parameters: 0.6 1.3 0.5 200 50 # 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/T0368/ # command:# Making conformation for sequence T0368 numbered 1 through 174 Created new target T0368 from T0368.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0368/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0368//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0368/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0368//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0368/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0368/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0368/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1na0A/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/T0368/1na0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1na0A/merged-good-all-a2m.gz for input Trying 1na0A/merged-good-all-a2m Error: Couldn't open file 1na0A/merged-good-all-a2m or 1na0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wao1/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/T0368/1wao1/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1wao1/merged-good-all-a2m.gz for input Trying 1wao1/merged-good-all-a2m Error: Couldn't open file 1wao1/merged-good-all-a2m or 1wao1/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fo7A/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/T0368/2fo7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/2fo7A/merged-good-all-a2m.gz for input Trying 2fo7A/merged-good-all-a2m Error: Couldn't open file 2fo7A/merged-good-all-a2m or 2fo7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ouvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ouvA expands to /projects/compbio/data/pdb/1ouv.pdb.gz 1ouvA:# T0368 read from 1ouvA/merged-good-all-a2m # 1ouvA read from 1ouvA/merged-good-all-a2m # adding 1ouvA to template set # found chain 1ouvA in template set T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEIS 1ouvA 32 :LVGLGAKSYKEKDFTQAKKYFEKACDLK # choosing archetypes in rotamer library T0368 54 :FDAFCHAGLAEALAGLR 1ouvA 60 :ENSGCFNLGVLYYQGQG T0368 71 :SFDEALHSADKALHY 1ouvA 80 :NLKKAASFYAKACDL T0368 103 :AVYSRALALDGLGRG 1ouvA 100 :CHLLGNLYYSGQGVS T0368 118 :AEAMPEFKKVVE 1ouvA 118 :NKALQYYSKACD T0368 130 :MIEERKGETPGKERMMEVAIDRIA 1ouvA 142 :IYHDGKVVTRDFKKAVEYFTKACD Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1ouvA read from 1ouvA/merged-good-all-a2m # found chain 1ouvA in template set T0368 5 :KE 1ouvA 30 :KE T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEISH 1ouvA 32 :LVGLGAKSYKEKDFTQAKKYFEKACDLKE T0368 55 :DAFCHAGLAEALAGLR 1ouvA 61 :NSGCFNLGVLYYQGQG T0368 71 :SFDEALHSADKALHY 1ouvA 80 :NLKKAASFYAKACDL T0368 103 :AVYSRALALDGLGRG 1ouvA 100 :CHLLGNLYYSGQGVS T0368 118 :AEAMPEFKKVVE 1ouvA 118 :NKALQYYSKACD T0368 130 :MIEERKGETPGKERMMEVAIDRIA 1ouvA 142 :IYHDGKVVTRDFKKAVEYFTKACD Number of specific fragments extracted= 7 number of extra gaps= 0 total=13 Number of alignments=2 # 1ouvA read from 1ouvA/merged-good-all-a2m # found chain 1ouvA in template set Warning: unaligning (T0368)G9 because first residue in template chain is (1ouvA)D28 T0368 10 :AYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1ouvA 29 :PKELVGLGAKSYKEKDFTQAKKYFEKACDLKEN T0368 57 :FCHAGLAEALAGLR 1ouvA 62 :SGCFNLGVLYYQGQ T0368 71 :SFDEALHSADKALHY 1ouvA 80 :NLKKAASFYAKACDL T0368 88 :RRGE 1ouvA 95 :NYSN T0368 103 :AVYSRALALDGLG 1ouvA 99 :GCHLLGNLYYSGQ T0368 116 :RGAEAMPEFKKVVEM 1ouvA 116 :NTNKALQYYSKACDL T0368 133 :ERKGETPGKERMM 1ouvA 131 :KYAEGCASLGGIY T0368 149 :IDRIAQLGASNQQKKPG 1ouvA 151 :RDFKKAVEYFTKACDLN Number of specific fragments extracted= 8 number of extra gaps= 0 total=21 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wfdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wfdA expands to /projects/compbio/data/pdb/1wfd.pdb.gz 1wfdA:# T0368 read from 1wfdA/merged-good-all-a2m # 1wfdA read from 1wfdA/merged-good-all-a2m # adding 1wfdA to template set # found chain 1wfdA in template set T0368 6 :EVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEI 1wfdA 11 :DSTAAVAVLKRAVELDAESRYQQALVCYQEGIDM T0368 62 :LAEALAGLRS 1wfdA 45 :LLQVLKGTKE T0368 118 :AEAMPEFKKVVEMIEER 1wfdA 55 :SSKRCVLRTKISGYMDR T0368 145 :MEVAIDRIAQLGASNQQKKP 1wfdA 72 :AENIKKYLDQEKEDGKSGPS Number of specific fragments extracted= 4 number of extra gaps= 0 total=25 Number of alignments=4 # 1wfdA read from 1wfdA/merged-good-all-a2m # found chain 1wfdA in template set T0368 6 :EVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEI 1wfdA 11 :DSTAAVAVLKRAVELDAESRYQQALVCYQEGIDM T0368 62 :LAEALAGLRSFDEALHSADKALHY 1wfdA 45 :LLQVLKGTKESSKRCVLRTKISGY T0368 105 :YSRA 1wfdA 69 :MDRA T0368 122 :PEFKKVVEMIEERKGETPG 1wfdA 73 :ENIKKYLDQEKEDGKSGPS Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 Number of alignments=5 # 1wfdA read from 1wfdA/merged-good-all-a2m # found chain 1wfdA in template set T0368 5 :KEVVGAYLALSDAQRQLVAGEYDEAAANCRR 1wfdA 10 :SDSTAAVAVLKRAVELDAESRYQQALVCYQE T0368 75 :ALHSADKALHYFNRRGE 1wfdA 41 :GIDMLLQVLKGTKESSK T0368 134 :RKGETPGKERMMEVAIDRIAQLGASNQ 1wfdA 58 :RCVLRTKISGYMDRAENIKKYLDQEKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d8dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d8dA expands to /projects/compbio/data/pdb/1d8d.pdb.gz 1d8dA:# T0368 read from 1d8dA/merged-good-all-a2m # 1d8dA read from 1d8dA/merged-good-all-a2m # adding 1d8dA to template set # found chain 1d8dA in template set T0368 5 :KEVVGAYLALSDA 1d8dA 234 :NSVWNQRHFVISN T0368 22 :VAGEYDEAAANCRRAMEISHT 1d8dA 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1d8dA 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKAL 1d8dA 289 :LSRYPNLLNQLLDLQ T0368 97 :GKLWISAV 1d8dA 308 :SPYLIAFL T0368 105 :YSRALAL 1d8dA 317 :DIYEDML T0368 112 :DGLGRGAEAMPEFKKVVEMIEERK 1d8dA 325 :NQCDNKEDILNKALELCEILAKEK T0368 137 :ETPGKERMMEVAIDRIAQLG 1d8dA 349 :DTIRKEYWRYIGRSLQSKHS T0368 159 :NQQKKP 1d8dA 369 :RESDIP Number of specific fragments extracted= 9 number of extra gaps= 0 total=41 Number of alignments=7 # 1d8dA read from 1d8dA/merged-good-all-a2m # found chain 1d8dA in template set T0368 6 :EVVGAYLALSDAQRQ 1d8dA 235 :SVWNQRHFVISNTTG T0368 22 :VAGEYDEAAANCRRAMEISHT 1d8dA 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1d8dA 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKA 1d8dA 289 :LSRYPNLLNQLLDL T0368 93 :NQDEGK 1d8dA 303 :QPSHSS T0368 99 :LWISAVYSRALAL 1d8dA 310 :YLIAFLVDIYEDM T0368 112 :DGLGRGAEAMPEFKKVVEMIEE 1d8dA 325 :NQCDNKEDILNKALELCEILAK T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQ 1d8dA 347 :EKDTIRKEYWRYIGRSLQSKHSRESD T0368 163 :KP 1d8dA 373 :IP Number of specific fragments extracted= 9 number of extra gaps= 0 total=50 Number of alignments=8 # 1d8dA read from 1d8dA/merged-good-all-a2m # found chain 1d8dA in template set T0368 8 :VGAYLALSDAQRQLVAG 1d8dA 94 :EKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1d8dA 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1d8dA 130 :NYTVWHFRRVLLRSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1d8dA 147 :DLQEEMNYIIAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1d8dA 168 :VWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=55 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xnfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xnfA expands to /projects/compbio/data/pdb/1xnf.pdb.gz 1xnfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0368 read from 1xnfA/merged-good-all-a2m # 1xnfA read from 1xnfA/merged-good-all-a2m # adding 1xnfA to template set # found chain 1xnfA in template set Warning: unaligning (T0368)E96 because of BadResidue code BAD_PEPTIDE in next template residue (1xnfA)N130 Warning: unaligning (T0368)G97 because of BadResidue code BAD_PEPTIDE at template residue (1xnfA)N130 T0368 8 :VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPP 1xnfA 60 :ERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPE T0368 58 :CHAGLAEALAGLRSFDEALHSADKALHY 1xnfA 98 :VFNYLGIYLTQAGNFDAAYEAFDSVLEL T0368 93 :NQD 1xnfA 126 :DPT T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVE 1xnfA 131 :YAHLNRGIALYYGGRDKLAQDDLLAFYQ T0368 130 :MIEERKG 1xnfA 171 :YLAEQKL T0368 140 :GKERMMEVAIDRIAQLGASN 1xnfA 178 :DEKQAKEVLKQHFEKSDKEQ Number of specific fragments extracted= 6 number of extra gaps= 1 total=61 Number of alignments=10 # 1xnfA read from 1xnfA/merged-good-all-a2m # found chain 1xnfA in template set Warning: unaligning (T0368)R89 because of BadResidue code BAD_PEPTIDE in next template residue (1xnfA)N130 Warning: unaligning (T0368)G90 because of BadResidue code BAD_PEPTIDE at template residue (1xnfA)N130 T0368 2 :KPLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMP 1xnfA 54 :RALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMP T0368 57 :FCHAGLAEALAGLRSFDEALHSADKALHYFNR 1xnfA 97 :EVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVE 1xnfA 131 :YAHLNRGIALYYGGRDKLAQDDLLAFYQ T0368 131 :IEERK 1xnfA 172 :LAEQK T0368 140 :GKERMMEVAIDRIAQLGAS 1xnfA 178 :DEKQAKEVLKQHFEKSDKE Number of specific fragments extracted= 5 number of extra gaps= 1 total=66 Number of alignments=11 # 1xnfA read from 1xnfA/merged-good-all-a2m # found chain 1xnfA in template set Warning: unaligning (T0368)R89 because of BadResidue code BAD_PEPTIDE in next template residue (1xnfA)N130 Warning: unaligning (T0368)G90 because of BadResidue code BAD_PEPTIDE at template residue (1xnfA)N130 T0368 5 :KEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1xnfA 57 :TDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1xnfA 95 :MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT T0368 91 :E 1xnfA 131 :Y T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEV 1xnfA 132 :AHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQK T0368 149 :IDRIAQLGASNQQKKP 1xnfA 177 :LDEKQAKEVLKQHFEK Number of specific fragments extracted= 5 number of extra gaps= 1 total=71 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jcqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jcqA expands to /projects/compbio/data/pdb/1jcq.pdb.gz 1jcqA:# T0368 read from 1jcqA/merged-good-all-a2m # 1jcqA read from 1jcqA/merged-good-all-a2m # adding 1jcqA to template set # found chain 1jcqA in template set T0368 5 :KEVVGAYLA 1jcqA 234 :NSVWNQRYF T0368 131 :IEERKGETPGKERMMEVAIDRIAQLGAS 1jcqA 243 :VISNTTGYNDRAVLEREVQYTLEMIKLV Number of specific fragments extracted= 2 number of extra gaps= 0 total=73 Number of alignments=13 # 1jcqA read from 1jcqA/merged-good-all-a2m # found chain 1jcqA in template set T0368 6 :EVVGAYLALSDAQRQ 1jcqA 235 :SVWNQRYFVISNTTG T0368 22 :VAGEYDEAAANCRRAMEISHT 1jcqA 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1jcqA 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKA 1jcqA 289 :LSKYPNLLNQLLDL T0368 93 :NQDEGKLWISAVY 1jcqA 303 :QPSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEE 1jcqA 319 :YEDMLENQCDNKEDILNKALELCEILAK T0368 135 :KGETPGKERMMEVAIDRIAQ 1jcqA 347 :EKDTIRKEYWRYIGRSLQSK Number of specific fragments extracted= 7 number of extra gaps= 0 total=80 Number of alignments=14 # 1jcqA read from 1jcqA/merged-good-all-a2m # found chain 1jcqA in template set T0368 2 :KPLKEVVGAYLALSDAQRQLVAG 1jcqA 123 :AIELNAANYTVWHFRRVLLKSLQ T0368 25 :EYDEAAANCRRAMEISHT 1jcqA 147 :DLHEEMNYITAIIEEQPK T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1jcqA 165 :NYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYH T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAID 1jcqA 202 :AWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTG T0368 151 :RIAQLGASNQQKKPGYK 1jcqA 256 :LEREVQYTLEMIKLVPH Number of specific fragments extracted= 5 number of extra gaps= 0 total=85 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qqeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qqeA expands to /projects/compbio/data/pdb/1qqe.pdb.gz 1qqeA:# T0368 read from 1qqeA/merged-good-all-a2m # 1qqeA read from 1qqeA/merged-good-all-a2m # adding 1qqeA to template set # found chain 1qqeA in template set T0368 4 :LKEVVGAY 1qqeA 33 :FEEAADLC T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISH 1qqeA 41 :VQAATIYRLRKELNLAGDSFLKAADYQK T0368 51 :HAGF 1qqeA 69 :KAGN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQ 1qqeA 76 :AGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRR T0368 100 :WISAVYSRALALDG 1qqeA 116 :GANFKFELGEILEN T0368 114 :LGRGAEAMPEFKKVVEMIEERK 1qqeA 131 :LHDYAKAIDCYELAGEWYAQDQ T0368 139 :PGKERMMEVAIDRIAQLGASNQ 1qqeA 172 :GQYIEASDIYSKLIKSSMGNRL Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 Number of alignments=16 # 1qqeA read from 1qqeA/merged-good-all-a2m # found chain 1qqeA in template set T0368 4 :LKEVVGAYL 1qqeA 33 :FEEAADLCV T0368 15 :SDAQRQLVAGEYDEAAANCRRAMEISHT 1qqeA 42 :QAATIYRLRKELNLAGDSFLKAADYQKK T0368 49 :FDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQ 1qqeA 70 :AGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRR T0368 100 :WISAVYSRALAL 1qqeA 116 :GANFKFELGEIL T0368 112 :DGLGRGAEAMPEFKKVVEMIEERKG 1qqeA 129 :NDLHDYAKAIDCYELAGEWYAQDQS T0368 139 :PGKERMMEVAIDRIAQLGASNQ 1qqeA 172 :GQYIEASDIYSKLIKSSMGNRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=98 Number of alignments=17 # 1qqeA read from 1qqeA/merged-good-all-a2m # found chain 1qqeA in template set T0368 8 :VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1qqeA 35 :EAADLCVQAATIYRLRKELNLAGDSFLKAADYQKK T0368 49 :FDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1qqeA 70 :AGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQ T0368 97 :GKLWISAVYSRALALD 1qqeA 113 :FRRGANFKFELGEILE T0368 113 :GLGRGAEAMPEFKKVVEMIEER 1qqeA 130 :DLHDYAKAIDCYELAGEWYAQD T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQKK 1qqeA 158 :NKCFIKCADLKALDGQYIEASDIYSKLIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=103 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c2lA/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/T0368/2c2lA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/2c2lA/merged-good-all-a2m.gz for input Trying 2c2lA/merged-good-all-a2m Error: Couldn't open file 2c2lA/merged-good-all-a2m or 2c2lA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qbqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qbqA expands to /projects/compbio/data/pdb/1qbq.pdb.gz 1qbqA:# T0368 read from 1qbqA/merged-good-all-a2m # 1qbqA read from 1qbqA/merged-good-all-a2m # adding 1qbqA to template set # found chain 1qbqA in template set T0368 5 :KEVVGAYLALSDAQRQL 1qbqA 234 :NSVWNQRHFVISNTTGY T0368 22 :VAGEYDEA 1qbqA 252 :DRAVLERE T0368 33 :CRRAMEISHTMPP 1qbqA 260 :VQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1qbqA 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKALH 1qbqA 289 :LSRYPNLLNQLLDLQP T0368 96 :EGKL 1qbqA 305 :SHSS T0368 106 :SRALAL 1qbqA 309 :PYLIAF T0368 123 :EFKKVVEMIE 1qbqA 315 :LVDIYEDMLE T0368 136 :GETPGKERMMEVAIDRIAQLGASNQQ 1qbqA 325 :NQCDNKEDILNKALELCEILAKEKDT Number of specific fragments extracted= 9 number of extra gaps= 0 total=112 Number of alignments=19 # 1qbqA read from 1qbqA/merged-good-all-a2m # found chain 1qbqA in template set T0368 2 :KPLKEVVGAYLALSDAQ 1qbqA 146 :KDLQEEMNYITAIIEEQ T0368 24 :GEYDEAAANCRRAMEISHTMPPEE 1qbqA 163 :PKNYQVWHHRRVLVEWLKDPSQEL T0368 48 :AFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1qbqA 192 :ILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVR T0368 97 :GKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMI 1qbqA 233 :NNSVWNQRHFVISNTTGYSDRAVLEREVQYTLEMI T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQ 1qbqA 324 :ENQCDNKEDILNKALELCEILAKEKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=117 Number of alignments=20 # 1qbqA read from 1qbqA/merged-good-all-a2m # found chain 1qbqA in template set T0368 8 :VGAYLALSDAQRQLVAG 1qbqA 94 :EKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1qbqA 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1qbqA 130 :NYTVWHFRRVLLRSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1qbqA 147 :DLQEEMNYITAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1qbqA 168 :VWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=122 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a17/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a17 expands to /projects/compbio/data/pdb/1a17.pdb.gz 1a17:Warning: there is no chain 1a17 will retry with 1a17A # T0368 read from 1a17/merged-good-all-a2m # 1a17 read from 1a17/merged-good-all-a2m # adding 1a17 to template set # found chain 1a17 in template set T0368 6 :EVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1a17 24 :ALKRAEELKTQANDYFKAKDYENAIKFYSQAIELNPS T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1a17 61 :NAIYYGNRSLAYLRTECYGYALGDATRAIELDKK T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVV 1a17 95 :YIKGYYRRAASNMALGKFRAALRDYETVV T0368 133 :ERKGETPGKERMMEVAIDRIAQLG 1a17 124 :KVKPHDKDAKMKYQECNKIVKQKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=126 Number of alignments=22 # 1a17 read from 1a17/merged-good-all-a2m # found chain 1a17 in template set T0368 1 :MKPLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1a17 19 :PPADGALKRAEELKTQANDYFKAKDYENAIKFYSQAIELNPS T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1a17 61 :NAIYYGNRSLAYLRTECYGYALGDATRAIELDKK T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVVE 1a17 95 :YIKGYYRRAASNMALGKFRAALRDYETVVK T0368 134 :RKGETPGKERMMEVAIDRIAQLG 1a17 125 :VKPHDKDAKMKYQECNKIVKQKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=130 Number of alignments=23 # 1a17 read from 1a17/merged-good-all-a2m # found chain 1a17 in template set T0368 8 :VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1a17 26 :KRAEELKTQANDYFKAKDYENAIKFYSQAIELNPS T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1a17 61 :NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIK T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKP 1a17 98 :GYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR Number of specific fragments extracted= 3 number of extra gaps= 0 total=133 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbaA/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/T0368/2dbaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/2dbaA/merged-good-all-a2m.gz for input Trying 2dbaA/merged-good-all-a2m Error: Couldn't open file 2dbaA/merged-good-all-a2m or 2dbaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1elwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0368 read from 1elwA/merged-good-all-a2m # 1elwA read from 1elwA/merged-good-all-a2m # found chain 1elwA in training set Warning: unaligning (T0368)K2 because first residue in template chain is (1elwA)E2 T0368 3 :PLKEVV 1elwA 3 :QVNELK T0368 15 :SDAQRQLVAGEYDEAAANCRRAMEISHT 1elwA 9 :EKGNKALSVGNIDDALQCYSEAIKLDPH T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHY 1elwA 37 :NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL T0368 93 :NQDEGK 1elwA 68 :KPDWGK T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVE 1elwA 74 :GYSRKAAALEFLNRFEEAKRTYEEGLK T0368 137 :ETPGKERM 1elwA 101 :HEANNPQL T0368 149 :IDRIAQLGA 1elwA 109 :KEGLQNMEA Number of specific fragments extracted= 7 number of extra gaps= 0 total=140 Number of alignments=25 # 1elwA read from 1elwA/merged-good-all-a2m # found chain 1elwA in training set T0368 4 :LK 1elwA 4 :VN T0368 12 :LALSDAQRQLVAGEYDEAAANCRRAMEISHT 1elwA 6 :ELKEKGNKALSVGNIDDALQCYSEAIKLDPH T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHY 1elwA 37 :NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL T0368 93 :NQDEG 1elwA 68 :KPDWG T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVE 1elwA 73 :KGYSRKAAALEFLNRFEEAKRTYEEGLK T0368 137 :ETPGKERM 1elwA 101 :HEANNPQL T0368 149 :IDRIAQLGA 1elwA 109 :KEGLQNMEA Number of specific fragments extracted= 7 number of extra gaps= 0 total=147 Number of alignments=26 # 1elwA read from 1elwA/merged-good-all-a2m # found chain 1elwA in training set T0368 9 :GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1elwA 3 :QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPH T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1elwA 37 :NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGK T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERM 1elwA 74 :GYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNM Number of specific fragments extracted= 3 number of extra gaps= 0 total=150 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qz2A/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/T0368/1qz2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1qz2A/merged-good-all-a2m.gz for input Trying 1qz2A/merged-good-all-a2m Error: Couldn't open file 1qz2A/merged-good-all-a2m or 1qz2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3bA/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/T0368/1w3bA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1w3bA/merged-good-all-a2m.gz for input Trying 1w3bA/merged-good-all-a2m Error: Couldn't open file 1w3bA/merged-good-all-a2m or 1w3bA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ff4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ff4A expands to /projects/compbio/data/pdb/2ff4.pdb.gz 2ff4A:# T0368 read from 2ff4A/merged-good-all-a2m # 2ff4A read from 2ff4A/merged-good-all-a2m # adding 2ff4A to template set # found chain 2ff4A in template set T0368 7 :VVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGF 2ff4A 112 :LGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFV T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG 2ff4A 170 :KVLAHTAKAEAEIACGRASAVIAELEALTFEHPYRE T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGK 2ff4A 206 :PLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP T0368 142 :ERMMEVA 2ff4A 248 :RALNERI T0368 149 :IDRIAQLGASNQQKKPGYKAWWE 2ff4A 271 :AGTVTVLDQRTMASGQQAVAYLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=155 Number of alignments=28 # 2ff4A read from 2ff4A/merged-good-all-a2m # found chain 2ff4A in template set T0368 7 :VVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAF 2ff4A 112 :LGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPF T0368 58 :CHAGLAEALAGLRSFDEALHSADKALHYFNRRG 2ff4A 173 :AHTAKAEAEIACGRASAVIAELEALTFEHPYRE T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGK 2ff4A 206 :PLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP T0368 142 :ERMMEVA 2ff4A 248 :RALNERI T0368 149 :IDRIAQLGASNQQKKPGYKAWWE 2ff4A 271 :AGTVTVLDQRTMASGQQAVAYLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=160 Number of alignments=29 # 2ff4A read from 2ff4A/merged-good-all-a2m # found chain 2ff4A in template set T0368 7 :VVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMP 2ff4A 112 :LGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPV T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 2ff4A 170 :KVLAHTAKAEAEIACGRASAVIAELEALTFEHPYREP T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERK 2ff4A 207 :LWTQLITAYYLSDRQSDALGAYRRVKTTLADDL T0368 136 :GE 2ff4A 245 :PT T0368 154 :QLGASNQQKK 2ff4A 247 :LRALNERILR Number of specific fragments extracted= 5 number of extra gaps= 0 total=165 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hh8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0368 read from 1hh8A/merged-good-all-a2m # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set T0368 2 :KPLKEVVGAYLA 1hh8A 20 :KDWKGALDAFSA T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISHTM 1hh8A 41 :FNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1hh8A 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 94 :QDEG 1hh8A 110 :KILG T0368 98 :KLWI 1hh8A 117 :KLFA T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVE 1hh8A 123 :VLYNIAFMYAKKEEWKKAEEQLALATS T0368 135 :KGETPGKER 1hh8A 150 :MKSEPRHSK T0368 148 :AIDRIAQLGASNQ 1hh8A 159 :IDKAMECVWKQKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=173 Number of alignments=31 # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set T0368 3 :PLKEVVGAYLA 1hh8A 21 :DWKGALDAFSA T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISHTM 1hh8A 41 :FNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1hh8A 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 95 :DE 1hh8A 110 :KI T0368 98 :KLWIS 1hh8A 116 :FKLFA T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVE 1hh8A 123 :VLYNIAFMYAKKEEWKKAEEQLALATS T0368 135 :KGETPGKERMME 1hh8A 150 :MKSEPRHSKIDK T0368 148 :AIDRIAQLGASN 1hh8A 162 :AMECVWKQKLYE Number of specific fragments extracted= 8 number of extra gaps= 0 total=181 Number of alignments=32 # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set Warning: unaligning (T0368)E6 because first residue in template chain is (1hh8A)S2 T0368 7 :VVGAYLALSDAQRQLVAGEYDEAAANC 1hh8A 3 :LVEAISLWNEGVLAADKKDWKGALDAF T0368 49 :FDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1hh8A 30 :SAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAV T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEER 1hh8A 73 :AYFQRGMLYYQTEKYDLAIKDLKEALIQLRGN T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQKKPG 1hh8A 121 :CEVLYNIAFMYAKKEEWKKAEEQLALATSMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=185 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ihgA expands to /projects/compbio/data/pdb/1ihg.pdb.gz 1ihgA:# T0368 read from 1ihgA/merged-good-all-a2m # 1ihgA read from 1ihgA/merged-good-all-a2m # adding 1ihgA to template set # found chain 1ihgA in template set Warning: unaligning (T0368)K163 because last residue in template chain is (1ihgA)Y365 T0368 3 :PLKEVVGAYLALSD 1ihgA 215 :DVDKILLISEDLKN T0368 17 :AQRQLVAGEYDEAAANCR 1ihgA 230 :GNTFFKSQNWEMAIKKYT T0368 35 :RAMEISH 1ihgA 251 :RYVEGSR T0368 42 :TMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHY 1ihgA 259 :AAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI T0368 93 :NQD 1ihgA 303 :DPS T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVVEM 1ihgA 306 :NTKALYRRAQGWQGLKEYDQALADLKKAQEI T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQK 1ihgA 337 :APEDKAIQAELLKVKQKIKAQKDKEKAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=192 Number of alignments=34 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set Warning: unaligning (T0368)K163 because last residue in template chain is (1ihgA)Y365 T0368 3 :PLKEVVGAYLALSD 1ihgA 215 :DVDKILLISEDLKN T0368 17 :AQRQLVAGEYDEAAANCR 1ihgA 230 :GNTFFKSQNWEMAIKKYT T0368 35 :RAMEISHT 1ihgA 251 :RYVEGSRA T0368 43 :MPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHY 1ihgA 260 :AEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI T0368 93 :NQD 1ihgA 303 :DPS T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVVEM 1ihgA 306 :NTKALYRRAQGWQGLKEYDQALADLKKAQEI T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQK 1ihgA 337 :APEDKAIQAELLKVKQKIKAQKDKEKAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=199 Number of alignments=35 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set T0368 8 :VGAYLALSDAQRQLVAGEYDEAAANCRRAM 1ihgA 221 :LISEDLKNIGNTFFKSQNWEMAIKKYTKVL T0368 38 :EISHT 1ihgA 258 :AAAED T0368 46 :EEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1ihgA 263 :ADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTK T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMME 1ihgA 309 :ALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQ T0368 151 :RIAQLGASNQ 1ihgA 353 :KIKAQKDKEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=204 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wy6A expands to /projects/compbio/data/pdb/1wy6.pdb.gz 1wy6A:# T0368 read from 1wy6A/merged-good-all-a2m # 1wy6A read from 1wy6A/merged-good-all-a2m # adding 1wy6A to template set # found chain 1wy6A in template set Warning: unaligning (T0368)N87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy6A)N122 Warning: unaligning (T0368)G90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy6A)N122 T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEIS 1wy6A 11 :KLMDAKKFLLDGYIDEGVKIVLEITKSS T0368 44 :PPEE 1wy6A 39 :TKSE T0368 51 :HAGFDAFCHA 1wy6A 43 :YNWFICNLLE T0368 61 :GLAEALAGLRSF 1wy6A 58 :YMFQVLDKIGSY T0368 73 :DEALH 1wy6A 96 :NKALD T0368 78 :SADKALHYF 1wy6A 110 :KLEEIGREI T0368 91 :ELNQ 1wy6A 123 :EVSA T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVE 1wy6A 127 :SILVAIANALRRVGDERDATTLLIEACK T0368 135 :KGE 1wy6A 155 :KGE T0368 142 :ERMMEVAI 1wy6A 158 :KEACNAVN T0368 154 :Q 1wy6A 166 :T Number of specific fragments extracted= 11 number of extra gaps= 0 total=215 Number of alignments=37 # 1wy6A read from 1wy6A/merged-good-all-a2m # found chain 1wy6A in template set Warning: unaligning (T0368)N87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy6A)N122 Warning: unaligning (T0368)G90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy6A)N122 T0368 12 :LALSDAQRQLVAGEYDEAAANCRRAMEIS 1wy6A 10 :RKLMDAKKFLLDGYIDEGVKIVLEITKSS T0368 44 :PPEE 1wy6A 39 :TKSE T0368 51 :HAGFDAFCHA 1wy6A 43 :YNWFICNLLE T0368 61 :GLAEALAGLRSF 1wy6A 58 :YMFQVLDKIGSY T0368 73 :DEALH 1wy6A 96 :NKALD T0368 78 :SADKALHYF 1wy6A 110 :KLEEIGREI T0368 91 :ELNQ 1wy6A 123 :EVSA T0368 102 :SAVYSRALALDGLGRGAEAMPEFKKVVE 1wy6A 127 :SILVAIANALRRVGDERDATTLLIEACK T0368 139 :PGKERMMEVAID 1wy6A 155 :KGEKEACNAVNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=224 Number of alignments=38 # 1wy6A read from 1wy6A/merged-good-all-a2m # found chain 1wy6A in template set Warning: unaligning (T0368)L83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy6A)N122 Warning: unaligning (T0368)F86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy6A)N122 T0368 12 :LALSDAQRQLVAGEYDEAAANCRRAMEISHTMP 1wy6A 10 :RKLMDAKKFLLDGYIDEGVKIVLEITKSSTKSE T0368 54 :FD 1wy6A 91 :LN T0368 57 :FCHAGLAEALAGLRSFDEALHSADKA 1wy6A 93 :EHVNKALDILVIQGKRDKLEEIGREI T0368 87 :NRRGE 1wy6A 123 :EVSAS T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEM 1wy6A 128 :ILVAIANALRRVGDERDATTLLIEACKK T0368 134 :R 1wy6A 157 :E T0368 152 :IAQLGASN 1wy6A 158 :KEACNAVN Number of specific fragments extracted= 7 number of extra gaps= 0 total=231 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e96B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e96B expands to /projects/compbio/data/pdb/1e96.pdb.gz 1e96B:# T0368 read from 1e96B/merged-good-all-a2m # 1e96B read from 1e96B/merged-good-all-a2m # adding 1e96B to template set # found chain 1e96B in template set T0368 3 :PLKEVVGAY 1e96B 21 :DWKGALDAF T0368 12 :LALSDAQRQLVAGEYDEAAANCRRAMEISHTM 1e96B 39 :ICFNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1e96B 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 94 :QDE 1e96B 111 :ILG T0368 98 :KLW 1e96B 117 :KLF T0368 101 :ISAVYSRALALDGLGRGAEAMPEFKKVVEM 1e96B 121 :CEVLYNIAFMYAKKEEWKKAEEQLALATSM T0368 137 :ETPGKE 1e96B 152 :SEPRHS T0368 147 :VAIDRIAQLGASNQQK 1e96B 158 :KIDKAMECVWKQKLYE Number of specific fragments extracted= 8 number of extra gaps= 0 total=239 Number of alignments=40 # 1e96B read from 1e96B/merged-good-all-a2m # found chain 1e96B in template set T0368 3 :PLKEVVGAYLA 1e96B 21 :DWKGALDAFSA T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISHTM 1e96B 41 :FNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1e96B 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 94 :QDE 1e96B 111 :ILG T0368 98 :KLW 1e96B 117 :KLF T0368 101 :ISAVYSRALALDGLGRGAEAMPEFKKVVEM 1e96B 121 :CEVLYNIAFMYAKKEEWKKAEEQLALATSM T0368 136 :GETPGKERM 1e96B 151 :KSEPRHSKI T0368 149 :IDRIAQLGASNQQK 1e96B 160 :DKAMECVWKQKLYE Number of specific fragments extracted= 8 number of extra gaps= 0 total=247 Number of alignments=41 # 1e96B read from 1e96B/merged-good-all-a2m # found chain 1e96B in template set T0368 7 :VVGAYLALSDAQRQLVAGEYDEAAANCR 1e96B 3 :LVEAISLWNEGVLAADKKDWKGALDAFS T0368 50 :DHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1e96B 31 :AVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAV T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEER 1e96B 73 :AYFQRGMLYYQTEKYDLAIKDLKEALIQLRGN T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQKKPGYKA 1e96B 121 :CEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP Number of specific fragments extracted= 4 number of extra gaps= 0 total=251 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ft1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ft1A expands to /projects/compbio/data/pdb/1ft1.pdb.gz 1ft1A:# T0368 read from 1ft1A/merged-good-all-a2m # 1ft1A read from 1ft1A/merged-good-all-a2m # adding 1ft1A to template set # found chain 1ft1A in template set T0368 6 :EVVGAYLALSD 1ft1A 235 :SVWNQRHFVIS T0368 22 :VAGEYDEAAANCRRAMEISHT 1ft1A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1ft1A 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSAD 1ft1A 289 :LSRYPNLLNQLL T0368 91 :ELNQDEGKLWISAVY 1ft1A 301 :DLQPSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEER 1ft1A 319 :YEDMLENQCDNKEDILNKALELCEILAKE T0368 136 :GETPGKERMMEVAIDR 1ft1A 348 :KDTIRKEYWRYIGRSL Number of specific fragments extracted= 7 number of extra gaps= 0 total=258 Number of alignments=43 # 1ft1A read from 1ft1A/merged-good-all-a2m # found chain 1ft1A in template set T0368 22 :VAGEYDEAAANCRRAMEISHT 1ft1A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALA 1ft1A 273 :NESAWNYLKGILQ T0368 68 :GLRSFDEALHSAD 1ft1A 288 :GLSRYPNLLNQLL T0368 91 :ELNQDEGKLWISAVY 1ft1A 301 :DLQPSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEE 1ft1A 319 :YEDMLENQCDNKEDILNKALELCEILAK T0368 135 :KGETPGKERMMEVAIDRI 1ft1A 347 :EKDTIRKEYWRYIGRSLQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=264 Number of alignments=44 # 1ft1A read from 1ft1A/merged-good-all-a2m # found chain 1ft1A in template set T0368 7 :VVGAYLALSDAQRQLVAG 1ft1A 93 :SEKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1ft1A 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1ft1A 130 :NYTVWHFRRVLLRSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1ft1A 147 :DLQEEMNYIIAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1ft1A 168 :VWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=269 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p5qA/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/T0368/1p5qA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1p5qA/merged-good-all-a2m.gz for input Trying 1p5qA/merged-good-all-a2m Error: Couldn't open file 1p5qA/merged-good-all-a2m or 1p5qA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kt1A/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/T0368/1kt1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1kt1A/merged-good-all-a2m.gz for input Trying 1kt1A/merged-good-all-a2m Error: Couldn't open file 1kt1A/merged-good-all-a2m or 1kt1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hz4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0368 read from 1hz4A/merged-good-all-a2m # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set T0368 4 :LKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAME 1hz4A 6 :REDTMHAEFNALRAQVAINDGNPDEAERLAKLALE T0368 42 :TMPPEEAFD 1hz4A 41 :ELPPGWFYS T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1hz4A 50 :RIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWH T0368 99 :LWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE 1hz4A 89 :YALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLE T0368 138 :TP 1hz4A 129 :LP T0368 140 :GKERMMEVAIDRIAQLGASNQQK 1hz4A 148 :RLDEAEASARSGIEVLSSYQPQQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=275 Number of alignments=46 # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set T0368 1 :MKPLKEVVG 1hz4A 2 :IKDIREDTM T0368 10 :AYLALSDAQRQLVAGEYDEAAANCRRAME 1hz4A 12 :AEFNALRAQVAINDGNPDEAERLAKLALE T0368 42 :TMPPEEAFD 1hz4A 41 :ELPPGWFYS T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG 1hz4A 50 :RIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHD T0368 96 :EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE 1hz4A 86 :VWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLE T0368 140 :GK 1hz4A 128 :QL T0368 142 :ERMMEVAIDRIAQLGASNQQK 1hz4A 150 :DEAEASARSGIEVLSSYQPQQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=282 Number of alignments=47 # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set T0368 2 :KPLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1hz4A 4 :DIREDTMHAEFNALRAQVAINDGNPDEAERLAKLALEELPP T0368 50 :DHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1hz4A 45 :GWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDV T0368 97 :GKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM 1hz4A 87 :WHYALWSLIQQSEILFAQGFLQTAWETQEKAFQL T0368 131 :IEERKGETPGKERMMEVAIDRIAQLGASNQQKK 1hz4A 129 :LPMHEFLVRIRAQLLWAWARLDEAEASARSGIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=286 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1iP/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i1iP expands to /projects/compbio/data/pdb/1i1i.pdb.gz 1i1iP:# T0368 read from 1i1iP/merged-good-all-a2m # 1i1iP read from 1i1iP/merged-good-all-a2m # adding 1i1iP to template set # found chain 1i1iP in template set T0368 20 :QLV 1i1iP 33 :QIK T0368 24 :GEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAG 1i1iP 36 :TRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVER T0368 69 :LRSFDEALHSADKALHYFNR 1i1iP 89 :VSSDREVRAASTEADKKLSR T0368 104 :VYSRALALDGLGRGAE 1i1iP 119 :VFQRIVHLQETCDLEK T0368 120 :AMPEFKKVVEMIEERKGETPG 1i1iP 139 :ARRYLEKSIKMGKRNGLHLSE T0368 143 :RMMEVAIDRIAQLGA 1i1iP 160 :HIRNEIKSMKKRMSE Number of specific fragments extracted= 6 number of extra gaps= 0 total=292 Number of alignments=49 # 1i1iP read from 1i1iP/merged-good-all-a2m # found chain 1i1iP in template set T0368 4 :LKEVVGAY 1i1iP 31 :PEQIKTRT T0368 27 :DEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLR 1i1iP 39 :EQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTM T0368 71 :SFDEALHSADKALHYFNR 1i1iP 91 :SDREVRAASTEADKKLSR T0368 102 :SAVYSRALALDGLGRGAEAMPE 1i1iP 117 :EDVFQRIVHLQETCDLEKIKPE T0368 124 :FKKVVEMIEERKGETP 1i1iP 143 :LEKSIKMGKRNGLHLS T0368 142 :ERMMEVAIDRIAQLGA 1i1iP 159 :EHIRNEIKSMKKRMSE Number of specific fragments extracted= 6 number of extra gaps= 0 total=298 Number of alignments=50 # 1i1iP read from 1i1iP/merged-good-all-a2m # found chain 1i1iP in template set T0368 6 :EVVGAYLAL 1i1iP 30 :SPEQIKTRT T0368 18 :QRQ 1i1iP 39 :EQL T0368 30 :AANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLR 1i1iP 42 :IAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTM T0368 71 :SFDEALHSADKALHYFNRRGE 1i1iP 91 :SDREVRAASTEADKKLSRFDI T0368 96 :EGKLWISAVYSRALALDG 1i1iP 112 :EMSMREDVFQRIVHLQET T0368 114 :LGR 1i1iP 132 :LEK T0368 117 :GAEAMPEFKKVVEMIEER 1i1iP 136 :KPEARRYLEKSIKMGKRN T0368 138 :TPGKERMMEVAIDRIAQLGASNQQKKP 1i1iP 159 :EHIRNEIKSMKKRMSELCIDFNKNLNE Number of specific fragments extracted= 8 number of extra gaps= 0 total=306 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2avpA expands to /projects/compbio/data/pdb/2avp.pdb.gz 2avpA:# T0368 read from 2avpA/merged-good-all-a2m # 2avpA read from 2avpA/merged-good-all-a2m # adding 2avpA to template set # found chain 2avpA in template set T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEISHTM 2avpA 4 :WYNLGNAYYKQGDYDEAIEYYQKALELDPRS T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHY 2avpA 35 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL Number of specific fragments extracted= 2 number of extra gaps= 0 total=308 Number of alignments=52 # 2avpA read from 2avpA/merged-good-all-a2m # found chain 2avpA in template set T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEISHTM 2avpA 4 :WYNLGNAYYKQGDYDEAIEYYQKALELDPRS T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFN 2avpA 35 :AEAWYNLGNAYYKQGDYDEAIEYYQKALELDP Number of specific fragments extracted= 2 number of extra gaps= 0 total=310 Number of alignments=53 # 2avpA read from 2avpA/merged-good-all-a2m # found chain 2avpA in template set Warning: unaligning (T0368)R89 because last residue in template chain is (2avpA)S68 T0368 11 :YLALSDAQRQLVAGEYDEAAANCRRAMEISHT 2avpA 2 :EAWYNLGNAYYKQGDYDEAIEYYQKALELDPR T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 2avpA 34 :SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR Number of specific fragments extracted= 2 number of extra gaps= 0 total=312 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fchA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fchA expands to /projects/compbio/data/pdb/1fch.pdb.gz 1fchA:# T0368 read from 1fchA/merged-good-all-a2m # 1fchA read from 1fchA/merged-good-all-a2m # adding 1fchA to template set # found chain 1fchA in template set Warning: unaligning (T0368)R134 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fchA)G559 T0368 4 :LKEVVGAYLALSDAQ 1fchA 431 :FLEVKELFLAAVRLD T0368 24 :GEYDEAAANCRRAMEISHT 1fchA 465 :GEYDKAVDCFTAALSVRPN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1fchA 484 :DYLLWNKLGATLANGNQSEEAVAAYRRALELQPG T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVVEMIEE 1fchA 518 :YIRSRYNLGISCINLGAHREAVEHFLEALNMQRK T0368 142 :ERMMEVAIDRIAQLGASN 1fchA 564 :ENIWSTLRLALSMLGQSD Number of specific fragments extracted= 5 number of extra gaps= 0 total=317 Number of alignments=55 # 1fchA read from 1fchA/merged-good-all-a2m # found chain 1fchA in template set Warning: unaligning (T0368)R134 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fchA)G559 Warning: unaligning (T0368)K141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fchA)G559 T0368 4 :LKEVVGAYLALSDAQ 1fchA 431 :FLEVKELFLAAVRLD T0368 24 :GEYDEAAANCRRAMEISHT 1fchA 465 :GEYDKAVDCFTAALSVRPN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNR 1fchA 484 :DYLLWNKLGATLANGNQSEEAVAAYRRALELQPG T0368 100 :WISAVYSRALALDGLGRGAEAMPEFKKVVEMIEE 1fchA 518 :YIRSRYNLGISCINLGAHREAVEHFLEALNMQRK T0368 142 :ERMMEVAIDRIAQLGASN 1fchA 564 :ENIWSTLRLALSMLGQSD Number of specific fragments extracted= 5 number of extra gaps= 0 total=322 Number of alignments=56 # 1fchA read from 1fchA/merged-good-all-a2m # found chain 1fchA in template set T0368 2 :KPLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMP 1fchA 358 :CLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYA T0368 49 :FDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1fchA 444 :LDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYL T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQK 1fchA 487 :LWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEAL Number of specific fragments extracted= 3 number of extra gaps= 0 total=325 Number of alignments=57 # 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 # T0368 read from 1na3A/merged-good-all-a2m # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0368 10 :AYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHY 1na3A 37 :NAEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0368 93 :NQ 1na3A 68 :DP T0368 116 :RGAEAMPEFKKVVEM 1na3A 70 :NNAEAKQDLGNAKQK Number of specific fragments extracted= 4 number of extra gaps= 0 total=329 Number of alignments=58 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0368 6 :E 1na3A 3 :S T0368 10 :AYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYF 1na3A 37 :NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD T0368 115 :GRGAEAMPEFKKVVEM 1na3A 69 :PNNAEAKQDLGNAKQK Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=59 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0368 8 :VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1na3A 2 :NSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1na3A 37 :NAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAE T0368 120 :AMPEFKKVVE 1na3A 74 :AKQDLGNAKQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=336 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbnA expands to /projects/compbio/data/pdb/2fbn.pdb.gz 2fbnA:# T0368 read from 2fbnA/merged-good-all-a2m # 2fbnA read from 2fbnA/merged-good-all-a2m # adding 2fbnA to template set # found chain 2fbnA in template set Warning: unaligning (T0368)A157 because last residue in template chain is (2fbnA)K174 T0368 4 :LKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEI 2fbnA 32 :EEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDF T0368 40 :SHTMPPEEAFD 2fbnA 71 :TEEWDDQILLD T0368 51 :HAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR 2fbnA 83 :KKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNN T0368 101 :ISAVYSRALALDGLGRGAEAMPEFKKVVEM 2fbnA 122 :VKALYKLGVANMYFGFLEEAKENLYKAASL T0368 135 :KGETPGKERMMEVAIDRIAQLG 2fbnA 152 :NPNNLDIRNSYELCVNKLKEAR Number of specific fragments extracted= 5 number of extra gaps= 0 total=341 Number of alignments=61 # 2fbnA read from 2fbnA/merged-good-all-a2m # found chain 2fbnA in template set Warning: unaligning (T0368)A157 because last residue in template chain is (2fbnA)K174 T0368 5 :KEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEI 2fbnA 33 :EKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDF T0368 40 :SHTMPPEEAFD 2fbnA 71 :TEEWDDQILLD T0368 51 :HAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR 2fbnA 83 :KKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNN T0368 101 :ISAVYSRALALDGLGRGAEAMPEFKKVVEM 2fbnA 122 :VKALYKLGVANMYFGFLEEAKENLYKAASL T0368 135 :KGETPGKERMMEVAIDRIAQLG 2fbnA 152 :NPNNLDIRNSYELCVNKLKEAR Number of specific fragments extracted= 5 number of extra gaps= 0 total=346 Number of alignments=62 # 2fbnA read from 2fbnA/merged-good-all-a2m # found chain 2fbnA in template set T0368 3 :PLKEVVGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMP 2fbnA 31 :DEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTE T0368 45 :PEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 2fbnA 77 :QILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVK T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRI 2fbnA 124 :ALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=349 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bugA/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/T0368/2bugA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/2bugA/merged-good-all-a2m.gz for input Trying 2bugA/merged-good-all-a2m Error: Couldn't open file 2bugA/merged-good-all-a2m or 2bugA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jcrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jcrA expands to /projects/compbio/data/pdb/1jcr.pdb.gz 1jcrA:# T0368 read from 1jcrA/merged-good-all-a2m # 1jcrA read from 1jcrA/merged-good-all-a2m # adding 1jcrA to template set # found chain 1jcrA in template set T0368 5 :KEVVGAYLALSDA 1jcrA 131 :YTVWHFRRVLLRS T0368 21 :L 1jcrA 144 :L T0368 23 :AGEYDEAAANCRRAMEISHT 1jcrA 145 :QKDLQEEMNYIIAIIEEQPK T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR 1jcrA 165 :NYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKN T0368 103 :AVYS 1jcrA 201 :HAWQ T0368 107 :RALALDGLGRGAEAMPEFKKVVE 1jcrA 206 :RQWVIQEFRLWDNELQYVDQLLK T0368 130 :MIEERKGETPGKERMMEVAIDRIAQLGAS 1jcrA 242 :FVISNTTGYSDRAVLEREVQYTLEMIKLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=356 Number of alignments=64 # 1jcrA read from 1jcrA/merged-good-all-a2m # found chain 1jcrA in template set T0368 2 :KPLKEVVGAYLALSDAQ 1jcrA 146 :KDLQEEMNYIIAIIEEQ T0368 24 :GEYDEAAANCRRAMEISHTMPPEE 1jcrA 163 :PKNYQVWHHRRVLVEWLKDPSQEL T0368 48 :AFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYF 1jcrA 192 :ILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKED T0368 95 :DEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIE 1jcrA 231 :VRNNSVWNQRHFVISNTTGYSDRAVLEREVQYTLEMIK T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQ 1jcrA 324 :ENQCDNKEDILNKALELCEILAKEKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=361 Number of alignments=65 # 1jcrA read from 1jcrA/merged-good-all-a2m # found chain 1jcrA in template set T0368 8 :VGAYLALSDAQRQLVAG 1jcrA 94 :EKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1jcrA 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1jcrA 130 :NYTVWHFRRVLLRSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1jcrA 147 :DLQEEMNYIIAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1jcrA 168 :VWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=366 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zbpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zbpA expands to /projects/compbio/data/pdb/1zbp.pdb.gz 1zbpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0368 read from 1zbpA/merged-good-all-a2m # 1zbpA read from 1zbpA/merged-good-all-a2m # adding 1zbpA to template set # found chain 1zbpA in template set T0368 17 :AQRQLVAGEYDEAAANCRRAMEISHT 1zbpA 4 :WKNALSEGQLQQALELLIEAIKASPK T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR 1zbpA 30 :DASLRSSFIELLCIDGDFERADEQLMQSIKLFPEY T0368 101 :ISAVYSRALALDG 1zbpA 71 :LRHLVKAAQARKD T0368 114 :LGRGAEAMPEFKKVVEMIEE 1zbpA 94 :LGENEELTKSLVSFNLSMVS T0368 139 :PGKERMMEVAIDRIAQLGAS 1zbpA 114 :QDYEQVSELALQIEELRQEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=371 Number of alignments=67 # 1zbpA read from 1zbpA/merged-good-all-a2m # found chain 1zbpA in template set T0368 18 :QRQLVAGEYDEAAANCRRAMEISHT 1zbpA 5 :KNALSEGQLQQALELLIEAIKASPK T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR 1zbpA 30 :DASLRSSFIELLCIDGDFERADEQLMQSIKLFPEY T0368 96 :EG 1zbpA 67 :GA T0368 99 :LWISAVYSRALALDG 1zbpA 69 :SQLRHLVKAAQARKD T0368 114 :LGRGAEAMPEFKKVVEMIEE 1zbpA 94 :LGENEELTKSLVSFNLSMVS T0368 139 :PGKERMMEVAIDRIAQLGA 1zbpA 114 :QDYEQVSELALQIEELRQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=377 Number of alignments=68 # 1zbpA read from 1zbpA/merged-good-all-a2m # found chain 1zbpA in template set T0368 19 :RQLVAGEYDEAAANCRRAMEISHT 1zbpA 6 :NALSEGQLQQALELLIEAIKASPK T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1zbpA 30 :DASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLP T0368 97 :GKLWISAVYSRALALDGL 1zbpA 67 :GASQLRHLVKAAQARKDF T0368 131 :IEERKGETPGKERMMEVA 1zbpA 94 :LGENEELTKSLVSFNLSM T0368 149 :IDRIAQLGASNQQKKP 1zbpA 114 :QDYEQVSELALQIEEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=382 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wm5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wm5A expands to /projects/compbio/data/pdb/1wm5.pdb.gz 1wm5A:# T0368 read from 1wm5A/merged-good-all-a2m # 1wm5A read from 1wm5A/merged-good-all-a2m # adding 1wm5A to template set # found chain 1wm5A in template set T0368 2 :KPLKEVVGAY 1wm5A 20 :KDWKGALDAF T0368 12 :LALSDAQRQLVAGEYDEAAANCRRAMEISHTM 1wm5A 39 :ICFNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1wm5A 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 94 :QDEG 1wm5A 110 :KILG T0368 98 :KLWI 1wm5A 117 :KLFA T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEM 1wm5A 123 :VLYNIAFMYAKKEEWKKAEEQLALATSM T0368 136 :GETPGKERMMEVAI 1wm5A 154 :PRHSKIDKAMECVW Number of specific fragments extracted= 7 number of extra gaps= 0 total=389 Number of alignments=70 # 1wm5A read from 1wm5A/merged-good-all-a2m # found chain 1wm5A in template set T0368 3 :PLKEVVGAYLA 1wm5A 21 :DWKGALDAFSA T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISHTM 1wm5A 41 :FNIGCMYTILKNMTEAEKAFTRSINRDKHL T0368 56 :AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1wm5A 71 :AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLID T0368 95 :DE 1wm5A 110 :KI T0368 98 :KLWIS 1wm5A 116 :FKLFA T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEM 1wm5A 123 :VLYNIAFMYAKKEEWKKAEEQLALATSM T0368 136 :GETPGKERMM 1wm5A 151 :KSEPRHSKID T0368 147 :VAIDRIAQLGASNQQ 1wm5A 161 :KAMECVWKQKLYEPV Number of specific fragments extracted= 8 number of extra gaps= 0 total=397 Number of alignments=71 # 1wm5A read from 1wm5A/merged-good-all-a2m # found chain 1wm5A in template set T0368 6 :EVVGAYLALSDAQRQLVAGEYDEAAANCRR 1wm5A 2 :SLVEAISLWNEGVLAADKKDWKGALDAFSA T0368 51 :HAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1wm5A 32 :VQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAV T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEER 1wm5A 73 :AYFQRGMLYYQTEKYDLAIKDLKEALIQLRGN T0368 135 :KGETPGKERMMEVAIDRIAQLGASNQQKKPGYKAWWEF 1wm5A 121 :CEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSK Number of specific fragments extracted= 4 number of extra gaps= 0 total=401 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1elrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1elrA expands to /projects/compbio/data/pdb/1elr.pdb.gz 1elrA:# T0368 read from 1elrA/merged-good-all-a2m # 1elrA read from 1elrA/merged-good-all-a2m # adding 1elrA to template set # found chain 1elrA in template set Warning: unaligning (T0368)S158 because last residue in template chain is (1elrA)Q349 T0368 9 :GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1elrA 224 :QALKEKELGNDAYKKKDFDTALKHYDKAKELDPT T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL 1elrA 258 :NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENRED T0368 97 :GKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM 1elrA 296 :YRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE T0368 139 :PGKERMMEVAIDRIAQLGA 1elrA 330 :HRTPDVLKKCQQAEKILKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=405 Number of alignments=73 # 1elrA read from 1elrA/merged-good-all-a2m # found chain 1elrA in template set Warning: unaligning (T0368)S158 because last residue in template chain is (1elrA)Q349 T0368 9 :GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1elrA 224 :QALKEKELGNDAYKKKDFDTALKHYDKAKELDPT T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN 1elrA 258 :NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDY T0368 98 :KLWISAVYSRALALDGLGRGAEAMPEFKKVVEM 1elrA 297 :RQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE T0368 139 :PGKERMMEVAIDRIAQLGA 1elrA 330 :HRTPDVLKKCQQAEKILKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=409 Number of alignments=74 # 1elrA read from 1elrA/merged-good-all-a2m # found chain 1elrA in template set T0368 9 :GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHT 1elrA 224 :QALKEKELGNDAYKKKDFDTALKHYDKAKELDPT T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE 1elrA 258 :NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENRE T0368 96 :EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM 1elrA 295 :DYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE T0368 149 :IDRIAQLGASNQQKKP 1elrA 330 :HRTPDVLKKCQQAEKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=413 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hxiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0368 read from 1hxiA/merged-good-all-a2m # 1hxiA read from 1hxiA/merged-good-all-a2m # found chain 1hxiA in training set Warning: unaligning (T0368)A157 because last residue in template chain is (1hxiA)L445 T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISHT 1hxiA 353 :MEEGLSMLKLANLAEAALAFEAVCQKEPE T0368 55 :DAFCHAGLAEALAGLRSFDEALHSADKALHY 1hxiA 382 :REEAWRSLGLTQAENEKDGLAIIALNHARML T0368 93 :NQD 1hxiA 413 :DPK T0368 117 :GAEAMPEFKKVVEMIE 1hxiA 416 :DIAVHAALAVSHTNEH T0368 144 :MMEVAIDRIAQLG 1hxiA 432 :NANAALASLRAWL Number of specific fragments extracted= 5 number of extra gaps= 0 total=418 Number of alignments=76 # 1hxiA read from 1hxiA/merged-good-all-a2m # found chain 1hxiA in training set T0368 14 :LSDAQRQLVAGEYDEAAANCRRAMEISH 1hxiA 353 :MEEGLSMLKLANLAEAALAFEAVCQKEP T0368 54 :FDAFCHAGLAEALAGLRSFDEALHSADKALHYFN 1hxiA 381 :EREEAWRSLGLTQAENEKDGLAIIALNHARMLDP T0368 116 :RGAEAMPEFKKVVEMIEE 1hxiA 415 :KDIAVHAALAVSHTNEHN T0368 144 :MMEVAIDRIAQL 1hxiA 433 :ANAALASLRAWL Number of specific fragments extracted= 4 number of extra gaps= 0 total=422 Number of alignments=77 # 1hxiA read from 1hxiA/merged-good-all-a2m # found chain 1hxiA in training set Warning: unaligning (T0368)K163 because last residue in template chain is (1hxiA)L445 T0368 13 :ALSDAQRQLVAGEYDEAAANCRRAMEISHT 1hxiA 352 :PMEEGLSMLKLANLAEAALAFEAVCQKEPE T0368 55 :DAFCHAGLAEALAGLRSFDEALHS 1hxiA 382 :REEAWRSLGLTQAENEKDGLAIIA T0368 124 :FKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQK 1hxiA 406 :LNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWL Number of specific fragments extracted= 3 number of extra gaps= 0 total=425 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ld8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ld8A expands to /projects/compbio/data/pdb/1ld8.pdb.gz 1ld8A:# T0368 read from 1ld8A/merged-good-all-a2m # 1ld8A read from 1ld8A/merged-good-all-a2m # adding 1ld8A to template set # found chain 1ld8A in template set Warning: unaligning (T0368)L155 because last residue in template chain is (1ld8A)H367 T0368 5 :KEVVGAYLALSDA 1ld8A 234 :NSVWNQRYFVISN T0368 22 :VAGEYDEAAANCRRAMEISHT 1ld8A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1ld8A 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKAL 1ld8A 289 :LSKYPNLLNQLLDLQ T0368 84 :HY 1ld8A 309 :PY T0368 100 :WISAVY 1ld8A 311 :LIAFLV T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEERK 1ld8A 319 :YEDMLENQCDNKEDILNKALELCEILAKEK T0368 137 :ETPGKERMMEVAIDRIAQ 1ld8A 349 :DTIRKEYWRYIGRSLQSK Number of specific fragments extracted= 8 number of extra gaps= 0 total=433 Number of alignments=79 # 1ld8A read from 1ld8A/merged-good-all-a2m # found chain 1ld8A in template set Warning: unaligning (T0368)L155 because last residue in template chain is (1ld8A)H367 T0368 6 :EVVGAYLALSDAQRQ 1ld8A 235 :SVWNQRYFVISNTTG T0368 22 :VAGEYDEAAANCRRAMEISHT 1ld8A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1ld8A 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKAL 1ld8A 289 :LSKYPNLLNQLLDLQ T0368 94 :QDEGKLWISAVY 1ld8A 304 :PSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEER 1ld8A 319 :YEDMLENQCDNKEDILNKALELCEILAKE T0368 136 :GETPGKERMMEVAIDRIAQ 1ld8A 348 :KDTIRKEYWRYIGRSLQSK Number of specific fragments extracted= 7 number of extra gaps= 0 total=440 Number of alignments=80 # 1ld8A read from 1ld8A/merged-good-all-a2m # found chain 1ld8A in template set T0368 8 :VGAYLALSDAQRQLVAG 1ld8A 94 :DKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1ld8A 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1ld8A 130 :NYTVWHFRRVLLKSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1ld8A 147 :DLHEEMNYITAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1ld8A 168 :VWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=445 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gw1A/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/T0368/2gw1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/2gw1A/merged-good-all-a2m.gz for input Trying 2gw1A/merged-good-all-a2m Error: Couldn't open file 2gw1A/merged-good-all-a2m or 2gw1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kt0A/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/T0368/1kt0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0368/1kt0A/merged-good-all-a2m.gz for input Trying 1kt0A/merged-good-all-a2m Error: Couldn't open file 1kt0A/merged-good-all-a2m or 1kt0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tn6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0368 read from 1tn6A/merged-good-all-a2m # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set Warning: unaligning (T0368)A157 because last residue in template chain is (1tn6A)T369 T0368 5 :KEVVGAYLALSDAQR 1tn6A 234 :NSVWNQRYFVISNTT T0368 22 :VAGEYDEAAANCRRAMEISHT 1tn6A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALAG 1tn6A 273 :NESAWNYLKGILQD T0368 69 :LRSFDEALHSADKA 1tn6A 289 :LSKYPNLLNQLLDL T0368 93 :NQDEGKLWISAVY 1tn6A 303 :QPSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEERK 1tn6A 319 :YEDMLENQCDNKEDILNKALELCEILAKEK T0368 137 :ETPGKERMMEVAIDRIAQLG 1tn6A 349 :DTIRKEYWRYIGRSLQSKHS Number of specific fragments extracted= 7 number of extra gaps= 0 total=452 Number of alignments=82 # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set Warning: unaligning (T0368)A157 because last residue in template chain is (1tn6A)T369 T0368 6 :EVVGAYLALSDAQRQL 1tn6A 235 :SVWNQRYFVISNTTGY T0368 22 :VAGEYDEAAANCRRAMEISHT 1tn6A 252 :DRAVLEREVQYTLEMIKLVPH T0368 55 :DAFCHAGLAEALA 1tn6A 273 :NESAWNYLKGILQ T0368 68 :GLRSFDEALHSADKA 1tn6A 288 :GLSKYPNLLNQLLDL T0368 86 :F 1tn6A 303 :Q T0368 94 :QDEGKLWISAVY 1tn6A 304 :PSHSSPYLIAFL T0368 106 :SRALALDGLGRGAEAMPEFKKVVEMIEER 1tn6A 319 :YEDMLENQCDNKEDILNKALELCEILAKE T0368 136 :GETPGKERMMEVAIDRIAQLG 1tn6A 348 :KDTIRKEYWRYIGRSLQSKHS Number of specific fragments extracted= 8 number of extra gaps= 0 total=460 Number of alignments=83 # 1tn6A read from 1tn6A/merged-good-all-a2m # found chain 1tn6A in training set T0368 8 :VGAYLALSDAQRQLVAG 1tn6A 94 :DKFRDVYDYFRAVLQRD T0368 25 :EYDEAAANCRRAMEISHT 1tn6A 112 :RSERAFKLTRDAIELNAA T0368 55 :DAFCHAGLAEALAGLR 1tn6A 130 :NYTVWHFRRVLLKSLQ T0368 71 :SFDEALHSADKALHYFNRRGE 1tn6A 147 :DLHEEMNYITAIIEEQPKNYQ T0368 103 :AVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAIDRIAQLGASNQQKKPGYK 1tn6A 168 :VWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=465 Number of alignments=84 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 84 Done printing distance constraints # command: