# 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:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 66 Adding 3861 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -547.3101, CN propb: -547.3101 weights: 0.1707 constraints: 579 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 579 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 579 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 3282 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 3282 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 3861 # command: