNING: atoms too close: (T0353)S60.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)H59.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)C58.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)G44.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)Q61.O only 0.000 apart, marking (T0353)Q61.O as missing WARNING: atoms too close: (T0353)S60.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)H59.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)C58.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)G44.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)Q61.C only 0.000 apart, marking (T0353)Q61.C as missing WARNING: atoms too close: (T0353)Q61.N and (T0353)K62.N only 0.000 apart, marking (T0353)Q61.N as missing WARNING: atoms too close: (T0353)S60.N and (T0353)K62.N only 0.000 apart, marking (T0353)S60.N as missing WARNING: atoms too close: (T0353)H59.N and (T0353)K62.N only 0.000 apart, marking (T0353)H59.N as missing WARNING: atoms too close: (T0353)C58.N and (T0353)K62.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.N and (T0353)K62.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)K62.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)K62.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)K62.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)K62.N only 0.000 apart, marking (T0353)K62.N as missing WARNING: atoms too close: (T0353)Q61.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)S60.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)H59.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)C58.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)K62.CA only 0.000 apart, marking (T0353)K62.CA as missing WARNING: atoms too close: (T0353)Q61.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)S60.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)H59.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)C58.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)G44.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)K62.O only 0.000 apart, marking (T0353)K62.O as missing WARNING: atoms too close: (T0353)Q61.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)S60.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)H59.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)C58.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)G44.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)K62.C only 0.000 apart, marking (T0353)K62.C as missing WARNING: atoms too close: (T0353)K62.N and (T0353)A63.N only 0.000 apart, marking (T0353)K62.N as missing WARNING: atoms too close: (T0353)Q61.N and (T0353)A63.N only 0.000 apart, marking (T0353)Q61.N as missing WARNING: atoms too close: (T0353)S60.N and (T0353)A63.N only 0.000 apart, marking (T0353)S60.N as missing WARNING: atoms too close: (T0353)H59.N and (T0353)A63.N only 0.000 apart, marking (T0353)H59.N as missing WARNING: atoms too close: (T0353)C58.N and (T0353)A63.N only 0.000 apart, marking (T0353)C58.N as missing WARNING: atoms too close: (T0353)G44.N and (T0353)A63.N only 0.000 apart, marking (T0353)G44.N as missing WARNING: atoms too close: (T0353)V22.N and (T0353)A63.N only 0.000 apart, marking (T0353)V22.N as missing WARNING: atoms too close: (T0353)M18.N and (T0353)A63.N only 0.000 apart, marking (T0353)M18.N as missing WARNING: atoms too close: (T0353)V17.N and (T0353)A63.N only 0.000 apart, marking (T0353)V17.N as missing WARNING: atoms too close: (T0353)H16.N and (T0353)A63.N only 0.000 apart, marking (T0353)A63.N as missing WARNING: atoms too close: (T0353)K62.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)Q61.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)S60.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)H59.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)C58.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)G44.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)V22.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)M18.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)V17.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)H16.CA and (T0353)A63.CA only 0.000 apart, marking (T0353)A63.CA as missing WARNING: atoms too close: (T0353)K62.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)Q61.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)S60.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)H59.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)C58.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)G44.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)V22.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)M18.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)V17.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)H16.O and (T0353)A63.O only 0.000 apart, marking (T0353)A63.O as missing WARNING: atoms too close: (T0353)K62.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)Q61.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)S60.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)H59.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)C58.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)G44.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)V22.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)M18.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)V17.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing WARNING: atoms too close: (T0353)H16.C and (T0353)A63.C only 0.000 apart, marking (T0353)A63.C as missing # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0353 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.0257 model score 1.2734 model score 1.1332 model score 1.0717 model score 1.0681 model score 1.3554 model score 1.3276 model score 0.9761 model score 1.3268 model score 0.9343 model score 1.6625 model score 0.9235 model score 1.4735 model score 1.3051 model score 1.5177 model score 1.6413 model score 0.6833 model score 0.6748 model score 1.6287 model score 2.1997 model score 0.6833 model score 0.6748 model score 0.8191 model score 0.6160 model score 0.7399 model score 2.0728 model score 2.2928 model score 1.0237 model score 1.0178 model score 1.1144 model score 0.8774 model score 1.9582 model score 1.4239 model score 1.1723 model score 1.2281 model score 0.9782 model score 1.0675 model score 1.2305 model score 1.4094 model score 1.1978 model score 1.4392 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.1723 model score 1.2176 model score 1.4841 model score 1.1891 model score 1.3113 model score 1.1404 model score 1.2281 model score 1.9582 model score 0.9782 model score 1.6838 model score 2.0323 model score 2.1362 model score 2.0318 model score 2.0806 model score 1.8121 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.9444 model score 1.8306 model score 2.0957 model score 2.1126 model score 2.1103 model score 2.3560 model score 1.0273 model score 1.9035 model score 1.1823 model score 1.7993 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6838 model score 1.1275 model score 1.1105 model score 1.4750 model score 1.5025 model score 1.3726 model score 2.2354 model score 1.8553 model score 1.8032 model score 1.0900 model score 1.3366 model score 1.4320 model score 1.1788 model score 1.0364 model score 2.0242 model score 2.0242 model score 1.1455 model score 1.3969 model score 1.3447 model score 1.1145 model score 1.1994 model score 0.6803 model score 1.1463 model score 1.1759 model score 1.2023 model score 1.1238 model score 1.2771 model score 1.1224 model score 1.8356 model score 1.7885 model score 1.6506 model score 1.7481 model score 1.3614 model score 1.5680 model score 1.2049 model score 1.8003 model score 1.3475 model score 0.6686 model score 0.7483 model score 0.7416 model score 0.9956 model score 1.0259 model score 1.2771 model score 1.7990 model score 1.3845 model score 1.3679 model score 1.4125 model score 1.7990 model score 1.1745 model score 0.9970 model score 1.0971 model score 1.1605 model score 1.1745 model score 0.9970 model score 0.9902 model score 1.0356 model score 1.1745 model score 1.0181 model score 1.2990 model score 1.2990 model score 1.6975 model score 1.0189 model score 1.7189 model score 1.1661 model score 1.4436 model score 1.0567 model score 0.9382 model score 1.4577 model score 1.2491 model score 1.1874 model score 1.2119 model score 1.3244 model score 1.1794 model score 1.3871 model score 1.1271 model score 0.9752 model score 1.1702 model score 1.1713 model score 1.0483 model score 1.1352 model score 0.8568 model score 1.3950 model score 1.6026 model score 1.2343 model score 1.1036 model score 0.8684 model score 1.3860 model score 1.5958 model score 1.2838 model score 0.7732 model score 0.6364 model score 0.7876 model score 0.7985 model score 0.8116 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.9342 model score 1.2345 model score 0.6857 model score 1.0184 model score 0.8265 model score 2.0833 model score 1.3364 model score 1.5881 model score 2.0803 model score 0.9752 model score 2.0833 model score 2.1362 model score 1.9524 model score 1.1652 model score 1.9730 model score 1.8439 model score 1.8608 model score 1.7217 model score 1.7422 model score 1.4632 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6437 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.6265 model score 0.4657 model score 0.5392 model score 0.5737 model score 0.5735 model score 0.7613 model score 1.1177 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0461 model score 1.6080 model score 2.1268 model score 1.8139 model score 1.2700 model score 1.4969 model score 1.6035 model score 1.5578 model score 1.1671 model score 1.2387 model score 1.0399 model score 1.1540 model score 1.2535 model score 1.2483 model score 0.6745 model score 1.8543 model score 1.9019 model score 1.7457 model score 1.5910 model score 1.0327 model score 1.1140 model score 1.3909 model score 1.0362 model score 2.1063 model score 1.1942 model score 1.2207 model score 1.9612 model score 1.2915 model score 0.9186 USE_META, weight: 0.7334 cost: 1.0257 min: 0.4657 max: 2.3560 USE_META, weight: 0.6154 cost: 1.2734 min: 0.4657 max: 2.3560 USE_META, weight: 0.6822 cost: 1.1332 min: 0.4657 max: 2.3560 USE_META, weight: 0.7115 cost: 1.0717 min: 0.4657 max: 2.3560 USE_META, weight: 0.7132 cost: 1.0681 min: 0.4657 max: 2.3560 USE_META, weight: 0.5764 cost: 1.3554 min: 0.4657 max: 2.3560 USE_META, weight: 0.5896 cost: 1.3276 min: 0.4657 max: 2.3560 USE_META, weight: 0.7570 cost: 0.9761 min: 0.4657 max: 2.3560 USE_META, weight: 0.5900 cost: 1.3268 min: 0.4657 max: 2.3560 USE_META, weight: 0.7769 cost: 0.9343 min: 0.4657 max: 2.3560 USE_META, weight: 0.4302 cost: 1.6625 min: 0.4657 max: 2.3560 USE_META, weight: 0.7820 cost: 0.9235 min: 0.4657 max: 2.3560 USE_META, weight: 0.5202 cost: 1.4735 min: 0.4657 max: 2.3560 USE_META, weight: 0.6004 cost: 1.3051 min: 0.4657 max: 2.3560 USE_META, weight: 0.4991 cost: 1.5177 min: 0.4657 max: 2.3560 USE_META, weight: 0.4403 cost: 1.6413 min: 0.4657 max: 2.3560 USE_META, weight: 0.8964 cost: 0.6833 min: 0.4657 max: 2.3560 USE_META, weight: 0.9005 cost: 0.6748 min: 0.4657 max: 2.3560 USE_META, weight: 0.4463 cost: 1.6287 min: 0.4657 max: 2.3560 USE_META, weight: 0.1744 cost: 2.1997 min: 0.4657 max: 2.3560 USE_META, weight: 0.8964 cost: 0.6833 min: 0.4657 max: 2.3560 USE_META, weight: 0.9005 cost: 0.6748 min: 0.4657 max: 2.3560 USE_META, weight: 0.8317 cost: 0.8191 min: 0.4657 max: 2.3560 USE_META, weight: 0.9285 cost: 0.6160 min: 0.4657 max: 2.3560 USE_META, weight: 0.8695 cost: 0.7399 min: 0.4657 max: 2.3560 USE_META, weight: 0.2348 cost: 2.0728 min: 0.4657 max: 2.3560 USE_META, weight: 0.1301 cost: 2.2928 min: 0.4657 max: 2.3560 USE_META, weight: 0.7343 cost: 1.0237 min: 0.4657 max: 2.3560 USE_META, weight: 0.7372 cost: 1.0178 min: 0.4657 max: 2.3560 USE_META, weight: 0.6912 cost: 1.1144 min: 0.4657 max: 2.3560 USE_META, weight: 0.8040 cost: 0.8774 min: 0.4657 max: 2.3560 USE_META, weight: 0.2894 cost: 1.9582 min: 0.4657 max: 2.3560 USE_META, weight: 0.5438 cost: 1.4239 min: 0.4657 max: 2.3560 USE_META, weight: 0.6636 cost: 1.1723 min: 0.4657 max: 2.3560 USE_META, weight: 0.6370 cost: 1.2281 min: 0.4657 max: 2.3560 USE_META, weight: 0.7560 cost: 0.9782 min: 0.4657 max: 2.3560 USE_META, weight: 0.7135 cost: 1.0675 min: 0.4657 max: 2.3560 USE_META, weight: 0.6359 cost: 1.2305 min: 0.4657 max: 2.3560 USE_META, weight: 0.5507 cost: 1.4094 min: 0.4657 max: 2.3560 USE_META, weight: 0.6514 cost: 1.1978 min: 0.4657 max: 2.3560 USE_META, weight: 0.5365 cost: 1.4392 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6636 cost: 1.1723 min: 0.4657 max: 2.3560 USE_META, weight: 0.6420 cost: 1.2176 min: 0.4657 max: 2.3560 USE_META, weight: 0.5151 cost: 1.4841 min: 0.4657 max: 2.3560 USE_META, weight: 0.6556 cost: 1.1891 min: 0.4657 max: 2.3560 USE_META, weight: 0.5974 cost: 1.3113 min: 0.4657 max: 2.3560 USE_META, weight: 0.6788 cost: 1.1404 min: 0.4657 max: 2.3560 USE_META, weight: 0.6370 cost: 1.2281 min: 0.4657 max: 2.3560 USE_META, weight: 0.2894 cost: 1.9582 min: 0.4657 max: 2.3560 USE_META, weight: 0.7560 cost: 0.9782 min: 0.4657 max: 2.3560 USE_META, weight: 0.4200 cost: 1.6838 min: 0.4657 max: 2.3560 USE_META, weight: 0.2541 cost: 2.0323 min: 0.4657 max: 2.3560 USE_META, weight: 0.2047 cost: 2.1362 min: 0.4657 max: 2.3560 USE_META, weight: 0.2544 cost: 2.0318 min: 0.4657 max: 2.3560 USE_META, weight: 0.2311 cost: 2.0806 min: 0.4657 max: 2.3560 USE_META, weight: 0.3589 cost: 1.8121 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.2960 cost: 1.9444 min: 0.4657 max: 2.3560 USE_META, weight: 0.3501 cost: 1.8306 min: 0.4657 max: 2.3560 USE_META, weight: 0.2239 cost: 2.0957 min: 0.4657 max: 2.3560 USE_META, weight: 0.2159 cost: 2.1126 min: 0.4657 max: 2.3560 USE_META, weight: 0.2170 cost: 2.1103 min: 0.4657 max: 2.3560 USE_META, weight: 0.1000 cost: 2.3560 min: 0.4657 max: 2.3560 USE_META, weight: 0.7326 cost: 1.0273 min: 0.4657 max: 2.3560 USE_META, weight: 0.3154 cost: 1.9035 min: 0.4657 max: 2.3560 USE_META, weight: 0.6588 cost: 1.1823 min: 0.4657 max: 2.3560 USE_META, weight: 0.3651 cost: 1.7993 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.4200 cost: 1.6838 min: 0.4657 max: 2.3560 USE_META, weight: 0.6849 cost: 1.1275 min: 0.4657 max: 2.3560 USE_META, weight: 0.6930 cost: 1.1105 min: 0.4657 max: 2.3560 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USE_META, weight: 0.6692 cost: 1.1605 min: 0.4657 max: 2.3560 USE_META, weight: 0.6625 cost: 1.1745 min: 0.4657 max: 2.3560 USE_META, weight: 0.7471 cost: 0.9970 min: 0.4657 max: 2.3560 USE_META, weight: 0.7503 cost: 0.9902 min: 0.4657 max: 2.3560 USE_META, weight: 0.7287 cost: 1.0356 min: 0.4657 max: 2.3560 USE_META, weight: 0.6625 cost: 1.1745 min: 0.4657 max: 2.3560 USE_META, weight: 0.7370 cost: 1.0181 min: 0.4657 max: 2.3560 USE_META, weight: 0.6033 cost: 1.2990 min: 0.4657 max: 2.3560 USE_META, weight: 0.6033 cost: 1.2990 min: 0.4657 max: 2.3560 USE_META, weight: 0.4135 cost: 1.6975 min: 0.4657 max: 2.3560 USE_META, weight: 0.7366 cost: 1.0189 min: 0.4657 max: 2.3560 USE_META, weight: 0.4033 cost: 1.7189 min: 0.4657 max: 2.3560 USE_META, weight: 0.6665 cost: 1.1661 min: 0.4657 max: 2.3560 USE_META, weight: 0.5344 cost: 1.4436 min: 0.4657 max: 2.3560 USE_META, weight: 0.7186 cost: 1.0567 min: 0.4657 max: 2.3560 USE_META, weight: 0.7750 cost: 0.9382 min: 0.4657 max: 2.3560 USE_META, weight: 0.5277 cost: 1.4577 min: 0.4657 max: 2.3560 USE_META, weight: 0.6270 cost: 1.2491 min: 0.4657 max: 2.3560 USE_META, weight: 0.6564 cost: 1.1874 min: 0.4657 max: 2.3560 USE_META, weight: 0.6447 cost: 1.2119 min: 0.4657 max: 2.3560 USE_META, weight: 0.5912 cost: 1.3244 min: 0.4657 max: 2.3560 USE_META, weight: 0.6602 cost: 1.1794 min: 0.4657 max: 2.3560 USE_META, weight: 0.5613 cost: 1.3871 min: 0.4657 max: 2.3560 USE_META, weight: 0.6851 cost: 1.1271 min: 0.4657 max: 2.3560 USE_META, weight: 0.7574 cost: 0.9752 min: 0.4657 max: 2.3560 USE_META, weight: 0.6646 cost: 1.1702 min: 0.4657 max: 2.3560 USE_META, weight: 0.6640 cost: 1.1713 min: 0.4657 max: 2.3560 USE_META, weight: 0.7226 cost: 1.0483 min: 0.4657 max: 2.3560 USE_META, weight: 0.6812 cost: 1.1352 min: 0.4657 max: 2.3560 USE_META, weight: 0.8138 cost: 0.8568 min: 0.4657 max: 2.3560 USE_META, weight: 0.5575 cost: 1.3950 min: 0.4657 max: 2.3560 USE_META, weight: 0.4587 cost: 1.6026 min: 0.4657 max: 2.3560 USE_META, weight: 0.6341 cost: 1.2343 min: 0.4657 max: 2.3560 USE_META, weight: 0.6963 cost: 1.1036 min: 0.4657 max: 2.3560 USE_META, weight: 0.8083 cost: 0.8684 min: 0.4657 max: 2.3560 USE_META, weight: 0.5618 cost: 1.3860 min: 0.4657 max: 2.3560 USE_META, weight: 0.4619 cost: 1.5958 min: 0.4657 max: 2.3560 USE_META, weight: 0.6105 cost: 1.2838 min: 0.4657 max: 2.3560 USE_META, weight: 0.8536 cost: 0.7732 min: 0.4657 max: 2.3560 USE_META, weight: 0.9187 cost: 0.6364 min: 0.4657 max: 2.3560 USE_META, weight: 0.8467 cost: 0.7876 min: 0.4657 max: 2.3560 USE_META, weight: 0.8416 cost: 0.7985 min: 0.4657 max: 2.3560 USE_META, weight: 0.8353 cost: 0.8116 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.7770 cost: 0.9342 min: 0.4657 max: 2.3560 USE_META, weight: 0.6340 cost: 1.2345 min: 0.4657 max: 2.3560 USE_META, weight: 0.8953 cost: 0.6857 min: 0.4657 max: 2.3560 USE_META, weight: 0.7369 cost: 1.0184 min: 0.4657 max: 2.3560 USE_META, weight: 0.8282 cost: 0.8265 min: 0.4657 max: 2.3560 USE_META, weight: 0.2298 cost: 2.0833 min: 0.4657 max: 2.3560 USE_META, weight: 0.5855 cost: 1.3364 min: 0.4657 max: 2.3560 USE_META, weight: 0.4656 cost: 1.5881 min: 0.4657 max: 2.3560 USE_META, weight: 0.2313 cost: 2.0803 min: 0.4657 max: 2.3560 USE_META, weight: 0.7574 cost: 0.9752 min: 0.4657 max: 2.3560 USE_META, weight: 0.2298 cost: 2.0833 min: 0.4657 max: 2.3560 USE_META, weight: 0.2046 cost: 2.1362 min: 0.4657 max: 2.3560 USE_META, weight: 0.2922 cost: 1.9524 min: 0.4657 max: 2.3560 USE_META, weight: 0.6670 cost: 1.1652 min: 0.4657 max: 2.3560 USE_META, weight: 0.2823 cost: 1.9730 min: 0.4657 max: 2.3560 USE_META, weight: 0.3438 cost: 1.8439 min: 0.4657 max: 2.3560 USE_META, weight: 0.3358 cost: 1.8608 min: 0.4657 max: 2.3560 USE_META, weight: 0.4020 cost: 1.7217 min: 0.4657 max: 2.3560 USE_META, weight: 0.3922 cost: 1.7422 min: 0.4657 max: 2.3560 USE_META, weight: 0.5251 cost: 1.4632 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.4391 cost: 1.6437 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.9234 cost: 0.6265 min: 0.4657 max: 2.3560 USE_META, weight: 1.0000 cost: 0.4657 min: 0.4657 max: 2.3560 USE_META, weight: 0.9650 cost: 0.5392 min: 0.4657 max: 2.3560 USE_META, weight: 0.9486 cost: 0.5737 min: 0.4657 max: 2.3560 USE_META, weight: 0.9487 cost: 0.5735 min: 0.4657 max: 2.3560 USE_META, weight: 0.8593 cost: 0.7613 min: 0.4657 max: 2.3560 USE_META, weight: 0.6896 cost: 1.1177 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.6137 cost: 1.2771 min: 0.4657 max: 2.3560 USE_META, weight: 0.2475 cost: 2.0461 min: 0.4657 max: 2.3560 USE_META, weight: 0.4561 cost: 1.6080 min: 0.4657 max: 2.3560 USE_META, weight: 0.2091 cost: 2.1268 min: 0.4657 max: 2.3560 USE_META, weight: 0.3581 cost: 1.8139 min: 0.4657 max: 2.3560 USE_META, weight: 0.6171 cost: 1.2700 min: 0.4657 max: 2.3560 USE_META, weight: 0.5090 cost: 1.4969 min: 0.4657 max: 2.3560 USE_META, weight: 0.4583 cost: 1.6035 min: 0.4657 max: 2.3560 USE_META, weight: 0.4800 cost: 1.5578 min: 0.4657 max: 2.3560 USE_META, weight: 0.6660 cost: 1.1671 min: 0.4657 max: 2.3560 USE_META, weight: 0.6320 cost: 1.2387 min: 0.4657 max: 2.3560 USE_META, weight: 0.7266 cost: 1.0399 min: 0.4657 max: 2.3560 USE_META, weight: 0.6723 cost: 1.1540 min: 0.4657 max: 2.3560 USE_META, weight: 0.6249 cost: 1.2535 min: 0.4657 max: 2.3560 USE_META, weight: 0.6274 cost: 1.2483 min: 0.4657 max: 2.3560 USE_META, weight: 0.9006 cost: 0.6745 min: 0.4657 max: 2.3560 USE_META, weight: 0.3389 cost: 1.8543 min: 0.4657 max: 2.3560 USE_META, weight: 0.3162 cost: 1.9019 min: 0.4657 max: 2.3560 USE_META, weight: 0.3906 cost: 1.7457 min: 0.4657 max: 2.3560 USE_META, weight: 0.4642 cost: 1.5910 min: 0.4657 max: 2.3560 USE_META, weight: 0.7300 cost: 1.0327 min: 0.4657 max: 2.3560 USE_META, weight: 0.6913 cost: 1.1140 min: 0.4657 max: 2.3560 USE_META, weight: 0.5595 cost: 1.3909 min: 0.4657 max: 2.3560 USE_META, weight: 0.7284 cost: 1.0362 min: 0.4657 max: 2.3560 USE_META, weight: 0.2189 cost: 2.1063 min: 0.4657 max: 2.3560 USE_META, weight: 0.6531 cost: 1.1942 min: 0.4657 max: 2.3560 USE_META, weight: 0.6406 cost: 1.2207 min: 0.4657 max: 2.3560 USE_META, weight: 0.2880 cost: 1.9612 min: 0.4657 max: 2.3560 USE_META, weight: 0.6069 cost: 1.2915 min: 0.4657 max: 2.3560 USE_META, weight: 0.7844 cost: 0.9186 min: 0.4657 max: 2.3560 USE_EVALUE, weight: 0.8355 eval: 10.7870 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8355 eval: 10.7870 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8355 eval: 10.7870 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8509 eval: 9.8756 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8509 eval: 9.8756 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8509 eval: 9.8756 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8451 eval: 10.2140 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8451 eval: 10.2140 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8451 eval: 10.2140 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7946 eval: 13.2060 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7946 eval: 13.2060 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7946 eval: 13.2060 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 1.0000 eval: 1.0523 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 1.0000 eval: 1.0523 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 1.0000 eval: 1.0523 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9273 eval: 5.3543 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9273 eval: 5.3543 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9273 eval: 5.3543 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7355 eval: 16.7000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7085 eval: 18.3000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7085 eval: 18.3000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7085 eval: 18.3000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8795 eval: 8.1823 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8795 eval: 8.1823 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8795 eval: 8.1823 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7898 eval: 13.4910 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7898 eval: 13.4910 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7898 eval: 13.4910 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8504 eval: 9.9045 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8504 eval: 9.9045 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8504 eval: 9.9045 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9330 eval: 5.0148 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9330 eval: 5.0148 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8744 eval: 8.4828 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8744 eval: 8.4828 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8744 eval: 8.4828 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9240 eval: 5.5500 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9240 eval: 5.5500 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9240 eval: 5.5500 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7321 eval: 16.9000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7321 eval: 16.9000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.7321 eval: 16.9000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8750 eval: 8.4494 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8750 eval: 8.4494 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8750 eval: 8.4494 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9595 eval: 3.4459 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9595 eval: 3.4459 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.9595 eval: 3.4459 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8592 eval: 9.3820 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8592 eval: 9.3820 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.8592 eval: 9.3820 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.1000 eval: 54.3000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.1000 eval: 54.3000 min: 1.0523 max: 54.3000 USE_EVALUE, weight: 0.1000 eval: 54.3000 min: 1.0523 max: 54.3000 Number of contacts in models: 262 Number of contacts in alignments: 54 NUMB_ALIGNS: 54 Adding 2666 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -133.5018, CN propb: -133.5018 weights: 0.2738 constraints: 223 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 223 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 223 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2443 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2443 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2666 # command: