# 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/T0386/ # command:# Making conformation for sequence T0386 numbered 1 through 299 Created new target T0386 from T0386.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0386/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0386//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0386//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y5eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y5eA expands to /projects/compbio/data/pdb/1y5e.pdb.gz 1y5eA: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 # T0386 read from 1y5eA/merged-good-all-a2m # 1y5eA read from 1y5eA/merged-good-all-a2m # adding 1y5eA to template set # found chain 1y5eA in template set T0386 173 :FENLAKAAGHQLNFSLI 1y5eA 36 :LHELLKEAGHKVTSYEI # choosing archetypes in rotamer library T0386 190 :TKERMMVASVAVAEN 1y5eA 56 :DKESIQQAVLAGYHK T0386 205 :GD 1y5eA 87 :RD T0386 209 :PMQHLFEDISNPEKIRLLKEFMHTMKNTGRNVN 1y5eA 89 :VTIEAVSALLDKEIVGFGELFRMISYLEDIGSS T0386 287 :L 1y5eA 122 :A Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1y5eA read from 1y5eA/merged-good-all-a2m # found chain 1y5eA in template set T0386 172 :FFENLAKAAGHQLNFSLI 1y5eA 35 :LLHELLKEAGHKVTSYEI T0386 190 :TKERMMVASVAVAEN 1y5eA 56 :DKESIQQAVLAGYHK T0386 209 :PMQHLFEDISNPEKIRLLKEFMHTMKNTGRNVN 1y5eA 89 :VTIEAVSALLDKEIVGFGELFRMISYLEDIGSS T0386 242 :DRPVMVAKEGETY 1y5eA 123 :MLSRAIGGTIGRK T0386 264 :EGFALNVKGAYIIGNID 1y5eA 136 :VVFSMPGSSGAVRLAMN Number of specific fragments extracted= 5 number of extra gaps= 0 total=10 Number of alignments=2 # 1y5eA read from 1y5eA/merged-good-all-a2m # found chain 1y5eA in template set T0386 172 :FFENLAKAAGHQLNFSLI 1y5eA 35 :LLHELLKEAGHKVTSYEI T0386 190 :TKERMMVASVAVAENGDLEP 1y5eA 56 :DKESIQQAVLAGYHKEDVDV T0386 210 :MQHLFEDISNPEKIRLLKEFMHTMKNTGRNVND 1y5eA 90 :TIEAVSALLDKEIVGFGELFRMISYLEDIGSSA T0386 261 :AGLEGFALNVKGAYII 1y5eA 123 :MLSRAIGGTIGRKVVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=14 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v4eA expands to /projects/compbio/data/pdb/1v4e.pdb.gz 1v4eA:# T0386 read from 1v4eA/merged-good-all-a2m # 1v4eA read from 1v4eA/merged-good-all-a2m # adding 1v4eA to template set # found chain 1v4eA in template set Warning: unaligning (T0386)R243 because last residue in template chain is (1v4eA)F288 T0386 27 :LKNKYGIKNLNAFLE 1v4eA 96 :INFMYGDKAAVAAGD T0386 43 :CSHDTAKAMINLR 1v4eA 111 :LVLVSAFHTVEEI T0386 66 :AYLCHIHQQLFKN 1v4eA 126 :NKLRRAFLNVIGK T0386 123 :LQRLDQTLAEKNN 1v4eA 139 :MSEAELIEQLSRY T0386 137 :QGLTREEFN 1v4eA 152 :KPITKEEYL T0386 147 :EAIELFN 1v4eA 161 :RIVEGKS T0386 166 :GRTQRLFFENLAKAAG 1v4eA 168 :GALFGLALQLPALLEG T0386 182 :HQLNFSLITKERMMVA 1v4eA 221 :LDLKNGVASFPLVTAM T0386 198 :SVAVAENGDLEPMQHLFEDI 1v4eA 242 :ARQMFENRDWSGLMSFMREK T0386 218 :SNPEKIRLLKEFMHTMKNTGRNVND 1v4eA 263 :ILKECEETLKVLVKNVIIENSWLRD Number of specific fragments extracted= 10 number of extra gaps= 0 total=24 Number of alignments=4 # 1v4eA read from 1v4eA/merged-good-all-a2m # found chain 1v4eA in template set Warning: unaligning (T0386)R243 because last residue in template chain is (1v4eA)F288 T0386 27 :LKNKYGIKNLNAFLE 1v4eA 96 :INFMYGDKAAVAAGD T0386 43 :CSHDTAKAMINLR 1v4eA 111 :LVLVSAFHTVEEI T0386 66 :AYLCHIHQQLFKN 1v4eA 126 :NKLRRAFLNVIGK T0386 123 :LQRLDQTLAEKNN 1v4eA 139 :MSEAELIEQLSRY T0386 137 :QGLTREEFN 1v4eA 152 :KPITKEEYL T0386 147 :EAIELFN 1v4eA 161 :RIVEGKS T0386 166 :GRTQRLFFENLAKAAG 1v4eA 168 :GALFGLALQLPALLEG T0386 182 :HQLNFSLI 1v4eA 221 :LDLKNGVA T0386 190 :TKE 1v4eA 239 :FPE T0386 198 :SVAVAENGDLEPMQHLFEDI 1v4eA 242 :ARQMFENRDWSGLMSFMREK T0386 218 :SNPEKIRLLKEFMHTMKNTGRNVND 1v4eA 263 :ILKECEETLKVLVKNVIIENSWLRD Number of specific fragments extracted= 11 number of extra gaps= 0 total=35 Number of alignments=5 # 1v4eA read from 1v4eA/merged-good-all-a2m # found chain 1v4eA in template set Warning: unaligning (T0386)R243 because last residue in template chain is (1v4eA)F288 T0386 30 :KYGIKNLNAFLEKCSH 1v4eA 122 :EIGNNKLRRAFLNVIG T0386 47 :TAKAMINLREESLPEYFDTAYLCHIHQQLFKNTFEW 1v4eA 138 :KMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGL T0386 130 :LAEKNNLQGLTREEFNSEAIELFNS 1v4eA 175 :LQLPALLEGELGEDLYNLGVTIGTI T0386 170 :RLFFENLAKAAG 1v4eA 200 :YQMFDDIMDFAG T0386 182 :HQLNFSLI 1v4eA 221 :LDLKNGVA T0386 190 :TKERMMVA 1v4eA 231 :PLVTAMEK T0386 198 :SVAVAENGDLEPMQHLFEDIS 1v4eA 242 :ARQMFENRDWSGLMSFMREKG T0386 219 :NPEKIRLLKEFMHTMKNTGRNVND 1v4eA 264 :LKECEETLKVLVKNVIIENSWLRD Number of specific fragments extracted= 8 number of extra gaps= 0 total=43 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f3yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f3yA expands to /projects/compbio/data/pdb/2f3y.pdb.gz 2f3yA:# T0386 read from 2f3yA/merged-good-all-a2m # 2f3yA read from 2f3yA/merged-good-all-a2m # adding 2f3yA to template set # found chain 2f3yA in template set T0386 41 :E 2f3yA 6 :E T0386 43 :CSHDTAKAMINLREESLPEYFDTAYLCHIHQQ 2f3yA 7 :EQIAEFKEAFSLFDKDGDGTITTKELGTVMRS T0386 83 :AG 2f3yA 39 :LG T0386 94 :ADGT 2f3yA 41 :QNPT T0386 120 :QEGLQRLDQTLAE 2f3yA 45 :EAELQDMINEVDA T0386 138 :GLT 2f3yA 58 :DGN T0386 141 :REEFNSEAIELF 2f3yA 65 :FPEFLTMMARKM T0386 181 :G 2f3yA 80 :D T0386 190 :TKERMMVASVAVAENGD 2f3yA 81 :SEEEIREAFRVFDKDGN T0386 207 :LEPMQHLFEDISN 2f3yA 102 :AAELRHVMTNLGE T0386 220 :PEKIRLLKEF 2f3yA 119 :EEVDEMIREA T0386 239 :NVNDRPVMVAKEGETYT 2f3yA 129 :DIDGDGQVNYEEFVQMM Number of specific fragments extracted= 12 number of extra gaps= 0 total=55 Number of alignments=7 # 2f3yA read from 2f3yA/merged-good-all-a2m # found chain 2f3yA in template set T0386 15 :SPHHYVYPNTTTLKNKYGIK 2f3yA 23 :GDGTITTKELGTVMRSLGQN T0386 35 :NLNAFLE 2f3yA 44 :TEAELQD T0386 51 :MINLREESLPEYFDTAYLCHIHQQLFKN 2f3yA 51 :MINEVDADGNGTIDFPEFLTMMARKMKD T0386 94 :ADGT 2f3yA 79 :TDSE T0386 121 :EGLQRLDQTLAEKN 2f3yA 83 :EEIREAFRVFDKDG T0386 137 :QG 2f3yA 97 :NG T0386 139 :LTREEFNSE 2f3yA 100 :ISAAELRHV T0386 149 :I 2f3yA 109 :M T0386 178 :KAAG 2f3yA 110 :TNLG T0386 187 :SLITKERMMVASVAVAENGD 2f3yA 114 :EKLTDEEVDEMIREADIDGD T0386 207 :LEPMQHLFE 2f3yA 138 :YEEFVQMMT Number of specific fragments extracted= 11 number of extra gaps= 0 total=66 Number of alignments=8 # 2f3yA read from 2f3yA/merged-good-all-a2m # found chain 2f3yA in template set T0386 44 :SHDTAKAMINLREESLPEYFDTAYLCHIHQQLFK 2f3yA 8 :QIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQ T0386 113 :FAIGDEIQEGLQRL 2f3yA 42 :NPTEAELQDMINEV T0386 131 :AEK 2f3yA 56 :DAD T0386 138 :GLT 2f3yA 59 :GNG T0386 141 :REEFNSEAIELFN 2f3yA 65 :FPEFLTMMARKMK T0386 188 :LITKERMMVASVAVAEN 2f3yA 78 :DTDSEEEIREAFRVFDK T0386 205 :GD 2f3yA 96 :GN T0386 207 :LEPMQHLFEDIS 2f3yA 102 :AAELRHVMTNLG T0386 219 :NPEKIRLLKEF 2f3yA 118 :DEEVDEMIREA T0386 236 :TGRNVNDRPVM 2f3yA 129 :DIDGDGQVNYE Number of specific fragments extracted= 10 number of extra gaps= 0 total=76 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z2nX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z2nX expands to /projects/compbio/data/pdb/1z2n.pdb.gz 1z2nX:# T0386 read from 1z2nX/merged-good-all-a2m # 1z2nX read from 1z2nX/merged-good-all-a2m # adding 1z2nX to template set # found chain 1z2nX in template set Warning: unaligning (T0386)T140 because of BadResidue code BAD_PEPTIDE at template residue (1z2nX)E83 T0386 72 :HQQLFKNTFE 1z2nX 18 :QKTLFISTKN T0386 88 :HIPFTFADGTTAA 1z2nX 28 :HTQFELNNIIFDV T0386 102 :PEMKRTGWKNAFAI 1z2nX 44 :TELPDKEPNAIITK T0386 116 :GD 1z2nX 61 :PV T0386 120 :QEGLQRLDQTLAEK 1z2nX 63 :GKMADEMRKYEKDH T0386 137 :QGL 1z2nX 77 :PKV T0386 141 :REEFNSE 1z2nX 84 :SSAIHDM T0386 155 :LNQ 1z2nX 91 :MSS T0386 170 :RLFFENLAKAAGHQL 1z2nX 94 :REEINALLIKNNIPI T0386 185 :NFSLI 1z2nX 110 :NSFSV T0386 190 :TKERMMVASV 1z2nX 116 :SKEEVIQLLQ T0386 204 :NGDL 1z2nX 126 :SKQL Number of specific fragments extracted= 12 number of extra gaps= 1 total=88 Number of alignments=10 # 1z2nX read from 1z2nX/merged-good-all-a2m # found chain 1z2nX in template set T0386 72 :HQQLFKNTFE 1z2nX 18 :QKTLFISTKN T0386 88 :HIPFTFADGTTAAM 1z2nX 28 :HTQFELNNIIFDVT T0386 102 :PEMKRTGWKNAFAIGDE 1z2nX 44 :TELPDKEPNAIITKRTH T0386 119 :IQEGLQRLDQTLAEK 1z2nX 62 :VGKMADEMRKYEKDH T0386 137 :QGL 1z2nX 77 :PKV T0386 140 :T 1z2nX 84 :S T0386 142 :EEFNSEA 1z2nX 85 :SAIHDMM T0386 156 :NQ 1z2nX 92 :SS T0386 170 :RLFFENLAKAAGHQL 1z2nX 94 :REEINALLIKNNIPI T0386 185 :NFSLI 1z2nX 110 :NSFSV T0386 190 :TKERMMVASVA 1z2nX 116 :SKEEVIQLLQS T0386 205 :GD 1z2nX 127 :KQ T0386 243 :R 1z2nX 129 :L Number of specific fragments extracted= 13 number of extra gaps= 0 total=101 Number of alignments=11 # 1z2nX read from 1z2nX/merged-good-all-a2m # found chain 1z2nX in template set T0386 91 :FTFADGT 1z2nX 40 :VTLSTEL T0386 102 :PEMKRTGWKNAFAIGDE 1z2nX 47 :PDKEPNAIITKRTHPVG T0386 121 :EGLQRLDQTLAEK 1z2nX 64 :KMADEMRKYEKDH T0386 137 :QG 1z2nX 77 :PK T0386 151 :LFNSLNQ 1z2nX 87 :IHDMMSS T0386 170 :RLFFENLAKAAGHQ 1z2nX 94 :REEINALLIKNNIP T0386 184 :LNFSLITKERMMVASVA 1z2nX 109 :PNSFSVKSKEEVIQLLQ T0386 204 :NGDL 1z2nX 126 :SKQL T0386 265 :GFALNVKGA 1z2nX 130 :ILPFIVKPE T0386 274 :YIIGNIDHLPP 1z2nX 150 :KIVLEQEGIDD Number of specific fragments extracted= 10 number of extra gaps= 0 total=111 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h16A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0386 read from 1h16A/merged-good-all-a2m # 1h16A read from 1h16A/merged-good-all-a2m # found chain 1h16A in training set T0386 97 :T 1h16A 462 :S T0386 103 :EMKRTG 1h16A 463 :EPIKGD T0386 113 :FAIGDEIQEGLQRLDQTLAE 1h16A 469 :VLNYDEVMERMDHFMDWLAK T0386 140 :TREEFNSEAIELFNS 1h16A 489 :QYITALNIIHYMHDK T0386 155 :LNQLH 1h16A 510 :LMALH T0386 168 :TQRLFFENLAKAA 1h16A 529 :LSVAADSLSAIKY T0386 181 :G 1h16A 543 :K T0386 182 :HQ 1h16A 563 :YP T0386 205 :GDLEPMQHLFEDISN 1h16A 568 :NNDPRVDDLAVDLVE T0386 228 :EFMHTMKNTG 1h16A 583 :RFMKKIQKLH Number of specific fragments extracted= 10 number of extra gaps= 0 total=121 Number of alignments=13 # 1h16A read from 1h16A/merged-good-all-a2m # found chain 1h16A in training set T0386 47 :TAKAMINLREESLPE 1h16A 24 :NVRDFIQKNYTPYEG T0386 62 :YFD 1h16A 42 :FLA T0386 65 :TAYLCHIHQQLFKNT 1h16A 47 :TEATTTLWDKVMEGV T0386 93 :FADGT 1h16A 465 :IKGDV T0386 114 :AIGDEIQEGLQRLDQTLAEKN 1h16A 470 :LNYDEVMERMDHFMDWLAKQY T0386 141 :REEFN 1h16A 491 :ITALN T0386 147 :EAIELFNS 1h16A 496 :IIHYMHDK T0386 155 :LNQLH 1h16A 510 :LMALH T0386 168 :TQRLFFENLAKAA 1h16A 529 :LSVAADSLSAIKY T0386 181 :G 1h16A 543 :K T0386 183 :QLNFSLI 1h16A 556 :DFEIEGE T0386 205 :GDLEPMQHLFEDIS 1h16A 568 :NNDPRVDDLAVDLV T0386 227 :KEFMHTMKNTGRN 1h16A 582 :ERFMKKIQKLHTY Number of specific fragments extracted= 13 number of extra gaps= 0 total=134 Number of alignments=14 # 1h16A read from 1h16A/merged-good-all-a2m # found chain 1h16A in training set T0386 84 :GYLRHIPFTFADGT 1h16A 449 :GVDEKLKMQVGPKS T0386 107 :TGWKNAFAIGDEIQEGLQRLDQTLAEK 1h16A 463 :EPIKGDVLNYDEVMERMDHFMDWLAKQ T0386 141 :REEFNSEAIELFNS 1h16A 490 :YITALNIIHYMHDK T0386 155 :LNQLH 1h16A 510 :LMALH T0386 166 :GRTQRLFFENLAKAAG 1h16A 528 :GLSVAADSLSAIKYAK T0386 182 :HQLNFSLITKERMMVASVAVAE 1h16A 561 :GEYPQFGNNDPRVDDLAVDLVE T0386 228 :EFMHTMKNTG 1h16A 583 :RFMKKIQKLH Number of specific fragments extracted= 7 number of extra gaps= 0 total=141 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1osa/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1osa expands to /projects/compbio/data/pdb/1osa.pdb.gz 1osa:Warning: there is no chain 1osa will retry with 1osaA # T0386 read from 1osa/merged-good-all-a2m # 1osa read from 1osa/merged-good-all-a2m # adding 1osa to template set # found chain 1osa in template set T0386 43 :CSHDTAKAMINLREESLPEYFDTAYLCHIHQQ 1osa 7 :EQIAEFKEAFALFDKDGDGTITTKELGTVMRS T0386 94 :ADGT 1osa 39 :LGQN T0386 114 :AI 1osa 43 :PT T0386 120 :QEGLQRLDQTLAEKNN 1osa 45 :EAELQDMINEVDADGN T0386 137 :QGLTREEFNSEAIE 1osa 61 :GTIDFPEFLSLMAR T0386 190 :TKERMMVASVAVAENG 1osa 81 :SEEELIEAFKVFDRDG T0386 206 :DLEPMQHLFEDIS 1osa 101 :SAAELRHVMTNLG T0386 219 :NPEKIRLLK 1osa 118 :DDEVDEMIR T0386 235 :NTGRNVN 1osa 127 :EADIDGD T0386 244 :PVMVAKEGETY 1osa 134 :GHINYEEFVRM Number of specific fragments extracted= 10 number of extra gaps= 0 total=151 Number of alignments=16 # 1osa read from 1osa/merged-good-all-a2m # found chain 1osa in template set T0386 15 :SPHHYVYPNTTTLKNKYGIK 1osa 23 :GDGTITTKELGTVMRSLGQN T0386 35 :NLNAFLE 1osa 44 :TEAELQD T0386 51 :MINLREESLPEYFDTAYLCHIHQQLFKN 1osa 51 :MINEVDADGNGTIDFPEFLSLMARKMKE T0386 120 :QEGLQRLDQTLAEKN 1osa 79 :QDSEEELIEAFKVFD T0386 162 :REGNGRTQRLFFENLAKAAGH 1osa 94 :RDGNGLISAAELRHVMTNLGE T0386 188 :LITKERMMVASVAVAENG 1osa 115 :KLTDDEVDEMIREADIDG T0386 206 :DLEPMQHLF 1osa 137 :NYEEFVRMM Number of specific fragments extracted= 7 number of extra gaps= 0 total=158 Number of alignments=17 # 1osa read from 1osa/merged-good-all-a2m # found chain 1osa in template set T0386 44 :SHDTAKAMINLREESLPEYFDTAYLCHIHQQ 1osa 8 :QIAEFKEAFALFDKDGDGTITTKELGTVMRS T0386 94 :A 1osa 39 :L T0386 96 :GT 1osa 40 :GQ T0386 113 :FAIGDEIQEGLQRL 1osa 42 :NPTEAELQDMINEV T0386 138 :GLTREEFNSEAIELFNS 1osa 62 :TIDFPEFLSLMARKMKE T0386 190 :TKERMMVASVAVAEN 1osa 80 :DSEEELIEAFKVFDR T0386 205 :GD 1osa 96 :GN T0386 207 :LEPMQH 1osa 102 :AAELRH T0386 246 :MVAKEGETYTG 1osa 108 :VMTNLGEKLTD Number of specific fragments extracted= 9 number of extra gaps= 0 total=167 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g03A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g03A expands to /projects/compbio/data/pdb/2g03.pdb.gz 2g03A: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 50, because occupancy 0.5 <= existing 0.500 in 2g03A Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 441, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2g03A 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 658, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2g03A 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 711, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 714, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 717, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 720, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 723, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 726, because occupancy 0.250 <= existing 0.250 in 2g03A Skipped atom 729, because occupancy 0.250 <= existing 0.250 in 2g03A 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 884, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 2g03A 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 1290, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1298, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1300, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1302, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1304, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1509, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 2g03A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2g03A # T0386 read from 2g03A/merged-good-all-a2m # 2g03A read from 2g03A/merged-good-all-a2m # adding 2g03A to template set # found chain 2g03A in template set Warning: unaligning (T0386)L36 because first residue in template chain is (2g03A)M11 Warning: unaligning (T0386)N37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g03A)S13 Warning: unaligning (T0386)A38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g03A)S13 Warning: unaligning (T0386)F39 because of BadResidue code BAD_PEPTIDE at template residue (2g03A)I14 T0386 40 :LE 2g03A 15 :DE T0386 43 :CSHDTAKAMIN 2g03A 17 :QSLHNARRLFE T0386 58 :SLP 2g03A 28 :SGD T0386 61 :EYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGT 2g03A 35 :EVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFR T0386 113 :FAIGDEIQEGLQRLDQT 2g03A 72 :FANAMYLKEALVKIEQM T0386 137 :QGLTREEFNSE 2g03A 89 :PERTFEEIIAK T0386 152 :FNSLNQLHPFREGNGRTQRLFFENLAKAA 2g03A 100 :YVEMNIAHPFLEGNGRSTRIWLDLVLKKN T0386 181 :GHQLNFSLITKERMMVASVAVAE 2g03A 130 :KKVVNWQNVSKTLYLQAMERSPV T0386 206 :DLEPMQHLFEDIS 2g03A 153 :NDLELRFLLKDNL T0386 219 :NPEKIRLLKEFMH 2g03A 172 :REIIFKGIEQSYY Number of specific fragments extracted= 10 number of extra gaps= 0 total=177 Number of alignments=19 # 2g03A read from 2g03A/merged-good-all-a2m # found chain 2g03A in template set Warning: unaligning (T0386)L36 because first residue in template chain is (2g03A)M11 Warning: unaligning (T0386)N37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g03A)S13 Warning: unaligning (T0386)A38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g03A)S13 Warning: unaligning (T0386)F39 because of BadResidue code BAD_PEPTIDE at template residue (2g03A)I14 T0386 40 :LE 2g03A 15 :DE T0386 43 :CSHDTAKAMIN 2g03A 17 :QSLHNARRLFE T0386 56 :EESLPE 2g03A 28 :SGDIDR T0386 62 :YFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGT 2g03A 36 :VGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFR T0386 113 :FAIGDEIQEGLQRLDQT 2g03A 72 :FANAMYLKEALVKIEQM T0386 137 :Q 2g03A 91 :R T0386 140 :TREEFNSE 2g03A 92 :TFEEIIAK T0386 152 :FNSLNQLHPFREGNGRTQRLFFENLAKAA 2g03A 100 :YVEMNIAHPFLEGNGRSTRIWLDLVLKKN T0386 181 :GHQLNFSLITKERMMVASVAVAE 2g03A 130 :KKVVNWQNVSKTLYLQAMERSPV T0386 206 :DLEPMQHLFEDIS 2g03A 153 :NDLELRFLLKDNL T0386 219 :NPEKIRLLKEFM 2g03A 172 :REIIFKGIEQSY T0386 235 :N 2g03A 184 :Y Number of specific fragments extracted= 12 number of extra gaps= 0 total=189 Number of alignments=20 # 2g03A read from 2g03A/merged-good-all-a2m # found chain 2g03A in template set T0386 37 :N 2g03A 15 :D T0386 45 :HDTAKAMINLREES 2g03A 16 :EQSLHNARRLFESG T0386 59 :LPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPFTFADGT 2g03A 33 :RIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFR T0386 113 :FAIGDEIQEGLQRLDQT 2g03A 72 :FANAMYLKEALVKIEQM T0386 138 :GLT 2g03A 89 :PER T0386 144 :FNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERMMVASVAVAEN 2g03A 92 :TFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPV T0386 206 :DLEPMQHLFEDIS 2g03A 153 :NDLELRFLLKDNL T0386 219 :NPEKIRLLKEFMH 2g03A 172 :REIIFKGIEQSYY Number of specific fragments extracted= 8 number of extra gaps= 0 total=197 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r2rA expands to /projects/compbio/data/pdb/1r2r.pdb.gz 1r2rA:Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 1r2rA Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 1r2rA # T0386 read from 1r2rA/merged-good-all-a2m # 1r2rA read from 1r2rA/merged-good-all-a2m # adding 1r2rA to template set # found chain 1r2rA in template set T0386 41 :EKCSHDTAKAMINL 1r2rA 106 :DELIGQKVAHALSE T0386 56 :EESLPEYFDTAYLCHIHQQLFKNTFEW 1r2rA 131 :LDEREAGITEKVVFEQTKVIADNVKDW T0386 93 :FADGT 1r2rA 170 :IGTGK T0386 113 :FAIGDEIQEGLQRLDQTLAEK 1r2rA 175 :TATPQQAQEVHEKLRGWLKSN Number of specific fragments extracted= 4 number of extra gaps= 0 total=201 Number of alignments=22 # 1r2rA read from 1r2rA/merged-good-all-a2m # found chain 1r2rA in template set T0386 32 :GIKNLNAFLE 1r2rA 76 :GEISPGMIKD T0386 52 :INLREE 1r2rA 96 :SERRHV T0386 61 :EYFDTAYLCHIHQQLFKN 1r2rA 102 :FGESDELIGQKVAHALSE T0386 108 :GWKNAFAIGDE 1r2rA 120 :GLGVIACIGEK T0386 119 :IQEGLQRLDQTLAEKNN 1r2rA 139 :TEKVVFEQTKVIADNVK T0386 185 :NFSLI 1r2rA 156 :DWSKV T0386 190 :TKERMMVASVA 1r2rA 177 :TPQQAQEVHEK T0386 210 :MQHLFEDISNPEKIRL 1r2rA 188 :LRGWLKSNVSDAVAQS T0386 263 :LEGF 1r2rA 204 :TRII T0386 267 :ALNVKGAYIIGNID 1r2rA 209 :GGSVTGATCKELAS Number of specific fragments extracted= 10 number of extra gaps= 0 total=211 Number of alignments=23 # 1r2rA read from 1r2rA/merged-good-all-a2m # found chain 1r2rA in template set T0386 55 :REES 1r2rA 134 :REAG T0386 63 :FDTAYLCHIHQQLFKNTFEW 1r2rA 138 :ITEKVVFEQTKVIADNVKDW T0386 92 :TFADGT 1r2rA 169 :AIGTGK T0386 113 :FAIGDEIQEGLQRLDQTLAE 1r2rA 175 :TATPQQAQEVHEKLRGWLKS T0386 138 :GLTRE 1r2rA 195 :NVSDA Number of specific fragments extracted= 5 number of extra gaps= 0 total=216 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ywfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ywfA expands to /projects/compbio/data/pdb/1ywf.pdb.gz 1ywfA:# T0386 read from 1ywfA/merged-good-all-a2m # 1ywfA read from 1ywfA/merged-good-all-a2m # adding 1ywfA to template set # found chain 1ywfA in template set Warning: unaligning (T0386)Q120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ywfA)D120 T0386 121 :EGLQRLDQTLAEKNNLQ 1ywfA 121 :AATRYMTDEYRQFPTRN T0386 140 :TREEFNSEAIELFNS 1ywfA 138 :GAQRALHRVVTLLAA T0386 156 :NQLHPFR 1ywfA 156 :VLTHCFA T0386 164 :GNGRTQRL 1ywfA 163 :GKDRTGFV T0386 173 :FENLAKAAG 1ywfA 171 :VALVLEAVG T0386 186 :FSLITKERMMVASVAVAEN 1ywfA 191 :RSNDSVPQLRARISEMIQQ T0386 206 :DLE 1ywfA 212 :DTE T0386 209 :PMQHLFEDI 1ywfA 217 :PEVVTFTKA T0386 218 :SNPEK 1ywfA 227 :LSDGV T0386 223 :IRLLKEFMHTMKNT 1ywfA 236 :AEYLAAARQTIDET T0386 240 :VNDRPVMVAK 1ywfA 250 :YGSLGGYLRD T0386 250 :EGETYTG 1ywfA 266 :TVNRMRG Number of specific fragments extracted= 12 number of extra gaps= 1 total=228 Number of alignments=25 # 1ywfA read from 1ywfA/merged-good-all-a2m # found chain 1ywfA in template set Warning: unaligning (T0386)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywfA)S117 Warning: unaligning (T0386)E118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ywfA)N119 Warning: unaligning (T0386)I119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ywfA)N119 Warning: unaligning (T0386)Q120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ywfA)D120 T0386 12 :EII 1ywfA 31 :SEL T0386 18 :H 1ywfA 34 :S T0386 19 :YVYPNTTTLKNKYGI 1ywfA 36 :LDDAGRATLRRLGIT T0386 36 :LN 1ywfA 57 :SS T0386 50 :AMINLREE 1ywfA 59 :REVARRGP T0386 58 :SLPE 1ywfA 68 :RVPD T0386 62 :YFD 1ywfA 79 :PFP T0386 121 :EGLQRLDQTLAEKNNLQG 1ywfA 121 :AATRYMTDEYRQFPTRNG T0386 141 :REEFNSEAIELFN 1ywfA 139 :AQRALHRVVTLLA T0386 156 :NQLHPFR 1ywfA 156 :VLTHCFA T0386 164 :GNGRTQR 1ywfA 163 :GKDRTGF T0386 172 :FFENLAKAAG 1ywfA 170 :VVALVLEAVG T0386 191 :KERMMVASVAVAEN 1ywfA 196 :VPQLRARISEMIQQ T0386 206 :DLE 1ywfA 212 :DTE T0386 209 :PMQHLFEDI 1ywfA 217 :PEVVTFTKA T0386 218 :SNPEK 1ywfA 227 :LSDGV T0386 223 :IRLLKEFMHTMKNTG 1ywfA 236 :AEYLAAARQTIDETY T0386 261 :AGLEGF 1ywfA 251 :GSLGGY T0386 267 :ALNVKGAYIIGN 1ywfA 259 :DAGISQATVNRM Number of specific fragments extracted= 19 number of extra gaps= 0 total=247 Number of alignments=26 # 1ywfA read from 1ywfA/merged-good-all-a2m # found chain 1ywfA in template set Warning: unaligning (T0386)Q120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ywfA)D120 T0386 121 :EGLQRLDQTLAEKNNL 1ywfA 121 :AATRYMTDEYRQFPTR T0386 138 :G 1ywfA 137 :N T0386 140 :TREEFNSEAIELFNS 1ywfA 138 :GAQRALHRVVTLLAA T0386 158 :LHPFR 1ywfA 158 :THCFA T0386 164 :GNGRT 1ywfA 163 :GKDRT T0386 170 :RLFFENLAKAAGHQ 1ywfA 168 :GFVVALVLEAVGLD T0386 184 :LNFSLITKERMMVASVAVAENGDLEPMQHLFEDIS 1ywfA 192 :SNDSVPQLRARISEMIQQRFDTELAPEVVTFTKAR T0386 220 :PEK 1ywfA 229 :DGV T0386 223 :IRLLKEFMHTMKNTGRNVNDRPV 1ywfA 236 :AEYLAAARQTIDETYGSLGGYLR Number of specific fragments extracted= 9 number of extra gaps= 1 total=256 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d5rA expands to /projects/compbio/data/pdb/1d5r.pdb.gz 1d5rA:# T0386 read from 1d5rA/merged-good-all-a2m # 1d5rA read from 1d5rA/merged-good-all-a2m # adding 1d5rA to template set # found chain 1d5rA in template set T0386 58 :SLPEYFD 1d5rA 41 :RLEGVYR T0386 65 :TAYLCHIHQ 1d5rA 50 :IDDVVRFLD T0386 77 :KNTFEW 1d5rA 59 :SKHKNH T0386 85 :YLRHIPFTFADGTTAAMP 1d5rA 72 :AERHYDTAKFNCRVAQYP T0386 112 :AFAIGDEIQEGLQRLDQTLAEK 1d5rA 94 :NPPQLELIKPFCEDLDQWLSED T0386 140 :TRE 1d5rA 116 :DNH T0386 156 :NQLHP 1d5rA 120 :AAIHC T0386 162 :REGNGRTQRLFFENLAKA 1d5rA 125 :KAGKGRTGVMICAYLLHR T0386 181 :G 1d5rA 143 :G T0386 188 :LI 1d5rA 144 :KF T0386 190 :TKERMMVASVAVAENG 1d5rA 147 :KAQEALDFYGEVRTRD T0386 206 :DLEPMQHLF 1d5rA 167 :TIPSQRRYV T0386 227 :KEFMHTMKN 1d5rA 176 :YYYSYLLKN T0386 260 :GAGLEGFALNVKGAYII 1d5rA 185 :HLDYRPVALLFHKMMFE Number of specific fragments extracted= 14 number of extra gaps= 0 total=270 Number of alignments=28 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set T0386 57 :ESLPE 1d5rA 40 :ERLEG T0386 62 :YFDTAYLCHIHQQLFKNT 1d5rA 47 :RNNIDDVVRFLDSKHKNH T0386 87 :RHIPFTFADGTTAAMP 1d5rA 74 :RHYDTAKFNCRVAQYP T0386 113 :F 1d5rA 90 :F T0386 114 :AIGDE 1d5rA 94 :NPPQL T0386 119 :IQEGLQRLDQTLAEK 1d5rA 101 :IKPFCEDLDQWLSED T0386 140 :TRE 1d5rA 116 :DNH T0386 155 :LNQLHP 1d5rA 119 :VAAIHC T0386 162 :REGNGRTQRLFFENLAKAAG 1d5rA 125 :KAGKGRTGVMICAYLLHRGK T0386 188 :LITKERMMVASVAVAENG 1d5rA 145 :FLKAQEALDFYGEVRTRD T0386 206 :DLEPMQHLFEDI 1d5rA 167 :TIPSQRRYVYYY T0386 223 :IRLLKE 1d5rA 179 :SYLLKN T0386 240 :VNDRPVMVAKEGE 1d5rA 185 :HLDYRPVALLFHK T0386 253 :TYTGT 1d5rA 199 :MFETI T0386 258 :YRGAGLEGFAL 1d5rA 206 :FSGGTCNPQFV T0386 284 :PEQLKILKPGDKITFT 1d5rA 220 :LKVKIYSSNSGPTRRE Number of specific fragments extracted= 16 number of extra gaps= 0 total=286 Number of alignments=29 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set T0386 50 :AMINLREESLPEYF 1d5rA 52 :DVVRFLDSKHKNHY T0386 77 :KNTFEW 1d5rA 73 :ERHYDT T0386 83 :AGYLR 1d5rA 82 :NCRVA T0386 90 :PFTFADGT 1d5rA 87 :QYPFEDHN T0386 113 :FAIGDEIQEGLQRLDQTLAEK 1d5rA 95 :PPQLELIKPFCEDLDQWLSED T0386 140 :TRE 1d5rA 116 :DNH T0386 162 :REGNGRTQRLFFENLAKA 1d5rA 125 :KAGKGRTGVMICAYLLHR T0386 188 :LITKERMMVASVAVAENGDL 1d5rA 145 :FLKAQEALDFYGEVRTRDKK T0386 217 :ISNPEKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETYTGTYRGAGLEGFAL 1d5rA 166 :VTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVV Number of specific fragments extracted= 9 number of extra gaps= 0 total=295 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mxrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0386 read from 1mxrA/merged-good-all-a2m # 1mxrA read from 1mxrA/merged-good-all-a2m # found chain 1mxrA in training set T0386 26 :TLKNKY 1mxrA 106 :TWVETW T0386 42 :KCSHDTAK 1mxrA 112 :AFSETIHS T0386 70 :HIHQQLFKNTFEW 1mxrA 120 :RSYTHIIRNIVND T0386 117 :DEIQEGLQRLDQTLAEKNNLQG 1mxrA 151 :EGISSYYDELIEMTSYWHLLGE T0386 140 :TREEFNSEAIELFNSLNQL 1mxrA 185 :SLRELKKKLYLCLMSVNAL T0386 167 :RT 1mxrA 207 :RF T0386 169 :QRLFFENLAKAAG 1mxrA 210 :VSFACSFAFAERE T0386 195 :MVASVAVAENGDLEPMQHLFEDISNP 1mxrA 246 :QHMLNLLRSGADDPEMAEIAEECKQE T0386 221 :EKIRLLKEFMHTMKNTGRN 1mxrA 275 :LFVQAAQQEKDWADYLFRD T0386 240 :VNDRPVMVAKEGETYTGTY 1mxrA 297 :IGLNKDILCQYVEYITNIR Number of specific fragments extracted= 10 number of extra gaps= 0 total=305 Number of alignments=31 # 1mxrA read from 1mxrA/merged-good-all-a2m # found chain 1mxrA in training set T0386 19 :YVYPNTTTLKNKY 1mxrA 99 :ISIPELETWVETW T0386 42 :KCSHDTAKAMINLREESL 1mxrA 112 :AFSETIHSRSYTHIIRNI T0386 62 :YFDTAYLCH 1mxrA 130 :VNDPSVVFD T0386 78 :NTFEW 1mxrA 139 :DIVTN T0386 117 :DEIQEGLQRLDQTLAEKNNLQG 1mxrA 151 :EGISSYYDELIEMTSYWHLLGE T0386 139 :LTREEFNSEAIELFNSLNQL 1mxrA 184 :VSLRELKKKLYLCLMSVNAL T0386 168 :TQRLFFENLAKAAG 1mxrA 209 :YVSFACSFAFAERE T0386 195 :MVASVAVAENGDLEPMQHLFEDI 1mxrA 246 :QHMLNLLRSGADDPEMAEIAEEC T0386 219 :NPEKIRLLKEFMHTMKNTGRNVND 1mxrA 269 :KQECYDLFVQAAQQEKDWADYLFR T0386 264 :EGFALNVKGAYIIGNI 1mxrA 293 :DGSMIGLNKDILCQYV Number of specific fragments extracted= 10 number of extra gaps= 0 total=315 Number of alignments=32 # 1mxrA read from 1mxrA/merged-good-all-a2m # found chain 1mxrA in training set T0386 22 :PNTTTLKNKYGIKNLNAFLE 1mxrA 132 :DPSVVFDDIVTNEQIQKRAE T0386 42 :KCSHDTAKAMINLREES 1mxrA 155 :SYYDELIEMTSYWHLLG T0386 88 :HIPFTFADGT 1mxrA 172 :EGTHTVNGKT T0386 139 :LTREEFNSEAIELFNSLNQL 1mxrA 184 :VSLRELKKKLYLCLMSVNAL T0386 168 :TQRLFFENLAKAAG 1mxrA 209 :YVSFACSFAFAERE T0386 190 :TKERMMV 1mxrA 236 :RDEALHL T0386 197 :ASVAVAE 1mxrA 247 :HMLNLLR T0386 204 :NGDLEPMQHLFEDISNP 1mxrA 255 :GADDPEMAEIAEECKQE T0386 222 :KIRLLKEFMHTMKNTG 1mxrA 272 :CYDLFVQAAQQEKDWA Number of specific fragments extracted= 9 number of extra gaps= 0 total=324 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1na3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0386 read from 1na3A/merged-good-all-a2m # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set Warning: unaligning (T0386)G116 because first residue in template chain is (1na3A)G1 T0386 117 :DEIQEGLQRLDQTLAE 1na3A 2 :NSAEAWYNLGNAYYKQ T0386 138 :G 1na3A 18 :G T0386 140 :TREEFNSEAIELFNS 1na3A 19 :DYDEAIEYYQKALEL T0386 190 :TKERMMVASVAVAENGDLEPMQHLFEDIS 1na3A 37 :NAEAWYNLGNAYYKQGDYDEAIEYYQKAL T0386 220 :PEKIRLLKEFMHTM 1na3A 72 :AEAKQDLGNAKQKQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=329 Number of alignments=34 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set Warning: unaligning (T0386)G116 because first residue in template chain is (1na3A)G1 T0386 117 :DEIQEGLQRLDQTLAEK 1na3A 2 :NSAEAWYNLGNAYYKQG T0386 140 :TREEFNSEAIELFNS 1na3A 19 :DYDEAIEYYQKALEL T0386 190 :TKERMMVASVAVAENGDLEPMQHLFEDIS 1na3A 37 :NAEAWYNLGNAYYKQGDYDEAIEYYQKAL T0386 219 :NPEKIRLLKEFMHTM 1na3A 71 :NAEAKQDLGNAKQKQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=35 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0386 119 :IQEGLQRLDQTLAEK 1na3A 4 :AEAWYNLGNAYYKQG T0386 140 :TREEFNSEAIELFNS 1na3A 19 :DYDEAIEYYQKALEL T0386 189 :ITKERMMVASVAVAENGDLEPMQHLFEDISN 1na3A 36 :NNAEAWYNLGNAYYKQGDYDEAIEYYQKALE T0386 220 :PEKIRLLKEFMHTM 1na3A 72 :AEAKQDLGNAKQKQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=337 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ggzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ggzA expands to /projects/compbio/data/pdb/1ggz.pdb.gz 1ggzA:# T0386 read from 1ggzA/merged-good-all-a2m # 1ggzA read from 1ggzA/merged-good-all-a2m # adding 1ggzA to template set # found chain 1ggzA in template set T0386 43 :CSHDTAKAMINLREESLPEYFDTAYLCHIHQQ 1ggzA 7 :EQVTEFKEAFSLFDKDGDGCITTRELGTVMRS T0386 94 :ADGT 1ggzA 39 :LGQN T0386 114 :AIGDEIQEGLQ 1ggzA 43 :PTEAELRDMMS T0386 125 :RLDQTLAEK 1ggzA 67 :EFLGMMARK T0386 136 :LQGLTREEFNSEAIELF 1ggzA 76 :MKDTDNEEEIREAFRVF T0386 162 :REGNG 1ggzA 94 :KDGNG T0386 172 :FFENLAKAAGHQL 1ggzA 104 :ELRHVMTRLGEKL T0386 190 :TKERMMVASVAVAENGD 1ggzA 117 :SDEEVDEMIRAADTDGD T0386 207 :LEPMQHLFE 1ggzA 138 :YEEFVRVLV Number of specific fragments extracted= 9 number of extra gaps= 0 total=346 Number of alignments=37 # 1ggzA read from 1ggzA/merged-good-all-a2m # found chain 1ggzA in template set T0386 15 :SPHHYVYPNTTTLKNKYGIK 1ggzA 23 :GDGCITTRELGTVMRSLGQN T0386 35 :NLNAFLE 1ggzA 44 :TEAELRD T0386 51 :MINLREESLPEYFDTAYLCHIHQQLFKNTFE 1ggzA 51 :MMSEIDRDGNGTVDFPEFLGMMARKMKDTDN T0386 120 :QEGLQRLDQTLAEKN 1ggzA 82 :EEEIREAFRVFDKDG T0386 137 :QG 1ggzA 97 :NG T0386 139 :LTREEFN 1ggzA 100 :VSAAELR T0386 147 :E 1ggzA 107 :H T0386 176 :LAKAAGHQ 1ggzA 108 :VMTRLGEK T0386 189 :ITKERMMVASVAVAENGD 1ggzA 116 :LSDEEVDEMIRAADTDGD T0386 207 :LEPMQHLFE 1ggzA 138 :YEEFVRVLV Number of specific fragments extracted= 10 number of extra gaps= 0 total=356 Number of alignments=38 # 1ggzA read from 1ggzA/merged-good-all-a2m # found chain 1ggzA in template set T0386 45 :HDTAKAMINLREESLPEYFDTAYLCHIHQQ 1ggzA 9 :VTEFKEAFSLFDKDGDGCITTRELGTVMRS T0386 94 :A 1ggzA 39 :L T0386 96 :GT 1ggzA 40 :GQ T0386 113 :FAIGDEIQEGLQR 1ggzA 42 :NPTEAELRDMMSE T0386 126 :LDQTLAEK 1ggzA 68 :FLGMMARK T0386 136 :LQGLTREEFNSEAIELFN 1ggzA 76 :MKDTDNEEEIREAFRVFD T0386 162 :REGNG 1ggzA 94 :KDGNG T0386 173 :FENLAKAAGHQL 1ggzA 105 :LRHVMTRLGEKL T0386 191 :KERMMVASVAVAEN 1ggzA 117 :SDEEVDEMIRAADT T0386 205 :GD 1ggzA 132 :GD T0386 207 :LEPMQHLF 1ggzA 138 :YEEFVRVL Number of specific fragments extracted= 11 number of extra gaps= 0 total=367 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sxjE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sxjE expands to /projects/compbio/data/pdb/1sxj.pdb.gz 1sxjE:# T0386 read from 1sxjE/merged-good-all-a2m # 1sxjE read from 1sxjE/merged-good-all-a2m # adding 1sxjE to template set # found chain 1sxjE in template set Warning: unaligning (T0386)N35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sxjE)R134 Warning: unaligning (T0386)S58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sxjE)R134 T0386 24 :TTTLKNKYGIK 1sxjE 110 :QELLKEVAQME T0386 61 :EYFDTA 1sxjE 144 :NSLTKD T0386 71 :IHQQLFKNTFEWAGYLR 1sxjE 150 :AQAALRRTMEKYSKNIR T0386 97 :T 1sxjE 173 :S T0386 101 :MPEMKR 1sxjE 174 :MSPIIA T0386 107 :TGWKNAFAI 1sxjE 183 :SQCLLIRCP T0386 116 :GD 1sxjE 193 :PS T0386 118 :EIQEGLQRL 1sxjE 197 :EISTILSDV T0386 130 :LAEKN 1sxjE 206 :VTNER T0386 137 :QGLTREEFNSEAIELF 1sxjE 211 :IQLETKDILKRIAQAS T0386 163 :EGNGRTQRLFFENLAKAAGHQL 1sxjE 227 :NGNLRVSLLMLESMALNNELAL T0386 185 :NFSLI 1sxjE 251 :SSPII T0386 190 :TKERMMVASVAVAENG 1sxjE 278 :SLIECRAVLYDLLAHC T0386 206 :DLEPMQHLFEDIS 1sxjE 295 :PANIILKELTFSL T0386 219 :NPEKIRLLKEFMHTMKN 1sxjE 318 :KSSIIEYSSVFDERLSL T0386 240 :VNDRPVMVAKEGETYTGTY 1sxjE 335 :GNKAIFHLEGFIAKVMCCL Number of specific fragments extracted= 16 number of extra gaps= 0 total=383 Number of alignments=40 # 1sxjE read from 1sxjE/merged-good-all-a2m # found chain 1sxjE in template set Warning: unaligning (T0386)N35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sxjE)R134 Warning: unaligning (T0386)E61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sxjE)R134 T0386 21 :YPN 1sxjE 106 :RIV T0386 24 :TTTLKNKYGIK 1sxjE 110 :QELLKEVAQME T0386 62 :YFDTAYLCHIHQQLFKNT 1sxjE 145 :SLTKDAQAALRRTMEKYS T0386 107 :TGWKNAFAIGDE 1sxjE 183 :SQCLLIRCPAPS T0386 119 :IQEG 1sxjE 198 :ISTI T0386 126 :LDQTLAEKNN 1sxjE 202 :LSDVVTNERI T0386 139 :LTREEFNSEAIELF 1sxjE 213 :LETKDILKRIAQAS T0386 163 :EGNGRTQRLFFENLAKAAGHQLNFSLI 1sxjE 227 :NGNLRVSLLMLESMALNNELALKSSSP T0386 190 :TKERMMV 1sxjE 275 :SVNSLIE T0386 197 :ASVAVAENG 1sxjE 285 :VLYDLLAHC T0386 206 :DLEPMQHLFEDIS 1sxjE 295 :PANIILKELTFSL T0386 219 :NPEKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETY 1sxjE 318 :KSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCL Number of specific fragments extracted= 12 number of extra gaps= 0 total=395 Number of alignments=41 # 1sxjE read from 1sxjE/merged-good-all-a2m # found chain 1sxjE in template set T0386 46 :DT 1sxjE 149 :DA T0386 72 :HQQLFKNTFEWAGYLRHIPFTFADGTTAAMPEMKRTGWKNAFAIGDEIQEGLQRLDQTLAE 1sxjE 151 :QAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI T0386 138 :GLTREEFNSEAIELF 1sxjE 212 :QLETKDILKRIAQAS T0386 163 :EGNGRTQRLFFENLAKAAGHQLNFSLI 1sxjE 227 :NGNLRVSLLMLESMALNNELALKSSSP T0386 190 :TKERMMVASVAVAE 1sxjE 255 :IKPDWIIVIHKLTR T0386 212 :HLFEDISNPEK 1sxjE 269 :KIVKERSVNSL T0386 224 :RLLKEFMHTMKNTGRNVNDRPVMVAKE 1sxjE 280 :IECRAVLYDLLAHCIPANIILKELTFS T0386 276 :IGNIDHLPPEQL 1sxjE 307 :LLDVETLNTTNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=403 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y1xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y1xA expands to /projects/compbio/data/pdb/1y1x.pdb.gz 1y1xA:# T0386 read from 1y1xA/merged-good-all-a2m # 1y1xA read from 1y1xA/merged-good-all-a2m # adding 1y1xA to template set # found chain 1y1xA in template set Warning: unaligning (T0386)M246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y1xA)T179 T0386 11 :T 1y1xA 41 :S T0386 17 :HHYVYPNTTTLKNKYGIK 1y1xA 42 :GAISVPELNAALSSAGVP T0386 43 :CSHDTAKAMINLREESLPEYFDTAYLCHIHQQLF 1y1xA 60 :FSLATTEKLLHMYDKNHSGEITFDEFKDLHHFIL T0386 121 :EGLQRLDQTLAEKN 1y1xA 94 :SMREGFRKRDSSGD T0386 137 :QGLTREEFN 1y1xA 108 :GRLDSNEVR T0386 175 :NLAKAAGHQLN 1y1xA 117 :AALLSSGYQVS T0386 191 :KERMMVASVAVAEN 1y1xA 128 :EQTFQALMRKFDRQ T0386 205 :GDL 1y1xA 144 :GSL T0386 209 :PMQHLFE 1y1xA 147 :GFDDYVE T0386 222 :KIRLLKEFMHTMKNTGRNVNDRPV 1y1xA 154 :LSIFVCRVRNVFAFYDRERTGQVT Number of specific fragments extracted= 10 number of extra gaps= 1 total=413 Number of alignments=43 # 1y1xA read from 1y1xA/merged-good-all-a2m # found chain 1y1xA in template set T0386 11 :T 1y1xA 41 :S T0386 17 :HHYVYPNTTTLKNKYGIKNLNAFLE 1y1xA 42 :GAISVPELNAALSSAGVPFSLATTE T0386 50 :AMINLREESLPEYFDTAYLCHIHQQLF 1y1xA 67 :KLLHMYDKNHSGEITFDEFKDLHHFIL T0386 121 :EGLQRLDQTLAE 1y1xA 94 :SMREGFRKRDSS T0386 137 :QG 1y1xA 106 :GD T0386 139 :LTREEFN 1y1xA 110 :LDSNEVR T0386 147 :E 1y1xA 117 :A T0386 176 :LAKAAGHQL 1y1xA 118 :ALLSSGYQV T0386 190 :TKERMMVASVAVAEN 1y1xA 127 :SEQTFQALMRKFDRQ T0386 205 :GDL 1y1xA 144 :GSL T0386 209 :PMQHLFE 1y1xA 147 :GFDDYVE T0386 222 :KIRLLKEFMHTMKNTGRNVND 1y1xA 154 :LSIFVCRVRNVFAFYDRERTG Number of specific fragments extracted= 12 number of extra gaps= 0 total=425 Number of alignments=44 # 1y1xA read from 1y1xA/merged-good-all-a2m # found chain 1y1xA in template set T0386 45 :HDTAKAMINLREESLPEYFDTAYLCHIHQQLF 1y1xA 62 :LATTEKLLHMYDKNHSGEITFDEFKDLHHFIL T0386 121 :EGLQRLDQTLAEKN 1y1xA 94 :SMREGFRKRDSSGD T0386 138 :GLTR 1y1xA 109 :RLDS T0386 143 :EF 1y1xA 113 :NE T0386 173 :FENLAKAAGHQL 1y1xA 115 :VRAALLSSGYQV T0386 191 :KERMMVASVAVAEN 1y1xA 127 :SEQTFQALMRKFDR T0386 205 :GDLEPMQHLFEDISNPEKIRLLKE 1y1xA 144 :GSLGFDDYVELSIFVCRVRNVFAF T0386 232 :TM 1y1xA 168 :YD Number of specific fragments extracted= 8 number of extra gaps= 0 total=433 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pi1A expands to /projects/compbio/data/pdb/1pi1.pdb.gz 1pi1A:# T0386 read from 1pi1A/merged-good-all-a2m # 1pi1A read from 1pi1A/merged-good-all-a2m # adding 1pi1A to template set # found chain 1pi1A in template set T0386 21 :YPNTTTLKNKYGIKNLNAFLE 1pi1A 14 :TLGSGNLRQAVMLPEGEDLNE T0386 43 :CSHDTAKAMINLR 1pi1A 35 :WIAVNTVDFFNQI T0386 73 :QQLFKNTFEW 1pi1A 48 :NMLYGTITEF T0386 83 :AG 1pi1A 68 :AG T0386 94 :ADGTTAAMPEMKRTGWKNA 1pi1A 70 :PRYEYHWADGTNIKKPIKC T0386 118 :EIQEGLQRLDQTLAEK 1pi1A 89 :SAPKYIDYLMTWVQDQ T0386 137 :QGL 1pi1A 115 :IGV T0386 140 :TREEFNSEAIE 1pi1A 122 :NFMSVAKTILK T0386 167 :RTQRLFFENLAKAA 1pi1A 133 :RLFRVYAHIYHQHF T0386 192 :E 1pi1A 147 :D T0386 200 :AVAENGDLEPMQHLFEDISN 1pi1A 148 :SVMQLQEEAHLNTSFKHFIF T0386 232 :TMKN 1pi1A 168 :FVQE T0386 240 :VNDRPVMVAKEGETYTGTYRG 1pi1A 172 :FNLIDRRELAPLQELIEKLGS Number of specific fragments extracted= 13 number of extra gaps= 0 total=446 Number of alignments=46 # 1pi1A read from 1pi1A/merged-good-all-a2m # found chain 1pi1A in template set T0386 27 :LKNKYGIKNLNAFLE 1pi1A 20 :LRQAVMLPEGEDLNE T0386 43 :CSHDTAKAMINLR 1pi1A 35 :WIAVNTVDFFNQI T0386 73 :QQLFKNTFEW 1pi1A 48 :NMLYGTITEF T0386 83 :AG 1pi1A 68 :AG T0386 94 :ADGTTAAMPEMKRTGWKNA 1pi1A 70 :PRYEYHWADGTNIKKPIKC T0386 118 :EIQEGLQRLDQTLAEKNNLQGL 1pi1A 89 :SAPKYIDYLMTWVQDQLDDETL T0386 140 :TREEFNSEAIE 1pi1A 122 :NFMSVAKTILK T0386 167 :RTQRLFFENLAKAA 1pi1A 133 :RLFRVYAHIYHQHF T0386 192 :ERMMV 1pi1A 147 :DSVMQ T0386 204 :NGDLEPMQHLFEDIS 1pi1A 152 :LQEEAHLNTSFKHFI T0386 231 :HTMKNTG 1pi1A 167 :FFVQEFN T0386 238 :RNVN 1pi1A 178 :RELA Number of specific fragments extracted= 12 number of extra gaps= 0 total=458 Number of alignments=47 # 1pi1A read from 1pi1A/merged-good-all-a2m # found chain 1pi1A in template set T0386 32 :GIKNLNAF 1pi1A 16 :GSGNLRQA T0386 44 :SHDTAKAMINLR 1pi1A 33 :NEWIAVNTVDFF T0386 70 :HIHQQLFKNTFEW 1pi1A 45 :NQINMLYGTITEF T0386 83 :AGYLRHIPFTFADGT 1pi1A 68 :AGPRYEYHWADGTNI T0386 106 :RTGWKNA 1pi1A 83 :KKPIKCS T0386 119 :IQEGLQRLDQTLAEKNNLQGL 1pi1A 90 :APKYIDYLMTWVQDQLDDETL T0386 140 :TREEFNSEAIELFNSLN 1pi1A 122 :NFMSVAKTILKRLFRVY T0386 171 :LFFENLAK 1pi1A 139 :AHIYHQHF T0386 181 :G 1pi1A 147 :D T0386 188 :LITKERMMVASVA 1pi1A 151 :QLQEEAHLNTSFK T0386 209 :PMQHLFEDI 1pi1A 164 :HFIFFVQEF T0386 280 :DHLPPEQLKIL 1pi1A 173 :NLIDRRELAPL Number of specific fragments extracted= 12 number of extra gaps= 0 total=470 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0386 read from 1exrA/merged-good-all-a2m # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set Warning: unaligning (T0386)T47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1exrA)F12 Warning: unaligning (T0386)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1exrA)F12 Warning: unaligning (T0386)H212 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1exrA)M144 Warning: unaligning (T0386)L213 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1exrA)M144 T0386 43 :CSHD 1exrA 7 :EQIA T0386 49 :KAMINLREESLPEYFDTAYLCHIHQQL 1exrA 13 :KEAFALFDKDGDGTITTKELGTVMRSL T0386 95 :DGT 1exrA 40 :GQN T0386 114 :AIGDEIQEGLQR 1exrA 43 :PTEAELQDMINE T0386 126 :LDQTLAEKNNLQG 1exrA 68 :FLSLMARKMKEQD T0386 140 :TREEFNSEAIEL 1exrA 81 :SEEELIEAFKVF T0386 162 :REGNGRTQRLFFENLAKAAGHQL 1exrA 94 :RDGNGLISAAELRHVMTNLGEKL T0386 190 :TKERMMVASVAVAENG 1exrA 117 :TDDEVDEMIREADIDG T0386 206 :DLEPMQ 1exrA 137 :NYEEFV T0386 214 :FE 1exrA 145 :MV Number of specific fragments extracted= 10 number of extra gaps= 2 total=480 Number of alignments=49 # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set Warning: unaligning (T0386)T47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1exrA)F12 Warning: unaligning (T0386)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1exrA)F12 Warning: unaligning (T0386)H212 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1exrA)M144 Warning: unaligning (T0386)L213 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1exrA)M144 T0386 45 :HD 1exrA 9 :IA T0386 49 :KAMINLREESLPEYFDTAYLCHIHQQL 1exrA 13 :KEAFALFDKDGDGTITTKELGTVMRSL T0386 94 :ADGT 1exrA 40 :GQNP T0386 119 :IQEGLQRLDQTLAEKNN 1exrA 44 :TEAELQDMINEVDADGN T0386 137 :QGLTREEFNSEAIELFNS 1exrA 61 :GTIDFPEFLSLMARKMKE T0386 162 :REGNGRTQRLFFENLAKAAGHQ 1exrA 94 :RDGNGLISAAELRHVMTNLGEK T0386 189 :ITKERMMVASVAVAENG 1exrA 116 :LTDDEVDEMIREADIDG T0386 206 :DLEPMQ 1exrA 137 :NYEEFV T0386 214 :FE 1exrA 145 :MV Number of specific fragments extracted= 9 number of extra gaps= 2 total=489 Number of alignments=50 # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set Warning: unaligning (T0386)H212 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1exrA)M144 Warning: unaligning (T0386)L213 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1exrA)M144 T0386 7 :KTKNTEIISPHHYVYPNT 1exrA 13 :KEAFALFDKDGDGTITTK T0386 25 :TTLKNKYGIKNLNAFLEKCSH 1exrA 34 :TVMRSLGQNPTEAELQDMINE T0386 55 :REESLPEYFDTAYLCHIHQQLFKN 1exrA 55 :VDADGNGTIDFPEFLSLMARKMKE T0386 120 :QEGLQRLDQTLAEK 1exrA 79 :QDSEEELIEAFKVF T0386 162 :REGNG 1exrA 94 :RDGNG T0386 172 :FFENLAKAAGHQL 1exrA 104 :ELRHVMTNLGEKL T0386 191 :KERMMVASVAVAE 1exrA 117 :TDDEVDEMIREAD T0386 204 :NGDLEPMQ 1exrA 135 :HINYEEFV T0386 214 :FE 1exrA 145 :MV Number of specific fragments extracted= 9 number of extra gaps= 1 total=498 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fnaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fnaA expands to /projects/compbio/data/pdb/2fna.pdb.gz 2fnaA: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 996, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fnaA 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 1457, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 2fnaA 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 # T0386 read from 2fnaA/merged-good-all-a2m # 2fnaA read from 2fnaA/merged-good-all-a2m # adding 2fnaA to template set # found chain 2fnaA in template set Warning: unaligning (T0386)A94 because of BadResidue code BAD_PEPTIDE in next template residue (2fnaA)G108 Warning: unaligning (T0386)D95 because of BadResidue code BAD_PEPTIDE at template residue (2fnaA)G108 Warning: unaligning (T0386)M101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fnaA)R120 Warning: unaligning (T0386)F113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fnaA)R120 T0386 17 :HHYVYPN 2fnaA 69 :NYISYKD T0386 44 :SHDTAKAMINLREESLPE 2fnaA 76 :FLLELQKEINKLVKRLPS T0386 75 :LFKNTFEWAG 2fnaA 94 :LLKALKNIQG T0386 91 :FTF 2fnaA 104 :IVI T0386 96 :GTTAA 2fnaA 109 :NEIKF T0386 114 :AI 2fnaA 121 :LS T0386 123 :LQRLDQTLAEK 2fnaA 123 :FANLLESFEQA T0386 134 :NNLQGLTREEFNSEAIE 2fnaA 149 :VKLRGVNLLPALAYAYD T0386 174 :ENLAKAA 2fnaA 179 :MGLLYDY T0386 181 :G 2fnaA 189 :E T0386 182 :HQLNFSLI 2fnaA 198 :RAFSTVEL T0386 190 :TKERMMVASVAVAEN 2fnaA 209 :SREEAIEFLRRGFQE T0386 205 :GDLEPMQHLFEDISNP 2fnaA 239 :GGIPGWLTYFGFIYLD T0386 221 :EKIRLLKEFMHTMKNTGRNVNDRPVMVAKEGETYTGTYRGAG 2fnaA 261 :AINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSKCG Number of specific fragments extracted= 14 number of extra gaps= 1 total=512 Number of alignments=52 # 2fnaA read from 2fnaA/merged-good-all-a2m # found chain 2fnaA in template set Warning: unaligning (T0386)A94 because of BadResidue code BAD_PEPTIDE in next template residue (2fnaA)G108 Warning: unaligning (T0386)D95 because of BadResidue code BAD_PEPTIDE at template residue (2fnaA)G108 Warning: unaligning (T0386)M101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fnaA)R120 Warning: unaligning (T0386)G108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fnaA)R120 T0386 16 :PHH 2fnaA 66 :EER T0386 19 :YVYPN 2fnaA 71 :ISYKD T0386 44 :SHDTAKAMINLREESLPE 2fnaA 76 :FLLELQKEINKLVKRLPS T0386 75 :LFKNTFEWAG 2fnaA 94 :LLKALKNIQG T0386 91 :FTF 2fnaA 104 :IVI T0386 96 :GTTAA 2fnaA 109 :NEIKF T0386 109 :WK 2fnaA 121 :LS T0386 123 :LQRLDQTLAEKN 2fnaA 123 :FANLLESFEQAS T0386 135 :NLQGLTREE 2fnaA 150 :KLRGVNLLP T0386 147 :EAIELFNSLNQL 2fnaA 159 :ALAYAYDNLKRI T0386 174 :ENLAKAA 2fnaA 179 :MGLLYDY T0386 181 :G 2fnaA 189 :E T0386 182 :H 2fnaA 200 :F T0386 183 :QLNFSLITKERMMVASVAVAEN 2fnaA 202 :TVELKPFSREEAIEFLRRGFQE T0386 205 :GDLEPMQHLFEDIS 2fnaA 239 :GGIPGWLTYFGFIY T0386 219 :NPEK 2fnaA 258 :LDFA T0386 223 :IRLLKEFMHTMKNTG 2fnaA 263 :NQTLEYAKKLILKEF T0386 238 :RNVNDRPVMVAKEGETYTGTYRGAGLEGFAL 2fnaA 282 :HGREIARKRYLNIMRTLSKCGKWSDVKRALE T0386 269 :NVKGAYIIGNIDHLPPEQLKILKPGD 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEK Number of specific fragments extracted= 19 number of extra gaps= 1 total=531 Number of alignments=53 # 2fnaA read from 2fnaA/merged-good-all-a2m # found chain 2fnaA in template set T0386 97 :T 2fnaA 192 :E T0386 99 :AAMPEMKRTGWKNAFAIGDEIQEGLQRLDQTLAE 2fnaA 193 :SPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI T0386 138 :GLTR 2fnaA 227 :DFKD T0386 142 :EEFNSEA 2fnaA 232 :EVVYEKI T0386 191 :KERMMVASVAVAENGDLEPMQHLFEDISNPEKIRLLKEFMHTMK 2fnaA 242 :PGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=536 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nh1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nh1A expands to /projects/compbio/data/pdb/1nh1.pdb.gz 1nh1A:# T0386 read from 1nh1A/merged-good-all-a2m # 1nh1A read from 1nh1A/merged-good-all-a2m # adding 1nh1A to template set # found chain 1nh1A in template set T0386 24 :TTTLKNK 1nh1A 184 :TEYLRDR T0386 36 :LNAFLEKCSHDTAKAMINLR 1nh1A 191 :VAHLRTELGAKALKQHLQRY T0386 94 :ADGT 1nh1A 211 :NPDR T0386 111 :NAFAIGDEIQEGLQRLDQTLAEK 1nh1A 215 :IDHTNASYLPIIKDHLNDLYRQA T0386 135 :NLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLI 1nh1A 238 :ISSDLSQAELISLIARTHWWAASAMPDQRGSAAKAEFAARAIASAHGIELPPFRN T0386 197 :ASVAVAE 1nh1A 296 :SDIEAML T0386 205 :GDLEPMQHL 1nh1A 303 :SGEEEFVEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=543 Number of alignments=55 # 1nh1A read from 1nh1A/merged-good-all-a2m # found chain 1nh1A in template set T0386 34 :KNLNAFLE 1nh1A 57 :SNTPENRA T0386 42 :KCSHDTAKAMINLREES 1nh1A 67 :QSMYNSIRSAGDEISRG T0386 62 :YFD 1nh1A 84 :GIT T0386 68 :LCHIHQQLFKNT 1nh1A 88 :FEELWGRATEWR T0386 86 :LRHIPFTFADGT 1nh1A 161 :VYRQTAYLHGNV T0386 99 :AAMPEM 1nh1A 173 :IPLNTF T0386 105 :KRTGWKNAFAIGDEIQEGLQRLDQTLAEKNN 1nh1A 209 :RYNPDRIDHTNASYLPIIKDHLNDLYRQAIS T0386 137 :QGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLI 1nh1A 240 :SDLSQAELISLIARTHWWAASAMPDQRGSAAKAEFAARAIASAHGIELPPFRN T0386 206 :DLEPMQH 1nh1A 304 :GEEEFVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=552 Number of alignments=56 # 1nh1A read from 1nh1A/merged-good-all-a2m # found chain 1nh1A in template set T0386 23 :NTTTLKNK 1nh1A 183 :DTEYLRDR T0386 36 :LNAFLEKCSHDTAKAMINLR 1nh1A 191 :VAHLRTELGAKALKQHLQRY T0386 58 :S 1nh1A 211 :N T0386 95 :DG 1nh1A 212 :PD T0386 110 :KNAFAIGDEIQEGLQRLDQTLAEK 1nh1A 214 :RIDHTNASYLPIIKDHLNDLYRQA T0386 135 :NLQGLTREEFNSEAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERMMVA 1nh1A 238 :ISSDLSQAELISLIARTHWWAASAMPDQRGSAAKAEFAARAIASAHGIELPPFRNGNVSDIEA T0386 203 :ENGDLEPMQH 1nh1A 301 :MLSGEEEFVE T0386 232 :TMKNT 1nh1A 311 :KYRSL Number of specific fragments extracted= 8 number of extra gaps= 0 total=560 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fpwA/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/T0386/1fpwA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0386/1fpwA/merged-good-all-a2m.gz for input Trying 1fpwA/merged-good-all-a2m Error: Couldn't open file 1fpwA/merged-good-all-a2m or 1fpwA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g8lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g8lA expands to /projects/compbio/data/pdb/1g8l.pdb.gz 1g8lA:# T0386 read from 1g8lA/merged-good-all-a2m # 1g8lA read from 1g8lA/merged-good-all-a2m # adding 1g8lA to template set # found chain 1g8lA in template set T0386 16 :PHHYVYPNTTTLKNK 1g8lA 153 :GTRLTTAELPVIASL T0386 32 :GIK 1g8lA 168 :GIA T0386 90 :PFTFADGT 1g8lA 171 :EVPVIRKV T0386 109 :WKNAFAIGDEI 1g8lA 179 :RVALFSTGDEL T0386 131 :AE 1g8lA 190 :QL T0386 137 :QGLTREE 1g8lA 192 :PGQPLGD T0386 164 :G 1g8lA 199 :G T0386 169 :QRLFFENLAKAAGHQLNFSLI 1g8lA 205 :NRLAVHLMLEQLGCEVINLGI T0386 190 :TKERMMVASVAVAEN 1g8lA 229 :DPHALRAAFIEADSQ T0386 205 :GDLEPMQHLFEDIS 1g8lA 256 :GEADYTKTILEELG Number of specific fragments extracted= 10 number of extra gaps= 0 total=570 Number of alignments=58 # 1g8lA read from 1g8lA/merged-good-all-a2m # found chain 1g8lA in template set T0386 15 :SPHH 1g8lA 151 :PAGT T0386 19 :YVYPNTTTLKNKYGI 1g8lA 156 :LTTAELPVIASLGIA T0386 90 :PFTFADGT 1g8lA 171 :EVPVIRKV T0386 109 :WKNAFAIGDE 1g8lA 179 :RVALFSTGDE T0386 137 :QGLTRE 1g8lA 192 :PGQPLG T0386 163 :EG 1g8lA 198 :DG T0386 169 :QRLFFENLAKAAGHQLNFSLI 1g8lA 205 :NRLAVHLMLEQLGCEVINLGI T0386 190 :TKERMMVASVAVAEN 1g8lA 229 :DPHALRAAFIEADSQ T0386 205 :GDLEPMQHLFEDIS 1g8lA 256 :GEADYTKTILEELG Number of specific fragments extracted= 9 number of extra gaps= 0 total=579 Number of alignments=59 # 1g8lA read from 1g8lA/merged-good-all-a2m # found chain 1g8lA in template set T0386 169 :QRLFFENLAKAAGHQLNFSLI 1g8lA 205 :NRLAVHLMLEQLGCEVINLGI T0386 190 :TKERMMVASVAVAE 1g8lA 228 :DDPHALRAAFIEAD T0386 204 :N 1g8lA 254 :S T0386 205 :GDLEPMQHLFEDI 1g8lA 256 :GEADYTKTILEEL T0386 251 :GETYTGTYRGAGLEGFALN 1g8lA 269 :GEIAFWKLAIKPGKPFAFG T0386 270 :VKGAYI 1g8lA 289 :LSNSWF Number of specific fragments extracted= 6 number of extra gaps= 0 total=585 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b3oA expands to /projects/compbio/data/pdb/2b3o.pdb.gz 2b3oA:# T0386 read from 2b3oA/merged-good-all-a2m # 2b3oA read from 2b3oA/merged-good-all-a2m # adding 2b3oA to template set # found chain 2b3oA in template set Warning: unaligning (T0386)R243 because last residue in template chain is (2b3oA)L526 T0386 79 :TFEWAGYLRHIP 2b3oA 364 :YWPEVGMQRAYG T0386 91 :FTFADGTTAAMP 2b3oA 377 :YSVTNCGEHDTT T0386 103 :EMKRTGWKNA 2b3oA 403 :GDLIREIWHY T0386 113 :FAIGDEIQEGLQRLDQTLAEK 2b3oA 423 :PSEPGGVLSFLDQINQRQESL T0386 137 :QGLTR 2b3oA 444 :PHAGP T0386 158 :LHPFREGNGRTQRLFFENLAKAA 2b3oA 450 :IVHCSAGIGRTGTIIVIDMLMEN T0386 181 :GHQLN 2b3oA 479 :DCDID T0386 194 :MMVASVAVAEN 2b3oA 484 :IQKTIQMVRAQ T0386 206 :DLEPMQHLFEDISNPEKIR 2b3oA 500 :QTEAQYKFIYVAIAQFIET T0386 236 :TGRNVND 2b3oA 519 :TKKKLEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=595 Number of alignments=61 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set T0386 46 :DTAKAMINLREES 2b3oA 185 :DSLTDLVEHFKKT T0386 80 :FEWAGYLRHIP 2b3oA 365 :WPEVGMQRAYG T0386 91 :FTFADGTTAAM 2b3oA 377 :YSVTNCGEHDT T0386 102 :PEMKRTGWK 2b3oA 398 :SPLDNGDLI T0386 111 :NAF 2b3oA 410 :WHY T0386 116 :GDE 2b3oA 423 :PSE T0386 119 :IQEGLQRLDQTLAEK 2b3oA 429 :VLSFLDQINQRQESL T0386 137 :QGLTR 2b3oA 444 :PHAGP T0386 157 :QLHPFREGNGRTQRLFFENLAKAA 2b3oA 449 :IIVHCSAGIGRTGTIIVIDMLMEN T0386 181 :GHQLN 2b3oA 479 :DCDID T0386 194 :MMVASVAVAEN 2b3oA 484 :IQKTIQMVRAQ T0386 205 :G 2b3oA 497 :G T0386 206 :DLEPMQHLFEDISNPEKIRL 2b3oA 500 :QTEAQYKFIYVAIAQFIETT Number of specific fragments extracted= 13 number of extra gaps= 0 total=608 Number of alignments=62 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set Warning: unaligning (T0386)V240 because last residue in template chain is (2b3oA)L526 T0386 80 :FEWAGYLRHIPFTFADGT 2b3oA 400 :LDNGDLIREIWHYQYLSW T0386 108 :GWKNAFAIGDEIQEGLQRLDQTLAEKN 2b3oA 418 :PDHGVPSEPGGVLSFLDQINQRQESLP T0386 138 :GLTR 2b3oA 445 :HAGP T0386 162 :REGNGRTQRLFFENLAKA 2b3oA 454 :SAGIGRTGTIIVIDMLME T0386 180 :AGHQLN 2b3oA 478 :LDCDID T0386 195 :MVASVAVAEN 2b3oA 484 :IQKTIQMVRA T0386 216 :DISNPEKIRLLKEFMHTMKNTGRN 2b3oA 502 :EAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 7 number of extra gaps= 0 total=615 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f6sA expands to /projects/compbio/data/pdb/2f6s.pdb.gz 2f6sA: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 # T0386 read from 2f6sA/merged-good-all-a2m # 2f6sA read from 2f6sA/merged-good-all-a2m # adding 2f6sA to template set # found chain 2f6sA in template set Warning: unaligning (T0386)N35 because first residue in template chain is (2f6sA)G-1 Warning: unaligning (T0386)T92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f6sA)K56 Warning: unaligning (T0386)F93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f6sA)K56 T0386 36 :LNAFLE 2f6sA 0 :HMHLDR T0386 43 :CSHDTAKAMIN 2f6sA 6 :QSLEKAKHLIQ T0386 57 :ESLP 2f6sA 18 :GLID T0386 61 :EYFDTAYLCHIHQQLFKNTFEWAGYLRHIPF 2f6sA 24 :EVGTIKGLQEIHRFLFEGLYEFAGKIRDKNI T0386 94 :ADGT 2f6sA 57 :GNFR T0386 113 :FAIGDEIQEGLQRLDQT 2f6sA 61 :FANCLYLDLILPRIESM T0386 137 :QGLTREEFNSE 2f6sA 78 :PQNNFNQIVEK T0386 152 :FNSLNQLHPFREGNGRTQRLFFENLAKAA 2f6sA 89 :YVEMNIAHPFLEGNGRATRIWLDLLLKKE T0386 183 :Q 2f6sA 120 :K T0386 184 :LNFSLITKERMMVASVAVAE 2f6sA 122 :VLWDRIDKAAYLSAMERSPV T0386 206 :DLEPMQHLFEDIS 2f6sA 142 :NDLEIKTLLKKHL T0386 222 :KIRLLKEFMHTMKNTG 2f6sA 161 :PLTLIKGITQSYYYEG Number of specific fragments extracted= 12 number of extra gaps= 1 total=627 Number of alignments=64 # 2f6sA read from 2f6sA/merged-good-all-a2m # found chain 2f6sA in template set Warning: unaligning (T0386)K34 because first residue in template chain is (2f6sA)G-1 Warning: unaligning (T0386)T92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f6sA)K56 Warning: unaligning (T0386)F93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f6sA)K56 T0386 35 :NLNA 2f6sA 0 :HMHL T0386 40 :LE 2f6sA 4 :DR T0386 43 :CSHDTAKAMIN 2f6sA 6 :QSLEKAKHLIQ T0386 56 :EESLPE 2f6sA 17 :SGLIDT T0386 62 :YFDTAYLCHIHQQLFKNTFEWAGYLRHIPF 2f6sA 25 :VGTIKGLQEIHRFLFEGLYEFAGKIRDKNI T0386 94 :ADGT 2f6sA 57 :GNFR T0386 113 :FAIGDEIQEGLQRLDQT 2f6sA 61 :FANCLYLDLILPRIESM T0386 135 :NLQ 2f6sA 78 :PQN T0386 140 :TREEFNSE 2f6sA 81 :NFNQIVEK T0386 152 :FNSLNQLHPFREGNGRTQRLFFENLAKAA 2f6sA 89 :YVEMNIAHPFLEGNGRATRIWLDLLLKKE T0386 181 :GHQLNFSLITKERMMVASVAVAE 2f6sA 119 :KKIVLWDRIDKAAYLSAMERSPV T0386 206 :DLEPMQHLFEDIS 2f6sA 142 :NDLEIKTLLKKHL T0386 219 :NPEKIRLLKEFMHTMKNTGR 2f6sA 158 :TNDPLTLIKGITQSYYYEGL Number of specific fragments extracted= 13 number of extra gaps= 1 total=640 Number of alignments=65 # 2f6sA read from 2f6sA/merged-good-all-a2m # found chain 2f6sA in template set Warning: unaligning (T0386)T92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f6sA)K56 Warning: unaligning (T0386)F93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f6sA)K56 T0386 44 :SHDTAKAMINLREES 2f6sA 4 :DRQSLEKAKHLIQSG T0386 59 :LPEYFDTAYLCHIHQQLFKNTFEWAGYLRHIPF 2f6sA 22 :TIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNI T0386 94 :ADGT 2f6sA 57 :GNFR T0386 113 :FAIGDEIQEGLQRLDQT 2f6sA 61 :FANCLYLDLILPRIESM T0386 138 :GLTREE 2f6sA 78 :PQNNFN T0386 147 :EAIELFNSLNQLHPFREGNGRTQRLFFENLAKAAGHQLNFSLITKERMMVASVAVAEN 2f6sA 84 :QIVEKYVEMNIAHPFLEGNGRATRIWLDLLLKKELKKIVLWDRIDKAAYLSAMERSPV T0386 206 :DLEPMQHLF 2f6sA 142 :NDLEIKTLL T0386 234 :KNTG 2f6sA 151 :KKHL T0386 238 :RNVNDRPVM 2f6sA 156 :SNTNDPLTL Number of specific fragments extracted= 9 number of extra gaps= 1 total=649 Number of alignments=66 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0386//projects/compbio/experiments/protein-predict/casp7/T0386/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0386//projects/compbio/experiments/protein-predict/casp7/T0386/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0386/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0386/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((T0386)V201.CB, (T0386)M210.CB) [> 3.3772 = 5.6286 < 7.3172] w=1.0000 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)L184.CB) [> 3.3670 = 5.6116 < 7.2951] w=0.8771 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)E147.CB) [> 3.5749 = 5.9582 < 7.7456] w=0.7538 to align # Constraint # added constraint: constraint((T0386)R55.CB, (T0386)I71.CB) [> 3.1588 = 5.2647 < 6.8442] w=0.6962 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)F214.CB) [> 4.0558 = 6.7597 < 8.7876] w=0.6957 to align # Constraint # added constraint: constraint((T0386)R55.CB, (T0386)L68.CB) [> 4.0908 = 6.8180 < 8.8634] w=0.6588 to align # Constraint # added constraint: constraint((T0386)L54.CB, (T0386)I71.CB) [> 4.1070 = 6.8449 < 8.8984] w=0.6184 to align # Constraint # added constraint: constraint((T0386)L130.CB, (T0386)L139.CB) [> 3.4108 = 5.6846 < 7.3900] w=0.6117 to align # Constraint # added constraint: constraint((T0386)E56.CB, (T0386)Y67.CB) [> 3.6943 = 6.1572 < 8.0044] w=0.6103 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)L123.CB) [> 2.9770 = 4.9616 < 6.4501] w=0.5893 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)L213.CB) [> 3.3677 = 5.6129 < 7.2967] w=0.5830 to align # Constraint # added constraint: constraint((T0386)I52.CB, (T0386)F63.CB) [> 4.1411 = 6.9018 < 8.9723] w=0.5677 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)M210.CB) [> 3.3538 = 5.5896 < 7.2665] w=0.5529 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)F172.CB) [> 4.3281 = 7.2135 < 9.3775] w=0.5513 to align # Constraint # added constraint: constraint((T0386)F173.CB, (T0386)S198.CB) [> 3.7020 = 6.1700 < 8.0210] w=0.5486 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)Q169.CB) [> 3.5867 = 5.9778 < 7.7712] w=0.5093 to align # Constraint # added constraint: constraint((T0386)L155.CB, (T0386)F173.CB) [> 4.4309 = 7.3848 < 9.6003] w=0.5050 to align # Constraint # added constraint: constraint((T0386)L155.CB, (T0386)F172.CB) [> 4.0515 = 6.7525 < 8.7782] w=0.5050 to align # Constraint # added constraint: constraint((T0386)A177.CB, (T0386)M194.CB) [> 3.9716 = 6.6194 < 8.6053] w=0.5022 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)F173.CB) [> 2.8891 = 4.8151 < 6.2596] w=0.4702 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)L176.CB) [> 4.1068 = 6.8447 < 8.8981] w=0.4640 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)F113.CB) [> 4.2636 = 7.1061 < 9.2379] w=0.4635 to align # Constraint # added constraint: constraint((T0386)I119.CB, (T0386)L158.CB) [> 3.8542 = 6.4237 < 8.3508] w=0.4633 to align # Constraint # added constraint: constraint((T0386)E147.CB, (T0386)L176.CB) [> 4.1837 = 6.9728 < 9.0647] w=0.4596 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)L151.CB) [> 3.6305 = 6.0509 < 7.8661] w=0.4553 to align # Constraint # added constraint: constraint((T0386)A148.CB, (T0386)L176.CB) [> 3.7454 = 6.2423 < 8.1150] w=0.4545 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)E143.CB) [> 3.5069 = 5.8449 < 7.5984] w=0.4470 to align # Constraint # added constraint: constraint((T0386)M195.CB, (T0386)L213.CB) [> 3.6784 = 6.1306 < 7.9698] w=0.4469 to align # Constraint # added constraint: constraint((T0386)L130.CB, (T0386)F144.CB) [> 3.6148 = 6.0246 < 7.8320] w=0.4436 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)Q211.CB) [> 4.0537 = 6.7562 < 8.7831] w=0.4411 to align # Constraint # added constraint: constraint((T0386)N145.CB, (T0386)Q211.CB) [> 3.8355 = 6.3926 < 8.3103] w=0.4267 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)M210.CB) [> 3.7414 = 6.2357 < 8.1064] w=0.4258 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)L155.CB) [> 3.5615 = 5.9358 < 7.7166] w=0.4258 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)S154.CB) [> 3.0901 = 5.1502 < 6.6953] w=0.4258 to align # Constraint # added constraint: constraint((T0386)M51.CB, (T0386)Q74.CB) [> 3.9362 = 6.5604 < 8.5285] w=0.4247 to align # Constraint # added constraint: constraint((T0386)M51.CB, (T0386)L75.CB) [> 4.1965 = 6.9942 < 9.0925] w=0.4247 to align # Constraint # added constraint: constraint((T0386)G166.CA, (T0386)L207.CB) [> 4.1976 = 6.9960 < 9.0948] w=0.4230 to align # Constraint # added constraint: constraint((T0386)F144.CB, (T0386)A177.CB) [> 3.9298 = 6.5497 < 8.5146] w=0.4197 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)F186.CB) [> 4.3745 = 7.2908 < 9.4781] w=0.4189 to align # Constraint # added constraint: constraint((T0386)F173.CB, (T0386)L184.CB) [> 4.4139 = 7.3564 < 9.5634] w=0.4153 to align # Constraint # added constraint: constraint((T0386)L184.CB, (T0386)M194.CB) [> 3.3826 = 5.6377 < 7.3291] w=0.4120 to align # Constraint # added constraint: constraint((T0386)I149.CB, (T0386)M210.CB) [> 3.5307 = 5.8845 < 7.6498] w=0.4120 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)F214.CB) [> 4.0349 = 6.7248 < 8.7422] w=0.4106 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)H159.CB) [> 2.5034 = 4.1723 < 5.4240] w=0.3861 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)Q157.CB) [> 3.7190 = 6.1983 < 8.0578] w=0.3861 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)L158.CB) [> 2.8383 = 4.7305 < 6.1497] w=0.3861 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)H159.CB) [> 3.8115 = 6.3526 < 8.2584] w=0.3861 to align # Constraint # added constraint: constraint((T0386)I119.CB, (T0386)P160.CB) [> 3.6479 = 6.0799 < 7.9038] w=0.3861 to align # Constraint # added constraint: constraint((T0386)G122.CA, (T0386)L158.CB) [> 3.8204 = 6.3673 < 8.2775] w=0.3861 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)P160.CB) [> 3.8268 = 6.3780 < 8.2915] w=0.3861 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)L158.CB) [> 4.0278 = 6.7129 < 8.7268] w=0.3861 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)S154.CB) [> 3.9858 = 6.6430 < 8.6359] w=0.3861 to align # Constraint # added constraint: constraint((T0386)L155.CB, (T0386)Q169.CB) [> 2.9251 = 4.8752 < 6.3378] w=0.3861 to align # Constraint # added constraint: constraint((T0386)N156.CB, (T0386)N165.CB) [> 4.1591 = 6.9319 < 9.0115] w=0.3861 to align # Constraint # added constraint: constraint((T0386)N156.CB, (T0386)Q169.CB) [> 3.2209 = 5.3682 < 6.9787] w=0.3861 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)D127.CB) [> 3.1925 = 5.3209 < 6.9171] w=0.3830 to align # Constraint # added constraint: constraint((T0386)D64.CB, (T0386)D127.CB) [> 3.8858 = 6.4763 < 8.4192] w=0.3830 to align # Constraint # added constraint: constraint((T0386)F173.CB, (T0386)A197.CB) [> 3.9836 = 6.6393 < 8.6311] w=0.3817 to align # Constraint # added constraint: constraint((T0386)F173.CB, (T0386)M194.CB) [> 3.2246 = 5.3743 < 6.9866] w=0.3817 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)E174.CB) [> 3.8868 = 6.4781 < 8.4215] w=0.3774 to align # Constraint # added constraint: constraint((T0386)I119.CB, (T0386)E174.CB) [> 3.5378 = 5.8962 < 7.6651] w=0.3774 to align # Constraint # added constraint: constraint((T0386)A148.CB, (T0386)F173.CB) [> 3.5120 = 5.8534 < 7.6094] w=0.3750 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)I217.CB) [> 3.6002 = 6.0003 < 7.8004] w=0.3743 to align # Constraint # added constraint: constraint((T0386)N145.CB, (T0386)M210.CB) [> 3.9489 = 6.5816 < 8.5560] w=0.3737 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)L123.CB) [> 3.6933 = 6.1555 < 8.0021] w=0.3701 to align # Constraint # added constraint: constraint((T0386)L130.CB, (T0386)R141.CB) [> 4.0649 = 6.7749 < 8.8073] w=0.3696 to align # Constraint # added constraint: constraint((T0386)A200.CB, (T0386)L213.CB) [> 4.1244 = 6.8740 < 8.9362] w=0.3640 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)H212.CB) [> 3.9484 = 6.5807 < 8.5549] w=0.3626 to align # Constraint # added constraint: constraint((T0386)M195.CB, (T0386)I217.CB) [> 3.2992 = 5.4987 < 7.1483] w=0.3612 to align # Constraint # added constraint: constraint((T0386)M195.CB, (T0386)F214.CB) [> 4.0343 = 6.7239 < 8.7410] w=0.3601 to align # Constraint # added constraint: constraint((T0386)R87.CB, (T0386)R162.CB) [> 3.2978 = 5.4963 < 7.1452] w=0.3477 to align # Constraint # added constraint: constraint((T0386)T47.CB, (T0386)L75.CB) [> 3.3881 = 5.6468 < 7.3408] w=0.3437 to align # Constraint # added constraint: constraint((T0386)L151.CB, (T0386)L176.CB) [> 3.9215 = 6.5359 < 8.4966] w=0.3390 to align # Constraint # added constraint: constraint((T0386)M51.CB, (T0386)I71.CB) [> 4.4302 = 7.3836 < 9.5987] w=0.3378 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)N175.CB) [> 3.4762 = 5.7937 < 7.5318] w=0.3370 to align # Constraint # added constraint: constraint((T0386)F144.CB, (T0386)L176.CB) [> 3.3562 = 5.5937 < 7.2718] w=0.3337 to align # Constraint # added constraint: constraint((T0386)N156.CB, (T0386)S198.CB) [> 3.7934 = 6.3223 < 8.2190] w=0.3325 to align # Constraint # added constraint: constraint((T0386)N145.CB, (T0386)L207.CB) [> 4.1387 = 6.8979 < 8.9673] w=0.3323 to align # Constraint # added constraint: constraint((T0386)H72.CB, (T0386)A94.CB) [> 3.7652 = 6.2754 < 8.1580] w=0.3313 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)Q120.CB) [> 3.6697 = 6.1162 < 7.9511] w=0.3284 to align # Constraint # added constraint: constraint((T0386)G122.CA, (T0386)S154.CB) [> 4.2272 = 7.0453 < 9.1589] w=0.3199 to align # Constraint # added constraint: constraint((T0386)F144.CB, (T0386)A197.CB) [> 4.3623 = 7.2705 < 9.4516] w=0.3187 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)F144.CB) [> 3.1927 = 5.3211 < 6.9174] w=0.3124 to align # Constraint # added constraint: constraint((T0386)L75.CB, (T0386)T168.CB) [> 3.4148 = 5.6913 < 7.3987] w=0.3113 to align # Constraint # added constraint: constraint((T0386)L75.CB, (T0386)R167.CB) [> 3.7612 = 6.2687 < 8.1493] w=0.3113 to align # Constraint # added constraint: constraint((T0386)I71.CB, (T0386)L171.CB) [> 3.3016 = 5.5027 < 7.1535] w=0.3113 to align # Constraint # added constraint: constraint((T0386)L184.CB, (T0386)S218.CB) [> 4.0113 = 6.6855 < 8.6912] w=0.3032 to align # Constraint # added constraint: constraint((T0386)A177.CB, (T0386)S218.CB) [> 4.0424 = 6.7373 < 8.7585] w=0.3032 to align # Constraint # added constraint: constraint((T0386)H72.CB, (T0386)T168.CB) [> 2.6321 = 4.3869 < 5.7030] w=0.3026 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)F172.CB) [> 3.1298 = 5.2163 < 6.7812] w=0.3026 to align # Constraint # added constraint: constraint((T0386)H72.CB, (T0386)A83.CB) [> 3.6533 = 6.0888 < 7.9154] w=0.3021 to align # Constraint # added constraint: constraint((T0386)N145.CB, (T0386)F214.CB) [> 3.7756 = 6.2927 < 8.1805] w=0.3015 to align # Constraint # added constraint: constraint((T0386)T97.CB, (T0386)I115.CB) [> 4.2114 = 7.0189 < 9.1246] w=0.2999 to align # Constraint # added constraint: constraint((T0386)F144.CB, (T0386)A180.CB) [> 3.6598 = 6.0997 < 7.9296] w=0.2992 to align # Constraint # added constraint: constraint((T0386)L139.CB, (T0386)A180.CB) [> 3.9907 = 6.6512 < 8.6466] w=0.2992 to align # Constraint # added constraint: constraint((T0386)I149.CB, (T0386)Q211.CB) [> 3.3342 = 5.5570 < 7.2241] w=0.2963 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)M194.CB) [> 3.6282 = 6.0470 < 7.8611] w=0.2959 to align # Constraint # added constraint: constraint((T0386)A197.CB, (T0386)M210.CB) [> 2.8577 = 4.7629 < 6.1917] w=0.2949 to align # Constraint # added constraint: constraint((T0386)H159.CB, (T0386)T168.CB) [> 3.3079 = 5.5132 < 7.1672] w=0.2918 to align # Constraint # added constraint: constraint((T0386)L151.CB, (T0386)F172.CB) [> 3.8758 = 6.4596 < 8.3975] w=0.2911 to align # Constraint # added constraint: constraint((T0386)N145.CB, (T0386)A177.CB) [> 4.1836 = 6.9727 < 9.0645] w=0.2893 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)L126.CB) [> 3.7681 = 6.2802 < 8.1642] w=0.2831 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)R243.CB) [> 3.6763 = 6.1272 < 7.9653] w=0.2809 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)A197.CB) [> 3.8381 = 6.3969 < 8.3159] w=0.2781 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)N145.CB) [> 3.5039 = 5.8398 < 7.5918] w=0.2781 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)E215.CB) [> 4.2558 = 7.0930 < 9.2209] w=0.2748 to align # Constraint # added constraint: constraint((T0386)T47.CB, (T0386)Q74.CB) [> 3.7924 = 6.3206 < 8.2168] w=0.2611 to align # Constraint # added constraint: constraint((T0386)F80.CB, (T0386)E163.CB) [> 3.7099 = 6.1832 < 8.0382] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F80.CB, (T0386)R162.CB) [> 4.4245 = 7.3742 < 9.5864] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F76.CB, (T0386)G164.CA) [> 4.0345 = 6.7242 < 8.7415] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F76.CB, (T0386)E163.CB) [> 4.5743 = 7.6239 < 9.9110] w=0.2609 to align # Constraint # added constraint: constraint((T0386)I71.CB, (T0386)T168.CB) [> 2.6995 = 4.4992 < 5.8489] w=0.2609 to align # Constraint # added constraint: constraint((T0386)C69.CB, (T0386)L86.CB) [> 4.5513 = 7.5854 < 9.8611] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)Q169.CB) [> 3.9755 = 6.6258 < 8.6136] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)P160.CB) [> 4.1734 = 6.9557 < 9.0425] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)L155.CB) [> 4.3150 = 7.1916 < 9.3491] w=0.2609 to align # Constraint # added constraint: constraint((T0386)Y67.CB, (T0386)F172.CB) [> 3.9336 = 6.5559 < 8.5227] w=0.2609 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)P160.CB) [> 4.3911 = 7.3186 < 9.5141] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F63.CB, (T0386)N175.CB) [> 4.3167 = 7.1945 < 9.3528] w=0.2609 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)A202.CB) [> 3.7828 = 6.3047 < 8.1961] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)L158.CB) [> 3.5538 = 5.9231 < 7.7000] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)L158.CB) [> 4.1021 = 6.8368 < 8.8878] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F91.CB, (T0386)H159.CB) [> 3.9208 = 6.5346 < 8.4950] w=0.2609 to align # Constraint # added constraint: constraint((T0386)F91.CB, (T0386)F113.CB) [> 3.2499 = 5.4166 < 7.0416] w=0.2609 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)G116.CA) [> 3.6399 = 6.0664 < 7.8864] w=0.2609 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)I115.CB) [> 3.5478 = 5.9130 < 7.6869] w=0.2609 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)F113.CB) [> 4.5821 = 7.6368 < 9.9279] w=0.2609 to align # Constraint # added constraint: constraint((T0386)I89.CB, (T0386)R162.CB) [> 3.6794 = 6.1324 < 7.9721] w=0.2609 to align # Constraint # added constraint: constraint((T0386)I89.CB, (T0386)G116.CA) [> 4.3929 = 7.3215 < 9.5180] w=0.2609 to align # Constraint # added constraint: constraint((T0386)H88.CB, (T0386)G116.CA) [> 3.9485 = 6.5808 < 8.5550] w=0.2609 to align # Constraint # added constraint: constraint((T0386)W82.CB, (T0386)F161.CB) [> 4.0816 = 6.8028 < 8.8436] w=0.2609 to align # Constraint # added constraint: constraint((T0386)Y85.CB, (T0386)F161.CB) [> 4.4762 = 7.4604 < 9.6985] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L86.CB, (T0386)I119.CB) [> 3.6140 = 6.0233 < 7.8303] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L86.CB, (T0386)L123.CB) [> 4.3968 = 7.3280 < 9.5263] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L86.CB, (T0386)P160.CB) [> 3.0339 = 5.0565 < 6.5735] w=0.2609 to align # Constraint # added constraint: constraint((T0386)L86.CB, (T0386)F161.CB) [> 4.3056 = 7.1761 < 9.3289] w=0.2609 to align # Constraint # added constraint: constraint((T0386)R87.CB, (T0386)G116.CA) [> 3.9758 = 6.6264 < 8.6143] w=0.2609 to align # Constraint # added constraint: constraint((T0386)R87.CB, (T0386)I119.CB) [> 4.4161 = 7.3602 < 9.5682] w=0.2609 to align # Constraint # added constraint: constraint((T0386)R87.CB, (T0386)P160.CB) [> 3.9460 = 6.5767 < 8.5497] w=0.2609 to align # Constraint # added constraint: constraint((T0386)R87.CB, (T0386)F161.CB) [> 3.4857 = 5.8094 < 7.5523] w=0.2609 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)L151.CB) [> 3.0980 = 5.1633 < 6.7123] w=0.2606 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)K178.CB) [> 3.0033 = 5.0055 < 6.5072] w=0.2590 to align # Constraint # added constraint: constraint((T0386)Q169.CB, (T0386)A202.CB) [> 4.2175 = 7.0292 < 9.1380] w=0.2590 to align # Constraint # added constraint: constraint((T0386)S146.CB, (T0386)L207.CB) [> 4.0957 = 6.8261 < 8.8739] w=0.2580 to align # Constraint # added constraint: constraint((T0386)Q169.CB, (T0386)S198.CB) [> 3.6126 = 6.0209 < 7.8272] w=0.2578 to align # Constraint # added constraint: constraint((T0386)L171.CB, (T0386)F229.CB) [> 4.3647 = 7.2745 < 9.4569] w=0.2571 to align # Constraint # added constraint: constraint((T0386)R167.CB, (T0386)F229.CB) [> 3.8304 = 6.3841 < 8.2993] w=0.2560 to align # Constraint # added constraint: constraint((T0386)A177.CB, (T0386)I189.CB) [> 3.6391 = 6.0651 < 7.8846] w=0.2532 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)L126.CB) [> 4.4023 = 7.3372 < 9.5384] w=0.2511 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)M210.CB) [> 4.5118 = 7.5197 < 9.7757] w=0.2490 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)R141.CB) [> 3.7601 = 6.2669 < 8.1469] w=0.2477 to align # Constraint # added constraint: constraint((T0386)F76.CB, (T0386)L123.CB) [> 3.6732 = 6.1220 < 7.9586] w=0.2456 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)F186.CB) [> 3.1983 = 5.3305 < 6.9297] w=0.2450 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)L188.CB) [> 3.8689 = 6.4481 < 8.3825] w=0.2450 to align # Constraint # added constraint: constraint((T0386)L158.CB, (T0386)T168.CB) [> 3.2554 = 5.4256 < 7.0533] w=0.2445 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)M210.CB) [> 3.5633 = 5.9387 < 7.7204] w=0.2444 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)A148.CB) [> 3.0690 = 5.1149 < 6.6494] w=0.2444 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)P209.CB) [> 3.5962 = 5.9936 < 7.7917] w=0.2442 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)M210.CB) [> 4.1141 = 6.8568 < 8.9138] w=0.2427 to align # Constraint # added constraint: constraint((T0386)V20.CB, (T0386)Y62.CB) [> 3.3250 = 5.5416 < 7.2042] w=0.2427 to align # Constraint # added constraint: constraint((T0386)I149.CB, (T0386)F214.CB) [> 3.8501 = 6.4169 < 8.3419] w=0.2424 to align # Constraint # added constraint: constraint((T0386)R55.CB, (T0386)H70.CB) [> 3.7510 = 6.2517 < 8.1273] w=0.2422 to align # Constraint # added constraint: constraint((T0386)A148.CB, (T0386)F172.CB) [> 3.6075 = 6.0125 < 7.8163] w=0.2422 to align # Constraint # added constraint: constraint((T0386)M51.CB, (T0386)A148.CB) [> 4.1223 = 6.8705 < 8.9317] w=0.2414 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)M233.CB) [> 4.0731 = 6.7885 < 8.8250] w=0.2414 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)A148.CB) [> 3.2783 = 5.4638 < 7.1029] w=0.2384 to align # Constraint # added constraint: constraint((T0386)L130.CB, (T0386)F229.CB) [> 3.6555 = 6.0925 < 7.9203] w=0.2361 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)Q211.CB) [> 3.7928 = 6.3213 < 8.2177] w=0.2344 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)L75.CB) [> 3.2668 = 5.4447 < 7.0781] w=0.2180 to align # Constraint # added constraint: constraint((T0386)Q183.CB, (T0386)S218.CB) [> 3.5984 = 5.9974 < 7.7966] w=0.2174 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)I217.CB) [> 3.1344 = 5.2239 < 6.7911] w=0.2174 to align # Constraint # added constraint: constraint((T0386)S187.CB, (T0386)E228.CB) [> 3.1017 = 5.1694 < 6.7203] w=0.2174 to align # Constraint # added constraint: constraint((T0386)I189.CB, (T0386)I217.CB) [> 3.0479 = 5.0798 < 6.6037] w=0.2174 to align # Constraint # added constraint: constraint((T0386)Q157.CB, (T0386)A202.CB) [> 3.4587 = 5.7645 < 7.4939] w=0.2157 to align # Constraint # added constraint: constraint((T0386)N156.CB, (T0386)V201.CB) [> 3.6886 = 6.1477 < 7.9920] w=0.2157 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)L171.CB) [> 4.3544 = 7.2573 < 9.4345] w=0.2157 to align # Constraint # added constraint: constraint((T0386)S44.CB, (T0386)R167.CB) [> 4.4797 = 7.4662 < 9.7061] w=0.2157 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)L184.CB) [> 4.3327 = 7.2212 < 9.3876] w=0.2136 to align # Constraint # added constraint: constraint((T0386)L54.CB, (T0386)Q74.CB) [> 3.5942 = 5.9903 < 7.7874] w=0.2125 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)F229.CB) [> 3.1717 = 5.2862 < 6.8720] w=0.2098 to align # Constraint # added constraint: constraint((T0386)T97.CB, (T0386)W109.CB) [> 3.9454 = 6.5757 < 8.5483] w=0.2064 to align # Constraint # added constraint: constraint((T0386)F63.CB, (T0386)L123.CB) [> 4.6132 = 7.6886 < 9.9952] w=0.2062 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)G116.CA) [> 3.9561 = 6.5935 < 8.5715] w=0.2062 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)F229.CB) [> 4.0034 = 6.6723 < 8.6740] w=0.2059 to align # Constraint # added constraint: constraint((T0386)F144.CB, (T0386)M194.CB) [> 4.0400 = 6.7334 < 8.7534] w=0.2056 to align # Constraint # added constraint: constraint((T0386)S187.CB, (T0386)A197.CB) [> 3.3535 = 5.5892 < 7.2660] w=0.2051 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)S198.CB) [> 3.9888 = 6.6480 < 8.6424] w=0.2044 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)L151.CB) [> 3.0022 = 5.0037 < 6.5048] w=0.2033 to align # Constraint # added constraint: constraint((T0386)Q74.CB, (T0386)A94.CB) [> 3.5161 = 5.8601 < 7.6182] w=0.2033 to align # Constraint # added constraint: constraint((T0386)I149.CB, (T0386)Q169.CB) [> 3.6758 = 6.1263 < 7.9641] w=0.2026 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)R170.CB) [> 4.1295 = 6.8825 < 8.9472] w=0.2026 to align # Constraint # added constraint: constraint((T0386)K49.CB, (T0386)R141.CB) [> 4.2786 = 7.1310 < 9.2703] w=0.2017 to align # Constraint # added constraint: constraint((T0386)L54.CB, (T0386)I217.CB) [> 4.3720 = 7.2867 < 9.4727] w=0.2011 to align # Constraint # added constraint: constraint((T0386)K191.CB, (T0386)L213.CB) [> 2.8863 = 4.8105 < 6.2536] w=0.2003 to align # Constraint # added constraint: constraint((T0386)T24.CB, (T0386)I52.CB) [> 3.6501 = 6.0835 < 7.9085] w=0.2000 to align # Constraint # added constraint: constraint((T0386)T24.CB, (T0386)M51.CB) [> 3.9806 = 6.6343 < 8.6246] w=0.2000 to align # Constraint # added constraint: constraint((T0386)Y21.CB, (T0386)I52.CB) [> 3.2425 = 5.4041 < 7.0254] w=0.2000 to align # Constraint # added constraint: constraint((T0386)Y19.CB, (T0386)L68.CB) [> 4.1514 = 6.9190 < 8.9946] w=0.2000 to align # Constraint # added constraint: constraint((T0386)Y19.CB, (T0386)Y62.CB) [> 3.6058 = 6.0096 < 7.8125] w=0.2000 to align # Constraint # added constraint: constraint((T0386)Y19.CB, (T0386)I52.CB) [> 4.4857 = 7.4761 < 9.7189] w=0.2000 to align # Constraint # added constraint: constraint((T0386)H18.CB, (T0386)F63.CB) [> 3.7380 = 6.2301 < 8.0991] w=0.2000 to align # Constraint # added constraint: constraint((T0386)H18.CB, (T0386)Y62.CB) [> 2.2935 = 3.8226 < 4.9693] w=0.2000 to align # Constraint # added constraint: constraint((T0386)H17.CB, (T0386)T65.CB) [> 3.9884 = 6.6473 < 8.6415] w=0.2000 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)M230.CB) [> 3.7435 = 6.2392 < 8.1110] w=0.1996 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)F229.CB) [> 3.3951 = 5.6585 < 7.3560] w=0.1996 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)A148.CB) [> 3.9560 = 6.5934 < 8.5714] w=0.1996 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)E215.CB) [> 4.0314 = 6.7190 < 8.7347] w=0.1976 to align # Constraint # added constraint: constraint((T0386)L213.CB, (T0386)K222.CB) [> 3.9678 = 6.6130 < 8.5969] w=0.1976 to align # Constraint # added constraint: constraint((T0386)R55.CB, (T0386)Q74.CB) [> 4.4354 = 7.3923 < 9.6100] w=0.1972 to align # Constraint # added constraint: constraint((T0386)M210.CB, (T0386)F229.CB) [> 2.9855 = 4.9758 < 6.4685] w=0.1965 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)F214.CB) [> 3.2951 = 5.4919 < 7.1395] w=0.1960 to align # Constraint # added constraint: constraint((T0386)C43.CB, (T0386)T79.CB) [> 3.5438 = 5.9063 < 7.6782] w=0.1783 to align # Constraint # added constraint: constraint((T0386)I52.CB, (T0386)K222.CB) [> 3.2824 = 5.4707 < 7.1119] w=0.1739 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)R167.CB) [> 4.2945 = 7.1575 < 9.3048] w=0.1739 to align # Constraint # added constraint: constraint((T0386)H45.CB, (T0386)M230.CB) [> 3.7387 = 6.2312 < 8.1006] w=0.1739 to align # Constraint # added constraint: constraint((T0386)V196.CB, (T0386)P209.CB) [> 4.0063 = 6.6771 < 8.6803] w=0.1739 to align # Constraint # added constraint: constraint((T0386)R193.CB, (T0386)L213.CB) [> 3.4051 = 5.6752 < 7.3778] w=0.1739 to align # Constraint # added constraint: constraint((T0386)L188.CB, (T0386)I217.CB) [> 3.0342 = 5.0569 < 6.5740] w=0.1739 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)F229.CB) [> 3.8956 = 6.4927 < 8.4405] w=0.1739 to align # Constraint # added constraint: constraint((T0386)L184.CB, (T0386)I217.CB) [> 3.7260 = 6.2100 < 8.0730] w=0.1739 to align # Constraint # added constraint: constraint((T0386)L184.CB, (T0386)F214.CB) [> 3.4691 = 5.7819 < 7.5165] w=0.1739 to align # Constraint # added constraint: constraint((T0386)R141.CB, (T0386)Q211.CB) [> 4.5044 = 7.5073 < 9.7595] w=0.1739 to align # Constraint # added constraint: constraint((T0386)F93.CB, (T0386)F113.CB) [> 4.5193 = 7.5321 < 9.7918] w=0.1738 to align # Constraint # added constraint: constraint((T0386)M101.CB, (T0386)G122.CA) [> 4.2927 = 7.1546 < 9.3009] w=0.1727 to align # Constraint # added constraint: constraint((T0386)R167.CB, (T0386)M210.CB) [> 4.5513 = 7.5855 < 9.8611] w=0.1727 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)M210.CB) [> 2.7712 = 4.6187 < 6.0043] w=0.1727 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)F214.CB) [> 3.5964 = 5.9941 < 7.7923] w=0.1727 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)F214.CB) [> 3.3914 = 5.6524 < 7.3481] w=0.1727 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)R170.CB) [> 3.2975 = 5.4958 < 7.1445] w=0.1711 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)R170.CB) [> 4.0607 = 6.7678 < 8.7982] w=0.1711 to align # Constraint # added constraint: constraint((T0386)S187.CB, (T0386)L225.CB) [> 3.3249 = 5.5414 < 7.2039] w=0.1701 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)L225.CB) [> 3.1182 = 5.1970 < 6.7561] w=0.1701 to align # Constraint # added constraint: constraint((T0386)T92.CB, (T0386)F113.CB) [> 3.8804 = 6.4673 < 8.4075] w=0.1701 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)M210.CB) [> 3.9197 = 6.5328 < 8.4926] w=0.1674 to align # Constraint # added constraint: constraint((T0386)L158.CB, (T0386)F172.CB) [> 3.5428 = 5.9047 < 7.6761] w=0.1662 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)K191.CB) [> 4.1250 = 6.8751 < 8.9376] w=0.1656 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)M194.CB) [> 3.4465 = 5.7441 < 7.4673] w=0.1654 to align # Constraint # added constraint: constraint((T0386)A83.CB, (T0386)T98.CB) [> 3.9174 = 6.5289 < 8.4876] w=0.1653 to align # Constraint # added constraint: constraint((T0386)A83.CB, (T0386)G96.CA) [> 3.6257 = 6.0429 < 7.8558] w=0.1653 to align # Constraint # added constraint: constraint((T0386)M195.CB, (T0386)K222.CB) [> 2.9810 = 4.9683 < 6.4588] w=0.1648 to align # Constraint # added constraint: constraint((T0386)T24.CB, (T0386)F39.CB) [> 3.5862 = 5.9769 < 7.7700] w=0.1642 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)F214.CB) [> 3.8694 = 6.4489 < 8.3836] w=0.1642 to align # Constraint # added constraint: constraint((T0386)L130.CB, (T0386)M210.CB) [> 3.7714 = 6.2856 < 8.1713] w=0.1642 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)M194.CB) [> 3.4457 = 5.7428 < 7.4657] w=0.1641 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)A114.CB) [> 4.0474 = 6.7457 < 8.7694] w=0.1620 to align # Constraint # added constraint: constraint((T0386)A48.CB, (T0386)I149.CB) [> 4.1756 = 6.9594 < 9.0471] w=0.1619 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)G251.CA) [> 4.5248 = 7.5414 < 9.8038] w=0.1616 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)F229.CB) [> 3.9114 = 6.5191 < 8.4748] w=0.1609 to align # Constraint # added constraint: constraint((T0386)K191.CB, (T0386)I217.CB) [> 3.3217 = 5.5362 < 7.1971] w=0.1609 to align # Constraint # added constraint: constraint((T0386)Y21.CB, (T0386)L40.CB) [> 3.3724 = 5.6206 < 7.3068] w=0.1608 to align # Constraint # added constraint: constraint((T0386)L40.CB, (T0386)M51.CB) [> 4.1803 = 6.9672 < 9.0574] w=0.1608 to align # Constraint # added constraint: constraint((T0386)L226.CB, (T0386)M246.CB) [> 3.5131 = 5.8551 < 7.6116] w=0.1593 to align # Constraint # added constraint: constraint((T0386)F91.CB, (T0386)A100.CB) [> 4.2726 = 7.1210 < 9.2573] w=0.1581 to align # Constraint # added constraint: constraint((T0386)A180.CB, (T0386)M210.CB) [> 4.7627 = 7.9378 < 10.3191] w=0.1574 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)L126.CB) [> 4.2686 = 7.1143 < 9.2486] w=0.1569 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)F229.CB) [> 3.7309 = 6.2181 < 8.0836] w=0.1565 to align # Constraint # added constraint: constraint((T0386)E118.CB, (T0386)S154.CB) [> 3.9618 = 6.6031 < 8.5840] w=0.1555 to align # Constraint # added constraint: constraint((T0386)L86.CB, (T0386)G116.CA) [> 4.7916 = 7.9860 < 10.3817] w=0.1304 to align # Constraint # added constraint: constraint((T0386)F80.CB, (T0386)F161.CB) [> 4.7819 = 7.9698 < 10.3607] w=0.1304 to align # Constraint # added constraint: constraint((T0386)P60.CB, (T0386)Q74.CB) [> 4.4823 = 7.4705 < 9.7116] w=0.1304 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)I217.CB) [> 4.2868 = 7.1447 < 9.2881] w=0.1304 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)L225.CB) [> 4.2301 = 7.0502 < 9.1653] w=0.1304 to align # Constraint # added constraint: constraint((T0386)Q183.CB, (T0386)L225.CB) [> 4.5193 = 7.5322 < 9.7919] w=0.1304 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)Q183.CB) [> 2.8007 = 4.6679 < 6.0683] w=0.1304 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)R170.CB) [> 4.0657 = 6.7762 < 8.8090] w=0.1296 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)I217.CB) [> 3.0742 = 5.1236 < 6.6607] w=0.1293 to align # Constraint # added constraint: constraint((T0386)Q157.CB, (T0386)E203.CB) [> 3.3705 = 5.6176 < 7.3029] w=0.1287 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)R170.CB) [> 4.0528 = 6.7547 < 8.7811] w=0.1272 to align # Constraint # added constraint: constraint((T0386)F63.CB, (T0386)L126.CB) [> 4.2699 = 7.1164 < 9.2514] w=0.1267 to align # Constraint # added constraint: constraint((T0386)L75.CB, (T0386)L123.CB) [> 3.7937 = 6.3229 < 8.2197] w=0.1265 to align # Constraint # added constraint: constraint((T0386)S187.CB, (T0386)V201.CB) [> 3.6471 = 6.0786 < 7.9021] w=0.1264 to align # Constraint # added constraint: constraint((T0386)R125.CB, (T0386)L151.CB) [> 4.6888 = 7.8146 < 10.1590] w=0.1262 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)A202.CB) [> 4.2616 = 7.1027 < 9.2336] w=0.1260 to align # Constraint # added constraint: constraint((T0386)E118.CB, (T0386)L158.CB) [> 4.1117 = 6.8528 < 8.9087] w=0.1253 to align # Constraint # added constraint: constraint((T0386)R125.CB, (T0386)S154.CB) [> 3.6789 = 6.1315 < 7.9710] w=0.1253 to align # Constraint # added constraint: constraint((T0386)E150.CB, (T0386)Q211.CB) [> 3.5687 = 5.9478 < 7.7322] w=0.1253 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)Q211.CB) [> 4.3537 = 7.2562 < 9.4330] w=0.1253 to align # Constraint # added constraint: constraint((T0386)L155.CB, (T0386)N165.CB) [> 4.1304 = 6.8839 < 8.9491] w=0.1253 to align # Constraint # added constraint: constraint((T0386)L155.CB, (T0386)T168.CB) [> 4.1225 = 6.8709 < 8.9321] w=0.1253 to align # Constraint # added constraint: constraint((T0386)N156.CB, (T0386)R170.CB) [> 4.5183 = 7.5306 < 9.7897] w=0.1253 to align # Constraint # added constraint: constraint((T0386)L184.CB, (T0386)S198.CB) [> 4.6232 = 7.7053 < 10.0169] w=0.1240 to align # Constraint # added constraint: constraint((T0386)Q120.CB, (T0386)I149.CB) [> 3.0928 = 5.1546 < 6.7010] w=0.1232 to align # Constraint # added constraint: constraint((T0386)F152.CB, (T0386)N165.CB) [> 2.4548 = 4.0912 < 5.3186] w=0.1232 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)M210.CB) [> 4.2453 = 7.0754 < 9.1981] w=0.1230 to align # Constraint # added constraint: constraint((T0386)Q74.CB, (T0386)D95.CB) [> 4.7613 = 7.9355 < 10.3161] w=0.1230 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)R125.CB) [> 4.4826 = 7.4710 < 9.7122] w=0.1224 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)I217.CB) [> 2.3414 = 3.9023 < 5.0730] w=0.1218 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)R243.CB) [> 3.4303 = 5.7171 < 7.4322] w=0.1217 to align # Constraint # added constraint: constraint((T0386)Y21.CB, (T0386)L36.CB) [> 4.1790 = 6.9651 < 9.0546] w=0.1215 to align # Constraint # added constraint: constraint((T0386)Y21.CB, (T0386)F39.CB) [> 2.5777 = 4.2962 < 5.5851] w=0.1215 to align # Constraint # added constraint: constraint((T0386)K28.CB, (T0386)F39.CB) [> 4.4548 = 7.4246 < 9.6520] w=0.1215 to align # Constraint # added constraint: constraint((T0386)Q73.CB, (T0386)F113.CB) [> 3.4506 = 5.7510 < 7.4763] w=0.1215 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)A100.CB) [> 4.1201 = 6.8669 < 8.9270] w=0.1209 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)A99.CB) [> 3.4487 = 5.7478 < 7.4722] w=0.1209 to align # Constraint # added constraint: constraint((T0386)I89.CB, (T0386)A100.CB) [> 3.4127 = 5.6878 < 7.3941] w=0.1209 to align # Constraint # added constraint: constraint((T0386)H88.CB, (T0386)A100.CB) [> 4.0372 = 6.7286 < 8.7472] w=0.1209 to align # Constraint # added constraint: constraint((T0386)S187.CB, (T0386)S198.CB) [> 3.3606 = 5.6010 < 7.2812] w=0.1207 to align # Constraint # added constraint: constraint((T0386)A83.CB, (T0386)E174.CB) [> 3.7082 = 6.1803 < 8.0344] w=0.1191 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)R125.CB) [> 3.9694 = 6.6157 < 8.6004] w=0.1191 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)E221.CB) [> 3.7684 = 6.2807 < 8.1649] w=0.1191 to align # Constraint # added constraint: constraint((T0386)R125.CB, (T0386)I217.CB) [> 4.3138 = 7.1896 < 9.3465] w=0.1191 to align # Constraint # added constraint: constraint((T0386)F161.CB, (T0386)M210.CB) [> 3.2990 = 5.4983 < 7.1478] w=0.1191 to align # Constraint # added constraint: constraint((T0386)A100.CB, (T0386)W109.CB) [> 3.9310 = 6.5517 < 8.5172] w=0.1189 to align # Constraint # added constraint: constraint((T0386)K110.CB, (T0386)R125.CB) [> 3.9735 = 6.6225 < 8.6093] w=0.1189 to align # Constraint # added constraint: constraint((T0386)I33.CB, (T0386)C43.CB) [> 3.4290 = 5.7149 < 7.4294] w=0.1187 to align # Constraint # added constraint: constraint((T0386)Q157.CB, (T0386)R170.CB) [> 3.4691 = 5.7819 < 7.5164] w=0.1187 to align # Constraint # added constraint: constraint((T0386)L171.CB, (T0386)L188.CB) [> 2.2922 = 3.8204 < 4.9665] w=0.1187 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)V247.CB) [> 3.3901 = 5.6502 < 7.3453] w=0.1180 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)T190.CB) [> 3.6872 = 6.1453 < 7.9889] w=0.1175 to align # Constraint # added constraint: constraint((T0386)L207.CB, (T0386)T232.CB) [> 2.8801 = 4.8002 < 6.2403] w=0.1175 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)F229.CB) [> 4.6535 = 7.7558 < 10.0825] w=0.1175 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)D216.CB) [> 2.7455 = 4.5759 < 5.9487] w=0.1175 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)V201.CB) [> 3.5305 = 5.8842 < 7.6494] w=0.1161 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)S187.CB) [> 4.4986 = 7.4976 < 9.7469] w=0.1161 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)L36.CB) [> 3.5115 = 5.8525 < 7.6083] w=0.0922 to align # Constraint # added constraint: constraint((T0386)A50.CB, (T0386)Q74.CB) [> 3.6935 = 6.1559 < 8.0026] w=0.0913 to align # Constraint # added constraint: constraint((T0386)E174.CB, (T0386)N185.CB) [> 3.8469 = 6.4116 < 8.3350] w=0.0913 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)A202.CB) [> 4.6065 = 7.6774 < 9.9807] w=0.0870 to align # Constraint # added constraint: constraint((T0386)L40.CB, (T0386)T236.CB) [> 3.8923 = 6.4872 < 8.4333] w=0.0870 to align # Constraint # added constraint: constraint((T0386)H45.CB, (T0386)L226.CB) [> 4.2741 = 7.1236 < 9.2606] w=0.0870 to align # Constraint # added constraint: constraint((T0386)H45.CB, (T0386)F229.CB) [> 4.3436 = 7.2393 < 9.4110] w=0.0870 to align # Constraint # added constraint: constraint((T0386)H45.CB, (T0386)M233.CB) [> 3.0589 = 5.0982 < 6.6277] w=0.0870 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)L226.CB) [> 4.6652 = 7.7753 < 10.1079] w=0.0870 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)E203.CB) [> 4.2450 = 7.0751 < 9.1976] w=0.0870 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)N185.CB) [> 4.7448 = 7.9080 < 10.2804] w=0.0870 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)F214.CB) [> 3.2364 = 5.3940 < 7.0122] w=0.0870 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)F229.CB) [> 4.7515 = 7.9192 < 10.2950] w=0.0868 to align # Constraint # added constraint: constraint((T0386)G116.CA, (T0386)F229.CB) [> 4.6683 = 7.7805 < 10.1146] w=0.0868 to align # Constraint # added constraint: constraint((T0386)M101.CB, (T0386)L171.CB) [> 4.1337 = 6.8895 < 8.9563] w=0.0868 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)F93.CB) [> 3.3279 = 5.5465 < 7.2105] w=0.0868 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)I89.CB) [> 3.7233 = 6.2054 < 8.0671] w=0.0868 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)Q211.CB) [> 4.7137 = 7.8562 < 10.2130] w=0.0868 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)N156.CB) [> 3.7631 = 6.2718 < 8.1533] w=0.0868 to align # Constraint # added constraint: constraint((T0386)Y85.CB, (T0386)A94.CB) [> 4.2208 = 7.0347 < 9.1451] w=0.0859 to align # Constraint # added constraint: constraint((T0386)M101.CB, (T0386)A114.CB) [> 3.9383 = 6.5638 < 8.5329] w=0.0852 to align # Constraint # added constraint: constraint((T0386)K110.CB, (T0386)A177.CB) [> 3.2465 = 5.4109 < 7.0342] w=0.0842 to align # Constraint # added constraint: constraint((T0386)K110.CB, (T0386)H182.CB) [> 2.9712 = 4.9521 < 6.4377] w=0.0842 to align # Constraint # added constraint: constraint((T0386)K110.CB, (T0386)Q183.CB) [> 4.2659 = 7.1098 < 9.2427] w=0.0842 to align # Constraint # added constraint: constraint((T0386)K110.CB, (T0386)L184.CB) [> 3.4964 = 5.8274 < 7.5756] w=0.0842 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)N185.CB) [> 2.7937 = 4.6562 < 6.0531] w=0.0842 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)E174.CB) [> 3.4845 = 5.8075 < 7.5497] w=0.0842 to align # Constraint # added constraint: constraint((T0386)W109.CB, (T0386)N185.CB) [> 3.9086 = 6.5144 < 8.4688] w=0.0842 to align # Constraint # added constraint: constraint((T0386)W109.CB, (T0386)Q183.CB) [> 2.8786 = 4.7977 < 6.2370] w=0.0842 to align # Constraint # added constraint: constraint((T0386)W109.CB, (T0386)H182.CB) [> 4.2070 = 7.0116 < 9.1151] w=0.0842 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)H182.CB) [> 3.7782 = 6.2970 < 8.1862] w=0.0842 to align # Constraint # added constraint: constraint((T0386)I33.CB, (T0386)P90.CB) [> 3.5523 = 5.9205 < 7.6966] w=0.0842 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)F91.CB) [> 3.7391 = 6.2318 < 8.1013] w=0.0842 to align # Constraint # added constraint: constraint((T0386)Y19.CB, (T0386)F91.CB) [> 4.6522 = 7.7537 < 10.0798] w=0.0842 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)I217.CB) [> 4.4124 = 7.3540 < 9.5602] w=0.0842 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)A197.CB) [> 4.6327 = 7.7212 < 10.0376] w=0.0842 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)M194.CB) [> 3.5773 = 5.9622 < 7.7509] w=0.0842 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)I189.CB) [> 4.0450 = 6.7416 < 8.7641] w=0.0842 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)N185.CB) [> 3.8939 = 6.4898 < 8.4367] w=0.0842 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)F186.CB) [> 2.8497 = 4.7495 < 6.1743] w=0.0842 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)V201.CB) [> 4.7404 = 7.9007 < 10.2709] w=0.0842 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)F186.CB) [> 4.2911 = 7.1519 < 9.2975] w=0.0842 to align # Constraint # added constraint: constraint((T0386)C69.CB, (T0386)G96.CA) [> 4.0952 = 6.8253 < 8.8729] w=0.0839 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)D95.CB) [> 3.7811 = 6.3018 < 8.1923] w=0.0835 to align # Constraint # added constraint: constraint((T0386)K30.CB, (T0386)F39.CB) [> 3.4583 = 5.7638 < 7.4929] w=0.0835 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)Q211.CB) [> 3.5162 = 5.8604 < 7.6185] w=0.0833 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)F214.CB) [> 3.0645 = 5.1075 < 6.6397] w=0.0833 to align # Constraint # added constraint: constraint((T0386)F76.CB, (T0386)L155.CB) [> 3.2793 = 5.4655 < 7.1052] w=0.0831 to align # Constraint # added constraint: constraint((T0386)F91.CB, (T0386)A114.CB) [> 4.5759 = 7.6266 < 9.9145] w=0.0829 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)L126.CB) [> 3.3334 = 5.5557 < 7.2224] w=0.0825 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)L123.CB) [> 4.0975 = 6.8292 < 8.8779] w=0.0825 to align # Constraint # added constraint: constraint((T0386)F93.CB, (T0386)A114.CB) [> 3.1955 = 5.3258 < 6.9235] w=0.0824 to align # Constraint # added constraint: constraint((T0386)F229.CB, (T0386)E250.CB) [> 2.8049 = 4.6748 < 6.0772] w=0.0823 to align # Constraint # added constraint: constraint((T0386)F229.CB, (T0386)T253.CB) [> 4.3713 = 7.2855 < 9.4711] w=0.0823 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)E174.CB) [> 4.6600 = 7.7667 < 10.0967] w=0.0821 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)R170.CB) [> 4.2625 = 7.1041 < 9.2354] w=0.0821 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)N78.CB) [> 3.8663 = 6.4438 < 8.3769] w=0.0821 to align # Constraint # added constraint: constraint((T0386)T24.CB, (T0386)Q74.CB) [> 3.1086 = 5.1809 < 6.7352] w=0.0821 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)V247.CB) [> 3.2033 = 5.3388 < 6.9404] w=0.0821 to align # Constraint # added constraint: constraint((T0386)M246.CB, (T0386)L268.CB) [> 3.8479 = 6.4131 < 8.3371] w=0.0821 to align # Constraint # added constraint: constraint((T0386)T253.CB, (T0386)A267.CB) [> 3.9727 = 6.6211 < 8.6074] w=0.0816 to align # Constraint # added constraint: constraint((T0386)F93.CB, (T0386)R125.CB) [> 3.9443 = 6.5738 < 8.5459] w=0.0815 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)T129.CB) [> 4.1055 = 6.8426 < 8.8954] w=0.0815 to align # Constraint # added constraint: constraint((T0386)H88.CB, (T0386)M101.CB) [> 3.8205 = 6.3674 < 8.2776] w=0.0813 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)Q211.CB) [> 3.2825 = 5.4708 < 7.1120] w=0.0809 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)M210.CB) [> 4.6861 = 7.8102 < 10.1533] w=0.0809 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)F214.CB) [> 4.4639 = 7.4398 < 9.6718] w=0.0809 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)A273.CB) [> 3.8527 = 6.4211 < 8.3475] w=0.0808 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)A267.CB) [> 3.4971 = 5.8284 < 7.5770] w=0.0808 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)I275.CB) [> 4.0962 = 6.8271 < 8.8752] w=0.0808 to align # Constraint # added constraint: constraint((T0386)I217.CB, (T0386)V270.CB) [> 3.8006 = 6.3344 < 8.2347] w=0.0808 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)L282.CB) [> 3.7530 = 6.2550 < 8.1315] w=0.0808 to align # Constraint # added constraint: constraint((T0386)E250.CB, (T0386)N278.CB) [> 3.4980 = 5.8300 < 7.5790] w=0.0805 to align # Constraint # added constraint: constraint((T0386)Q74.CB, (T0386)G96.CA) [> 4.1902 = 6.9836 < 9.0787] w=0.0803 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)V247.CB) [> 4.1070 = 6.8451 < 8.8986] w=0.0798 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)F214.CB) [> 3.1486 = 5.2476 < 6.8219] w=0.0796 to align # Constraint # added constraint: constraint((T0386)I217.CB, (T0386)M233.CB) [> 3.9404 = 6.5673 < 8.5375] w=0.0794 to align # Constraint # added constraint: constraint((T0386)T98.CB, (T0386)R170.CB) [> 3.5159 = 5.8599 < 7.6178] w=0.0794 to align # Constraint # added constraint: constraint((T0386)A99.CB, (T0386)W109.CB) [> 2.2259 = 3.7098 < 4.8227] w=0.0794 to align # Constraint # added constraint: constraint((T0386)A100.CB, (T0386)K110.CB) [> 3.0628 = 5.1047 < 6.6361] w=0.0794 to align # Constraint # added constraint: constraint((T0386)M101.CB, (T0386)K110.CB) [> 4.1915 = 6.9858 < 9.0815] w=0.0794 to align # Constraint # added constraint: constraint((T0386)A100.CB, (T0386)A112.CB) [> 3.7720 = 6.2867 < 8.1728] w=0.0794 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)R125.CB) [> 4.6257 = 7.7095 < 10.0224] w=0.0794 to align # Constraint # added constraint: constraint((T0386)G116.CA, (T0386)L126.CB) [> 3.9812 = 6.6354 < 8.6260] w=0.0793 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)L126.CB) [> 3.1466 = 5.2444 < 6.8177] w=0.0792 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)T129.CB) [> 4.6092 = 7.6820 < 9.9866] w=0.0791 to align # Constraint # added constraint: constraint((T0386)W109.CB, (T0386)L139.CB) [> 3.5386 = 5.8976 < 7.6669] w=0.0791 to align # Constraint # added constraint: constraint((T0386)N53.CB, (T0386)T98.CB) [> 3.9812 = 6.6353 < 8.6259] w=0.0790 to align # Constraint # added constraint: constraint((T0386)K49.CB, (T0386)T98.CB) [> 3.8800 = 6.4667 < 8.4068] w=0.0790 to align # Constraint # added constraint: constraint((T0386)L59.CB, (T0386)L130.CB) [> 4.4709 = 7.4514 < 9.6869] w=0.0790 to align # Constraint # added constraint: constraint((T0386)Y19.CB, (T0386)L136.CB) [> 2.7301 = 4.5502 < 5.9152] w=0.0790 to align # Constraint # added constraint: constraint((T0386)V20.CB, (T0386)L136.CB) [> 4.7383 = 7.8971 < 10.2662] w=0.0790 to align # Constraint # added constraint: constraint((T0386)P22.CB, (T0386)H45.CB) [> 3.5267 = 5.8778 < 7.6411] w=0.0790 to align # Constraint # added constraint: constraint((T0386)W82.CB, (T0386)R125.CB) [> 3.6510 = 6.0850 < 7.9105] w=0.0790 to align # Constraint # added constraint: constraint((T0386)W82.CB, (T0386)L126.CB) [> 3.8328 = 6.3880 < 8.3044] w=0.0790 to align # Constraint # added constraint: constraint((T0386)W82.CB, (T0386)T129.CB) [> 3.9203 = 6.5338 < 8.4939] w=0.0790 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)Q211.CB) [> 3.4778 = 5.7964 < 7.5353] w=0.0790 to align # Constraint # added constraint: constraint((T0386)T79.CB, (T0386)T98.CB) [> 3.4037 = 5.6727 < 7.3746] w=0.0790 to align # Constraint # added constraint: constraint((T0386)I33.CB, (T0386)M210.CB) [> 4.7984 = 7.9973 < 10.3965] w=0.0785 to align # Constraint # added constraint: constraint((T0386)K28.CB, (T0386)Q211.CB) [> 4.4339 = 7.3898 < 9.6068] w=0.0785 to align # Constraint # added constraint: constraint((T0386)K28.CB, (T0386)M210.CB) [> 4.3839 = 7.3064 < 9.4984] w=0.0785 to align # Constraint # added constraint: constraint((T0386)H18.CB, (T0386)Y67.CB) [> 4.7965 = 7.9942 < 10.3924] w=0.0785 to align # Constraint # added constraint: constraint((T0386)T11.CB, (T0386)Y62.CB) [> 4.7083 = 7.8471 < 10.2013] w=0.0785 to align # Constraint # added constraint: constraint((T0386)T11.CB, (T0386)V20.CB) [> 4.7225 = 7.8709 < 10.2322] w=0.0785 to align # Constraint # added constraint: constraint((T0386)H182.CB, (T0386)M233.CB) [> 4.4786 = 7.4644 < 9.7037] w=0.0785 to align # Constraint # added constraint: constraint((T0386)L268.CB, (T0386)N278.CB) [> 3.7092 = 6.1821 < 8.0367] w=0.0784 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)G265.CA) [> 4.0750 = 6.7917 < 8.8292] w=0.0784 to align # Constraint # added constraint: constraint((T0386)M210.CB, (T0386)G265.CA) [> 4.4356 = 7.3926 < 9.6104] w=0.0784 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)G265.CA) [> 4.0219 = 6.7031 < 8.7141] w=0.0784 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)L263.CB) [> 3.5265 = 5.8775 < 7.6408] w=0.0784 to align # Constraint # added constraint: constraint((T0386)A267.CB, (T0386)I276.CB) [> 3.4713 = 5.7854 < 7.5210] w=0.0783 to align # Constraint # added constraint: constraint((T0386)F266.CB, (T0386)N278.CB) [> 4.1021 = 6.8368 < 8.8878] w=0.0783 to align # Constraint # added constraint: constraint((T0386)F266.CB, (T0386)I276.CB) [> 4.5900 = 7.6500 < 9.9449] w=0.0783 to align # Constraint # added constraint: constraint((T0386)I217.CB, (T0386)F229.CB) [> 3.9153 = 6.5255 < 8.4831] w=0.0780 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)L123.CB) [> 3.5041 = 5.8402 < 7.5922] w=0.0778 to align # Constraint # added constraint: constraint((T0386)Y31.CB, (T0386)C43.CB) [> 4.3188 = 7.1980 < 9.3574] w=0.0771 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)S198.CB) [> 3.8537 = 6.4228 < 8.3496] w=0.0771 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)L226.CB) [> 4.5862 = 7.6437 < 9.9368] w=0.0771 to align # Constraint # added constraint: constraint((T0386)Q157.CB, (T0386)F229.CB) [> 2.6481 = 4.4135 < 5.7375] w=0.0771 to align # Constraint # added constraint: constraint((T0386)L59.CB, (T0386)L171.CB) [> 4.6663 = 7.7772 < 10.1104] w=0.0435 to align # Constraint # added constraint: constraint((T0386)G96.CA, (T0386)E203.CB) [> 4.5958 = 7.6596 < 9.9575] w=0.0435 to align # Constraint # added constraint: constraint((T0386)L136.CB, (T0386)L176.CB) [> 3.7853 = 6.3088 < 8.2014] w=0.0435 to align # Constraint # added constraint: constraint((T0386)Q183.CB, (T0386)V240.CB) [> 4.0217 = 6.7029 < 8.7137] w=0.0435 to align # Constraint # added constraint: constraint((T0386)F186.CB, (T0386)T236.CB) [> 3.1667 = 5.2778 < 6.8612] w=0.0435 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)R170.CB) [> 4.1286 = 6.8809 < 8.9452] w=0.0434 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)M210.CB) [> 3.0217 = 5.0361 < 6.5469] w=0.0434 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)M210.CB) [> 4.5146 = 7.5244 < 9.7817] w=0.0434 to align # Constraint # added constraint: constraint((T0386)M101.CB, (T0386)F113.CB) [> 4.4113 = 7.3522 < 9.5578] w=0.0434 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)I217.CB) [> 4.7544 = 7.9240 < 10.3012] w=0.0434 to align # Constraint # added constraint: constraint((T0386)D117.CB, (T0386)L263.CB) [> 3.7980 = 6.3300 < 8.2290] w=0.0434 to align # Constraint # added constraint: constraint((T0386)F93.CB, (T0386)I115.CB) [> 4.0317 = 6.7195 < 8.7354] w=0.0434 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)G260.CA) [> 3.7203 = 6.2005 < 8.0607] w=0.0434 to align # Constraint # added constraint: constraint((T0386)L268.CB, (T0386)K291.CB) [> 4.3469 = 7.2449 < 9.4183] w=0.0434 to align # Constraint # added constraint: constraint((T0386)L268.CB, (T0386)L290.CB) [> 2.9202 = 4.8671 < 6.3272] w=0.0434 to align # Constraint # added constraint: constraint((T0386)L268.CB, (T0386)I289.CB) [> 3.9948 = 6.6581 < 8.6555] w=0.0434 to align # Constraint # added constraint: constraint((T0386)L268.CB, (T0386)L287.CB) [> 3.3151 = 5.5252 < 7.1828] w=0.0434 to align # Constraint # added constraint: constraint((T0386)A267.CB, (T0386)K291.CB) [> 3.0263 = 5.0438 < 6.5569] w=0.0434 to align # Constraint # added constraint: constraint((T0386)A267.CB, (T0386)L290.CB) [> 4.7140 = 7.8567 < 10.2137] w=0.0434 to align # Constraint # added constraint: constraint((T0386)G265.CA, (T0386)K295.CB) [> 4.3854 = 7.3089 < 9.5016] w=0.0434 to align # Constraint # added constraint: constraint((T0386)T255.CB, (T0386)E264.CB) [> 3.9686 = 6.6144 < 8.5987] w=0.0434 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)K295.CB) [> 4.7872 = 7.9786 < 10.3722] w=0.0434 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)I217.CB) [> 3.3963 = 5.6605 < 7.3587] w=0.0434 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)T129.CB) [> 3.4592 = 5.7653 < 7.4949] w=0.0429 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)I217.CB) [> 2.9954 = 4.9924 < 6.4901] w=0.0429 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)L126.CB) [> 3.3539 = 5.5899 < 7.2668] w=0.0429 to align # Constraint # added constraint: constraint((T0386)A112.CB, (T0386)I217.CB) [> 2.9083 = 4.8471 < 6.3012] w=0.0429 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)R125.CB) [> 4.3716 = 7.2860 < 9.4718] w=0.0429 to align # Constraint # added constraint: constraint((T0386)T92.CB, (T0386)L126.CB) [> 3.3776 = 5.6294 < 7.3182] w=0.0429 to align # Constraint # added constraint: constraint((T0386)T92.CB, (T0386)R125.CB) [> 4.2919 = 7.1531 < 9.2991] w=0.0429 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)T129.CB) [> 3.3340 = 5.5567 < 7.2236] w=0.0429 to align # Constraint # added constraint: constraint((T0386)T79.CB, (T0386)I89.CB) [> 4.1852 = 6.9753 < 9.0679] w=0.0429 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)S198.CB) [> 3.6966 = 6.1611 < 8.0094] w=0.0429 to align # Constraint # added constraint: constraint((T0386)N23.CB, (T0386)L36.CB) [> 3.8520 = 6.4200 < 8.3460] w=0.0427 to align # Constraint # added constraint: constraint((T0386)S15.CB, (T0386)T25.CB) [> 3.6001 = 6.0001 < 7.8001] w=0.0427 to align # Constraint # added constraint: constraint((T0386)I13.CB, (T0386)L68.CB) [> 4.6169 = 7.6948 < 10.0033] w=0.0427 to align # Constraint # added constraint: constraint((T0386)I13.CB, (T0386)T26.CB) [> 3.3464 = 5.5774 < 7.2506] w=0.0427 to align # Constraint # added constraint: constraint((T0386)E12.CB, (T0386)T26.CB) [> 3.9326 = 6.5543 < 8.5206] w=0.0427 to align # Constraint # added constraint: constraint((T0386)N10.CB, (T0386)L68.CB) [> 3.0711 = 5.1185 < 6.6540] w=0.0427 to align # Constraint # added constraint: constraint((T0386)N10.CB, (T0386)T65.CB) [> 3.2105 = 5.3508 < 6.9560] w=0.0427 to align # Constraint # added constraint: constraint((T0386)K9.CB, (T0386)H72.CB) [> 4.2096 = 7.0160 < 9.1208] w=0.0427 to align # Constraint # added constraint: constraint((T0386)K9.CB, (T0386)L68.CB) [> 4.6570 = 7.7616 < 10.0901] w=0.0427 to align # Constraint # added constraint: constraint((T0386)K7.CB, (T0386)T65.CB) [> 4.0965 = 6.8274 < 8.8757] w=0.0427 to align # Constraint # added constraint: constraint((T0386)V199.CB, (T0386)V270.CB) [> 4.3121 = 7.1868 < 9.3429] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)I217.CB) [> 4.3637 = 7.2729 < 9.4548] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)V270.CB) [> 2.5912 = 4.3187 < 5.6143] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)K271.CB) [> 3.4485 = 5.7475 < 7.4717] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)G272.CA) [> 3.2309 = 5.3849 < 7.0003] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)A273.CB) [> 2.8357 = 4.7262 < 6.1440] w=0.0421 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)I275.CB) [> 4.7643 = 7.9405 < 10.3227] w=0.0421 to align # Constraint # added constraint: constraint((T0386)N185.CB, (T0386)A202.CB) [> 4.2474 = 7.0791 < 9.2028] w=0.0421 to align # Constraint # added constraint: constraint((T0386)T255.CB, (T0386)F266.CB) [> 4.5670 = 7.6116 < 9.8951] w=0.0421 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)N269.CB) [> 3.2456 = 5.4093 < 7.0321] w=0.0421 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)L268.CB) [> 3.1203 = 5.2006 < 6.7607] w=0.0421 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)A267.CB) [> 4.1986 = 6.9978 < 9.0971] w=0.0421 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)N269.CB) [> 4.4800 = 7.4666 < 9.7066] w=0.0421 to align # Constraint # added constraint: constraint((T0386)I217.CB, (T0386)K271.CB) [> 4.5395 = 7.5659 < 9.8357] w=0.0421 to align # Constraint # added constraint: constraint((T0386)G251.CA, (T0386)N269.CB) [> 3.5481 = 5.9135 < 7.6876] w=0.0421 to align # Constraint # added constraint: constraint((T0386)G251.CA, (T0386)V270.CB) [> 3.4239 = 5.7065 < 7.4185] w=0.0421 to align # Constraint # added constraint: constraint((T0386)I52.CB, (T0386)A94.CB) [> 2.6254 = 4.3758 < 5.6885] w=0.0418 to align # Constraint # added constraint: constraint((T0386)Q157.CB, (T0386)M194.CB) [> 4.4836 = 7.4726 < 9.7143] w=0.0418 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)E203.CB) [> 3.6402 = 6.0669 < 7.8870] w=0.0418 to align # Constraint # added constraint: constraint((T0386)M210.CB, (T0386)M233.CB) [> 3.7074 = 6.1789 < 8.0326] w=0.0418 to align # Constraint # added constraint: constraint((T0386)I89.CB, (T0386)M101.CB) [> 1.8300 = 3.0500 < 3.9650] w=0.0418 to align # Constraint # added constraint: constraint((T0386)I89.CB, (T0386)P102.CB) [> 2.7087 = 4.5145 < 5.8689] w=0.0418 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)E203.CB) [> 4.1859 = 6.9765 < 9.0695] w=0.0418 to align # Constraint # added constraint: constraint((T0386)T97.CB, (T0386)N111.CB) [> 3.2558 = 5.4264 < 7.0543] w=0.0418 to align # Constraint # added constraint: constraint((T0386)A83.CB, (T0386)A200.CB) [> 2.8932 = 4.8219 < 6.2685] w=0.0412 to align # Constraint # added constraint: constraint((T0386)Y31.CB, (T0386)T129.CB) [> 2.6727 = 4.4544 < 5.7907] w=0.0412 to align # Constraint # added constraint: constraint((T0386)T79.CB, (T0386)H88.CB) [> 3.6426 = 6.0711 < 7.8924] w=0.0411 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)E174.CB) [> 4.6521 = 7.7535 < 10.0795] w=0.0411 to align # Constraint # added constraint: constraint((T0386)T129.CB, (T0386)R170.CB) [> 4.0034 = 6.6723 < 8.6740] w=0.0411 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)Q74.CB) [> 3.1538 = 5.2563 < 6.8332] w=0.0411 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)I71.CB) [> 4.3590 = 7.2650 < 9.4445] w=0.0411 to align # Constraint # added constraint: constraint((T0386)D46.CB, (T0386)Q74.CB) [> 4.4017 = 7.3362 < 9.5371] w=0.0411 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)I279.CB) [> 3.6578 = 6.0964 < 7.9253] w=0.0411 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)I279.CB) [> 4.2330 = 7.0550 < 9.1715] w=0.0411 to align # Constraint # added constraint: constraint((T0386)G277.CA, (T0386)L287.CB) [> 2.9906 = 4.9843 < 6.4796] w=0.0411 to align # Constraint # added constraint: constraint((T0386)I276.CB, (T0386)L287.CB) [> 4.5085 = 7.5142 < 9.7684] w=0.0411 to align # Constraint # added constraint: constraint((T0386)L226.CB, (T0386)E250.CB) [> 3.8614 = 6.4356 < 8.3664] w=0.0411 to align # Constraint # added constraint: constraint((T0386)L225.CB, (T0386)T257.CB) [> 4.1795 = 6.9658 < 9.0555] w=0.0411 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)M233.CB) [> 3.4627 = 5.7712 < 7.5026] w=0.0411 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)M233.CB) [> 4.3502 = 7.2503 < 9.4254] w=0.0411 to align # Constraint # added constraint: constraint((T0386)F91.CB, (T0386)N111.CB) [> 3.5083 = 5.8472 < 7.6014] w=0.0397 to align # Constraint # added constraint: constraint((T0386)P90.CB, (T0386)N111.CB) [> 4.4817 = 7.4695 < 9.7103] w=0.0397 to align # Constraint # added constraint: constraint((T0386)A83.CB, (T0386)L290.CB) [> 4.4854 = 7.4756 < 9.7183] w=0.0397 to align # Constraint # added constraint: constraint((T0386)S218.CB, (T0386)Y258.CB) [> 3.4792 = 5.7987 < 7.5384] w=0.0397 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)R125.CB) [> 4.3535 = 7.2558 < 9.4326] w=0.0397 to align # Constraint # added constraint: constraint((T0386)F93.CB, (T0386)T129.CB) [> 3.2803 = 5.4671 < 7.1072] w=0.0397 to align # Constraint # added constraint: constraint((T0386)N153.CB, (T0386)L282.CB) [> 3.8285 = 6.3809 < 8.2951] w=0.0397 to align # Constraint # added constraint: constraint((T0386)E150.CB, (T0386)L282.CB) [> 2.8991 = 4.8318 < 6.2813] w=0.0397 to align # Constraint # added constraint: constraint((T0386)L68.CB, (T0386)F113.CB) [> 4.5711 = 7.6186 < 9.9041] w=0.0397 to align # Constraint # added constraint: constraint((T0386)T65.CB, (T0386)T129.CB) [> 2.7020 = 4.5034 < 5.8544] w=0.0397 to align # Constraint # added constraint: constraint((T0386)L36.CB, (T0386)Q74.CB) [> 3.6127 = 6.0211 < 7.8275] w=0.0397 to align # Constraint # added constraint: constraint((T0386)M194.CB, (T0386)L268.CB) [> 3.5826 = 5.9710 < 7.7623] w=0.0397 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)L263.CB) [> 3.6097 = 6.0162 < 7.8211] w=0.0397 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)A267.CB) [> 3.6554 = 6.0923 < 7.9200] w=0.0397 to align # Constraint # added constraint: constraint((T0386)E142.CB, (T0386)L268.CB) [> 2.3835 = 3.9725 < 5.1642] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I14.CB, (T0386)H159.CB) [> 3.7716 = 6.2860 < 8.1717] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I14.CB, (T0386)Q157.CB) [> 4.7906 = 7.9844 < 10.3797] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I14.CB, (T0386)L59.CB) [> 3.7542 = 6.2570 < 8.1341] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I14.CB, (T0386)S58.CB) [> 3.7038 = 6.1730 < 8.0249] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I14.CB, (T0386)N23.CB) [> 4.3241 = 7.2069 < 9.3689] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I13.CB, (T0386)P160.CB) [> 4.0764 = 6.7940 < 8.8322] w=0.0397 to align # Constraint # added constraint: constraint((T0386)I13.CB, (T0386)H159.CB) [> 3.5723 = 5.9538 < 7.7399] w=0.0397 to align # Constraint # added constraint: constraint((T0386)E12.CB, (T0386)M194.CB) [> 4.7651 = 7.9419 < 10.3245] w=0.0397 to align # Constraint # added constraint: constraint((T0386)E12.CB, (T0386)P160.CB) [> 4.1927 = 6.9878 < 9.0841] w=0.0397 to align # Constraint # added constraint: constraint((T0386)L27.CB, (T0386)L59.CB) [> 3.8424 = 6.4041 < 8.3253] w=0.0397 to align # Constraint # added constraint: constraint((T0386)A179.CB, (T0386)V270.CB) [> 4.6642 = 7.7737 < 10.1058] w=0.0397 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)F266.CB) [> 2.9281 = 4.8801 < 6.3442] w=0.0397 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)G262.CA) [> 3.6062 = 6.0104 < 7.8135] w=0.0397 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)K271.CB) [> 3.3950 = 5.6583 < 7.3558] w=0.0396 to align # Constraint # added constraint: constraint((T0386)R170.CB, (T0386)G272.CA) [> 3.8420 = 6.4034 < 8.3244] w=0.0396 to align # Constraint # added constraint: constraint((T0386)F113.CB, (T0386)L123.CB) [> 3.4464 = 5.7440 < 7.4672] w=0.0396 to align # Constraint # added constraint: constraint((T0386)N111.CB, (T0386)L126.CB) [> 4.3123 = 7.1871 < 9.3433] w=0.0396 to align # Constraint # added constraint: constraint((T0386)F266.CB, (T0386)I279.CB) [> 4.4449 = 7.4082 < 9.6306] w=0.0396 to align # Constraint # added constraint: constraint((T0386)L207.CB, (T0386)G265.CA) [> 2.8631 = 4.7719 < 6.2035] w=0.0396 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)A202.CB) [> 4.7029 = 7.8381 < 10.1896] w=0.0395 to align # Constraint # added constraint: constraint((T0386)L126.CB, (T0386)S198.CB) [> 2.8513 = 4.7521 < 6.1778] w=0.0395 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)S198.CB) [> 3.6236 = 6.0394 < 7.8512] w=0.0395 to align # Constraint # added constraint: constraint((T0386)L123.CB, (T0386)M194.CB) [> 3.9207 = 6.5345 < 8.4949] w=0.0395 to align # Constraint # added constraint: constraint((T0386)I115.CB, (T0386)R125.CB) [> 2.3422 = 3.9037 < 5.0748] w=0.0395 to align # Constraint # added constraint: constraint((T0386)P16.CB, (T0386)T236.CB) [> 4.7152 = 7.8587 < 10.2164] w=0.0395 to align # Constraint # added constraint: constraint((T0386)A114.CB, (T0386)M194.CB) [> 4.0781 = 6.7969 < 8.8360] w=0.0395 to align # Constraint # added constraint: constraint((T0386)V247.CB, (T0386)L282.CB) [> 4.2644 = 7.1073 < 9.2395] w=0.0395 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)L263.CB) [> 4.1570 = 6.9284 < 9.0069] w=0.0395 to align # Constraint # added constraint: constraint((T0386)G260.CA, (T0386)I275.CB) [> 4.2517 = 7.0861 < 9.2120] w=0.0395 to align # Constraint # added constraint: constraint((T0386)L263.CB, (T0386)I275.CB) [> 3.7569 = 6.2614 < 8.1398] w=0.0395 to align # Constraint # added constraint: constraint((T0386)N175.CB, (T0386)P283.CB) [> 3.7226 = 6.2043 < 8.0656] w=0.0395 to align # Constraint # added constraint: constraint((T0386)A94.CB, (T0386)L126.CB) [> 3.5918 = 5.9863 < 7.7822] w=0.0390 to align # Constraint # added constraint: constraint((T0386)E203.CB, (T0386)F229.CB) [> 4.6138 = 7.6897 < 9.9966] w=0.0390 to align # Constraint # added constraint: constraint((T0386)I217.CB, (T0386)I275.CB) [> 4.3491 = 7.2484 < 9.4229] w=0.0387 to align # Constraint # added constraint: constraint((T0386)A202.CB, (T0386)V270.CB) [> 3.2258 = 5.3763 < 6.9892] w=0.0387 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)I275.CB) [> 3.5100 = 5.8500 < 7.6050] w=0.0387 to align # Constraint # added constraint: constraint((T0386)S198.CB, (T0386)V270.CB) [> 4.6246 = 7.7077 < 10.0200] w=0.0387 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)F266.CB) [> 3.3917 = 5.6529 < 7.3488] w=0.0387 to align # Constraint # added constraint: constraint((T0386)F214.CB, (T0386)G265.CA) [> 4.4644 = 7.4407 < 9.6729] w=0.0387 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)A267.CB) [> 4.0145 = 6.6908 < 8.6981] w=0.0387 to align # Constraint # added constraint: constraint((T0386)Q211.CB, (T0386)F266.CB) [> 3.0135 = 5.0225 < 6.5292] w=0.0387 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)L287.CB) [> 2.3373 = 3.8955 < 5.0641] w=0.0387 to align # Constraint # added constraint: constraint((T0386)Y254.CB, (T0386)G265.CA) [> 4.1242 = 6.8736 < 8.9357] w=0.0387 to align # Constraint # added constraint: constraint((T0386)M246.CB, (T0386)Y274.CB) [> 4.5663 = 7.6105 < 9.8937] w=0.0387 to align # Constraint # added constraint: constraint((T0386)M233.CB, (T0386)Y274.CB) [> 4.3088 = 7.1814 < 9.3358] w=0.0387 to align # Constraint # added constraint: constraint((T0386)F229.CB, (T0386)Y274.CB) [> 4.7765 = 7.9609 < 10.3492] w=0.0387 to align # Constraint # added constraint: constraint((T0386)K222.CB, (T0386)Y258.CB) [> 4.5730 = 7.6217 < 9.9081] w=0.0386 to align # Constraint # added constraint: constraint((T0386)V240.CB, (T0386)G272.CA) [> 4.7327 = 7.8878 < 10.2542] w=0.0386 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0386/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0386/decoys/ # ReadConformPDB reading from PDB file T0386.chimera.pdb.gz looking for model 1 # Found a chain break before 293 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera3.pdb.gz looking for model 1 # Found a chain break before 293 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera4.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera5.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera6.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0386.chimera7.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera-4-1.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 265 # 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 255 # 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 262 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # 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 289 # 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 296 # 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 294 # 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 239 # 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 273 # 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 235 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 263 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 298 # 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 288 # 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 298 # 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 228 # 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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: atoms too close: (T0386)N235.C and (T0386)T236.N only 0.000 apart, marking (T0386)T236.N as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CA only 0.000 apart, marking (T0386)T236.CA as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CA only 0.000 apart, marking (T0386)T236.CA as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.CB only 0.000 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CB only 0.000 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CB only 0.000 apart, marking (T0386)T236.CB as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.CG2 only 0.000 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.CG2 only 0.000 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.CG2 only 0.000 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.CG2 only 0.000 apart, marking (T0386)T236.CG2 as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.OG1 only 0.000 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.OG1 only 0.000 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.OG1 only 0.000 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.OG1 only 0.000 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.OG1 only 0.000 apart, marking (T0386)T236.OG1 as missing WARNING: atoms too close: (T0386)T236.OG1 and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.O only 0.000 apart, marking (T0386)T236.O as missing WARNING: atoms too close: (T0386)T236.O and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.OG1 and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CG2 and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CB and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.CA and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)T236.N and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing WARNING: atoms too close: (T0386)N235.C and (T0386)T236.C only 0.000 apart, marking (T0386)T236.C as missing # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 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 296 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 291 # 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 T0386 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 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 265 # 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 252 # 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 294 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 188 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 112 # 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 T0386 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 269 # 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 283 # 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 274 # 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 224 # 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 248 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 268 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 202 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 250, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 252, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 339, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 341, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 345, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 347, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 418, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 420, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 610, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 612, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 706, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 708, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 710, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz Skipped atom 712, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL1.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 295 # 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 292 # 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 291 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 291 # 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 239 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 203 # 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 236 # 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 236 # 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 T0386 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 T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 297 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 285 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 297 # 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 172 # 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 160 # 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 273 # 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 298 # 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 279 # 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 298 # 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 293 # 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 297 # 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 T0386 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # 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 221 # 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 223 # 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 207 # 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 # Found a chain break before 251 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 296 # 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 296 # 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 296 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 246 # 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 249 # 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 T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 132 # 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 295 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 283 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 218 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 216 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 216 # copying to AlignedFragments data structure # 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 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 221 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 217 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)K5.CA and (T0386)K5.CB only 0.000 apart, marking (T0386)K5.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)N23.CA and (T0386)N23.CB only 0.000 apart, marking (T0386)N23.CB as missing WARNING: atoms too close: (T0386)V245.CA and (T0386)V245.CB only 0.000 apart, marking (T0386)V245.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)T253.CA and (T0386)T253.CB only 0.000 apart, marking (T0386)T253.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)T253.CA and (T0386)T253.CB only 0.000 apart, marking (T0386)T253.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)A267.CA and (T0386)A267.CB only 0.000 apart, marking (T0386)A267.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing WARNING: atoms too close: (T0386)P284.CA and (T0386)P284.CB only 0.000 apart, marking (T0386)P284.CB as missing # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)M1.CA and (T0386)M1.CB only 0.000 apart, marking (T0386)M1.CB as missing WARNING: atoms too close: (T0386)T11.CA and (T0386)T11.CB only 0.000 apart, marking (T0386)T11.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)H18.CA and (T0386)H18.CB only 0.000 apart, marking (T0386)H18.CB as missing WARNING: atoms too close: (T0386)N23.CA and (T0386)N23.CB only 0.000 apart, marking (T0386)N23.CB as missing WARNING: atoms too close: (T0386)V245.CA and (T0386)V245.CB only 0.000 apart, marking (T0386)V245.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)A261.CA and (T0386)A261.CB only 0.000 apart, marking (T0386)A261.CB as missing WARNING: atoms too close: (T0386)V270.CA and (T0386)V270.CB only 0.000 apart, marking (T0386)V270.CB as missing # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)P2.CA and (T0386)P2.CB only 0.000 apart, marking (T0386)P2.CB as missing WARNING: atoms too close: (T0386)A4.CA and (T0386)A4.CB only 0.000 apart, marking (T0386)A4.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)H17.CA and (T0386)H17.CB only 0.000 apart, marking (T0386)H17.CB as missing WARNING: atoms too close: (T0386)Y19.CA and (T0386)Y19.CB only 0.000 apart, marking (T0386)Y19.CB as missing WARNING: atoms too close: (T0386)Y21.CA and (T0386)Y21.CB only 0.000 apart, marking (T0386)Y21.CB as missing WARNING: atoms too close: (T0386)T24.CA and (T0386)T24.CB only 0.000 apart, marking (T0386)T24.CB as missing WARNING: atoms too close: (T0386)N29.CA and (T0386)N29.CB only 0.000 apart, marking (T0386)N29.CB as missing WARNING: atoms too close: (T0386)T232.CA and (T0386)T232.CB only 0.000 apart, marking (T0386)T232.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)T257.CA and (T0386)T257.CB only 0.000 apart, marking (T0386)T257.CB as missing WARNING: atoms too close: (T0386)T297.CA and (T0386)T297.CB only 0.000 apart, marking (T0386)T297.CB as missing # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)K5.CA and (T0386)K5.CB only 0.000 apart, marking (T0386)K5.CB as missing WARNING: atoms too close: (T0386)K7.CA and (T0386)K7.CB only 0.000 apart, marking (T0386)K7.CB as missing WARNING: atoms too close: (T0386)P16.CA and (T0386)P16.CB only 0.000 apart, marking (T0386)P16.CB as missing WARNING: atoms too close: (T0386)V20.CA and (T0386)V20.CB only 0.000 apart, marking (T0386)V20.CB as missing WARNING: atoms too close: (T0386)Y21.CA and (T0386)Y21.CB only 0.000 apart, marking (T0386)Y21.CB as missing WARNING: atoms too close: (T0386)P22.CA and (T0386)P22.CB only 0.000 apart, marking (T0386)P22.CB as missing WARNING: atoms too close: (T0386)P244.CA and (T0386)P244.CB only 0.000 apart, marking (T0386)P244.CB as missing WARNING: atoms too close: (T0386)A248.CA and (T0386)A248.CB only 0.000 apart, marking (T0386)A248.CB as missing WARNING: atoms too close: (T0386)A261.CA and (T0386)A261.CB only 0.000 apart, marking (T0386)A261.CB as missing # WARNING: incomplete conformation T0386 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 Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 154, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 156, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 319, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 321, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 325, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 327, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 598, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 600, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 602, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 604, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 303, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 305, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 309, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 311, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 295 # 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 T0386 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 T0386 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 T0386 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 T0386 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 249 # 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 219 # 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 95 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 291 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 188 # 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 183 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 282 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 271 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 265 # 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 275 # 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0386)T129.CA and (T0386)N135.CA only 0.000 apart, marking (T0386)N135.CA as missing WARNING: atoms too close: (T0386)L130.CA and (T0386)L136.CA only 0.000 apart, marking (T0386)L136.CA as missing WARNING: atoms too close: (T0386)L130.C and (T0386)L136.C only 0.000 apart, marking (T0386)L136.C as missing WARNING: atoms too close: (T0386)A131.CA and (T0386)Q137.CA only 0.000 apart, marking (T0386)Q137.CA as missing WARNING: atoms too close: (T0386)E132.CA and (T0386)E142.CA only 0.000 apart, marking (T0386)E142.CA as missing WARNING: atoms too close: (T0386)K133.CA and (T0386)E143.CA only 0.000 apart, marking (T0386)E143.CA as missing # WARNING: incomplete conformation T0386 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 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 46, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 48, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 218, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 220, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 351, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 353, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 357, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 359, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 438, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 440, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 630, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 632, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 297 # 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 292 # 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 283 # 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 281 # 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 296 # 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 298 # 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 257 # 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 211 # 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 258 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 T0386 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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: atom 1 has residue number 1 < previous residue 252 in servers/nFOLD_TS1.pdb.gz # WARNING: incomplete conformation T0386 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 T0386 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: atom 1 has residue number 1 < previous residue 259 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 252 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0386 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0386 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 T0386 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 T0386 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 1.5089 model score 1.4050 model score 1.4131 model score 1.3530 model score 1.0557 model score 1.0399 model score 1.0516 model score 1.2673 model score 1.8616 model score 1.8167 model score 1.8584 model score 1.8646 model score 1.7949 model score 1.4290 model score 1.4267 model score 1.4267 model score 1.4213 model score 1.6854 model score 1.6066 model score 1.7510 model score 1.4098 model score 1.3613 model score 1.2083 model score 1.0544 model score 1.3318 model score 0.8335 model score 1.5131 model score 1.5060 model score 1.5423 model score 1.5607 model score 1.5155 model score 0.8434 model score 1.9250 model score 1.0984 model score 1.9255 model score 1.1332 model score 1.1578 model score 0.7997 model score 0.6373 model score 0.6645 model score 0.7096 model score 0.6590 model score 1.0734 model score 0.7154 model score 0.7134 model score 1.8898 model score 1.8387 model score 1.5437 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.9050 model score 0.7666 model score 0.7733 model score 0.7793 model score 2.1973 model score 0.8351 model score 0.6590 model score 0.6645 model score 0.7096 model score 0.7997 model score 1.4314 model score 1.2258 model score 0.8335 model score 0.9950 model score 0.8381 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 2.2515 model score 2.1486 model score 2.3137 model score 2.1627 model score 2.1186 model score 1.4353 model score 2.1540 model score 1.7653 model score 1.9760 model score 1.5464 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.9075 model score 1.0052 model score 1.9816 model score 1.8647 model score 2.0986 model score 2.2660 model score 2.1024 model score 1.8001 model score 2.2916 model score 2.2916 model score 0.7151 model score 0.9636 model score 0.9134 model score 1.3798 model score 0.9589 model score 0.8711 model score 0.9954 model score 0.9954 model score 1.4487 model score 1.7797 model score 1.5952 model score 1.6251 model score 1.6082 model score 1.0408 model score 1.2413 model score 1.2269 model score 1.0370 model score 1.8438 model score 0.9357 model score 1.1053 model score 1.8772 model score 1.7573 model score 2.0557 model score 1.2301 model score 1.1053 model score 1.8098 model score 1.6514 model score 1.9902 model score 0.8610 model score 0.8793 model score 0.8715 model score 0.9034 model score 2.1033 model score 1.0408 model score 1.2862 model score 1.2946 model score 1.2911 model score 1.2901 model score 1.2907 model score 0.9468 model score 0.9476 model score 0.9468 model score 0.9418 model score 0.9510 model score 2.0821 model score 0.7489 model score 1.1607 model score 0.9476 model score 0.9485 model score 0.7755 model score 0.9448 model score 0.8556 model score 1.3760 model score 0.7053 model score 1.5431 model score 0.8563 model score 0.8514 model score 0.8059 model score 0.8968 model score 0.8941 model score 0.7583 model score 0.8067 model score 0.8653 model score 0.7755 model score 0.7538 model score 0.8776 model score 1.0691 model score 0.9128 model score 0.8975 model score 1.6355 model score 2.0043 model score 0.8665 model score 0.9046 model score 2.4925 model score 2.3979 model score 2.3979 model score 0.8499 model score 0.8505 model score 0.8935 model score 2.4972 model score 0.8067 model score 0.8211 model score 0.7996 model score 0.7583 model score 0.8653 model score 1.7903 model score 1.7857 model score 1.7737 model score 1.7273 model score 1.8553 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 1.2798 model score 0.5041 model score 0.6138 model score 1.3178 model score 0.9460 model score 1.0691 model score 1.6900 model score 1.4744 model score 1.7467 model score 1.9570 model score 1.0395 model score 1.9708 model score 1.5178 model score 1.5165 model score 1.6780 model score 1.0857 model score 1.4875 model score 1.9874 model score 2.2449 model score 1.9928 model score 1.2771 model score 1.2771 model score 0.6425 model score 1.2771 model score 1.2771 model score 0.6766 model score 0.6790 model score 0.7213 model score 0.6902 model score 0.6941 model score 1.3739 model score 0.8916 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1112 model score 2.2849 model score 2.0243 model score 2.2075 model score 2.2673 model score 2.1261 model score 1.7339 model score 1.6581 model score 1.8054 model score 2.0024 model score 0.8258 model score 1.9555 model score 1.8868 model score 1.5475 model score 1.4852 model score 0.6908 model score 0.7171 model score 1.8748 model score 1.5163 model score 1.3480 model score 0.8695 model score 1.3890 model score 1.2999 model score 0.7828 USE_META, weight: 0.5463 cost: 1.5089 min: 0.5041 max: 2.4972 USE_META, weight: 0.5932 cost: 1.4050 min: 0.5041 max: 2.4972 USE_META, weight: 0.5895 cost: 1.4131 min: 0.5041 max: 2.4972 USE_META, weight: 0.6167 cost: 1.3530 min: 0.5041 max: 2.4972 USE_META, weight: 0.7509 cost: 1.0557 min: 0.5041 max: 2.4972 USE_META, weight: 0.7581 cost: 1.0399 min: 0.5041 max: 2.4972 USE_META, weight: 0.7528 cost: 1.0516 min: 0.5041 max: 2.4972 USE_META, weight: 0.6554 cost: 1.2673 min: 0.5041 max: 2.4972 USE_META, weight: 0.3870 cost: 1.8616 min: 0.5041 max: 2.4972 USE_META, weight: 0.4073 cost: 1.8167 min: 0.5041 max: 2.4972 USE_META, weight: 0.3884 cost: 1.8584 min: 0.5041 max: 2.4972 USE_META, weight: 0.3857 cost: 1.8646 min: 0.5041 max: 2.4972 USE_META, weight: 0.4172 cost: 1.7949 min: 0.5041 max: 2.4972 USE_META, weight: 0.5823 cost: 1.4290 min: 0.5041 max: 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USE_META, weight: 0.6510 cost: 1.2771 min: 0.5041 max: 2.4972 USE_META, weight: 0.2743 cost: 2.1112 min: 0.5041 max: 2.4972 USE_META, weight: 0.1959 cost: 2.2849 min: 0.5041 max: 2.4972 USE_META, weight: 0.3136 cost: 2.0243 min: 0.5041 max: 2.4972 USE_META, weight: 0.2308 cost: 2.2075 min: 0.5041 max: 2.4972 USE_META, weight: 0.2038 cost: 2.2673 min: 0.5041 max: 2.4972 USE_META, weight: 0.2676 cost: 2.1261 min: 0.5041 max: 2.4972 USE_META, weight: 0.4447 cost: 1.7339 min: 0.5041 max: 2.4972 USE_META, weight: 0.4789 cost: 1.6581 min: 0.5041 max: 2.4972 USE_META, weight: 0.4124 cost: 1.8054 min: 0.5041 max: 2.4972 USE_META, weight: 0.3234 cost: 2.0024 min: 0.5041 max: 2.4972 USE_META, weight: 0.8547 cost: 0.8258 min: 0.5041 max: 2.4972 USE_META, weight: 0.3446 cost: 1.9555 min: 0.5041 max: 2.4972 USE_META, weight: 0.3756 cost: 1.8868 min: 0.5041 max: 2.4972 USE_META, weight: 0.5288 cost: 1.5475 min: 0.5041 max: 2.4972 USE_META, weight: 0.5570 cost: 1.4852 min: 0.5041 max: 2.4972 USE_META, weight: 0.9157 cost: 0.6908 min: 0.5041 max: 2.4972 USE_META, weight: 0.9038 cost: 0.7171 min: 0.5041 max: 2.4972 USE_META, weight: 0.3811 cost: 1.8748 min: 0.5041 max: 2.4972 USE_META, weight: 0.5429 cost: 1.5163 min: 0.5041 max: 2.4972 USE_META, weight: 0.6189 cost: 1.3480 min: 0.5041 max: 2.4972 USE_META, weight: 0.8350 cost: 0.8695 min: 0.5041 max: 2.4972 USE_META, weight: 0.6004 cost: 1.3890 min: 0.5041 max: 2.4972 USE_META, weight: 0.6407 cost: 1.2999 min: 0.5041 max: 2.4972 USE_META, weight: 0.8742 cost: 0.7828 min: 0.5041 max: 2.4972 USE_EVALUE, weight: 0.8901 eval: 10.3510 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8901 eval: 10.3510 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8901 eval: 10.3510 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.1000 eval: 84.8000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.1000 eval: 84.8000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.1000 eval: 84.8000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9483 eval: 4.8723 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9483 eval: 4.8723 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9483 eval: 4.8723 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9099 eval: 8.4910 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9099 eval: 8.4910 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9099 eval: 8.4910 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8971 eval: 9.6978 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8971 eval: 9.6978 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8971 eval: 9.6978 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8801 eval: 11.2960 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8801 eval: 11.2960 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8801 eval: 11.2960 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9134 eval: 8.1594 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9134 eval: 8.1594 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9134 eval: 8.1594 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9133 eval: 8.1728 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9133 eval: 8.1728 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9133 eval: 8.1728 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9984 eval: 0.1554 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9984 eval: 0.1554 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9984 eval: 0.1554 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8872 eval: 10.6320 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8872 eval: 10.6320 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.8872 eval: 10.6320 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9007 eval: 9.3533 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9007 eval: 9.3533 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9007 eval: 9.3533 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9668 eval: 3.1250 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9668 eval: 3.1250 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9668 eval: 3.1250 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9444 eval: 5.2342 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9444 eval: 5.2342 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9444 eval: 5.2342 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9028 eval: 9.1569 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9028 eval: 9.1569 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9028 eval: 9.1569 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9135 eval: 8.1538 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9135 eval: 8.1538 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9135 eval: 8.1538 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9814 eval: 1.7513 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9814 eval: 1.7513 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9814 eval: 1.7513 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9082 eval: 8.6484 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9082 eval: 8.6484 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9082 eval: 8.6484 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9604 eval: 3.7312 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9604 eval: 3.7312 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9604 eval: 3.7312 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9688 eval: 2.9372 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9688 eval: 2.9372 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9688 eval: 2.9372 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9874 eval: 1.1900 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9874 eval: 1.1900 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 0.9874 eval: 1.1900 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 84.8000 Number of contacts in models: 263 Number of contacts in alignments: 66 NUMB_ALIGNS: 66 Adding 22622 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: -514.8974, CN propb: -514.8974 weights: 0.2272 constraints: 618 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 618 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 618 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 22004 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 22004 # 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 22622 # command: