# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0326 numbered 1 through 304 Created new target T0326 from T0326.a2m # command:CPU_time= 6.366 sec, elapsed time= 6.406 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ghrA/T0326-2ghrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ghrA expands to /projects/compbio/data/pdb/2ghr.pdb.gz 2ghrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 2ghrA/T0326-2ghrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ghrA read from 2ghrA/T0326-2ghrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ghrA to template set # found chain 2ghrA in template set Warning: unaligning (T0326)K17 because first residue in template chain is (2ghrA)E17 Warning: unaligning (T0326)T74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ghrA)S87 Warning: unaligning (T0326)K87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ghrA)S87 Warning: unaligning (T0326)T296 because last residue in template chain is (2ghrA)T297 T0326 18 :EGIFVMTEKRAIHQDIRPLEILILNLMPDKIKTEIQLLRLLGNTPLQVNVTLLYTE 2ghrA 18 :ENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGNTPLQLDVHLLHME # choosing archetypes in rotamer library T0326 88 :FYTTFSAVKDRKFDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKDS 2ghrA 88 :FYKTFRDIENEKFDGLIITGAPVETLSFEEVDYWEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQH T0326 177 :VLFRGHDDFFWAPHSRYTEVKKEDIDKVPELEILAESDEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRNLKVPIPANYFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQK 2ghrA 178 :KLLQGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSCDTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQE Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ghrA/T0326-2ghrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2ghrA/T0326-2ghrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ghrA read from 2ghrA/T0326-2ghrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ghrA in template set Warning: unaligning (T0326)K17 because first residue in template chain is (2ghrA)E17 Warning: unaligning (T0326)V65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ghrA)S87 Warning: unaligning (T0326)K87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ghrA)S87 Warning: unaligning (T0326)T296 because last residue in template chain is (2ghrA)T297 T0326 18 :EGIFVMTEKRAIHQDIRPLEILILNLMPDKIKTEI 2ghrA 18 :ENIFVMTKERAETQDIRALKIAILNLMPTKQETEA T0326 53 :QLLR 2ghrA 59 :GNTP T0326 57 :LLGNTPLQ 2ghrA 66 :DVHLLHME T0326 88 :FYTTFSAVKDRKFDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKDS 2ghrA 88 :FYKTFRDIENEKFDGLIITGAPVETLSFEEVDYWEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQH T0326 177 :VLFRGHDDFFWAPHSRYTEVKKEDIDKVPELEILAESDEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRNLKVPIPANYFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQK 2ghrA 178 :KLLQGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSCDTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQE Number of specific fragments extracted= 5 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ghrA/T0326-2ghrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2ghrA/T0326-2ghrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ghrA read from 2ghrA/T0326-2ghrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ghrA in template set Warning: unaligning (T0326)K17 because first residue in template chain is (2ghrA)E17 Warning: unaligning (T0326)T74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ghrA)S87 Warning: unaligning (T0326)K87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ghrA)S87 Warning: unaligning (T0326)T296 because last residue in template chain is (2ghrA)T297 T0326 18 :EGIFVMTEKRAIHQDIRPLEILILNLMPDKIKTEIQLLRLLGNTPLQVNVTLLYTE 2ghrA 18 :ENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGNTPLQLDVHLLHME T0326 88 :FYTTFSAVKDRKFDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 2ghrA 88 :FYKTFRDIENEKFDGLIITGAPVETLSFEEVDYWEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQ T0326 176 :SVLFRGHDDFFWAPHSRYTEVKKEDIDKVPELEILAESDEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRNLKVPIPANYFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQK 2ghrA 177 :VKLLQGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSCDTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQE Number of specific fragments extracted= 3 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wl8A/T0326-1wl8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wl8A expands to /projects/compbio/data/pdb/1wl8.pdb.gz 1wl8A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: N3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Bad short name: O5 for alphabet: pdb_atoms Bad short name: OD for alphabet: pdb_atoms # T0326 read from 1wl8A/T0326-1wl8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wl8A read from 1wl8A/T0326-1wl8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wl8A to template set # found chain 1wl8A in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1wl8A)M1 Warning: unaligning (T0326)D175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)E113 Warning: unaligning (T0326)V177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)E113 Warning: unaligning (T0326)L178 because of BadResidue code BAD_PEPTIDE at template residue (1wl8A)I114 Warning: unaligning (T0326)E215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)P149 Warning: unaligning (T0326)G217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)P149 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1wl8A 2 :MIVIMDNGGQYVHRIWRTLRYLG T0326 65 :VNVTLLYTE 1wl8A 25 :VETKIIPNT T0326 90 :TTFSAVKDRKFDGFIITGAPV 1wl8A 34 :TPLEEIKAMNPKGIIFSGGPS T0326 115 :FE 1wl8A 55 :LE T0326 128 :MEWSRHN 1wl8A 61 :CEKVLEH T0326 135 :VYSTMFICWAAQAGLYYFYGIPK 1wl8A 72 :NVPILGICLGHQLIAKFFGGKVG T0326 159 :ELPQKLSGVYKHRVAK 1wl8A 95 :RGEKAEYSLVEIEIID T0326 179 :FRGHDDFFWA 1wl8A 115 :FKGLPKRLKV T0326 194 :TEVKKEDIDKVP 1wl8A 125 :WESHMDEVKELP T0326 206 :ELEILAESD 1wl8A 138 :KFKILARSE T0326 218 :VYVVANKSERQIFVTGHPEYDRYTL 1wl8A 150 :IEAMKHEELPIYGVQFHPEVAHTEK T0326 280 :AHLFFSNWLNYC 1wl8A 175 :GEEILRNFAKLC Number of specific fragments extracted= 12 number of extra gaps= 0 total=23 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wl8A/T0326-1wl8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1wl8A/T0326-1wl8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wl8A read from 1wl8A/T0326-1wl8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wl8A in template set Warning: unaligning (T0326)D175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)E113 Warning: unaligning (T0326)V177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)E113 Warning: unaligning (T0326)L178 because of BadResidue code BAD_PEPTIDE at template residue (1wl8A)I114 Warning: unaligning (T0326)E215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)P149 Warning: unaligning (T0326)G217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)P149 T0326 57 :LLGNTPLQVNVTLLYTETHKPKHTPIEHI 1wl8A 2 :MIVIMDNGGQYVHRIWRTLRYLGVETKII T0326 87 :KFYTTFSAVKDRKFDGFIITGAPV 1wl8A 31 :PNTTPLEEIKAMNPKGIIFSGGPS T0326 115 :FEEVDYW 1wl8A 55 :LENTGNC T0326 129 :EWSRHN 1wl8A 62 :EKVLEH T0326 135 :VYSTMFICWAAQAGLYYF 1wl8A 72 :NVPILGICLGHQLIAKFF T0326 154 :GIPKYELPQKLSGVYKHRVAK 1wl8A 90 :GGKVGRGEKAEYSLVEIEIID T0326 179 :FRGHDDFFWA 1wl8A 115 :FKGLPKRLKV T0326 193 :YTEVK 1wl8A 125 :WESHM T0326 199 :EDIDKVPE 1wl8A 130 :DEVKELPP T0326 207 :LEILAESD 1wl8A 139 :FKILARSE T0326 218 :VYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRN 1wl8A 150 :IEAMKHEELPIYGVQFHPEVAHTEKGEEILRNFAKL Number of specific fragments extracted= 11 number of extra gaps= 0 total=34 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wl8A/T0326-1wl8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1wl8A/T0326-1wl8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wl8A read from 1wl8A/T0326-1wl8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wl8A in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1wl8A)M1 Warning: unaligning (T0326)D175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)E113 Warning: unaligning (T0326)V177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)E113 Warning: unaligning (T0326)L178 because of BadResidue code BAD_PEPTIDE at template residue (1wl8A)I114 Warning: unaligning (T0326)E215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wl8A)P149 Warning: unaligning (T0326)G217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wl8A)P149 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1wl8A 2 :MIVIMDNGGQYVHRIWRTLRYLG T0326 65 :VNVTLLYTE 1wl8A 25 :VETKIIPNT T0326 90 :TTFSAVKDRKFDGFIITGAPV 1wl8A 34 :TPLEEIKAMNPKGIIFSGGPS T0326 115 :FEEVDY 1wl8A 55 :LENTGN T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGLYYFYG 1wl8A 61 :CEKVLEHYDEFNVPILGICLGHQLIAKFFGG T0326 156 :PKYELPQKLSGVYKHRVAK 1wl8A 92 :KVGRGEKAEYSLVEIEIID T0326 179 :FRGHDDFFWAPHSRYTEVK 1wl8A 115 :FKGLPKRLKVWESHMDEVK T0326 202 :DKVPELEILAESD 1wl8A 134 :ELPPKFKILARSE T0326 218 :VYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIG 1wl8A 150 :IEAMKHEELPIYGVQFHPEVAHTEKGEEILRNFA Number of specific fragments extracted= 9 number of extra gaps= 0 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpmA/T0326-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gpmA expands to /projects/compbio/data/pdb/1gpm.pdb.gz 1gpmA:# T0326 read from 1gpmA/T0326-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0326-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gpmA to template set # found chain 1gpmA in template set Warning: unaligning (T0326)Q31 because first residue in template chain is (1gpmA)E3 T0326 32 :DIRPLEILILNLMPDKIKTEIQLLRLLG 1gpmA 4 :NIHKHRILILDFGSQYTQLVARRVRELG T0326 65 :VNVTLL 1gpmA 32 :VYCELW T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVELLP 1gpmA 38 :AWDVTEAQIRDFNPSGIILSGGPESTTE T0326 115 :FEEV 1gpmA 72 :PQYV T0326 133 :HNVYSTMFICWAAQAGLYYFYGIPK 1gpmA 77 :EAGVPVFGVCYGMQTMAMQLGGHVE T0326 159 :ELPQKLSGVYKHRVAKDSVLFRGH 1gpmA 102 :ASNEREFGYAQVEVVNDSALVRGI T0326 183 :DD 1gpmA 132 :DG T0326 185 :FFWA 1gpmA 136 :LLDV T0326 194 :TEVKKEDIDKVP 1gpmA 140 :WMSHGDKVTAIP T0326 206 :ELEILAESDEAGVYVVANKSERQIFVTGHPEYDR 1gpmA 153 :DFITVASTESCPFAIMANEEKRFYGVQFHPEVTH T0326 240 :YTLRDEYYRDIGRNLKVPIPA 1gpmA 188 :RQGMRMLERFVRDICQCEALW T0326 275 :TWWSHAHLFFSNWLNY 1gpmA 209 :TPAKIIDDAVARIREQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpmA/T0326-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1gpmA/T0326-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0326-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpmA in template set Warning: unaligning (T0326)E51 because first residue in template chain is (1gpmA)E3 T0326 52 :IQLLRLLGNTPLQVNVTLLYTETHKPKHTPIEHI 1gpmA 4 :NIHKHRILILDFGSQYTQLVARRVRELGVYCELW T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVELLP 1gpmA 38 :AWDVTEAQIRDFNPSGIILSGGPESTTE T0326 115 :FEEV 1gpmA 72 :PQYV T0326 121 :W 1gpmA 76 :F T0326 133 :HNVYSTMFICWAAQAGLYYF 1gpmA 77 :EAGVPVFGVCYGMQTMAMQL T0326 154 :GIPKYELPQKLSGVYKHRVAKDSVLFRGH 1gpmA 97 :GGHVEASNEREFGYAQVEVVNDSALVRGI T0326 183 :DDFFWA 1gpmA 132 :DGKPLL T0326 191 :SRYTEVK 1gpmA 138 :DVWMSHG T0326 199 :EDIDKVPE 1gpmA 145 :DKVTAIPS T0326 207 :LEILAESDEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRNLKVP 1gpmA 154 :FITVASTESCPFAIMANEEKRFYGVQFHPEVTHTRQGMRMLERFVRDICQC T0326 259 :PANYF 1gpmA 205 :EALWT T0326 269 :TKTPILTWWSHAHLFFSNWLNYCIYQ 1gpmA 300 :GENDPEAKRKIIGRVFVEVFDEEALK Number of specific fragments extracted= 12 number of extra gaps= 0 total=67 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpmA/T0326-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1gpmA/T0326-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0326-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpmA in template set T0326 35 :PLEILILNLMPDKI 1gpmA 7 :KHRILILDFGSQYT T0326 52 :IQLLRLLGNTPLQVNVTLLYT 1gpmA 21 :QLVARRVRELGVYCELWAWDV T0326 91 :TFSAVKDRKFDGFIITGAPVELLPFEEVDYWEE 1gpmA 42 :TEAQIRDFNPSGIILSGGPESTTEENSPRAPQY T0326 131 :SRHNVYSTMFICWAAQAGLYYFYG 1gpmA 75 :VFEAGVPVFGVCYGMQTMAMQLGG T0326 156 :PKYELPQKLSGVYKHRVAKDSVLFRGHDDFF 1gpmA 99 :HVEASNEREFGYAQVEVVNDSALVRGIEDAL T0326 187 :WAPHSRYTEVK 1gpmA 138 :DVWMSHGDKVT T0326 204 :VPELEILAESDEAGVYVVANKSERQIFVTGHPEYDRY 1gpmA 151 :PSDFITVASTESCPFAIMANEEKRFYGVQFHPEVTHT T0326 241 :TLRDEYYRDIGRNLKVPIP 1gpmA 189 :QGMRMLERFVRDICQCEAL Number of specific fragments extracted= 8 number of extra gaps= 0 total=75 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o1yA/T0326-1o1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o1yA expands to /projects/compbio/data/pdb/1o1y.pdb.gz 1o1yA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 533, because occupancy 0.35 <= existing 0.650 in 1o1yA Skipped atom 535, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 537, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 539, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 665, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 667, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 669, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 671, because occupancy 0.350 <= existing 0.650 in 1o1yA Bad short name: OD3 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1031, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1033, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1035, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1037, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1093, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1095, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1097, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1099, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1101, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1155, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1157, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1159, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1161, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1418, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1420, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1422, because occupancy 0.350 <= existing 0.650 in 1o1yA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1879, because occupancy 0.350 <= existing 0.650 in 1o1yA Skipped atom 1881, because occupancy 0.350 <= existing 0.650 in 1o1yA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 1o1yA/T0326-1o1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o1yA read from 1o1yA/T0326-1o1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o1yA to template set # found chain 1o1yA in template set Warning: unaligning (T0326)I33 because first residue in template chain is (1o1yA)H-2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o1yA)L89 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o1yA)L89 T0326 34 :RPLEILILNLMPDK 1o1yA -1 :HHVRVLAIRHVEIE T0326 48 :IKTEIQLLRLLG 1o1yA 14 :LGMMEDIFREKN T0326 65 :VNVTLLYTE 1o1yA 26 :WSFDYLDTP T0326 74 :THKPKH 1o1yA 36 :GEKLER T0326 96 :KDRKFDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMF 1o1yA 42 :PLEEYSLVVLLGGYMGAYEEEKYPFLKYEFQLIEEILKKEIPFLG T0326 144 :AAQAGLYYFYGIPKYELPQKLSGVYKHRVAKDSVLFRGHDDFFWA 1o1yA 90 :GSQMLAKVLGASVYRGKNGEEIGWYFVEKVSDNKFFREFPDRLRV T0326 194 :TEVKKEDIDKVPELEILAESDEAGVYVVANKS 1o1yA 135 :FQWHGDTFDLPRRATRVFTSEKYENQGFVYGK T0326 228 :QIFVTGHPEYDRYTLRDEYY 1o1yA 167 :AVGLQFHIEVGARTMKRWIE T0326 248 :R 1o1yA 189 :K T0326 249 :DIGR 1o1yA 191 :ELEK T0326 269 :TKTPILTWWSHAHL 1o1yA 195 :KKIDPRLLLETAER T0326 283 :FFSNWLNYCI 1o1yA 216 :LLRSLLERMV Number of specific fragments extracted= 12 number of extra gaps= 0 total=87 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o1yA/T0326-1o1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1o1yA/T0326-1o1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o1yA read from 1o1yA/T0326-1o1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o1yA in template set Warning: unaligning (T0326)I52 because first residue in template chain is (1o1yA)H-2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o1yA)L89 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o1yA)L89 T0326 53 :QLLRLLGNTPLQVNVTLLYTETHKPKHTPIEHI 1o1yA -1 :HHVRVLAIRHVEIEDLGMMEDIFREKNWSFDYL T0326 86 :LKFYTTFSA 1o1yA 37 :EKLERPLEE T0326 100 :FDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMF 1o1yA 46 :YSLVVLLGGYMGAYEEEKYPFLKYEFQLIEEILKKEIPFLG T0326 144 :AAQAGLYYF 1o1yA 90 :GSQMLAKVL T0326 154 :GIPKYELPQKL 1o1yA 99 :GASVYRGKNGE T0326 165 :SGVYKHRVAKDSVLFRGHDDFFWA 1o1yA 111 :IGWYFVEKVSDNKFFREFPDRLRV T0326 193 :YTEVK 1o1yA 135 :FQWHG T0326 200 :DIDKVPE 1o1yA 140 :DTFDLPR T0326 207 :LEILAESDEAGVYVVANKS 1o1yA 148 :ATRVFTSEKYENQGFVYGK T0326 228 :QIFVTGHPEYDRYTLRDEYYRD 1o1yA 167 :AVGLQFHIEVGARTMKRWIEAY T0326 250 :IGRN 1o1yA 191 :ELEK T0326 269 :TKTPILTWWSHAHLFFSNWLNYCIY 1o1yA 195 :KKIDPRLLLETAEREEKVLKGLLRS Number of specific fragments extracted= 12 number of extra gaps= 0 total=99 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o1yA/T0326-1o1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1o1yA/T0326-1o1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o1yA read from 1o1yA/T0326-1o1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o1yA in template set Warning: unaligning (T0326)I33 because first residue in template chain is (1o1yA)H-2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o1yA)L89 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o1yA)L89 T0326 34 :RPLEILILNLMPDKI 1o1yA -1 :HHVRVLAIRHVEIED T0326 53 :QLLRLLGNT 1o1yA 16 :MMEDIFREK T0326 64 :QVNVTLLYTETHKPKHTPIE 1o1yA 25 :NWSFDYLDTPKGEKLERPLE T0326 99 :KFDGFIITGAPVELLPFEEVDYWEELTEIMEWSRHNVYSTMF 1o1yA 45 :EYSLVVLLGGYMGAYEEEKYPFLKYEFQLIEEILKKEIPFLG T0326 144 :AAQAGLY 1o1yA 90 :GSQMLAK T0326 152 :FYGIPKYELP 1o1yA 97 :VLGASVYRGK T0326 162 :QKLSGVYKHRVAKDSVLFRGHDDFFWAPHSRYTEVK 1o1yA 108 :GEEIGWYFVEKVSDNKFFREFPDRLRVFQWHGDTFD T0326 203 :KVPELEILAESDEAGVYVVANKS 1o1yA 144 :LPRRATRVFTSEKYENQGFVYGK T0326 228 :QIFVTGHPEYDRYTLRDEYYR 1o1yA 167 :AVGLQFHIEVGARTMKRWIEA Number of specific fragments extracted= 9 number of extra gaps= 0 total=108 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a9xB/T0326-1a9xB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a9xB expands to /projects/compbio/data/pdb/1a9x.pdb.gz 1a9xB:Skipped atom 9502, because occupancy 0.500 <= existing 0.500 in 1a9xB Skipped atom 9504, because occupancy 0.500 <= existing 0.500 in 1a9xB # T0326 read from 1a9xB/T0326-1a9xB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xB read from 1a9xB/T0326-1a9xB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a9xB to template set # found chain 1a9xB in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a9xB)L1770 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a9xB)L1770 T0326 31 :QDIRPLEILILNLM 1a9xB 1687 :EDELPFHVVAYDFG T0326 51 :EIQLLRLL 1a9xB 1702 :KRNILRML T0326 59 :G 1a9xB 1713 :G T0326 65 :VNVTLLYTE 1a9xB 1714 :CRLTIVPAQ T0326 90 :TTFSAVKDRKFDGFIITGAPVELLP 1a9xB 1723 :TSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMF 1a9xB 1748 :CDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1a9xB 1771 :GHQLLALASGAKTVKMKFGHHGGNHPVKDVEK T0326 183 :DDFFWAPHSRYTEVKKE 1a9xB 1803 :NVVMITAQNHGFAVDEA T0326 203 :KVP 1a9xB 1820 :TLP T0326 206 :ELEILAES 1a9xB 1824 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDR 1a9xB 1833 :FDGTLQGIHRTDKPAFSFQGNPEASP T0326 258 :IPAN 1a9xB 1859 :GPHD T0326 280 :AHLFFSNWLNYCI 1a9xB 1863 :AAPLFDHFIELIE Number of specific fragments extracted= 13 number of extra gaps= 0 total=121 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a9xB/T0326-1a9xB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1a9xB/T0326-1a9xB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xB read from 1a9xB/T0326-1a9xB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a9xB in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a9xB)L1770 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a9xB)L1770 T0326 10 :PAVKVLAKEGIFV 1a9xB 1617 :KLTRLLREKGAQN T0326 23 :MTEKRAIHQ 1a9xB 1638 :PDAALALEK T0326 32 :DIRPL 1a9xB 1652 :GLNGM T0326 37 :EILILNLMPD 1a9xB 1668 :YSWTQGSWTL T0326 47 :K 1a9xB 1679 :G T0326 48 :IKTEIQLLR 1a9xB 1683 :QAKKEDELP T0326 57 :LLGNTPLQ 1a9xB 1693 :HVVAYDFG T0326 67 :VTLLYTETHKPKHTPIEHI 1a9xB 1701 :AKRNILRMLVDRGCRLTIV T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVEL 1a9xB 1720 :PAQTSAEDVLKMNPDGIFLSNGPGDP T0326 116 :EE 1a9xB 1746 :AP T0326 121 :WEELTEIMEWSRHNVYSTMF 1a9xB 1748 :CDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYYF 1a9xB 1771 :GHQLLALAS T0326 154 :GIPKYELPQKL 1a9xB 1780 :GAKTVKMKFGH T0326 165 :SGVYKHRVAK 1a9xB 1792 :GGNHPVKDVE T0326 184 :DFFWAPHSRYTEVK 1a9xB 1802 :KNVVMITAQNHGFA T0326 199 :EDIDKVPE 1a9xB 1816 :VDEATLPA T0326 207 :LEILAES 1a9xB 1825 :LRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1a9xB 1833 :FDGTLQGIHRTDKPAFSFQGNPEASPGPHD T0326 282 :LFFSNWLNYCIY 1a9xB 1865 :PLFDHFIELIEQ Number of specific fragments extracted= 19 number of extra gaps= 0 total=140 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a9xB/T0326-1a9xB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1a9xB/T0326-1a9xB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xB read from 1a9xB/T0326-1a9xB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a9xB in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a9xB)L1770 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a9xB)L1770 T0326 31 :QDIRPLEILILNLMP 1a9xB 1687 :EDELPFHVVAYDFGA T0326 52 :IQLLRLL 1a9xB 1703 :RNILRML T0326 63 :LQVNVTLLYTET 1a9xB 1712 :RGCRLTIVPAQT T0326 91 :TFSAVKDRKFDGFIITGAPVEL 1a9xB 1724 :SAEDVLKMNPDGIFLSNGPGDP T0326 119 :DYWEELTEIMEWSRHNVYSTMF 1a9xB 1746 :APCDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLY 1a9xB 1771 :GHQLLAL T0326 152 :FYGIPKYELPQKLSGV 1a9xB 1778 :ASGAKTVKMKFGHHGG T0326 168 :YKHRVAKDS 1a9xB 1795 :HPVKDVEKN T0326 185 :FFWAPHSRYTEVK 1a9xB 1810 :QNHGFAVDEATLP T0326 205 :PELEILAESD 1a9xB 1823 :ANLRVTHKSL T0326 215 :EAGVYVVANKSERQIFVTGHPEYDR 1a9xB 1834 :DGTLQGIHRTDKPAFSFQGNPEASP T0326 240 :YTLRDEYYRDI 1a9xB 1864 :APLFDHFIELI Number of specific fragments extracted= 12 number of extra gaps= 0 total=152 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c30B/T0326-1c30B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c30B expands to /projects/compbio/data/pdb/1c30.pdb.gz 1c30B:# T0326 read from 1c30B/T0326-1c30B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c30B read from 1c30B/T0326-1c30B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c30B to template set # found chain 1c30B in template set T0326 31 :QDIRPLEILILNLM 1c30B 187 :EDELPFHVVAYDFG T0326 51 :EIQLLRLL 1c30B 202 :KRNILRML T0326 59 :G 1c30B 213 :G T0326 65 :VNVTLLYTE 1c30B 214 :CRLTIVPAQ T0326 90 :TTFSAVKDRKFDGFIITGAPVELLP 1c30B 223 :TSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1c30B 248 :CDYAITAIQKFLETDIPVFGISLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEK T0326 183 :DDFFWAPHSRYTEVKKE 1c30B 303 :NVVMITAQNHGFAVDEA T0326 203 :KVP 1c30B 320 :TLP T0326 206 :ELEILAES 1c30B 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPE 1c30B 333 :FDGTLQGIHRTDKPAFSFQGHPE T0326 237 :YDRYTLRDEYYRDIG 1c30B 365 :PLFDHFIELIEQYRK Number of specific fragments extracted= 11 number of extra gaps= 0 total=163 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c30B/T0326-1c30B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1c30B/T0326-1c30B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c30B read from 1c30B/T0326-1c30B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c30B in template set T0326 10 :PAVKVLAKEGIFV 1c30B 117 :KLTRLLREKGAQN T0326 23 :MTEKRAIHQ 1c30B 138 :PDAALALEK T0326 32 :DIRPL 1c30B 152 :GLNGM T0326 37 :EILILNLM 1c30B 168 :YSWTQGSW T0326 45 :PDK 1c30B 177 :LTG T0326 48 :IKTEIQLLR 1c30B 183 :EAKKEDELP T0326 57 :LLGNTPLQ 1c30B 193 :HVVAYDFG T0326 67 :VTLLYTETHKPKHTPIEHI 1c30B 201 :AKRNILRMLVDRGCRLTIV T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVEL 1c30B 220 :PAQTSAEDVLKMNPDGIFLSNGPGDP T0326 116 :E 1c30B 246 :A T0326 120 :YWEELTEIMEWSRHNVYSTMFICWAAQAGLYYF 1c30B 247 :PCDYAITAIQKFLETDIPVFGISLGHQLLALAS T0326 154 :GIPKYELPQKL 1c30B 280 :GAKTVKMKFGH T0326 165 :SGVYKHRVAKDS 1c30B 292 :GGNHPVKDVEKN T0326 186 :FWAPHSRYTEVK 1c30B 304 :VVMITAQNHGFA T0326 199 :EDIDKVPE 1c30B 316 :VDEATLPA T0326 207 :LEILAES 1c30B 325 :LRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1c30B 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD T0326 282 :LFFSNWLNYCIY 1c30B 365 :PLFDHFIELIEQ Number of specific fragments extracted= 18 number of extra gaps= 0 total=181 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c30B/T0326-1c30B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1c30B/T0326-1c30B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c30B read from 1c30B/T0326-1c30B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c30B in template set T0326 31 :QDIRPLEILILNLMP 1c30B 187 :EDELPFHVVAYDFGA T0326 52 :IQLLRLL 1c30B 203 :RNILRML T0326 63 :LQVNVTLLYTET 1c30B 212 :RGCRLTIVPAQT T0326 91 :TFSAVKDRKFDGFIITGAPVEL 1c30B 224 :SAEDVLKMNPDGIFLSNGPGDP T0326 119 :DYWEELTEIMEWSRHNVYSTMFICWAAQAGLY 1c30B 246 :APCDYAITAIQKFLETDIPVFGISLGHQLLAL T0326 152 :FYGIPKYELPQKLSGV 1c30B 278 :ASGAKTVKMKFGHHGG T0326 168 :YKHRVAKDS 1c30B 295 :HPVKDVEKN T0326 186 :FWAPHSRYTEVK 1c30B 311 :NHGFAVDEATLP T0326 205 :PELEILAESD 1c30B 323 :ANLRVTHKSL T0326 215 :EAGVYVVANKSERQIFVTGHPEYDR 1c30B 334 :DGTLQGIHRTDKPAFSFQGHPEASP T0326 240 :YTLRDEYYRDI 1c30B 364 :APLFDHFIELI Number of specific fragments extracted= 11 number of extra gaps= 0 total=192 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1qB/T0326-1i1qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i1qB expands to /projects/compbio/data/pdb/1i1q.pdb.gz 1i1qB:# T0326 read from 1i1qB/T0326-1i1qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1qB read from 1i1qB/T0326-1i1qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i1qB to template set # found chain 1i1qB in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1i1qB)A1 Warning: unaligning (T0326)Y158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)I103 Warning: unaligning (T0326)Q162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)I103 Warning: unaligning (T0326)K198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)S137 Warning: unaligning (T0326)D202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)S137 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1i1qB 2 :DILLLDNIDSFTWNLADQLRTNG T0326 65 :VNVTLLYTE 1i1qB 25 :HNVVIYRNH T0326 80 :TPIEHIL 1i1qB 34 :IPAQTLI T0326 93 :SAVKDRKFDGFIITGAPVE 1i1qB 41 :DRLATMKNPVLMLSPGPGV T0326 115 :FEEVD 1i1qB 60 :PSEAG T0326 123 :ELTEIMEWSRHN 1i1qB 65 :CMPELLTRLRGK T0326 136 :YSTMFICWAAQAGLYYFYGIPK 1i1qB 77 :LPIIGICLGHQAIVEAYGGYVG T0326 163 :KLSGVYKHRVAK 1i1qB 104 :LHGKATSIEHDG T0326 176 :SVLFRGHDDFFWA 1i1qB 116 :QAMFAGLANPLPV T0326 194 :TEVK 1i1qB 129 :ARYH T0326 203 :KVP 1i1qB 138 :NVP T0326 206 :ELEILAESDE 1i1qB 142 :GLTINAHFNG T0326 217 :GVYVVANKSERQIFVTGHPEYDR 1i1qB 152 :MVMAVRHDADRVCGFQFHPESIL T0326 278 :SHAHLFFSNWLNYC 1i1qB 176 :TQGARLLEQTLAWA Number of specific fragments extracted= 14 number of extra gaps= 0 total=206 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1qB/T0326-1i1qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1i1qB/T0326-1i1qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1qB read from 1i1qB/T0326-1i1qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1qB in template set Warning: unaligning (T0326)E159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)I103 Warning: unaligning (T0326)K163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)I103 Warning: unaligning (T0326)E195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)S137 Warning: unaligning (T0326)D202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)S137 T0326 57 :LLGNTPLQVNVTLLYTETHKPKHTPIEHI 1i1qB 2 :DILLLDNIDSFTWNLADQLRTNGHNVVIY T0326 87 :KFYTTFSAVKDR 1i1qB 31 :RNHIPAQTLIDR T0326 99 :KFDGFIITGAPVE 1i1qB 47 :KNPVLMLSPGPGV T0326 115 :FEEVDYW 1i1qB 60 :PSEAGCM T0326 125 :TEIMEWSR 1i1qB 67 :PELLTRLR T0326 134 :NVYSTMFICWAAQAGLYYF 1i1qB 75 :GKLPIIGICLGHQAIVEAY T0326 154 :GIPKY 1i1qB 94 :GGYVG T0326 164 :LSGV 1i1qB 104 :LHGK T0326 168 :YKHRV 1i1qB 109 :TSIEH T0326 174 :KDSVLFRGHDDFFWA 1i1qB 114 :DGQAMFAGLANPLPV T0326 191 :SRYT 1i1qB 129 :ARYH T0326 203 :KVPE 1i1qB 138 :NVPA T0326 207 :LEILAESDE 1i1qB 143 :LTINAHFNG T0326 217 :GVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIG 1i1qB 152 :MVMAVRHDADRVCGFQFHPESILTTQGARLLEQTL Number of specific fragments extracted= 14 number of extra gaps= 0 total=220 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1qB/T0326-1i1qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1i1qB/T0326-1i1qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1qB read from 1i1qB/T0326-1i1qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1qB in template set Warning: unaligning (T0326)E159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)I103 Warning: unaligning (T0326)K163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)I103 Warning: unaligning (T0326)S191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1qB)S137 Warning: unaligning (T0326)T194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1qB)S137 T0326 37 :EILILNLMPDK 1i1qB 2 :DILLLDNIDSF T0326 51 :EIQLLRLLGNTPLQVNVTL 1i1qB 13 :TWNLADQLRTNGHNVVIYR T0326 78 :KHTPIEHILK 1i1qB 32 :NHIPAQTLID T0326 94 :AVKDRKFDGFIITGAPV 1i1qB 42 :RLATMKNPVLMLSPGPG T0326 114 :PFEEVDY 1i1qB 59 :VPSEAGC T0326 124 :LTEIMEWSRH 1i1qB 66 :MPELLTRLRG T0326 135 :VYSTMFICWAAQAGLY 1i1qB 76 :KLPIIGICLGHQAIVE T0326 152 :FYGIPKY 1i1qB 92 :AYGGYVG T0326 164 :LSGVYKHRVAKDSVLFRGHDDFFWA 1i1qB 104 :LHGKATSIEHDGQAMFAGLANPLPV T0326 189 :PH 1i1qB 131 :YH T0326 195 :EVK 1i1qB 138 :NVP T0326 205 :PELEILAESDE 1i1qB 141 :AGLTINAHFNG T0326 217 :GVYVVANKSERQIFVTGHPEYDRYTLR 1i1qB 152 :MVMAVRHDADRVCGFQFHPESILTTQG T0326 281 :HLFFSNW 1i1qB 179 :ARLLEQT Number of specific fragments extracted= 14 number of extra gaps= 0 total=234 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i7qB/T0326-1i7qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i7qB expands to /projects/compbio/data/pdb/1i7q.pdb.gz 1i7qB:# T0326 read from 1i7qB/T0326-1i7qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i7qB read from 1i7qB/T0326-1i7qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i7qB to template set # found chain 1i7qB in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1i7qB)A2 Warning: unaligning (T0326)Y71 because of BadResidue code BAD_PEPTIDE in next template residue (1i7qB)N33 Warning: unaligning (T0326)T72 because of BadResidue code BAD_PEPTIDE at template residue (1i7qB)N33 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1i7qB 3 :DILLLDNVDSFTYNLVDQLRASG T0326 65 :VNVTLL 1i7qB 26 :HQVVIY T0326 73 :E 1i7qB 34 :Q T0326 90 :TTFSAV 1i7qB 35 :IGAEVI T0326 96 :KDRKFDGFIITGAPVE 1i7qB 45 :QHMEQPVLMLSPGPGT T0326 115 :FEEVD 1i7qB 62 :PSEAG T0326 123 :ELTEIMEWSRHN 1i7qB 67 :CMPELLQRLRGQ T0326 136 :YSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVA 1i7qB 79 :LPIIGICLGHQAIVEAYGGQVGQAGEILHGKASAIAHD T0326 175 :DSVLFRGHDDFFWA 1i7qB 117 :GEGMFAGMANPLPV T0326 191 :SRY 1i7qB 131 :ARY T0326 202 :DKVP 1i7qB 139 :SNIP T0326 206 :ELEILAESDE 1i7qB 145 :DLTVNARFGE T0326 217 :GVYVVANKSERQIFVTGHPEYDR 1i7qB 155 :MVMAVRDDRRRVCGFQFHPESIL T0326 277 :WSHAHLFFSNWLNYC 1i7qB 178 :TTHGARLLEQTLAWA Number of specific fragments extracted= 14 number of extra gaps= 1 total=248 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i7qB/T0326-1i7qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1i7qB/T0326-1i7qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i7qB read from 1i7qB/T0326-1i7qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i7qB in template set Warning: unaligning (T0326)R56 because first residue in template chain is (1i7qB)A2 Warning: unaligning (T0326)K87 because of BadResidue code BAD_PEPTIDE in next template residue (1i7qB)N33 Warning: unaligning (T0326)F88 because of BadResidue code BAD_PEPTIDE at template residue (1i7qB)N33 T0326 57 :LLGNTPLQVNVTLLYTETHKPKHTPIEHI 1i7qB 3 :DILLLDNVDSFTYNLVDQLRASGHQVVIY T0326 89 :YTTFSAVKDR 1i7qB 34 :QIGAEVIIER T0326 99 :KFDGFIITGAPVE 1i7qB 49 :EQPVLMLSPGPGT T0326 115 :FEEVDYW 1i7qB 62 :PSEAGCM T0326 125 :TEIMEWSR 1i7qB 69 :PELLQRLR T0326 134 :NVYSTMFICWAAQAGLYYFYG 1i7qB 77 :GQLPIIGICLGHQAIVEAYGG T0326 156 :PKYELPQKLSGV 1i7qB 98 :QVGQAGEILHGK T0326 168 :YKHRV 1i7qB 111 :SAIAH T0326 174 :KDSVLFRGHDDFFWA 1i7qB 116 :DGEGMFAGMANPLPV T0326 191 :SRYTEVK 1i7qB 131 :ARYHSLV T0326 201 :IDKVPE 1i7qB 138 :GSNIPA T0326 207 :LEILAESDEA 1i7qB 146 :LTVNARFGEM T0326 218 :VYVVANKSERQIFVTGHPEYDRYTLRDEYYRD 1i7qB 156 :VMAVRDDRRRVCGFQFHPESILTTHGARLLEQ T0326 287 :WLNY 1i7qB 188 :TLAW Number of specific fragments extracted= 14 number of extra gaps= 1 total=262 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i7qB/T0326-1i7qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1i7qB/T0326-1i7qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i7qB read from 1i7qB/T0326-1i7qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i7qB in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1i7qB)A2 Warning: unaligning (T0326)L69 because of BadResidue code BAD_PEPTIDE in next template residue (1i7qB)N33 Warning: unaligning (T0326)K78 because of BadResidue code BAD_PEPTIDE at template residue (1i7qB)N33 T0326 37 :EILILNLMPDK 1i7qB 3 :DILLLDNVDSF T0326 51 :EIQLLRLLGNTPLQVNVT 1i7qB 14 :TYNLVDQLRASGHQVVIY T0326 79 :HTPIEHILK 1i7qB 34 :QIGAEVIIE T0326 94 :AVKDRKFDGFIITGAPV 1i7qB 43 :RLQHMEQPVLMLSPGPG T0326 114 :PFEEVDY 1i7qB 61 :TPSEAGC T0326 124 :LTEIMEWSRH 1i7qB 68 :MPELLQRLRG T0326 135 :VYSTMFICWAAQAGLY 1i7qB 78 :QLPIIGICLGHQAIVE T0326 152 :FYGIPKYELPQKLSGVYKHRVAKDSVLFRGHDDFFWAPHSR 1i7qB 94 :AYGGQVGQAGEILHGKASAIAHDGEGMFAGMANPLPVARYH T0326 193 :YTEVK 1i7qB 138 :GSNIP T0326 205 :PELEILAESDEA 1i7qB 143 :ADLTVNARFGEM T0326 218 :VYVVANKSERQIFVTGHPEYDRY 1i7qB 156 :VMAVRDDRRRVCGFQFHPESILT T0326 278 :SHAHLFFSNWLNY 1i7qB 179 :THGARLLEQTLAW Number of specific fragments extracted= 12 number of extra gaps= 1 total=274 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0326-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0326 read from 1vcoA/T0326-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0326-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vcoA to template set # found chain 1vcoA in template set Warning: unaligning (T0326)D46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0326)H75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0326)T90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 Warning: unaligning (T0326)L160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)G438 T0326 11 :AVKVLAKEG 1vcoA 290 :AVRVLKHPE T0326 34 :RPLEILILNLM 1vcoA 299 :RTVKIAIAGKY T0326 47 :K 1vcoA 315 :A T0326 48 :IKTEIQLLRLLG 1vcoA 319 :LLEALRHAGIKN T0326 62 :PLQVNVTLLYTET 1vcoA 331 :RARVEVKWVDAES T0326 91 :TFSAV 1vcoA 348 :DLEEA T0326 97 :DRKFDGFIITGAP 1vcoA 353 :FRDVSGILVPGGF T0326 117 :EVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1vcoA 366 :GVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIE T0326 153 :YGIP 1vcoA 409 :KGAN T0326 161 :PQKLSGVYKHRVAKDSVLFRGH 1vcoA 439 :GTMRLGDWPMRIKPGTLLHRLY T0326 183 :DDFFWAPHSRYTEVK 1vcoA 462 :KEEVLERHRHRYEVN T0326 198 :KEDIDKV 1vcoA 480 :VDGLERA T0326 206 :ELEILAES 1vcoA 487 :GLVVSATT T0326 214 :DEAG 1vcoA 498 :RGRG T0326 218 :VYVVANKSER 1vcoA 505 :VEAIELKDHP T0326 228 :QIFVTGHPEYDR 1vcoA 516 :FLGLQSHPEFKS T0326 267 :DPTKTP 1vcoA 528 :RPMRPS T0326 282 :LFFSNWLNYCI 1vcoA 534 :PPFVGFVEAAL Number of specific fragments extracted= 18 number of extra gaps= 0 total=292 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0326-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1vcoA/T0326-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0326-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set Warning: unaligning (T0326)L58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)D314 Warning: unaligning (T0326)P62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0326)T90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 Warning: unaligning (T0326)K157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)G438 Warning: unaligning (T0326)P161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)G438 T0326 13 :KVLAK 1vcoA 288 :QEAVR T0326 28 :AIHQDIRPLEILILNLM 1vcoA 293 :VLKHPERTVKIAIAGKY T0326 63 :LQVNVTLLYTETHKPKHTPIEHILKF 1vcoA 315 :AYLSLLEALRHAGIKNRARVEVKWVD T0326 91 :TFSAV 1vcoA 348 :DLEEA T0326 97 :DRKFDGFIITGAP 1vcoA 353 :FRDVSGILVPGGF T0326 111 :EL 1vcoA 366 :GV T0326 119 :DYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYF 1vcoA 368 :RGIEGKVRAAQYARERKIPYLGICLGLQIAVIEF T0326 153 :YGI 1vcoA 409 :KGA T0326 156 :P 1vcoA 433 :E T0326 162 :QKL 1vcoA 439 :GTM T0326 165 :SGVYKHRVAKDSVLFRGHD 1vcoA 443 :LGDWPMRIKPGTLLHRLYG T0326 184 :DFFWA 1vcoA 463 :EEVLE T0326 193 :YTEVK 1vcoA 468 :RHRHR T0326 199 :EDID 1vcoA 473 :YEVN T0326 206 :ELEILAES 1vcoA 487 :GLVVSATT T0326 214 :D 1vcoA 498 :R T0326 215 :EAGVYVVANKSER 1vcoA 502 :AGLVEAIELKDHP T0326 228 :QIFVTGHPEYDRYTL 1vcoA 516 :FLGLQSHPEFKSRPM T0326 253 :NLK 1vcoA 531 :RPS T0326 282 :LFFSNWLNYCIY 1vcoA 534 :PPFVGFVEAALA Number of specific fragments extracted= 20 number of extra gaps= 0 total=312 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/T0326-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1vcoA/T0326-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0326-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set Warning: unaligning (T0326)D46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)D314 Warning: unaligning (T0326)H75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0326)T90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 Warning: unaligning (T0326)L160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)G438 T0326 27 :RAIHQDIRPLEILILNL 1vcoA 292 :RVLKHPERTVKIAIAGK T0326 47 :KIKTEIQLLRLL 1vcoA 315 :AYLSLLEALRHA T0326 60 :NTPLQVNVTLLYTET 1vcoA 329 :KNRARVEVKWVDAES T0326 91 :TFSAV 1vcoA 348 :DLEEA T0326 97 :DRKFDGFIITGAP 1vcoA 353 :FRDVSGILVPGGF T0326 117 :EVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYF 1vcoA 366 :GVRGIEGKVRAAQYARERKIPYLGICLGLQIAVIEF T0326 154 :GIPKY 1vcoA 419 :HTPHP T0326 161 :PQKLSGVYKHRVAKDSVLFR 1vcoA 439 :GTMRLGDWPMRIKPGTLLHR T0326 182 :HDDFFWAPHSRYTEVK 1vcoA 461 :GKEEVLERHRHRYEVN T0326 199 :EDIDKVP 1vcoA 481 :DGLERAG T0326 207 :LEILA 1vcoA 488 :LVVSA T0326 212 :ESDEAGVYVVANKSERQIFVTGHPEYD 1vcoA 500 :RGAGLVEAIELKDHPFFLGLQSHPEFK Number of specific fragments extracted= 12 number of extra gaps= 0 total=324 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9xA/T0326-1l9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l9xA expands to /projects/compbio/data/pdb/1l9x.pdb.gz 1l9xA:Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2259, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2261, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2263, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2265, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2267, because occupancy 0.500 <= existing 0.500 in 1l9xA Skipped atom 2269, because occupancy 0.500 <= existing 0.500 in 1l9xA # T0326 read from 1l9xA/T0326-1l9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9xA read from 1l9xA/T0326-1l9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l9xA to template set # found chain 1l9xA in template set Warning: unaligning (T0326)I33 because first residue in template chain is (1l9xA)A7 T0326 34 :RPLEILILNLMPDK 1l9xA 8 :KKPIIGILMQKCRN T0326 48 :IKTEIQLLRLLG 1l9xA 33 :AASYVKYLESAG T0326 65 :VNVTLLYTE 1l9xA 45 :ARVVPVRLD T0326 90 :TTFSAVK 1l9xA 54 :LTEKDYE T0326 100 :FDGFIITGAPVE 1l9xA 66 :INGILFPGGSVD T0326 115 :FEEVDYWEE 1l9xA 78 :LRRSDYAKV T0326 124 :LTEIMEWSRHNV 1l9xA 90 :FYNLSIQSFDDG T0326 136 :YSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1l9xA 104 :FPVWGTCLGFEELSLLISGECLLTATDTVDVAMPLNFTGG T0326 176 :SVLFRGHD 1l9xA 147 :SRMFQNFP T0326 184 :DFFWA 1l9xA 164 :EPLTA T0326 192 :R 1l9xA 171 :H T0326 194 :TEVKKEDIDKVP 1l9xA 173 :WSLSVKNFTMNE T0326 207 :LEILAES 1l9xA 190 :FNVLTTN T0326 214 :DEAG 1l9xA 199 :GKIE T0326 218 :VYVVANKSERQIFVTGHPEYDR 1l9xA 204 :ISTMEGYKYPVYGVQWHPEKAP T0326 262 :YFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQKTPYR 1l9xA 226 :YEWKNLDGISHAPNAVKTAFYLAEFFVNEARKNNHHFK Number of specific fragments extracted= 16 number of extra gaps= 0 total=340 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9xA/T0326-1l9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1l9xA/T0326-1l9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9xA read from 1l9xA/T0326-1l9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l9xA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1l9xA)A7 T0326 35 :PLEILILNLMPDKIKTEIQLLRLLGN 1l9xA 8 :KKPIIGILMQKCRNKVMKNYGRYYIA T0326 69 :LLYTETHKPKHTPIEHI 1l9xA 34 :ASYVKYLESAGARVVPV T0326 87 :KFYTTFSAVKDR 1l9xA 51 :RLDLTEKDYEIL T0326 99 :KFDGFIITGAPVE 1l9xA 65 :SINGILFPGGSVD T0326 115 :FEEVDYWEE 1l9xA 78 :LRRSDYAKV T0326 124 :LTEIMEWSRHNV 1l9xA 90 :FYNLSIQSFDDG T0326 136 :YSTMFICWAAQAGLYYFYG 1l9xA 104 :FPVWGTCLGFEELSLLISG T0326 156 :PKYELPQKL 1l9xA 123 :ECLLTATDT T0326 165 :SGVYKHRVAKD 1l9xA 133 :DVAMPLNFTGG T0326 176 :SVLFRGHDD 1l9xA 147 :SRMFQNFPT T0326 185 :FFWA 1l9xA 165 :PLTA T0326 191 :SRYTEVK 1l9xA 169 :NFHKWSL T0326 200 :DID 1l9xA 176 :SVK T0326 204 :VPE 1l9xA 186 :LKK T0326 207 :LEILAES 1l9xA 190 :FNVLTTN T0326 214 :DEA 1l9xA 199 :GKI T0326 217 :GVYVVANKSERQIFVTGHPEYDR 1l9xA 203 :FISTMEGYKYPVYGVQWHPEKAP T0326 262 :YFPNDDPTKTPILTWWSHAHLFFSNWLNYCIYQKTPYR 1l9xA 226 :YEWKNLDGISHAPNAVKTAFYLAEFFVNEARKNNHHFK Number of specific fragments extracted= 18 number of extra gaps= 0 total=358 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9xA/T0326-1l9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1l9xA/T0326-1l9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9xA read from 1l9xA/T0326-1l9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l9xA in template set Warning: unaligning (T0326)I33 because first residue in template chain is (1l9xA)A7 T0326 34 :RPLEILILNLMPDKIKTE 1l9xA 8 :KKPIIGILMQKCRNKVMK T0326 52 :IQLLRLLGNTP 1l9xA 34 :ASYVKYLESAG T0326 65 :VNVTLLYTE 1l9xA 45 :ARVVPVRLD T0326 80 :TPIEHILKFY 1l9xA 54 :LTEKDYEILF T0326 98 :RKFDGFIITGAPV 1l9xA 64 :KSINGILFPGGSV T0326 114 :PFEEVDYWEELTEIMEWSRH 1l9xA 77 :DLRRSDYAKVAKIFYNLSIQ T0326 134 :NVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1l9xA 102 :DYFPVWGTCLGFEELSLLISGECLLTATDTVDVAMPLNFTGG T0326 176 :SVLFRGHD 1l9xA 147 :SRMFQNFP T0326 185 :FF 1l9xA 165 :PL T0326 196 :VKKEDIDKVPE 1l9xA 175 :LSVKNFTMNEK T0326 207 :LEILAESDEA 1l9xA 192 :VLTTNTDGKI T0326 217 :GVYVVANKSERQIFVTGHPEYDRY 1l9xA 203 :FISTMEGYKYPVYGVQWHPEKAPY T0326 263 :FPNDDPTKTPILTWWSHAHLFFSNWLNYC 1l9xA 227 :EWKNLDGISHAPNAVKTAFYLAEFFVNEA Number of specific fragments extracted= 13 number of extra gaps= 0 total=371 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ka9H/T0326-1ka9H-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ka9H expands to /projects/compbio/data/pdb/1ka9.pdb.gz 1ka9H:# T0326 read from 1ka9H/T0326-1ka9H-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ka9H read from 1ka9H/T0326-1ka9H-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ka9H to template set # found chain 1ka9H in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1ka9H)M3 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1ka9H 4 :KALLIDYGSGNLRSAAKALEAAG T0326 65 :VNVTLLYTET 1ka9H 27 :FSVAVAQDPK T0326 96 :KDRKFDGFIITGAPV 1ka9H 37 :AHEEADLLVLPGQGH T0326 115 :FEE 1ka9H 52 :FGQ T0326 120 :YWEE 1ka9H 55 :VMRA T0326 124 :LTEIMEWSRHNVYSTMFICWAAQ 1ka9H 64 :FVERVRRHLERGLPFLGICVGMQ T0326 152 :FYGIP 1ka9H 95 :APGVR T0326 157 :KYELPQKLSGVYKHRVA 1ka9H 111 :FRAGRVPQMGWNALEFG T0326 177 :VLFRGH 1ka9H 128 :GAFAPL T0326 183 :DDFFWAPHSRY 1ka9H 135 :GRHFYFANSYY T0326 201 :IDKVPELEILAESDEAGVYVVANK 1ka9H 146 :GPLTPYSLGKGEYEGTPFTALLAK T0326 226 :ERQIFVTGHPEYDRYTLRDEYYRDIG 1ka9H 170 :ENLLAPQFHPEKSGKAGLAFLALARR Number of specific fragments extracted= 12 number of extra gaps= 0 total=383 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ka9H/T0326-1ka9H-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1ka9H/T0326-1ka9H-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ka9H read from 1ka9H/T0326-1ka9H-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ka9H in template set Warning: unaligning (T0326)R56 because first residue in template chain is (1ka9H)M3 T0326 57 :LLGNTPLQVNVTLLYTETHKPKHTPIEHILKFYTT 1ka9H 4 :KALLIDYGSGNLRSAAKALEAAGFSVAVAQDPKAH T0326 98 :RKFDGFII 1ka9H 39 :EEADLLVL T0326 107 :GAPVE 1ka9H 47 :PGQGH T0326 115 :FEEV 1ka9H 52 :FGQV T0326 121 :WEE 1ka9H 56 :MRA T0326 124 :LTEIMEWSRHNVYSTMFICWAAQ 1ka9H 64 :FVERVRRHLERGLPFLGICVGMQ T0326 153 :YGI 1ka9H 96 :PGV T0326 156 :PKYELPQK 1ka9H 107 :EVRRFRAG T0326 164 :LSGVYKHRV 1ka9H 118 :QMGWNALEF T0326 176 :SVLFRGH 1ka9H 127 :GGAFAPL T0326 184 :DFFWA 1ka9H 134 :TGRHF T0326 191 :SRYTEVK 1ka9H 139 :YFANSYY T0326 201 :I 1ka9H 146 :G T0326 203 :KVPE 1ka9H 147 :PLTP T0326 207 :LEILAESDEAGVYVVANKS 1ka9H 152 :SLGKGEYEGTPFTALLAKE T0326 227 :RQIFVTGHPEYD 1ka9H 171 :NLLAPQFHPEKS T0326 240 :YTLRDEYYRDI 1ka9H 183 :GKAGLAFLALA Number of specific fragments extracted= 17 number of extra gaps= 0 total=400 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ka9H/T0326-1ka9H-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1ka9H/T0326-1ka9H-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ka9H read from 1ka9H/T0326-1ka9H-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ka9H in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1ka9H)M3 T0326 37 :EILILNLMPDKI 1ka9H 4 :KALLIDYGSGNL T0326 52 :IQLLRLLGNTPLQVNVT 1ka9H 16 :RSAAKALEAAGFSVAVA T0326 75 :HKPKHT 1ka9H 33 :QDPKAH T0326 98 :RKFDGFIITGAPV 1ka9H 39 :EEADLLVLPGQGH T0326 114 :PFEEVDYWEELTEIME 1ka9H 58 :AFQESGFVERVRRHLE T0326 134 :NVYSTMFICWAAQ 1ka9H 74 :RGLPFLGICVGMQ T0326 153 :YGIPKYEL 1ka9H 96 :PGVRGLGL T0326 161 :PQKLSGVYKHRVAKDSVLFRGHD 1ka9H 115 :RVPQMGWNALEFGGAFAPLTGRH T0326 186 :FWAPHSRYT 1ka9H 138 :FYFANSYYG T0326 202 :DKVPELEILAESDEAGVYVVANK 1ka9H 147 :PLTPYSLGKGEYEGTPFTALLAK T0326 226 :ERQIFVTGHPEYDRYTLRDEYYRDIG 1ka9H 170 :ENLLAPQFHPEKSGKAGLAFLALARR Number of specific fragments extracted= 11 number of extra gaps= 0 total=411 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abwA/T0326-2abwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2abwA expands to /projects/compbio/data/pdb/2abw.pdb.gz 2abwA:Skipped atom 2, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 4, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 6, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 8, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 10, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 12, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 27, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 29, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 31, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 33, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 62, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 64, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 66, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 72, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 74, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 76, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 78, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 80, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 82, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 84, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 86, because occupancy 0.300 <= existing 0.700 in 2abwA Skipped atom 223, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 225, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 227, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 229, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 231, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 233, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 235, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 237, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 239, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 241, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 243, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 245, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 247, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 249, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 251, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 253, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 255, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 448, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 450, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 452, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 715, because occupancy 0.450 <= existing 0.550 in 2abwA Skipped atom 717, because occupancy 0.450 <= existing 0.550 in 2abwA Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 910, because occupancy 0.400 <= existing 0.600 in 2abwA Skipped atom 974, because occupancy 0.250 <= existing 0.750 in 2abwA Skipped atom 976, because occupancy 0.250 <= existing 0.750 in 2abwA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 2abwA Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 2abwA # T0326 read from 2abwA/T0326-2abwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abwA read from 2abwA/T0326-2abwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2abwA to template set # found chain 2abwA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (2abwA)S2 Warning: unaligning (T0326)K157 because of BadResidue code BAD_PEPTIDE in next template residue (2abwA)S104 Warning: unaligning (T0326)Y158 because of BadResidue code BAD_PEPTIDE at template residue (2abwA)S104 Warning: unaligning (T0326)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2abwA)S176 Warning: unaligning (T0326)E215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2abwA)S176 T0326 35 :PLEILILNLM 2abwA 3 :EITIGVLSLQ T0326 46 :DKIKTEIQLLRLLGNTPLQ 2abwA 13 :GDFEPHINHFIKLQIPSLN T0326 67 :VTLL 2abwA 32 :IIQV T0326 90 :TTFSA 2abwA 36 :RNVHD T0326 97 :DRKFDGFIITGA 2abwA 41 :LGLCDGLVIPGG T0326 115 :FEEVDYWEELTEIME 2abwA 63 :YENDTLYNALVHFIH T0326 133 :HNVYSTMFICWAAQAGL 2abwA 78 :VLKKPIWGTCAGCILLS T0326 154 :G 2abwA 99 :N T0326 155 :IP 2abwA 101 :KL T0326 159 :ELPQKLS 2abwA 105 :NFGNKFS T0326 166 :GVYKHRVAKDSVLFRG 2abwA 131 :FICSLNIISDSSAFKK T0326 183 :DDFFWA 2abwA 147 :DLTAAC T0326 191 :SRYTEVK 2abwA 153 :IRAPYIR T0326 203 :KVPELEILAE 2abwA 162 :LSDEVKVLAT T0326 213 :S 2abwA 174 :H T0326 216 :AG 2abwA 177 :YG T0326 218 :VYVVANKS 2abwA 182 :IAAVEQNN T0326 228 :QIFVTGHPEYDR 2abwA 190 :CLGTVFHPELLP T0326 273 :IL 2abwA 202 :HT T0326 278 :SHAHLFFSNWLNYC 2abwA 204 :AFQQYFYEKVKNYK Number of specific fragments extracted= 20 number of extra gaps= 2 total=431 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abwA/T0326-2abwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2abwA/T0326-2abwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abwA read from 2abwA/T0326-2abwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2abwA in template set Warning: unaligning (T0326)P156 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2abwA)F123 Warning: unaligning (T0326)K157 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2abwA)F123 Warning: unaligning (T0326)Q162 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2abwA)N128 Warning: unaligning (T0326)K163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2abwA)D129 Warning: unaligning (T0326)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2abwA)S176 Warning: unaligning (T0326)E215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2abwA)S176 Warning: unaligning (T0326)Q294 because of BadResidue code BAD_PEPTIDE in next template residue (2abwA)E221 Warning: unaligning (T0326)K295 because of BadResidue code BAD_PEPTIDE at template residue (2abwA)E221 T0326 57 :LLGNTPLQVNVTLLYTET 2abwA 5 :TIGVLSLQGDFEPHINHF T0326 75 :HKPKHTPIEHIL 2abwA 25 :LQIPSLNIIQVR T0326 91 :TFSAVK 2abwA 37 :NVHDLG T0326 99 :KFDGFIITGAP 2abwA 43 :LCDGLVIPGGE T0326 112 :L 2abwA 62 :A T0326 115 :FEEVDYWEELTEIME 2abwA 63 :YENDTLYNALVHFIH T0326 133 :HNVYSTMFICWAAQAG 2abwA 78 :VLKKPIWGTCAGCILL T0326 155 :I 2abwA 94 :S T0326 164 :L 2abwA 130 :S T0326 166 :GVYKHRVAKDS 2abwA 131 :FICSLNIISDS T0326 180 :RGHDDFFWAPHSRYTEVK 2abwA 142 :SAFKKDLTAACIRAPYIR T0326 200 :DI 2abwA 160 :EI T0326 204 :VPE 2abwA 162 :LSD T0326 207 :LEILAES 2abwA 166 :VKVLATF T0326 216 :A 2abwA 177 :Y T0326 217 :GVYVVANKS 2abwA 181 :IIAAVEQNN T0326 228 :QIFVTGHPEYDRYT 2abwA 190 :CLGTVFHPELLPHT T0326 278 :SHAHLFFSNWLNYCIY 2abwA 204 :AFQQYFYEKVKNYKYS Number of specific fragments extracted= 18 number of extra gaps= 3 total=449 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abwA/T0326-2abwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2abwA/T0326-2abwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abwA read from 2abwA/T0326-2abwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2abwA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (2abwA)S2 Warning: unaligning (T0326)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2abwA)S176 Warning: unaligning (T0326)E215 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2abwA)S176 T0326 35 :PLEILILNLMPDKIKTEIQLL 2abwA 3 :EITIGVLSLQGDFEPHINHFI T0326 59 :GNTPLQVNVTLLY 2abwA 24 :KLQIPSLNIIQVR T0326 91 :TFSAV 2abwA 37 :NVHDL T0326 98 :RKFDGFIITGAP 2abwA 42 :GLCDGLVIPGGE T0326 115 :FEEVDYWEELTEI 2abwA 63 :YENDTLYNALVHF T0326 131 :SRHNVYSTMFICWAAQA 2abwA 76 :IHVLKKPIWGTCAGCIL T0326 155 :IPK 2abwA 100 :IKL T0326 161 :PQKL 2abwA 108 :NKFS T0326 165 :SGVYKHRVAKDSV 2abwA 130 :SFICSLNIISDSS T0326 181 :GHDDFFWAPHSRYTEV 2abwA 143 :AFKKDLTAACIRAPYI T0326 205 :PELEIL 2abwA 164 :DEVKVL T0326 211 :AES 2abwA 172 :FSH T0326 216 :AG 2abwA 177 :YG T0326 218 :VYVVANKS 2abwA 182 :IAAVEQNN T0326 228 :QIFVTGHPEYDRYTLRDEYYRDI 2abwA 190 :CLGTVFHPELLPHTAFQQYFYEK Number of specific fragments extracted= 15 number of extra gaps= 1 total=464 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g2iA/T0326-1g2iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g2iA expands to /projects/compbio/data/pdb/1g2i.pdb.gz 1g2iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 1g2iA/T0326-1g2iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g2iA read from 1g2iA/T0326-1g2iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g2iA to template set # found chain 1g2iA in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1g2iA)M1 T0326 37 :EILILN 1g2iA 2 :KVLFLT T0326 44 :MPDKIKTE 1g2iA 8 :ANEFEDVE T0326 52 :IQLLRLLGNTPL 1g2iA 17 :IYPYHRLKEEGH T0326 66 :NVTLLYTET 1g2iA 29 :EVYIASFER T0326 79 :HTPIEHILKFYTTFSAVKDRKFDGFIITGAPV 1g2iA 41 :TGKHGYSVKVDLTFDKVNPEEFDALVLPGGRA T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1g2iA 73 :PERVRLNEKAVSIARKMFSEGKPVASICHGPQILISA T0326 152 :FYGIP 1g2iA 112 :LRGRK T0326 186 :FWA 1g2iA 117 :GTS T0326 194 :TEVKKEDIDKVP 1g2iA 120 :YPGIKDDMINAG T0326 209 :ILAESDEAGV 1g2iA 132 :VEWVDAEVVV T0326 223 :NKS 1g2iA 142 :DGN T0326 230 :FVTGHPEYDRYTLRDEYYRD 1g2iA 145 :WVSSRVPADLYAWMREFVKL Number of specific fragments extracted= 12 number of extra gaps= 0 total=476 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g2iA/T0326-1g2iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1g2iA/T0326-1g2iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g2iA read from 1g2iA/T0326-1g2iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g2iA in template set Warning: unaligning (T0326)L55 because first residue in template chain is (1g2iA)M1 T0326 56 :RLLGNTPLQVNVTLL 1g2iA 2 :KVLFLTANEFEDVEL T0326 71 :YTETHKPKHTPIEHILKF 1g2iA 19 :PYHRLKEEGHEVYIASFE T0326 89 :YTTFSAVKDRKFDGFIITGAPV 1g2iA 51 :DLTFDKVNPEEFDALVLPGGRA T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1g2iA 73 :PERVRLNEKAVSIARKMFSEGKPVASICHGPQILISA T0326 154 :GI 1g2iA 110 :GV Number of specific fragments extracted= 5 number of extra gaps= 0 total=481 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g2iA/T0326-1g2iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1g2iA/T0326-1g2iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g2iA read from 1g2iA/T0326-1g2iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g2iA in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1g2iA)M1 T0326 37 :EILILNL 1g2iA 2 :KVLFLTA T0326 46 :DKI 1g2iA 9 :NEF T0326 49 :KTEIQLLRLLGNTPLQVNVTL 1g2iA 14 :VELIYPYHRLKEEGHEVYIAS T0326 70 :LYTETHKP 1g2iA 40 :ITGKHGYS T0326 90 :TTFSAVKDRKFDGFIITGAPV 1g2iA 52 :LTFDKVNPEEFDALVLPGGRA T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1g2iA 73 :PERVRLNEKAVSIARKMFSEGKPVASICHGPQILISA T0326 154 :GI 1g2iA 110 :GV T0326 179 :FRGHD 1g2iA 112 :LRGRK T0326 190 :HSRYTEV 1g2iA 117 :GTSYPGI T0326 198 :KEDIDKVP 1g2iA 124 :KDDMINAG T0326 209 :ILAESDEAGV 1g2iA 132 :VEWVDAEVVV T0326 223 :NKS 1g2iA 142 :DGN T0326 230 :FVTGHPEYDRYTLRDEYYRDI 1g2iA 145 :WVSSRVPADLYAWMREFVKLL Number of specific fragments extracted= 13 number of extra gaps= 0 total=494 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qdlB/T0326-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qdlB expands to /projects/compbio/data/pdb/1qdl.pdb.gz 1qdlB:# T0326 read from 1qdlB/T0326-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0326-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qdlB to template set # found chain 1qdlB in template set T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1qdlB 3 :LTLIIDNYDSFVYNIAQIVGELG T0326 65 :VNVTLLYTETH 1qdlB 26 :SYPIVIRNDEI T0326 91 :TFSAVKDRKFDGFIITGAPVELLP 1qdlB 37 :SIKGIERIDPDRLIISPGPGTPEK T0326 121 :WEE 1qdlB 61 :RED T0326 124 :LTEIMEWSR 1qdlB 67 :SLDVIKYLG T0326 134 :NVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKDS 1qdlB 76 :KRTPILGVCLGHQAIGYAFGAKIRRARKVFHGKISNIILVNNS T0326 177 :VLFRGHDDFFWA 1qdlB 121 :SLYYGIAKEFKA T0326 201 :IDKVP 1qdlB 140 :VDEVH T0326 206 :ELEILAESDEAG 1qdlB 146 :PLIVDAISAEDN T0326 218 :VYVVANKSERQIFVTGHPEYDR 1qdlB 159 :IMAIHHEEYPIYGVQFHPESVG T0326 277 :WSHAHLFFSNWLNY 1qdlB 181 :TSLGYKILYNFLNR Number of specific fragments extracted= 11 number of extra gaps= 0 total=505 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qdlB/T0326-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1qdlB/T0326-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0326-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qdlB in template set Warning: unaligning (T0326)L55 because first residue in template chain is (1qdlB)M1 T0326 56 :RLLGNTPLQVNVTLLYTETHKPKHTPIEHILKFYTTFSAVKDRKFDGFIITGAPVELLPFEEVDYW 1qdlB 2 :DLTLIIDNYDSFVYNIAQIVGELGSYPIVIRNDEISIKGIERIDPDRLIISPGPGTPEKREDIGVS T0326 125 :TEIMEWS 1qdlB 68 :LDVIKYL T0326 133 :HNVYSTMFICWAAQAGLYYF 1qdlB 75 :GKRTPILGVCLGHQAIGYAF T0326 154 :GIPKYELPQKLSG 1qdlB 95 :GAKIRRARKVFHG T0326 167 :VYKHRVAKDSVL 1qdlB 109 :ISNIILVNNSPL T0326 179 :FRGHDDFFWA 1qdlB 123 :YYGIAKEFKA T0326 191 :SRYTEVK 1qdlB 133 :TRYHSLV T0326 201 :IDKVPE 1qdlB 140 :VDEVHR T0326 207 :LEILAES 1qdlB 147 :LIVDAIS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGR 1qdlB 155 :EDNEIMAIHHEEYPIYGVQFHPESVGTSLGYKILYNFLN Number of specific fragments extracted= 10 number of extra gaps= 0 total=515 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qdlB/T0326-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1qdlB/T0326-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0326-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qdlB in template set T0326 37 :EILILNLMPDKIKTEIQLLRLLGN 1qdlB 3 :LTLIIDNYDSFVYNIAQIVGELGS T0326 66 :NVTLLYTETH 1qdlB 27 :YPIVIRNDEI T0326 91 :TFSAVKDRKFDGFIITGAPVEL 1qdlB 37 :SIKGIERIDPDRLIISPGPGTP T0326 119 :DYWEEL 1qdlB 59 :EKREDI T0326 125 :TEIMEWSR 1qdlB 68 :LDVIKYLG T0326 134 :NVYSTMFICWAAQAGLY 1qdlB 76 :KRTPILGVCLGHQAIGY T0326 152 :FYGIPKYELPQKLSG 1qdlB 93 :AFGAKIRRARKVFHG T0326 167 :VYKHRVAKD 1qdlB 109 :ISNIILVNN T0326 176 :SVLFRGHDDFFWA 1qdlB 120 :LSLYYGIAKEFKA T0326 192 :RYTEVK 1qdlB 139 :VVDEVH T0326 205 :PELEILAESDEA 1qdlB 145 :RPLIVDAISAED T0326 217 :GVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDI 1qdlB 158 :EIMAIHHEEYPIYGVQFHPESVGTSLGYKILYNF Number of specific fragments extracted= 12 number of extra gaps= 0 total=527 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r9gA/T0326-1r9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r9gA expands to /projects/compbio/data/pdb/1r9g.pdb.gz 1r9gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 1r9gA/T0326-1r9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r9gA read from 1r9gA/T0326-1r9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r9gA to template set # found chain 1r9gA in template set Warning: unaligning (T0326)P35 because first residue in template chain is (1r9gA)M1 T0326 36 :LEILILNLMPD 1r9gA 2 :LTIGVLGLQGA T0326 48 :IKTEIQLLRLLG 1r9gA 13 :VREHIHAIEACG T0326 63 :LQ 1r9gA 25 :AA T0326 69 :LLYTE 1r9gA 27 :GLVVK T0326 91 :TFS 1r9gA 32 :RPE T0326 96 :KDRKFDGFIITGAPV 1r9gA 35 :QLNEVDGLILPGGES T0326 115 :FEEVDYWEE 1r9gA 50 :TTMRRLIDT T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGL 1r9gA 61 :FMEPLREFAAQGKPMFGTCAGLIILA T0326 155 :IPKYELPQKLSGVYKHRVAKD 1r9gA 87 :KEIAGSDNPHLGLLNVVVERN T0326 178 :LFRGHDDFFWAPHSRYTEV 1r9gA 121 :TIKGLDEPFTGVFIRAPHI T0326 205 :PELEILAESDEAGVYVVA 1r9gA 144 :ENVEVLSEHNGRIVAAKQ T0326 226 :ERQIFVTGHPEYD 1r9gA 162 :GQFLGCSFHPELT T0326 239 :RYTLRDEYYRDIGRNL 1r9gA 180 :TQLFVEMVEEYKQKAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=540 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r9gA/T0326-1r9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1r9gA/T0326-1r9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r9gA read from 1r9gA/T0326-1r9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r9gA in template set Warning: unaligning (T0326)L55 because first residue in template chain is (1r9gA)M1 T0326 56 :RLLGNTPLQVNVTLL 1r9gA 2 :LTIGVLGLQGAVREH T0326 72 :TETHKPKHTPIEHI 1r9gA 17 :IHAIEACGAAGLVV T0326 90 :TTFSAVK 1r9gA 31 :KRPEQLN T0326 99 :KFDGFIITGAPVE 1r9gA 38 :EVDGLILPGGEST T0326 116 :EEVDYWEE 1r9gA 51 :TMRRLIDT T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGL 1r9gA 61 :FMEPLREFAAQGKPMFGTCAGLIILA T0326 153 :YGI 1r9gA 90 :AGS T0326 157 :KYELPQKL 1r9gA 104 :VERNSFGR T0326 165 :SGVYKHRVA 1r9gA 113 :VDSFEADLT T0326 179 :FRGHDDFFWA 1r9gA 122 :IKGLDEPFTG T0326 193 :YTEVK 1r9gA 132 :VFIRA T0326 199 :EDIDKVPE 1r9gA 137 :PHILEAGE T0326 207 :LEILAESDEA 1r9gA 146 :VEVLSEHNGR T0326 218 :VYVVANKS 1r9gA 156 :IVAAKQGQ T0326 228 :QIFVTGHPEYDRYT 1r9gA 164 :FLGCSFHPELTEDH T0326 278 :S 1r9gA 178 :R T0326 280 :AHLFFSNWLNYC 1r9gA 179 :VTQLFVEMVEEY Number of specific fragments extracted= 17 number of extra gaps= 0 total=557 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r9gA/T0326-1r9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1r9gA/T0326-1r9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r9gA read from 1r9gA/T0326-1r9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r9gA in template set Warning: unaligning (T0326)P35 because first residue in template chain is (1r9gA)M1 T0326 36 :LEILILNLMPDKI 1r9gA 2 :LTIGVLGLQGAVR T0326 53 :QLLRLLGNTPLQVN 1r9gA 15 :EHIHAIEACGAAGL T0326 71 :YTE 1r9gA 29 :VVK T0326 81 :PIEHI 1r9gA 32 :RPEQL T0326 98 :RKFDGFIITGAP 1r9gA 37 :NEVDGLILPGGE T0326 115 :FEEVDYWEELTEIM 1r9gA 56 :IDTYQFMEPLREFA T0326 133 :HNVYSTMFICWAAQAGLYYFYG 1r9gA 70 :AQGKPMFGTCAGLIILAKEIAG T0326 160 :LPQKLSGVYKHRVA 1r9gA 92 :SDNPHLGLLNVVVE T0326 174 :KDS 1r9gA 111 :RQV T0326 179 :FRGHDDFF 1r9gA 122 :IKGLDEPF T0326 189 :PHSRYTEVK 1r9gA 135 :RAPHILEAG T0326 205 :PELEILAESDEAGVYVVA 1r9gA 144 :ENVEVLSEHNGRIVAAKQ T0326 226 :ERQIFVTGHPEYDR 1r9gA 162 :GQFLGCSFHPELTE T0326 240 :YTLRDEYYRDIGRNLK 1r9gA 180 :TQLFVEMVEEYKQKAL Number of specific fragments extracted= 14 number of extra gaps= 0 total=571 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ox6A/T0326-1ox6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ox6A expands to /projects/compbio/data/pdb/1ox6.pdb.gz 1ox6A:# T0326 read from 1ox6A/T0326-1ox6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ox6A read from 1ox6A/T0326-1ox6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ox6A to template set # found chain 1ox6A in template set T0326 36 :LEILILNLMPDKIKTEIQLLRLLG 1ox6A 2 :PVVHVIDVESGNLQSLTNAIEHLG T0326 65 :VNVTLL 1ox6A 26 :YEVQLV T0326 90 :TTFSAVKDRKFDGFIITG 1ox6A 32 :KSPKDFNISGTSRLILPG T0326 108 :AP 1ox6A 51 :GN T0326 115 :FEEV 1ox6A 53 :YGHF T0326 119 :DYWEE 1ox6A 59 :NLFNR T0326 124 :LTEIMEWSRHNVYSTMFICWAAQ 1ox6A 65 :FEKPIREYIESGKPIMGICVGLQ T0326 152 :FYGIP 1ox6A 96 :SPKST T0326 158 :YELPQKLSGVYKHRVAKDSVLFRGHDDFFWAPHSRYTEVKKEDIDKVP 1ox6A 115 :SEKPVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLE T0326 206 :ELEI 1ox6A 165 :GWKI T0326 210 :LAESDEAGVYVVANKS 1ox6A 170 :KAKYGSEEFIAAVNKN T0326 227 :RQIFVTGHPEYDRYTLRDEYYRDIGRNLK 1ox6A 186 :NIFATQFHPEKSGKAGLNVIENFLKQQSP T0326 257 :PIPA 1ox6A 215 :PIPN T0326 262 :Y 1ox6A 219 :Y T0326 268 :PTKTPILTWWSHAHLFFS 1ox6A 338 :DVDGTKIPALEVASLYFR Number of specific fragments extracted= 15 number of extra gaps= 0 total=586 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ox6A/T0326-1ox6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1ox6A/T0326-1ox6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ox6A read from 1ox6A/T0326-1ox6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ox6A in template set Warning: unaligning (T0326)I273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)L276 T0326 53 :QLLRLLGNTPLQVNVTLLYTETHKPKHTPIEHI 1ox6A -2 :SHMPVVHVIDVESGNLQSLTNAIEHLGYEVQLV T0326 90 :TTFSAVKDRKFDGFII 1ox6A 32 :KSPKDFNISGTSRLIL T0326 107 :GAPVE 1ox6A 48 :PGVGN T0326 115 :FEEV 1ox6A 53 :YGHF T0326 121 :WEELTE 1ox6A 57 :VDNLFN T0326 127 :IMEWSRHNVYSTMFICWAAQ 1ox6A 68 :PIREYIESGKPIMGICVGLQ T0326 154 :GI 1ox6A 92 :GS T0326 156 :PKYELPQK 1ox6A 108 :KLSRFDDS T0326 164 :LSGVYKHRVAKDSVL 1ox6A 121 :EIGWNSCIPSENLFF T0326 181 :GHDDFFWA 1ox6A 136 :GLDPYKRY T0326 191 :SRYTEVK 1ox6A 144 :YFVHSFA T0326 199 :EDID 1ox6A 151 :AILN T0326 205 :PELEIL 1ox6A 164 :DGWKIA T0326 211 :AESDEAGVYVVANKS 1ox6A 171 :AKYGSEEFIAAVNKN T0326 227 :RQIFVTGHPEYD 1ox6A 186 :NIFATQFHPEKS T0326 240 :YTLRDEYYRDIGRNLKVPIPA 1ox6A 198 :GKAGLNVIENFLKQQSPPIPN T0326 263 :FP 1ox6A 219 :YS T0326 274 :LTWWSHAHLFFS 1ox6A 277 :GKPVQLAQKYYQ Number of specific fragments extracted= 18 number of extra gaps= 0 total=604 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ox6A/T0326-1ox6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1ox6A/T0326-1ox6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ox6A read from 1ox6A/T0326-1ox6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ox6A in template set T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1ox6A 3 :VVHVIDVESGNLQSLTNAIEHLG T0326 65 :VNVTLLYTE 1ox6A 26 :YEVQLVKSP T0326 78 :KHTPIE 1ox6A 35 :KDFNIS T0326 99 :KFDGFIITGAPV 1ox6A 41 :GTSRLILPGVGN T0326 117 :EVDYWEELTEIME 1ox6A 62 :NRGFEKPIREYIE T0326 134 :NVYSTMFICWAAQA 1ox6A 75 :SGKPIMGICVGLQA T0326 153 :YGIPKYEL 1ox6A 97 :PKSTGLNY T0326 161 :PQKLSGVYKHRVAKDSVLFRGHDDFFWAPHSRYTEVKKEDIDKV 1ox6A 118 :PVPEIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNL T0326 205 :PELEIL 1ox6A 164 :DGWKIA T0326 211 :AE 1ox6A 171 :AK T0326 213 :SDEAGVYVVANKS 1ox6A 174 :GSEEFIAAVNKNN T0326 228 :QIFVTGHPEYDRYTLRDEYYRDIGRNLK 1ox6A 187 :IFATQFHPEKSGKAGLNVIENFLKQQSP T0326 257 :PIPAN 1ox6A 215 :PIPNY Number of specific fragments extracted= 13 number of extra gaps= 0 total=617 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs0B/T0326-1cs0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cs0B expands to /projects/compbio/data/pdb/1cs0.pdb.gz 1cs0B:# T0326 read from 1cs0B/T0326-1cs0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0B read from 1cs0B/T0326-1cs0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cs0B to template set # found chain 1cs0B in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs0B)L270 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs0B)L270 T0326 31 :QDIRPLEILILNLM 1cs0B 187 :EDELPFHVVAYDFG T0326 51 :EIQLLRLL 1cs0B 202 :KRNILRML T0326 59 :G 1cs0B 213 :G T0326 65 :VNVTLLYTE 1cs0B 214 :CRLTIVPAQ T0326 90 :TTFSAVKDRKFDGFIITGAPVELLP 1cs0B 223 :TSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMF 1cs0B 248 :CDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1cs0B 271 :GHQLLALASGAKTVKMKFGHHGGNHPVKDVEK T0326 183 :DDFFWAPHSRYTEVKKED 1cs0B 303 :NVVMITAQNHGFAVDEAT T0326 204 :VP 1cs0B 321 :LP T0326 206 :ELEILAES 1cs0B 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPE 1cs0B 333 :FDGTLQGIHRTDKPAFSFQGHPE T0326 281 :HLFFSNWLNYCI 1cs0B 364 :APLFDHFIELIE Number of specific fragments extracted= 12 number of extra gaps= 0 total=629 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs0B/T0326-1cs0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1cs0B/T0326-1cs0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0B read from 1cs0B/T0326-1cs0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs0B in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs0B)L270 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs0B)L270 T0326 10 :PAVKVLAKEGIFV 1cs0B 117 :KLTRLLREKGAQN T0326 23 :MTEKRAIHQ 1cs0B 138 :PDAALALEK T0326 32 :DIRPL 1cs0B 152 :GLNGM T0326 37 :EILILNLMPD 1cs0B 168 :YSWTQGSWTL T0326 47 :K 1cs0B 179 :G T0326 48 :IKTEIQLLR 1cs0B 183 :EAKKEDELP T0326 57 :LLGNTPLQ 1cs0B 193 :HVVAYDFG T0326 67 :VTLLYTETHKPKHTPIEHI 1cs0B 201 :AKRNILRMLVDRGCRLTIV T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVEL 1cs0B 220 :PAQTSAEDVLKMNPDGIFLSNGPGDP T0326 116 :E 1cs0B 246 :A T0326 120 :YWEELTEIMEWSRHNVYSTMF 1cs0B 247 :PCDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYYF 1cs0B 271 :GHQLLALAS T0326 154 :GIPKYELPQKL 1cs0B 280 :GAKTVKMKFGH T0326 165 :SGVYKHRVAKDS 1cs0B 292 :GGNHPVKDVEKN T0326 186 :FWAPHSRYTEVK 1cs0B 304 :VVMITAQNHGFA T0326 199 :EDIDKVPE 1cs0B 316 :VDEATLPA T0326 207 :LEILAES 1cs0B 325 :LRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1cs0B 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD T0326 283 :FFSNWLNYCIYQ 1cs0B 366 :LFDHFIELIEQY Number of specific fragments extracted= 19 number of extra gaps= 0 total=648 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs0B/T0326-1cs0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1cs0B/T0326-1cs0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0B read from 1cs0B/T0326-1cs0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs0B in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cs0B)L270 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cs0B)L270 T0326 31 :QDIRPLEILILNLMP 1cs0B 187 :EDELPFHVVAYDFGA T0326 52 :IQLLRLL 1cs0B 203 :RNILRML T0326 63 :LQVNVTLLYTET 1cs0B 212 :RGCRLTIVPAQT T0326 91 :TFSAVKDRKFDGFIITGAPVEL 1cs0B 224 :SAEDVLKMNPDGIFLSNGPGDP T0326 119 :DYWEELTEIMEWSRHNVYSTMF 1cs0B 246 :APCDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYY 1cs0B 271 :GHQLLALA T0326 153 :YGIPKYELPQKLSGV 1cs0B 279 :SGAKTVKMKFGHHGG T0326 168 :YKHRVAKDS 1cs0B 295 :HPVKDVEKN T0326 185 :FFWAPHSRYTEVK 1cs0B 310 :QNHGFAVDEATLP T0326 205 :PELEILAESD 1cs0B 323 :ANLRVTHKSL T0326 215 :EAGVYVVANKSERQIFVTGHPEYDR 1cs0B 334 :DGTLQGIHRTDKPAFSFQGHPEASP T0326 240 :YTLRDEYYRDI 1cs0B 364 :APLFDHFIELI Number of specific fragments extracted= 12 number of extra gaps= 0 total=660 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvnA/T0326-1jvnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jvnA expands to /projects/compbio/data/pdb/1jvn.pdb.gz 1jvnA:Bad short name: CI for alphabet: pdb_atoms Bad short name: NI for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: OJ1 for alphabet: pdb_atoms Bad short name: OJ2 for alphabet: pdb_atoms Bad short name: CF for alphabet: pdb_atoms Bad short name: OF for alphabet: pdb_atoms Bad short name: NX for alphabet: pdb_atoms # T0326 read from 1jvnA/T0326-1jvnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvnA read from 1jvnA/T0326-1jvnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jvnA to template set # found chain 1jvnA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)V84 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)V84 Warning: unaligning (T0326)Q162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)P120 Warning: unaligning (T0326)K163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)P120 Warning: unaligning (T0326)I273 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jvnA)I344 Warning: unaligning (T0326)L274 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)I344 T0326 36 :LEILILNLMPDKIKTEIQLLRLLG 1jvnA 2 :PVVHVIDVESGNLQSLTNAIEHLG T0326 65 :VNVTLL 1jvnA 26 :YEVQLV T0326 90 :TTFSAVKDRKFDGFIITG 1jvnA 32 :KSPKDFNISGTSRLILPG T0326 108 :AP 1jvnA 51 :GN T0326 115 :FEEV 1jvnA 53 :YGHF T0326 119 :DYWEE 1jvnA 59 :NLFNR T0326 124 :LTEIMEWSRHNVYSTMF 1jvnA 65 :FEKPIREYIESGKPIMG T0326 144 :AAQ 1jvnA 85 :GLQ T0326 153 :YGIP 1jvnA 97 :PKST T0326 157 :KYELP 1jvnA 114 :DSEKP T0326 164 :LSGVYKHRVAKDSVLFRGHDDFFWAPHSRYTEVKKEDIDKVP 1jvnA 121 :EIGWNSCIPSENLFFGLDPYKRYYFVHSFAAILNSEKKKNLE T0326 206 :ELEI 1jvnA 165 :GWKI T0326 210 :LAESDEAGVYVVANKS 1jvnA 170 :KAKYGSEEFIAAVNKN T0326 227 :RQIFVTGHPEYDRYTLRDEYYRDIGRNL 1jvnA 186 :NIFATQFHPEKSGKAGLNVIENFLKQQS T0326 256 :VPIPANY 1jvnA 214 :PPIPNYS T0326 268 :PTKTP 1jvnA 338 :DVDGT T0326 275 :TWWSHAHLFFS 1jvnA 345 :PALEVASLYFR Number of specific fragments extracted= 17 number of extra gaps= 2 total=677 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvnA/T0326-1jvnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1jvnA/T0326-1jvnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvnA read from 1jvnA/T0326-1jvnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvnA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)V84 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)V84 Warning: unaligning (T0326)Q162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)P120 Warning: unaligning (T0326)K163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)P120 Warning: unaligning (T0326)I273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)L276 T0326 53 :QLLRLLGNTPLQVNVTLLYTETHKPKHTPIEHI 1jvnA -2 :SHMPVVHVIDVESGNLQSLTNAIEHLGYEVQLV T0326 90 :TTFSAVKDRKFDGFII 1jvnA 32 :KSPKDFNISGTSRLIL T0326 107 :GAPVE 1jvnA 48 :PGVGN T0326 115 :FEEV 1jvnA 53 :YGHF T0326 121 :WEE 1jvnA 57 :VDN T0326 124 :LTEIMEWSRHNVYSTMF 1jvnA 65 :FEKPIREYIESGKPIMG T0326 144 :AAQ 1jvnA 85 :GLQ T0326 156 :PKYELP 1jvnA 108 :KLSRFD T0326 164 :LSGVYKHRVAKDSVL 1jvnA 121 :EIGWNSCIPSENLFF T0326 181 :GHDDFFWA 1jvnA 136 :GLDPYKRY T0326 191 :SRYTEVK 1jvnA 144 :YFVHSFA T0326 199 :EDID 1jvnA 151 :AILN T0326 205 :PELEIL 1jvnA 164 :DGWKIA T0326 211 :AESDEAGVYVVANKS 1jvnA 171 :AKYGSEEFIAAVNKN T0326 227 :RQIFVTGHPEYD 1jvnA 186 :NIFATQFHPEKS T0326 240 :YTLRDEYYRDIGRNLKVPIPA 1jvnA 198 :GKAGLNVIENFLKQQSPPIPN T0326 263 :FP 1jvnA 219 :YS T0326 274 :LTWWSHAHLFFS 1jvnA 277 :GKPVQLAQKYYQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=695 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvnA/T0326-1jvnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1jvnA/T0326-1jvnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvnA read from 1jvnA/T0326-1jvnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvnA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)V84 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)V84 Warning: unaligning (T0326)Q162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)P120 Warning: unaligning (T0326)K163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)P120 T0326 37 :EILILNLMPDKIKTEIQLLRLLG 1jvnA 3 :VVHVIDVESGNLQSLTNAIEHLG T0326 65 :VNVTLLYTETHKPK 1jvnA 26 :YEVQLVKSPKDFNI T0326 98 :RKFDGFIITGAPV 1jvnA 40 :SGTSRLILPGVGN T0326 117 :EVDYWEELTEIME 1jvnA 62 :NRGFEKPIREYIE T0326 134 :NVYSTMF 1jvnA 75 :SGKPIMG T0326 144 :AAQA 1jvnA 85 :GLQA T0326 153 :YGIPKYEL 1jvnA 97 :PKSTGLNY T0326 161 :P 1jvnA 118 :P T0326 164 :LSGVYKHRVAKDS 1jvnA 121 :EIGWNSCIPSENL T0326 179 :FRGHDDFF 1jvnA 134 :FFGLDPYK T0326 187 :WAPHSRYTEVKKEDIDKV 1jvnA 144 :YFVHSFAAILNSEKKKNL T0326 205 :PELEIL 1jvnA 164 :DGWKIA T0326 211 :AE 1jvnA 171 :AK T0326 213 :SDEAGVYVVANKS 1jvnA 174 :GSEEFIAAVNKNN T0326 228 :QIFVTGHPEYDRYTLRDEYYRDIGRNLK 1jvnA 187 :IFATQFHPEKSGKAGLNVIENFLKQQSP T0326 257 :PIPAN 1jvnA 215 :PIPNY Number of specific fragments extracted= 16 number of extra gaps= 1 total=711 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3tA/T0326-1t3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t3tA expands to /projects/compbio/data/pdb/1t3t.pdb.gz 1t3tA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: CA1 for alphabet: pdb_atoms Bad short name: CB1 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms # T0326 read from 1t3tA/T0326-1t3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3tA read from 1t3tA/T0326-1t3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t3tA to template set # found chain 1t3tA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t3tA)N1136 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3tA)N1136 T0326 1 :MPINVP 1t3tA 1017 :LNVKLS T0326 7 :SGLPAVKVLAKEGI 1t3tA 1026 :NEDIAAPYIATGAR T0326 36 :LEILILNLMPDK 1t3tA 1040 :PKVAVLREQGVN T0326 48 :IKTEIQLLRLLG 1t3tA 1053 :HVEMAAAFHRAG T0326 65 :VNVTLLY 1t3tA 1065 :FDAIDVH T0326 93 :SAVKDRKFDGFIITGAPV 1t3tA 1078 :GRIGLGNFHALVACGGFS T0326 115 :FE 1t3tA 1096 :YG T0326 117 :EVDYWEELTEIMEWSRHNV 1t3tA 1109 :SILFNHRVRDEFETFFHRP T0326 136 :YSTMF 1t3tA 1129 :TLALG T0326 144 :AAQAGLYY 1t3tA 1137 :GCQMMSNL T0326 152 :FYGIP 1t3tA 1148 :IPGSE T0326 157 :KYELPQKLSGVYKHRVAK 1t3tA 1159 :RNHSDRFEARFSLVEVTQ T0326 175 :DSVLFRGH 1t3tA 1178 :PSLLLQGM T0326 183 :DDFFWA 1t3tA 1187 :GSQMPI T0326 191 :SRY 1t3tA 1197 :GEG T0326 194 :TEVKKEDIDKVP 1t3tA 1202 :EVRDDAHLAALE T0326 206 :EL 1t3tA 1216 :GL T0326 209 :ILAE 1t3tA 1218 :VALR T0326 218 :VYVVANKSERQIFVTGHPEYDR 1t3tA 1244 :ITAVTTENGRVTIMMPHPERVF T0326 258 :IPAN 1t3tA 1266 :RTVA T0326 262 :YFPNDDPTKTPILTWWSHAHLFF 1t3tA 1272 :WHPENWGEDSPWMRIFRNARKQL Number of specific fragments extracted= 21 number of extra gaps= 0 total=732 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3tA/T0326-1t3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1t3tA/T0326-1t3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3tA read from 1t3tA/T0326-1t3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3tA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t3tA)N1136 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3tA)N1136 T0326 13 :KVLAKEGIFVMT 1t3tA 1007 :EAKANDTDPGLN T0326 25 :EKRAIHQDI 1t3tA 1031 :APYIATGAR T0326 55 :LRLLGNTPLQVNVTLLYTETHKPKHTPIEHIL 1t3tA 1040 :PKVAVLREQGVNSHVEMAAAFHRAGFDAIDVH T0326 92 :FSAVKDR 1t3tA 1072 :MSDLLGG T0326 99 :KFDGFIITGAPV 1t3tA 1084 :NFHALVACGGFS T0326 115 :FEEV 1t3tA 1096 :YGDV T0326 120 :YWEELTEIMEWSRHNV 1t3tA 1112 :FNHRVRDEFETFFHRP T0326 136 :YSTMF 1t3tA 1129 :TLALG T0326 144 :AAQAGL 1t3tA 1137 :GCQMMS T0326 153 :YGI 1t3tA 1149 :PGS T0326 156 :PKYELPQK 1t3tA 1156 :RFVRNHSD T0326 164 :LSGVYKHRVAK 1t3tA 1166 :EARFSLVEVTQ T0326 175 :DSVLFRGHD 1t3tA 1178 :PSLLLQGMV T0326 185 :FFWAPHSRYTEVKKEDID 1t3tA 1187 :GSQMPIAVSHGEGRVEVR T0326 205 :PE 1t3tA 1215 :KG T0326 207 :LEILAESDEA 1t3tA 1218 :VALRYVDNFG T0326 217 :GVYVVANKSERQIFVTGHPEYDRY 1t3tA 1243 :GITAVTTENGRVTIMMPHPERVFR T0326 252 :RNLK 1t3tA 1267 :TVAN T0326 261 :NYFPNDDPTKTPILTWWSHAHLFF 1t3tA 1271 :SWHPENWGEDSPWMRIFRNARKQL Number of specific fragments extracted= 19 number of extra gaps= 0 total=751 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3tA/T0326-1t3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1t3tA/T0326-1t3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3tA read from 1t3tA/T0326-1t3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3tA in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t3tA)N1136 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t3tA)N1136 T0326 2 :PINVPSG 1t3tA 1018 :NVKLSFD T0326 25 :EKRAIHQDIR 1t3tA 1031 :APYIATGARP T0326 37 :EILILNL 1t3tA 1041 :KVAVLRE T0326 50 :TEIQLLRLLGNTPL 1t3tA 1052 :SHVEMAAAFHRAGF T0326 66 :NVTLLYT 1t3tA 1066 :DAIDVHM T0326 93 :SAVKD 1t3tA 1073 :SDLLG T0326 98 :RKFDGFIITGAPV 1t3tA 1083 :GNFHALVACGGFS T0326 115 :FEEV 1t3tA 1096 :YGDV T0326 119 :DYWEELTEI 1t3tA 1115 :RVRDEFETF T0326 131 :SRHNVYSTMF 1t3tA 1124 :FHRPQTLALG T0326 144 :AAQAGLYY 1t3tA 1137 :GCQMMSNL T0326 153 :YGIP 1t3tA 1149 :PGSE T0326 157 :KYELPQKLSGVYKHRVAK 1t3tA 1159 :RNHSDRFEARFSLVEVTQ T0326 175 :DSVLFRGHDDFF 1t3tA 1178 :PSLLLQGMVGSQ T0326 187 :WAPHSRYTEVKKEDIDKV 1t3tA 1195 :SHGEGRVEVRDDAHLAAL T0326 205 :PELEILA 1t3tA 1215 :KGLVALR T0326 218 :VYVVANKSERQIFVTGHPEYDRYT 1t3tA 1244 :ITAVTTENGRVTIMMPHPERVFRT T0326 258 :IPANYFPNDDPTKTPI 1t3tA 1268 :VANSWHPENWGEDSPW T0326 281 :HLFFSNWLN 1t3tA 1284 :MRIFRNARK Number of specific fragments extracted= 19 number of extra gaps= 0 total=770 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fexA/T0326-2fexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fexA expands to /projects/compbio/data/pdb/2fex.pdb.gz 2fexA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 18, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2fexA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 440, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 2fexA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 2fexA # T0326 read from 2fexA/T0326-2fexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fexA read from 2fexA/T0326-2fexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fexA to template set # found chain 2fexA in template set Warning: unaligning (T0326)Y153 because of BadResidue code BAD_PEPTIDE in next template residue (2fexA)D115 Warning: unaligning (T0326)G154 because of BadResidue code BAD_PEPTIDE at template residue (2fexA)D115 T0326 36 :LEILILNLMP 2fexA 2 :TRIAIALAQD T0326 46 :DKIKTEIQLLRLL 2fexA 15 :WEPALLAAAARSY T0326 63 :LQVNVTLLYTETHKP 2fexA 28 :LGVEIVHATPDGMPV T0326 87 :KFYTTFSAVKDRKFDGFIITGA 2fexA 51 :TPDTSYDALDPVDIDALVIPGG T0326 121 :WEE 2fexA 75 :WEK T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGLYY 2fexA 83 :LGGLVKRFRDRDRLVAGICAAASALGGT T0326 152 :F 2fexA 113 :L T0326 155 :IPKYELPQ 2fexA 116 :VAHTGNAL T0326 177 :VLFRGHDD 2fexA 124 :ASHKAYPA T0326 186 :FWA 2fexA 132 :YRG T0326 198 :KEDIDKVPEL 2fexA 135 :EAHYRDQPRA T0326 222 :ANKSERQIF 2fexA 145 :VSDGGVVTA T0326 237 :YDRYTLRDEYYRDIG 2fexA 156 :SAPVSFAVEILKSLG Number of specific fragments extracted= 13 number of extra gaps= 1 total=783 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fexA/T0326-2fexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2fexA/T0326-2fexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fexA read from 2fexA/T0326-2fexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fexA in template set T0326 56 :RLLGNTPLQ 2fexA 2 :TRIAIALAQ T0326 65 :VNVTLLYTETHKPK 2fexA 14 :DWEPALLAAAARSY T0326 79 :HTPIEHILKF 2fexA 29 :GVEIVHATPD T0326 89 :YTTFSAVKDRKFDGFIITGA 2fexA 53 :DTSYDALDPVDIDALVIPGG T0326 110 :VELLP 2fexA 78 :GTAAD T0326 121 :W 2fexA 83 :L T0326 125 :TEIMEWSRHNVYSTMFICWAAQAGLYY 2fexA 84 :GGLVKRFRDRDRLVAGICAAASALGGT T0326 154 :GI 2fexA 111 :GV T0326 156 :PKYELPQKLSGV 2fexA 130 :PAYRGEAHYRDQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=792 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fexA/T0326-2fexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2fexA/T0326-2fexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fexA read from 2fexA/T0326-2fexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fexA in template set Warning: unaligning (T0326)R180 because of BadResidue code BAD_PEPTIDE in next template residue (2fexA)D115 Warning: unaligning (T0326)G181 because of BadResidue code BAD_PEPTIDE at template residue (2fexA)D115 T0326 37 :EILILNL 2fexA 3 :RIAIALA T0326 44 :MPDK 2fexA 13 :ADWE T0326 51 :EIQLLRLL 2fexA 17 :PALLAAAA T0326 63 :LQVNVTLLYTETHK 2fexA 28 :LGVEIVHATPDGMP T0326 78 :KHTPIEHIL 2fexA 52 :PDTSYDALD T0326 97 :DRKFDGFIITGA 2fexA 61 :PVDIDALVIPGG T0326 119 :DYWEE 2fexA 73 :LSWEK T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGLY 2fexA 83 :LGGLVKRFRDRDRLVAGICAAASALGG T0326 153 :YG 2fexA 110 :TG T0326 178 :LF 2fexA 112 :VL T0326 182 :HDD 2fexA 116 :VAH T0326 194 :TEVKKEDIDKVPELE 2fexA 119 :TGNALASHKAYPAYR T0326 209 :ILAESDEAGV 2fexA 137 :HYRDQPRAVS T0326 223 :NKS 2fexA 147 :DGG T0326 228 :QIFVTG 2fexA 150 :VVTAAG T0326 238 :DRYTLRDEYYRDIGR 2fexA 157 :APVSFAVEILKSLGL Number of specific fragments extracted= 16 number of extra gaps= 1 total=808 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p5fA/T0326-1p5fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1p5fA/T0326-1p5fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p5fA read from 1p5fA/T0326-1p5fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p5fA in training set Warning: unaligning (T0326)P35 because first residue in template chain is (1p5fA)S3 Warning: unaligning (T0326)L36 because of BadResidue code BAD_PEPTIDE at template residue (1p5fA)K4 Warning: unaligning (T0326)I141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p5fA)C106 Warning: unaligning (T0326)C142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)C106 Warning: unaligning (T0326)W143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)A107 T0326 37 :EILILNLMP 1p5fA 5 :RALVILAKG T0326 48 :IKTEIQLLRLLG 1p5fA 19 :TVIPVDVMRRAG T0326 65 :VNVTLLYTETHKPKHTPIEHILKFYTTFSAV 1p5fA 31 :IKVTVAGLAGKDPVQCSRDVVICPDASLEDA T0326 96 :KDRKFDGFIITGA 1p5fA 63 :KEGPYDVVVLPGG T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1p5fA 79 :AQNLSESAAVKEILKEQENRKGLIAA T0326 144 :AAQAGLYY 1p5fA 108 :GPTALLAH T0326 182 :HDDFFWA 1p5fA 119 :FGSKVTT T0326 194 :TEVKKEDIDK 1p5fA 126 :HPLAKDKMMN T0326 206 :ELEILAESD 1p5fA 136 :GGHYTYSEN T0326 217 :GVY 1p5fA 145 :RVE T0326 224 :KSERQIFV 1p5fA 148 :KDGLILTS T0326 237 :YDRYTLRDEY 1p5fA 156 :RGPGTSFEFA T0326 281 :HLFF 1p5fA 166 :LAIV Number of specific fragments extracted= 13 number of extra gaps= 1 total=821 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p5fA/T0326-1p5fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1p5fA/T0326-1p5fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p5fA read from 1p5fA/T0326-1p5fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p5fA in training set Warning: unaligning (T0326)I141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p5fA)C106 Warning: unaligning (T0326)C142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)C106 Warning: unaligning (T0326)W143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)A107 T0326 56 :RLLGNTPLQVNVT 1p5fA 5 :RALVILAKGAEEM T0326 69 :LLYTETHKPKHTPIEHI 1p5fA 20 :VIPVDVMRRAGIKVTVA T0326 86 :LKFYTTFSAVKDR 1p5fA 52 :ICPDASLEDAKKE T0326 99 :KFDGFIITGA 1p5fA 66 :PYDVVVLPGG T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1p5fA 79 :AQNLSESAAVKEILKEQENRKGLIAA T0326 144 :AAQAGLYY 1p5fA 108 :GPTALLAH T0326 153 :YGIPKYELPQ 1p5fA 119 :FGSKVTTHPL Number of specific fragments extracted= 7 number of extra gaps= 1 total=828 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p5fA/T0326-1p5fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1p5fA/T0326-1p5fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p5fA read from 1p5fA/T0326-1p5fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p5fA in training set Warning: unaligning (T0326)I141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p5fA)C106 Warning: unaligning (T0326)C142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)C106 Warning: unaligning (T0326)W143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p5fA)A107 T0326 37 :E 1p5fA 5 :R T0326 39 :LILNLMPDKI 1p5fA 6 :ALVILAKGAE T0326 49 :KTEIQLLRLLGNTPLQVNVTL 1p5fA 17 :METVIPVDVMRRAGIKVTVAG T0326 70 :LYTETHKP 1p5fA 44 :VQCSRDVV T0326 88 :FYTTFSAVKDR 1p5fA 54 :PDASLEDAKKE T0326 99 :KFDGFIITGA 1p5fA 66 :PYDVVVLPGG T0326 120 :YWEELTEIMEWSRHNVYSTMF 1p5fA 84 :ESAAVKEILKEQENRKGLIAA T0326 144 :AAQAGLYY 1p5fA 108 :GPTALLAH T0326 153 :YGIPKYELPQK 1p5fA 119 :FGSKVTTHPLA T0326 198 :KEDIDKVPE 1p5fA 130 :KDKMMNGGH T0326 209 :ILAESDEAGV 1p5fA 139 :YTYSENRVEK T0326 223 :N 1p5fA 149 :D T0326 226 :ERQIFVT 1p5fA 150 :GLILTSR T0326 238 :DRYTLRDEYY 1p5fA 157 :GPGTSFEFAL Number of specific fragments extracted= 14 number of extra gaps= 1 total=842 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7rA/T0326-1q7rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q7rA expands to /projects/compbio/data/pdb/1q7r.pdb.gz 1q7rA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 515, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 624, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1054, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1q7rA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1502, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1504, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 1q7rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 1q7rA # T0326 read from 1q7rA/T0326-1q7rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7rA read from 1q7rA/T0326-1q7rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q7rA to template set # found chain 1q7rA in template set T0326 34 :RPLEILILN 1q7rA -1 :SNMKIGVLG T0326 44 :MPDKIKTEIQLLRLLG 1q7rA 8 :LQGAVREHVRAIEACG T0326 65 :VNVTLLYTET 1q7rA 24 :AEAVIVKKSE T0326 96 :KDRKFDGFIITGAPV 1q7rA 34 :QLEGLDGLVLPGGES T0326 115 :FEEVDYWEE 1q7rA 49 :TTMRRLIDR T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGL 1q7rA 60 :LMEPLKQFAAAGKPMFGTCAGLILLA T0326 155 :IPKYELPQKLSGVYKHRV 1q7rA 86 :KRIVGYDEPHLGLMDITV T0326 175 :DSV 1q7rA 112 :RES T0326 178 :LFRGHDDFFWAPHSRYTEV 1q7rA 120 :SIKGVGDGFVGVFIRAPHI T0326 205 :PELEILAESDEAGVYVVA 1q7rA 143 :DGVDVLATYNDRIVAARQ T0326 226 :ERQIFVTGHPEYDRY 1q7rA 161 :GQFLGCSFHPELTDD T0326 281 :HLFFSNWLNYCI 1q7rA 176 :HRLMQYFLNMVK Number of specific fragments extracted= 12 number of extra gaps= 0 total=854 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7rA/T0326-1q7rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1q7rA/T0326-1q7rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7rA read from 1q7rA/T0326-1q7rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7rA in template set Warning: unaligning (T0326)T50 because first residue in template chain is (1q7rA)L-5 T0326 51 :EIQLLRLLGNTPLQVNVTL 1q7rA -4 :YFQSNMKIGVLGLQGAVRE T0326 71 :YTETHKPKHTPIEHILK 1q7rA 15 :HVRAIEACGAEAVIVKK T0326 92 :FS 1q7rA 32 :SE T0326 96 :KDRKFDGFIITGAP 1q7rA 34 :QLEGLDGLVLPGGE T0326 118 :VDYWEE 1q7rA 48 :STTMRR T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGL 1q7rA 60 :LMEPLKQFAAAGKPMFGTCAGLILLA T0326 156 :PKYELPQKLSGVYKHRVAKD 1q7rA 87 :RIVGYDEPHLGLMDITVERN T0326 179 :FRGHDDFFWA 1q7rA 121 :IKGVGDGFVG T0326 193 :YTEVK 1q7rA 131 :VFIRA T0326 199 :EDIDKVPE 1q7rA 136 :PHIVEAGD T0326 207 :LEILAESDEA 1q7rA 145 :VDVLATYNDR T0326 218 :VYVVANKS 1q7rA 155 :IVAARQGQ T0326 228 :QIFVTGHPEYDRYT 1q7rA 163 :FLGCSFHPELTDDH T0326 282 :LFFSNWLNYCIY 1q7rA 177 :RLMQYFLNMVKE Number of specific fragments extracted= 14 number of extra gaps= 0 total=868 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7rA/T0326-1q7rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1q7rA/T0326-1q7rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7rA read from 1q7rA/T0326-1q7rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7rA in template set T0326 33 :IRPLEILILNLMPDKI 1q7rA -2 :QSNMKIGVLGLQGAVR T0326 53 :QLLRLLGNTP 1q7rA 14 :EHVRAIEACG T0326 65 :VNVTLLYTETH 1q7rA 24 :AEAVIVKKSEQ T0326 97 :DRKFDGFIITGAP 1q7rA 35 :LEGLDGLVLPGGE T0326 121 :WEELTEIMEW 1q7rA 48 :STTMRRLIDR T0326 131 :SRHNVYSTMFICWAAQAGLY 1q7rA 67 :FAAAGKPMFGTCAGLILLAK T0326 156 :PKYELPQKLSGVYKHRVA 1q7rA 87 :RIVGYDEPHLGLMDITVE T0326 174 :KDSV 1q7rA 110 :RQRE T0326 179 :FRGHDDFFWAPHSRY 1q7rA 121 :IKGVGDGFVGVFIRA T0326 194 :TEVK 1q7rA 139 :VEAG T0326 205 :PELEILAESDEAGVYVVA 1q7rA 143 :DGVDVLATYNDRIVAARQ T0326 226 :ERQIFVTGHPEYDR 1q7rA 161 :GQFLGCSFHPELTD T0326 240 :YTLRDEYYRD 1q7rA 176 :HRLMQYFLNM Number of specific fragments extracted= 13 number of extra gaps= 0 total=881 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhqA/T0326-1vhqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vhqA expands to /projects/compbio/data/pdb/1vhq.pdb.gz 1vhqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OD for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1055, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 1vhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1303, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 1vhqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1509, because occupancy 0.500 <= existing 0.500 in 1vhqA Skipped atom 1560, because occupancy 0.500 <= existing 0.500 in 1vhqA # T0326 read from 1vhqA/T0326-1vhqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhqA read from 1vhqA/T0326-1vhqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vhqA to template set # found chain 1vhqA in template set Warning: unaligning (T0326)P35 because first residue in template chain is (1vhqA)M4 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhqA)I139 T0326 36 :LEILILNLMPDK 1vhqA 5 :KKIGVILSGCGV T0326 48 :IKTEIQLLRLLGNTPLQVNVTLL 1vhqA 22 :IHEAVLTLLAISRSGAQAVCFAP T0326 73 :ET 1vhqA 45 :DK T0326 75 :HKPKHTPIEH 1vhqA 57 :GEAMTETRNV T0326 89 :YTTFSAVKDRKFDGFIITGA 1vhqA 78 :IRPLAQADAAELDALIVPGG T0326 112 :LLP 1vhqA 104 :LSN T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1vhqA 111 :GSECTVDRELKALAQAMHQAGKPLGF T0326 144 :AAQAGLYY 1vhqA 140 :APAMLPKI T0326 182 :HDDFFWAPH 1vhqA 148 :FDFPLRLTI T0326 195 :EVKKEDIDKVP 1vhqA 157 :GTDIDTAEVLE T0326 206 :ELEI 1vhqA 170 :GAEH T0326 213 :SDEAGV 1vhqA 176 :CPVDDI T0326 221 :VANKSERQIFVTGHPE 1vhqA 182 :VVDEDNKIVTTPAYML T0326 270 :KTPILTWWSHAHLFFSNWLNYC 1vhqA 198 :AQNIAEAASGIDKLVSRVLVLA Number of specific fragments extracted= 14 number of extra gaps= 0 total=895 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhqA/T0326-1vhqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1vhqA/T0326-1vhqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhqA read from 1vhqA/T0326-1vhqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhqA in template set Warning: unaligning (T0326)L55 because first residue in template chain is (1vhqA)M4 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 T0326 56 :RLLGNTPLQVNVT 1vhqA 5 :KKIGVILSGCGVY T0326 69 :LLYTETHKPKHTPIEHILKF 1vhqA 26 :VLTLLAISRSGAQAVCFAPD T0326 89 :YTTF 1vhqA 63 :TRNV T0326 93 :SAVKDRKFDGFIITGAPV 1vhqA 82 :AQADAAELDALIVPGGFG T0326 112 :LLP 1vhqA 104 :LSN T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1vhqA 111 :GSECTVDRELKALAQAMHQAGKPLGF T0326 181 :GHDDFFWA 1vhqA 147 :IFDFPLRL T0326 195 :EVK 1vhqA 155 :TIG T0326 199 :EDID 1vhqA 158 :TDID T0326 203 :KVP 1vhqA 175 :PCP T0326 206 :E 1vhqA 179 :D T0326 207 :L 1vhqA 181 :I T0326 221 :VANKSERQIFV 1vhqA 182 :VVDEDNKIVTT T0326 235 :PEYDR 1vhqA 193 :PAYML T0326 270 :KTPILTWWSHAHLFFSNWLNYC 1vhqA 198 :AQNIAEAASGIDKLVSRVLVLA Number of specific fragments extracted= 15 number of extra gaps= 0 total=910 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhqA/T0326-1vhqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1vhqA/T0326-1vhqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhqA read from 1vhqA/T0326-1vhqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhqA in template set Warning: unaligning (T0326)P35 because first residue in template chain is (1vhqA)M4 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 T0326 36 :LEILILNLMPDKI 1vhqA 5 :KKIGVILSGCGVY T0326 49 :KTEIQLLRLLGNTPLQVNVTL 1vhqA 23 :HEAVLTLLAISRSGAQAVCFA T0326 71 :YT 1vhqA 53 :NH T0326 73 :ETHKPKHTPIEHILKFY 1vhqA 58 :EAMTETRNVLIEAARIT T0326 91 :TFSAVKDRKFDGFIITGA 1vhqA 80 :PLAQADAAELDALIVPGG T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1vhqA 111 :GSECTVDRELKALAQAMHQAGKPLGF T0326 176 :SVLF 1vhqA 140 :APAM T0326 182 :HDDFFWAPHSRYTEV 1vhqA 148 :FDFPLRLTIGTDIDT T0326 198 :KEDIDKV 1vhqA 163 :AEVLEEM T0326 206 :ELEILAESDEA 1vhqA 170 :GAEHVPCPVDD T0326 220 :VVANKSERQIFVTGH 1vhqA 181 :IVVDEDNKIVTTPAY T0326 238 :DRYTLRDEYYRDIG 1vhqA 200 :NIAEAASGIDKLVS Number of specific fragments extracted= 12 number of extra gaps= 0 total=922 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0bA/T0326-1t0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0bA expands to /projects/compbio/data/pdb/1t0b.pdb.gz 1t0bA:Skipped atom 28, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 40, because occupancy 0.400 <= existing 0.600 in 1t0bA Skipped atom 157, because occupancy 0.300 <= existing 0.500 in 1t0bA Skipped atom 159, because occupancy 0.300 <= existing 0.500 in 1t0bA Skipped atom 161, because occupancy 0.300 <= existing 0.500 in 1t0bA Skipped atom 163, because occupancy 0.300 <= existing 0.500 in 1t0bA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1t0bA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1t0bA # T0326 read from 1t0bA/T0326-1t0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0bA read from 1t0bA/T0326-1t0bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0bA to template set # found chain 1t0bA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1t0bA)T3 Warning: unaligning (T0326)N253 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)R226 Warning: unaligning (T0326)L254 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)R226 Warning: unaligning (T0326)K270 because last residue in template chain is (1t0bA)A242 T0326 35 :PLEILILNLM 1t0bA 4 :PIRVVVWNEF T0326 45 :PDK 1t0bA 27 :PEG T0326 48 :IKTEIQLLRLLG 1t0bA 31 :HTVIASYLAEAG T0326 65 :VNVTLLYTETHKPKHT 1t0bA 43 :FDAATAVLDEPEHGLT T0326 93 :SA 1t0bA 59 :DE T0326 97 :DRKFDGFIITGAPV 1t0bA 62 :LDRCDVLVWWGHIA T0326 115 :FEEV 1t0bA 76 :HDEV T0326 121 :WEELTEIMEWSRHNVYSTMFI 1t0bA 80 :KDEVVERVHRRVLEGMGLIVL T0326 148 :GLYYFYGIPK 1t0bA 108 :IFKKLMGTTC T0326 159 :ELPQKLSGV 1t0bA 118 :NLKWREADE T0326 168 :YKHR 1t0bA 128 :ERLW T0326 172 :VAKDSVLFRGHDDFFWA 1t0bA 133 :VAPGHPIVEGIGPYIEL T0326 201 :IDKVP 1t0bA 161 :IPEPD T0326 208 :EILAE 1t0bA 166 :ETIFI T0326 213 :SDEAG 1t0bA 173 :FEGGE T0326 218 :VYVVANKSERQIFVTG 1t0bA 182 :GCTFTRGKGKIFYFRP T0326 234 :HPEYDRYTLRDEYYRDIG 1t0bA 202 :YPTYHHPDVLKVIANAVR T0326 252 :R 1t0bA 224 :V T0326 255 :KVPIPANYFPNDDPT 1t0bA 227 :GEIVFGNVKPLEPIK Number of specific fragments extracted= 19 number of extra gaps= 1 total=941 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0bA/T0326-1t0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1t0bA/T0326-1t0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0bA read from 1t0bA/T0326-1t0bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0bA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1t0bA)T3 Warning: unaligning (T0326)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0bA)D19 Warning: unaligning (T0326)I48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0bA)D19 Warning: unaligning (T0326)E195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0bA)Y155 Warning: unaligning (T0326)V196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0bA)Y155 Warning: unaligning (T0326)D200 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)F158 Warning: unaligning (T0326)I201 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)F158 Warning: unaligning (T0326)I258 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)R226 Warning: unaligning (T0326)P259 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)R226 T0326 35 :PLEILILNLMP 1t0bA 4 :PIRVVVWNEFR T0326 46 :D 1t0bA 17 :K T0326 49 :KTEIQL 1t0bA 20 :EQVRAI T0326 63 :LQVNVTLLYTETHKPKHTPIEHI 1t0bA 26 :YPEGMHTVIASYLAEAGFDAATA T0326 87 :KFYTTF 1t0bA 49 :VLDEPE T0326 93 :SAVKD 1t0bA 59 :DEVLD T0326 99 :KFDGFIITG 1t0bA 64 :RCDVLVWWG T0326 112 :LLPFEEV 1t0bA 73 :HIAHDEV T0326 121 :WEELTEIMEWSRHNVYSTMFI 1t0bA 80 :KDEVVERVHRRVLEGMGLIVL T0326 148 :GLYYFYG 1t0bA 108 :IFKKLMG T0326 156 :PKYELPQKL 1t0bA 115 :TTCNLKWRE T0326 165 :SGVYKHRV 1t0bA 125 :DEKERLWV T0326 173 :AKDSVLFRGHDDFFWA 1t0bA 134 :APGHPIVEGIGPYIEL T0326 191 :SRYT 1t0bA 150 :EQEE T0326 197 :K 1t0bA 156 :G T0326 202 :DKVPE 1t0bA 159 :FDIPE T0326 207 :LEILAES 1t0bA 165 :DETIFIS T0326 214 :DEAG 1t0bA 174 :EGGE T0326 218 :VYVVANKSERQIFVT 1t0bA 182 :GCTFTRGKGKIFYFR T0326 233 :GHPEYD 1t0bA 198 :GHETYP T0326 239 :RYTLRDEYYRDIGRNLKVP 1t0bA 206 :HHPDVLKVIANAVRWAAPV T0326 260 :ANYFPNDDPTKTPI 1t0bA 227 :GEIVFGNVKPLEPI Number of specific fragments extracted= 22 number of extra gaps= 4 total=963 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0bA/T0326-1t0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1t0bA/T0326-1t0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0bA read from 1t0bA/T0326-1t0bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0bA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1t0bA)T3 Warning: unaligning (T0326)T194 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)F158 Warning: unaligning (T0326)E195 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)F158 Warning: unaligning (T0326)P257 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)R226 Warning: unaligning (T0326)I258 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)R226 Warning: unaligning (T0326)L274 because last residue in template chain is (1t0bA)A242 T0326 35 :PLEILILNLMPDKI 1t0bA 4 :PIRVVVWNEFRHEK T0326 50 :TEIQLLRLLGNTPLQVNVTLLYTETHKPK 1t0bA 30 :MHTVIASYLAEAGFDAATAVLDEPEHGLT T0326 93 :SAVK 1t0bA 59 :DEVL T0326 98 :RKFDGFIITG 1t0bA 63 :DRCDVLVWWG T0326 112 :LLPFEEVD 1t0bA 73 :HIAHDEVK T0326 120 :YWEELTEI 1t0bA 83 :VVERVHRR T0326 131 :SRHNV 1t0bA 91 :VLEGM T0326 137 :STMFI 1t0bA 96 :GLIVL T0326 148 :GLYYFYGIPKYELPQKLSGVYKHRVAKD 1t0bA 108 :IFKKLMGTTCNLKWREADEKERLWVVAP T0326 176 :SVLFRGHDDFFWAPHS 1t0bA 137 :HPIVEGIGPYIELEQE T0326 196 :VK 1t0bA 159 :FD T0326 204 :VPELEILA 1t0bA 161 :IPEPDETI T0326 212 :ESDEA 1t0bA 174 :EGGEV T0326 217 :G 1t0bA 180 :R T0326 218 :VYVVANKSERQIFVTG 1t0bA 182 :GCTFTRGKGKIFYFRP T0326 234 :H 1t0bA 199 :H T0326 235 :PEYDRYTLRDEYYRDIGRNLKV 1t0bA 203 :PTYHHPDVLKVIANAVRWAAPV T0326 259 :PANYFPNDDPTKTPI 1t0bA 227 :GEIVFGNVKPLEPIK Number of specific fragments extracted= 18 number of extra gaps= 2 total=981 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ab0A/T0326-2ab0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2ab0A/T0326-2ab0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ab0A read from 2ab0A/T0326-2ab0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ab0A in training set Warning: unaligning (T0326)R98 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E66 Warning: unaligning (T0326)K99 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E66 Warning: unaligning (T0326)F100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ab0A)Y67 Warning: unaligning (T0326)D183 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G122 Warning: unaligning (T0326)D184 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G122 Warning: unaligning (T0326)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ab0A)Q156 Warning: unaligning (T0326)T232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ab0A)Q156 Warning: unaligning (T0326)I258 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G190 Warning: unaligning (T0326)P259 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G190 Warning: unaligning (T0326)P264 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E196 Warning: unaligning (T0326)N265 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E196 T0326 37 :E 2ab0A 4 :S T0326 39 :LILNLMPDKIKTE 2ab0A 5 :ALVCLAPGSEETE T0326 52 :IQLLRLLG 2ab0A 22 :IDLLVRGG T0326 65 :VNVTLLYTETH 2ab0A 30 :IKVTTASVASD T0326 78 :KHTP 2ab0A 41 :GNLA T0326 82 :IEHILKFYTTFSAVKD 2ab0A 49 :RGVKLLADAPLVEVAD T0326 101 :DGFIITGA 2ab0A 68 :DVIVLPGG T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMFICWAAQAGLYYFY 2ab0A 79 :AECFRDSTLLVETVKQFHRSGRIVAAICAAPATVLVPHD T0326 181 :GH 2ab0A 118 :IF T0326 185 :FFWA 2ab0A 123 :NMTG T0326 194 :TEVKKEDIDK 2ab0A 127 :FPTLKDKIPA T0326 220 :VVANKSERQIF 2ab0A 144 :VVWDARVKLLT T0326 233 :GHPEYDRYTLR 2ab0A 157 :GPGTAIDFGLK T0326 244 :DEYYRDIGRNLKVP 2ab0A 175 :REKAHEVASQLVMA T0326 260 :ANYF 2ab0A 191 :IYNY Number of specific fragments extracted= 15 number of extra gaps= 5 total=996 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ab0A/T0326-2ab0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2ab0A/T0326-2ab0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ab0A read from 2ab0A/T0326-2ab0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ab0A in training set Warning: unaligning (T0326)R98 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E66 Warning: unaligning (T0326)K99 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E66 Warning: unaligning (T0326)F100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ab0A)Y67 Warning: unaligning (T0326)G181 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G122 Warning: unaligning (T0326)H182 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G122 Warning: unaligning (T0326)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ab0A)Q156 Warning: unaligning (T0326)T232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ab0A)Q156 Warning: unaligning (T0326)I258 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G190 Warning: unaligning (T0326)P259 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G190 Warning: unaligning (T0326)P264 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E196 Warning: unaligning (T0326)N265 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E196 T0326 56 :RLLGNTPLQVNVTLL 2ab0A 4 :SALVCLAPGSEETEA T0326 71 :YTETHKPKHTPIEHILKF 2ab0A 21 :TIDLLVRGGIKVTTASVA T0326 89 :YTTFSAVKD 2ab0A 56 :DAPLVEVAD T0326 101 :DGFIITGA 2ab0A 68 :DVIVLPGG T0326 116 :EEVDYWEE 2ab0A 77 :KGAECFRD T0326 124 :LTEIMEWSRHNVYSTMFICW 2ab0A 88 :LVETVKQFHRSGRIVAAICA T0326 147 :AGLYYFY 2ab0A 108 :APATVLV T0326 175 :DSVLFR 2ab0A 115 :PHDIFP T0326 185 :FFW 2ab0A 123 :NMT T0326 195 :EVK 2ab0A 126 :GFP T0326 199 :EDIDKVPE 2ab0A 129 :TLKDKIPA T0326 216 :A 2ab0A 139 :W T0326 220 :VVANKSERQIF 2ab0A 144 :VVWDARVKLLT T0326 233 :G 2ab0A 157 :G T0326 239 :RYT 2ab0A 158 :PGT T0326 242 :LRDEYYRDIGRNLKVP 2ab0A 173 :VGREKAHEVASQLVMA T0326 260 :ANYF 2ab0A 191 :IYNY Number of specific fragments extracted= 17 number of extra gaps= 5 total=1013 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ab0A/T0326-2ab0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2ab0A/T0326-2ab0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ab0A read from 2ab0A/T0326-2ab0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ab0A in training set Warning: unaligning (T0326)R98 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E66 Warning: unaligning (T0326)K99 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E66 Warning: unaligning (T0326)F100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ab0A)Y67 Warning: unaligning (T0326)S176 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G122 Warning: unaligning (T0326)V177 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G122 Warning: unaligning (T0326)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ab0A)Q156 Warning: unaligning (T0326)T232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ab0A)Q156 Warning: unaligning (T0326)I258 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)G190 Warning: unaligning (T0326)P259 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)G190 Warning: unaligning (T0326)P264 because of BadResidue code BAD_PEPTIDE in next template residue (2ab0A)E196 Warning: unaligning (T0326)N265 because of BadResidue code BAD_PEPTIDE at template residue (2ab0A)E196 T0326 39 :LILNLMPDKIKTE 2ab0A 5 :ALVCLAPGSEETE T0326 52 :IQLLRLLGNTPLQVNVTLLYTETHKP 2ab0A 19 :VTTIDLLVRGGIKVTTASVASDGNLA T0326 78 :KHTP 2ab0A 48 :SRGV T0326 88 :FYTTFSAVKD 2ab0A 55 :ADAPLVEVAD T0326 101 :DGFIITGA 2ab0A 68 :DVIVLPGG T0326 122 :EELTEIMEWSRHNVYSTMFICWAAQAG 2ab0A 86 :TLLVETVKQFHRSGRIVAAICAAPATV T0326 150 :YYFYGI 2ab0A 113 :LVPHDI T0326 174 :KD 2ab0A 119 :FP T0326 178 :L 2ab0A 123 :N T0326 186 :FWAPHSRYTEVKKEDI 2ab0A 124 :MTGFPTLKDKIPAEQW T0326 212 :ESDE 2ab0A 140 :LDKR T0326 220 :VVANKSERQIF 2ab0A 144 :VVWDARVKLLT T0326 233 :G 2ab0A 157 :G T0326 239 :RYTLR 2ab0A 158 :PGTAI T0326 244 :DEYYRDIGRNLKVP 2ab0A 175 :REKAHEVASQLVMA T0326 260 :ANYF 2ab0A 191 :IYNY Number of specific fragments extracted= 16 number of extra gaps= 5 total=1029 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u9cA/T0326-1u9cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u9cA expands to /projects/compbio/data/pdb/1u9c.pdb.gz 1u9cA:Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1u9cA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1u9cA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1u9cA # T0326 read from 1u9cA/T0326-1u9cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9cA read from 1u9cA/T0326-1u9cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u9cA to template set # found chain 1u9cA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1u9cA)M1 Warning: unaligning (T0326)G107 because of BadResidue code BAD_PEPTIDE in next template residue (1u9cA)G95 Warning: unaligning (T0326)A108 because of BadResidue code BAD_PEPTIDE at template residue (1u9cA)G95 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9cA)H127 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9cA)H127 T0326 35 :PLEILILNLMP 1u9cA 2 :SKRVLMVVTNH T0326 46 :DK 1u9cA 17 :DD T0326 48 :IKTEIQLLRLLGNTPLQVNVTLLY 1u9cA 25 :LEEFAVPYLVFQEKGYDVKVASIQ T0326 72 :TETHKPKHTPIEH 1u9cA 54 :LDPRSINEKDPSW T0326 85 :ILK 1u9cA 76 :TAR T0326 92 :FSAVKDRKFDGFIIT 1u9cA 79 :LSKDDAHGFDAIFLP T0326 109 :PVE 1u9cA 102 :FPD T0326 121 :WEELTEIMEWSRHNVYSTMF 1u9cA 105 :NETLQYVLQQFAEDGRIIAA T0326 144 :A 1u9cA 128 :G T0326 152 :FYGIP 1u9cA 132 :LVNAT T0326 173 :AKDS 1u9cA 137 :YKDG T0326 177 :VLFRG 1u9cA 142 :PIVKG T0326 184 :DFFWA 1u9cA 147 :KTVTS T0326 189 :PHSRYTEVKKEDIDKV 1u9cA 162 :LDVHMPFLLESTLRLR T0326 206 :ELEILAESDEAG 1u9cA 178 :GANFVRGGKWTD T0326 220 :VVANKS 1u9cA 191 :SVRDGN T0326 229 :IFVTGHPEYDR 1u9cA 197 :LITGQNPQSSR T0326 241 :TLRDEYYRDIGRN 1u9cA 208 :STAEKVVAALEER Number of specific fragments extracted= 18 number of extra gaps= 1 total=1047 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u9cA/T0326-1u9cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1u9cA/T0326-1u9cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9cA read from 1u9cA/T0326-1u9cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u9cA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1u9cA)M1 Warning: unaligning (T0326)G107 because of BadResidue code BAD_PEPTIDE in next template residue (1u9cA)G95 Warning: unaligning (T0326)A108 because of BadResidue code BAD_PEPTIDE at template residue (1u9cA)G95 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9cA)H127 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9cA)H127 T0326 35 :PLEILILNLMPDKIKTEIQ 1u9cA 2 :SKRVLMVVTNHTTITDDHK T0326 61 :TPLQVNVTLLYTETHKPKHTPIEHI 1u9cA 21 :TGLWLEEFAVPYLVFQEKGYDVKVA T0326 86 :LKFYTTFSAVKDR 1u9cA 60 :NEKDPSWAEAEAA T0326 99 :KFDGFIIT 1u9cA 86 :GFDAIFLP T0326 109 :PVE 1u9cA 96 :HGT T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1u9cA 99 :MFDFPDNETLQYVLQQFAEDGRIIAA T0326 144 :A 1u9cA 128 :G T0326 153 :YGI 1u9cA 133 :VNA T0326 157 :KYE 1u9cA 136 :TYK T0326 174 :KDSVLFRGH 1u9cA 139 :DGTPIVKGK T0326 187 :WA 1u9cA 148 :TV T0326 191 :SRYT 1u9cA 150 :TSFT T0326 199 :EDIDKVP 1u9cA 161 :GLDVHMP T0326 206 :ELEILAESDEAG 1u9cA 178 :GANFVRGGKWTD T0326 219 :YVVANKS 1u9cA 190 :FSVRDGN T0326 228 :QIFVTG 1u9cA 197 :LITGQN T0326 235 :PEYD 1u9cA 203 :PQSS T0326 277 :WSHAHLFFSN 1u9cA 207 :RSTAEKVVAA Number of specific fragments extracted= 18 number of extra gaps= 1 total=1065 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u9cA/T0326-1u9cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1u9cA/T0326-1u9cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9cA read from 1u9cA/T0326-1u9cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u9cA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1u9cA)M1 Warning: unaligning (T0326)G107 because of BadResidue code BAD_PEPTIDE in next template residue (1u9cA)G95 Warning: unaligning (T0326)A108 because of BadResidue code BAD_PEPTIDE at template residue (1u9cA)G95 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9cA)H127 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9cA)H127 T0326 35 :PLEILILNLMPDKI 1u9cA 2 :SKRVLMVVTNHTTI T0326 49 :KTEIQLLRLLGNTPLQVNVTLL 1u9cA 26 :EEFAVPYLVFQEKGYDVKVASI T0326 71 :YTETHKPKHTPIEHILKFYTT 1u9cA 55 :DPRSINEKDPSWAEAEAALKH T0326 98 :RKFDGFIIT 1u9cA 85 :HGFDAIFLP T0326 122 :EELTEIMEWSRHNVYSTMF 1u9cA 106 :ETLQYVLQQFAEDGRIIAA T0326 144 :A 1u9cA 128 :G T0326 164 :LSGVYKHRVAKDSVLFRGH 1u9cA 129 :PSGLVNATYKDGTPIVKGK T0326 187 :WAPH 1u9cA 148 :TVTS T0326 196 :VKKEDIDKVP 1u9cA 152 :FTDEEEREVG T0326 206 :ELEILAESDEAGV 1u9cA 178 :GANFVRGGKWTDF T0326 220 :VVANKS 1u9cA 191 :SVRDGN T0326 230 :FVTGHPEYDRYTLRDEYYRDIGRN 1u9cA 197 :LITGQNPQSSRSTAEKVVAALEER Number of specific fragments extracted= 12 number of extra gaps= 1 total=1077 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oB/T0326-1c3oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c3oB expands to /projects/compbio/data/pdb/1c3o.pdb.gz 1c3oB:# T0326 read from 1c3oB/T0326-1c3oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3oB read from 1c3oB/T0326-1c3oB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c3oB to template set # found chain 1c3oB in template set Warning: unaligning (T0326)L112 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oB)A246 Warning: unaligning (T0326)L113 because of BadResidue code BAD_PEPTIDE at template residue (1c3oB)A246 T0326 31 :QDIRPLEILILNLM 1c3oB 187 :EDELPFHVVAYDFG T0326 51 :EIQLLRLL 1c3oB 202 :KRNILRML T0326 59 :G 1c3oB 213 :G T0326 65 :VNVTLLYTE 1c3oB 214 :CRLTIVPAQ T0326 90 :TTFSAVKDRKFDGFIITGAPVE 1c3oB 223 :TSAEDVLKMNPDGIFLSNGPGD T0326 114 :P 1c3oB 247 :P T0326 121 :WEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHRVAKD 1c3oB 248 :CDYAITAIQKFLETDIPVFGISLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEK T0326 183 :DDFFWAPHSRYTEVKKED 1c3oB 303 :NVVMITAQNHGFAVDEAT T0326 204 :VP 1c3oB 321 :LP T0326 206 :ELEILAES 1c3oB 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPE 1c3oB 333 :FDGTLQGIHRTDKPAFSFQGHPE T0326 237 :YDRYTLRDEYYRDIG 1c3oB 365 :PLFDHFIELIEQYRK Number of specific fragments extracted= 12 number of extra gaps= 1 total=1089 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oB/T0326-1c3oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1c3oB/T0326-1c3oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3oB read from 1c3oB/T0326-1c3oB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c3oB in template set Warning: unaligning (T0326)L112 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oB)A246 Warning: unaligning (T0326)E116 because of BadResidue code BAD_PEPTIDE at template residue (1c3oB)A246 T0326 10 :PAVKVLAKEGIFV 1c3oB 117 :KLTRLLREKGAQN T0326 23 :MTEKRAIHQ 1c3oB 138 :PDAALALEK T0326 32 :DIRPLEILILNLMPD 1c3oB 163 :TTAEAYSWTQGSWTL T0326 47 :K 1c3oB 179 :G T0326 48 :IKTEIQLLR 1c3oB 183 :EAKKEDELP T0326 57 :LLGNTPLQ 1c3oB 193 :HVVAYDFG T0326 67 :VTLLYTETHKPKHTPIEHI 1c3oB 201 :AKRNILRMLVDRGCRLTIV T0326 87 :KFYTTFSAVKDRKFDGFIITGAPVE 1c3oB 220 :PAQTSAEDVLKMNPDGIFLSNGPGD T0326 120 :YWEELTEIMEWSRHNVYSTMFICWAAQAGLYYF 1c3oB 247 :PCDYAITAIQKFLETDIPVFGISLGHQLLALAS T0326 154 :GIPKYELPQKL 1c3oB 280 :GAKTVKMKFGH T0326 165 :SGVYKHRVAKDS 1c3oB 292 :GGNHPVKDVEKN T0326 186 :FWAPHSRYTEVK 1c3oB 304 :VVMITAQNHGFA T0326 199 :EDIDKVPE 1c3oB 316 :VDEATLPA T0326 207 :LEILAES 1c3oB 325 :LRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1c3oB 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD T0326 275 :T 1c3oB 365 :P T0326 283 :FFSNWLNYCIY 1c3oB 366 :LFDHFIELIEQ Number of specific fragments extracted= 17 number of extra gaps= 1 total=1106 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3oB/T0326-1c3oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1c3oB/T0326-1c3oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3oB read from 1c3oB/T0326-1c3oB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c3oB in template set Warning: unaligning (T0326)L112 because of BadResidue code BAD_PEPTIDE in next template residue (1c3oB)A246 Warning: unaligning (T0326)D119 because of BadResidue code BAD_PEPTIDE at template residue (1c3oB)A246 T0326 31 :QDIRPLEILILNLMP 1c3oB 187 :EDELPFHVVAYDFGA T0326 52 :IQLLRLL 1c3oB 203 :RNILRML T0326 63 :LQVNVTLLYTET 1c3oB 212 :RGCRLTIVPAQT T0326 91 :TFSAVKDRKFDGFIITGAPVE 1c3oB 224 :SAEDVLKMNPDGIFLSNGPGD T0326 120 :YWEELTEIMEWSRHNVYSTMFICWAAQAGLY 1c3oB 247 :PCDYAITAIQKFLETDIPVFGISLGHQLLAL T0326 152 :FYGIPKYELPQKLSG 1c3oB 278 :ASGAKTVKMKFGHHG T0326 167 :VYKHRVAKDS 1c3oB 294 :NHPVKDVEKN T0326 186 :FWAPHSRYTEVK 1c3oB 311 :NHGFAVDEATLP T0326 205 :PELEILAESD 1c3oB 323 :ANLRVTHKSL T0326 215 :EAGVYVVANKSERQIFVTGHPEYDR 1c3oB 334 :DGTLQGIHRTDKPAFSFQGHPEASP T0326 240 :YTLRDEYYRDI 1c3oB 364 :APLFDHFIELI Number of specific fragments extracted= 11 number of extra gaps= 1 total=1117 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gk3A/T0326-2gk3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gk3A expands to /projects/compbio/data/pdb/2gk3.pdb.gz 2gk3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1464, because occupancy 0.500 <= existing 0.500 in 2gk3A Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 2gk3A Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 2gk3A Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 2gk3A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 2gk3A/T0326-2gk3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gk3A read from 2gk3A/T0326-2gk3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gk3A to template set # found chain 2gk3A in template set Warning: unaligning (T0326)L36 because first residue in template chain is (2gk3A)L8 Warning: unaligning (T0326)P235 because of BadResidue code BAD_PEPTIDE in next template residue (2gk3A)H227 Warning: unaligning (T0326)E236 because of BadResidue code BAD_PEPTIDE at template residue (2gk3A)H227 T0326 37 :EILILNLM 2gk3A 9 :KVLFIGES T0326 45 :PDK 2gk3A 26 :GYD T0326 48 :IKTEIQLLRLLG 2gk3A 39 :ATWLLECLRKGG T0326 65 :VNVTLLY 2gk3A 51 :VDIDYMP T0326 83 :EHILKFYTTFSAVK 2gk3A 60 :TVQIAFPESIDELN T0326 99 :KFDGFIITGAP 2gk3A 74 :RYDVIVISDIG T0326 115 :FEEVDYWEE 2gk3A 85 :SNTFLLQNE T0326 124 :LTEIMEWSRHNVYSTMFICW 2gk3A 104 :ALESIKEYVKNGGGLLMIGG T0326 157 :KYELPQKLSGVYKHR 2gk3A 151 :DGDDRVEKPEGICAE T0326 172 :VAKDSVLFRGHDDFFWA 2gk3A 167 :VSPEHPVVNGFSDYPVF T0326 204 :VPELEILAESDEAGVYVVANKSERQIFVT 2gk3A 192 :RDDADVVLTINNDPLLVFGEYQQGKTACF T0326 233 :GH 2gk3A 224 :CS T0326 237 :YDRYTLR 2gk3A 228 :WGTQQFM T0326 255 :KVP 2gk3A 235 :SWP T0326 279 :HAHLFFSNWLNYC 2gk3A 238 :FYTDLWVNTLQFI Number of specific fragments extracted= 15 number of extra gaps= 1 total=1132 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gk3A/T0326-2gk3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2gk3A/T0326-2gk3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gk3A read from 2gk3A/T0326-2gk3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gk3A in template set Warning: unaligning (T0326)L36 because first residue in template chain is (2gk3A)L8 Warning: unaligning (T0326)R239 because of BadResidue code BAD_PEPTIDE in next template residue (2gk3A)H227 Warning: unaligning (T0326)Y240 because of BadResidue code BAD_PEPTIDE at template residue (2gk3A)H227 T0326 37 :EILILNL 2gk3A 9 :KVLFIGE T0326 44 :MPDKIKTEIQL 2gk3A 25 :KGYDSFTSSKY T0326 56 :RL 2gk3A 36 :EE T0326 67 :VTLLYTETHKPKHTPIEHIL 2gk3A 38 :GATWLLECLRKGGVDIDYMP T0326 87 :KFYTTFSAVK 2gk3A 64 :AFPESIDELN T0326 99 :KFDGFIITGA 2gk3A 74 :RYDVIVISDI T0326 111 :E 2gk3A 84 :G T0326 115 :FEEVDYWEE 2gk3A 85 :SNTFLLQNE T0326 124 :LTEIMEWSRHNVYSTMFI 2gk3A 104 :ALESIKEYVKNGGGLLMI T0326 154 :GI 2gk3A 122 :GG T0326 156 :PKYELPQKLSG 2gk3A 154 :DRVEKPEGICA T0326 170 :HRVAKDSVLFRGHDDFFW 2gk3A 165 :EAVSPEHPVVNGFSDYPV T0326 193 :YTEVK 2gk3A 183 :FLGYN T0326 200 :DIDKVPELEILAESDEAGVYVV 2gk3A 188 :QAVARDDADVVLTINNDPLLVF T0326 222 :ANKSERQIFVTG 2gk3A 211 :EYQQGKTACFMS T0326 236 :EYD 2gk3A 223 :DCS T0326 241 :TLRDEYY 2gk3A 228 :WGTQQFM T0326 257 :PIPA 2gk3A 235 :SWPF T0326 280 :AHLFFSNWLNYC 2gk3A 239 :YTDLWVNTLQFI Number of specific fragments extracted= 19 number of extra gaps= 1 total=1151 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gk3A/T0326-2gk3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2gk3A/T0326-2gk3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gk3A read from 2gk3A/T0326-2gk3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gk3A in template set Warning: unaligning (T0326)V118 because of BadResidue code BAD_PEPTIDE in next template residue (2gk3A)N135 Warning: unaligning (T0326)D119 because of BadResidue code BAD_PEPTIDE at template residue (2gk3A)N135 Warning: unaligning (T0326)R239 because of BadResidue code BAD_PEPTIDE in next template residue (2gk3A)H227 Warning: unaligning (T0326)Y240 because of BadResidue code BAD_PEPTIDE at template residue (2gk3A)H227 T0326 12 :VKVLAKEGIFV 2gk3A 43 :LECLRKGGVDI T0326 23 :MTEKRAIHQD 2gk3A 67 :ESIDELNRYD T0326 37 :EILILNLMPDKI 2gk3A 77 :VIVISDIGSNTF T0326 49 :KTEI 2gk3A 91 :QNET T0326 72 :TETHKPKHTPIEHILKF 2gk3A 95 :FYQLKIKPNALESIKEY T0326 95 :VKDR 2gk3A 112 :VKNG T0326 101 :DGFIITGAPVELLPFEE 2gk3A 116 :GGLLMIGGYLSFMGIEA T0326 120 :YWE 2gk3A 136 :YKN T0326 135 :VYSTM 2gk3A 144 :VLPVI T0326 153 :YGIPKYELPQK 2gk3A 151 :DGDDRVEKPEG T0326 168 :YKHRVAKD 2gk3A 162 :ICAEAVSP T0326 176 :SVLFRGHDDFFWAP 2gk3A 171 :HPVVNGFSDYPVFL T0326 204 :VPELEILAESDEAGVYVVANKSERQIFVTG 2gk3A 192 :RDDADVVLTINNDPLLVFGEYQQGKTACFM T0326 235 :PEYD 2gk3A 222 :SDCS T0326 241 :TLRDEYYR 2gk3A 228 :WGTQQFMS T0326 277 :WSHAHLFFSNWLNYC 2gk3A 236 :WPFYTDLWVNTLQFI Number of specific fragments extracted= 16 number of extra gaps= 2 total=1167 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9vA/T0326-2a9vA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a9vA expands to /projects/compbio/data/pdb/2a9v.pdb.gz 2a9vA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 211, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 2a9vA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2a9vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 2a9vA/T0326-2a9vA-t06-local-adpstyle5.a2m # 2a9vA read from 2a9vA/T0326-2a9vA-t06-local-adpstyle5.a2m # adding 2a9vA to template set # found chain 2a9vA in template set T0326 35 :PLEILILNLMPDKIKTEIQLLRLLGNTP 2a9vA 1 :MLKIYVVDNGGQWTHREWRVLRELGVDT T0326 86 :LKFYTTFSAVKDRKFDGFIITGAPVELLP 2a9vA 29 :KIVPNDIDSSELDGLDGLVLSGGAPNIDE T0326 117 :EVDYWEELTEIM 2a9vA 58 :ELDKLGSVGKYI T0326 132 :RHNVYSTMFICWAAQAGLYYFYGIPKYE 2a9vA 70 :DDHNYPILGICVGAQFIALHFGASVVKA T0326 161 :PQKLSGVYKHRVAKDSVLFRGHDDFFWA 2a9vA 98 :KHPEFGKTKVSVMHSENIFGGLPSEITV T0326 194 :TEVKKEDIDKVP 2a9vA 126 :WENHNDEIINLP T0326 206 :ELEILAESDEAGVYVVANKSERQIFVTGHPEYDRYTLRDEYYRDIGRNL 2a9vA 139 :DFTLAASSATCQVQGFYHKTRPIYATQFHPEVEHTQYGRDIFRNFIGIC Number of specific fragments extracted= 7 number of extra gaps= 0 total=1174 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n57A/T0326-1n57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n57A expands to /projects/compbio/data/pdb/1n57.pdb.gz 1n57A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0326 read from 1n57A/T0326-1n57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n57A read from 1n57A/T0326-1n57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n57A to template set # found chain 1n57A in template set Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)G154 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)G154 Warning: unaligning (T0326)S165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)C207 Warning: unaligning (T0326)G166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)C207 Warning: unaligning (T0326)H182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1n57A)P218 Warning: unaligning (T0326)D183 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1n57A)P218 T0326 3 :INVPSGLP 1n57A 39 :VDYPKPYR T0326 34 :RPLEILILNLMP 1n57A 47 :GKHKILVIAADE T0326 46 :DK 1n57A 66 :GK T0326 48 :IKTEIQLLRLLGNT 1n57A 76 :IETLLPLYHLHAAG T0326 65 :VNVTLLYTETHKPKHTPIEH 1n57A 90 :FEFEVATISGLMTKFEYWAM T0326 88 :FYTTFSAV 1n57A 129 :NPKKLADV T0326 96 :K 1n57A 141 :N T0326 97 :DRKFDGFIIT 1n57A 143 :DSEYAAIFVP T0326 109 :PVELLPFEE 1n57A 155 :HGALIGLPE T0326 121 :WEELTEIMEWSRHNVYSTMFICWA 1n57A 164 :SQDVAAALQWAIKNDRFVISLCHG T0326 152 :FYGIPK 1n57A 194 :LRHGDN T0326 159 :ELPQKL 1n57A 200 :PLNGYS T0326 167 :VY 1n57A 208 :AF T0326 175 :DSVLFRG 1n57A 210 :PDAADKQ T0326 184 :DFFWAP 1n57A 219 :EIGYMP T0326 191 :SRYTEVKKEDIDKVP 1n57A 225 :GHLTWYFGEELKKMG T0326 209 :ILAESDEAG 1n57A 240 :MNIINDDIT T0326 218 :V 1n57A 251 :V T0326 221 :VANKS 1n57A 252 :HKDRK T0326 229 :IFVTGHPEYD 1n57A 257 :LLTGDSPFAA T0326 277 :WSHAHLFFSNWLNYC 1n57A 267 :NALGKLAAQEMLAAY Number of specific fragments extracted= 21 number of extra gaps= 3 total=1195 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n57A/T0326-1n57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1n57A/T0326-1n57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n57A read from 1n57A/T0326-1n57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n57A in template set Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)G154 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)G154 Warning: unaligning (T0326)K157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)C207 Warning: unaligning (T0326)Y158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)C207 Warning: unaligning (T0326)H182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1n57A)P218 Warning: unaligning (T0326)D183 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1n57A)P218 T0326 19 :GIFVMTEKRAIHQDIRPLE 1n57A 16 :DNAFFPSEYSLSQYTSPVS T0326 42 :NLMPDKIKTEIQLLRLLGNTPLQVN 1n57A 35 :DLDGVDYPKPYRGKHKILVIAADER T0326 67 :VTLLYTETHKPKHTPIEHILKFYTTF 1n57A 77 :ETLLPLYHLHAAGFEFEVATISGLMT T0326 97 :DR 1n57A 125 :SL T0326 99 :KFDGFIIT 1n57A 145 :EYAAIFVP T0326 109 :PVELLPFEEVDYW 1n57A 155 :HGALIGLPESQDV T0326 125 :TEIMEWSRHNVYSTMFICWA 1n57A 168 :AAALQWAIKNDRFVISLCHG T0326 152 :FYGIP 1n57A 201 :LNGYS T0326 159 :ELPQK 1n57A 208 :AFPDA T0326 178 :LFRG 1n57A 213 :ADKQ T0326 184 :DFFWA 1n57A 219 :EIGYM T0326 190 :HSRYTEVK 1n57A 224 :PGHLTWYF T0326 201 :ID 1n57A 232 :GE T0326 205 :P 1n57A 239 :G T0326 209 :ILAESDEAGVYVVANKS 1n57A 240 :MNIINDDITGRVHKDRK T0326 228 :QIFV 1n57A 257 :LLTG T0326 257 :PIPAN 1n57A 261 :DSPFA T0326 276 :WWSHAHLFFSNWLNYC 1n57A 266 :ANALGKLAAQEMLAAY Number of specific fragments extracted= 18 number of extra gaps= 3 total=1213 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n57A/T0326-1n57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1n57A/T0326-1n57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n57A read from 1n57A/T0326-1n57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n57A in template set Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)G154 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)G154 Warning: unaligning (T0326)K157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1n57A)C207 Warning: unaligning (T0326)Y158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1n57A)C207 Warning: unaligning (T0326)H182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1n57A)P218 Warning: unaligning (T0326)D183 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1n57A)P218 T0326 35 :PLEILILNLMP 1n57A 48 :KHKILVIAADE T0326 47 :K 1n57A 67 :K T0326 49 :KTEIQLLRLLGNTPLQVNVTLLYT 1n57A 76 :IETLLPLYHLHAAGFEFEVATISG T0326 75 :HKPKHTPI 1n57A 100 :LMTKFEYW T0326 83 :EHILKFYTT 1n57A 114 :EKVMPFFEQ T0326 92 :FSAVK 1n57A 133 :LADVV T0326 97 :DRKFDGFIIT 1n57A 143 :DSEYAAIFVP T0326 109 :PVELLPFEEV 1n57A 155 :HGALIGLPES T0326 122 :EELTEIMEWSRHNVYSTMFICWA 1n57A 165 :QDVAAALQWAIKNDRFVISLCHG T0326 152 :FYGIP 1n57A 201 :LNGYS T0326 159 :EL 1n57A 208 :AF T0326 175 :DSVLFRG 1n57A 210 :PDAADKQ T0326 184 :DFFWAPH 1n57A 219 :EIGYMPG T0326 192 :RYTEVKKEDIDKVP 1n57A 226 :HLTWYFGEELKKMG T0326 209 :ILAESDEAGVYVVANKS 1n57A 240 :MNIINDDITGRVHKDRK T0326 230 :FVTGHPEYDRYTLRDEYYRDI 1n57A 257 :LLTGDSPFAANALGKLAAQEM Number of specific fragments extracted= 16 number of extra gaps= 3 total=1229 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k9vF/T0326-1k9vF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k9vF expands to /projects/compbio/data/pdb/1k9v.pdb.gz 1k9vF:# T0326 read from 1k9vF/T0326-1k9vF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k9vF read from 1k9vF/T0326-1k9vF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k9vF to template set # found chain 1k9vF in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1k9vF)M301 T0326 37 :EILILNLMPDKIKTEIQLLRLLGNTPLQVNVTLLYTE 1k9vF 302 :RIGIISVGPGNIMNLYRGVKRASENFEDVSIELVESP T0326 96 :KDRKFDGFIITGAPV 1k9vF 339 :RNDLYDLLFIPGVGH T0326 115 :FEEV 1k9vF 354 :FGEG T0326 119 :DYWEE 1k9vF 359 :RRLRE T0326 124 :LTEIMEWSRHNVYSTMFICWAAQ 1k9vF 366 :LIDFVRKHVEDERYVVGVCLGMQ T0326 152 :FYGIP 1k9vF 397 :APGVK T0326 157 :KYELPQKLSGVYKHRVAKD 1k9vF 413 :LRSRRLPHMGWNEVIFKDT T0326 182 :H 1k9vF 432 :F T0326 183 :DDFFWAPHSRYTEVKKED 1k9vF 434 :NGYYYFVHTYRAVCEEEH T0326 209 :ILAES 1k9vF 452 :VLGTT T0326 214 :DEAGVYVVANKS 1k9vF 459 :DGEIFPSAVRKG T0326 227 :RQIFVTGHPEYDRYTLRDEYYRD 1k9vF 471 :RILGFQFHPEKSSKIGRKLLEKV T0326 288 :LNY 1k9vF 494 :IEC Number of specific fragments extracted= 13 number of extra gaps= 0 total=1242 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k9vF/T0326-1k9vF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1k9vF/T0326-1k9vF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k9vF read from 1k9vF/T0326-1k9vF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k9vF in template set T0326 37 :EILILNL 1k9vF 302 :RIGIISV T0326 63 :LQVNVTLL 1k9vF 309 :GPGNIMNL T0326 71 :YTETHKPK 1k9vF 320 :VKRASENF T0326 79 :HTPIEHILKFYTT 1k9vF 329 :DVSIELVESPRND T0326 99 :KFDGFII 1k9vF 342 :LYDLLFI T0326 107 :GAPVE 1k9vF 349 :PGVGH T0326 115 :FEE 1k9vF 354 :FGE T0326 118 :VDYWEE 1k9vF 358 :MRRLRE T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAG 1k9vF 366 :LIDFVRKHVEDERYVVGVCLGMQLL T0326 153 :YGI 1k9vF 398 :PGV T0326 156 :PKYELPQKLSGVYKHRVAKD 1k9vF 412 :KLRSRRLPHMGWNEVIFKDT T0326 182 :H 1k9vF 432 :F T0326 184 :DFFWA 1k9vF 433 :PNGYY T0326 191 :SRYTEVK 1k9vF 438 :YFVHTYR T0326 199 :EDID 1k9vF 445 :AVCE T0326 205 :PE 1k9vF 449 :EE T0326 207 :LEILAESDEAG 1k9vF 452 :VLGTTEYDGEI T0326 218 :VYVVANKS 1k9vF 464 :PSAVRKGR T0326 228 :QIFVTGHPEYDR 1k9vF 472 :ILGFQFHPEKSS T0326 278 :SHAHLFFSNWLNYCI 1k9vF 484 :KIGRKLLEKVIECSL Number of specific fragments extracted= 20 number of extra gaps= 0 total=1262 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k9vF/T0326-1k9vF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1k9vF/T0326-1k9vF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k9vF read from 1k9vF/T0326-1k9vF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k9vF in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1k9vF)M301 T0326 37 :EILILNLMPDKIKTEIQLLRLLGNTPLQVNVTLLYTETHKP 1k9vF 302 :RIGIISVGPGNIMNLYRGVKRASENFEDVSIELVESPRNDL T0326 100 :FDGFIITGAPV 1k9vF 343 :YDLLFIPGVGH T0326 115 :F 1k9vF 354 :F T0326 118 :VDYWEELTE 1k9vF 355 :GEGMRRLRE T0326 127 :IMEWSRHNVYSTMFICWAAQ 1k9vF 369 :FVRKHVEDERYVVGVCLGMQ T0326 153 :YGIPKYEL 1k9vF 398 :PGVKGLSL T0326 161 :PQKLSGVYKHRVAKDSV 1k9vF 417 :RLPHMGWNEVIFKDTFP T0326 183 :DDFFWAPHSRYTEVKKED 1k9vF 434 :NGYYYFVHTYRAVCEEEH T0326 209 :ILAE 1k9vF 452 :VLGT T0326 213 :SDEAGVYVVANK 1k9vF 459 :DGEIFPSAVRKG T0326 227 :RQIFVTGHPEYDRYTLRDEYYRDIG 1k9vF 471 :RILGFQFHPEKSSKIGRKLLEKVIE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1273 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jdbC/T0326-1jdbC-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jdbC expands to /projects/compbio/data/pdb/1jdb.pdb.gz 1jdbC:# T0326 read from 1jdbC/T0326-1jdbC-t06-local-adpstyle5.a2m # 1jdbC read from 1jdbC/T0326-1jdbC-t06-local-adpstyle5.a2m # adding 1jdbC to template set # found chain 1jdbC in template set Warning: unaligning (T0326)F179 because of BadResidue code BAD_PEPTIDE in next template residue (1jdbC)T308 Warning: unaligning (T0326)R180 because of BadResidue code BAD_PEPTIDE at template residue (1jdbC)T308 T0326 48 :IKTEIQLLRLLGNTPLQVNVTLLYT 1jdbC 186 :KEDELPFHVVAYDFGAKRNILRMLV T0326 81 :PIEH 1jdbC 211 :DRGC T0326 85 :ILKFYTTFSAVKDRKFDGFIITGAPVELLP 1jdbC 218 :IVPAQTSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHR 1jdbC 248 :CDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK T0326 172 :VAKDSVL 1jdbC 300 :VEKNVVM T0326 181 :GHDDFFWA 1jdbC 309 :AQNHGFAV T0326 199 :ED 1jdbC 317 :DE T0326 202 :DKVP 1jdbC 319 :ATLP T0326 206 :ELEILAES 1jdbC 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1jdbC 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD Number of specific fragments extracted= 10 number of extra gaps= 1 total=1283 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t36B/T0326-1t36B-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t36B expands to /projects/compbio/data/pdb/1t36.pdb.gz 1t36B:# T0326 read from 1t36B/T0326-1t36B-t06-local-adpstyle5.a2m # 1t36B read from 1t36B/T0326-1t36B-t06-local-adpstyle5.a2m # adding 1t36B to template set # found chain 1t36B in template set Warning: unaligning (T0326)P114 because of BadResidue code BAD_PEPTIDE in next template residue (1t36B)D248 Warning: unaligning (T0326)W121 because of BadResidue code BAD_PEPTIDE at template residue (1t36B)D248 Warning: unaligning (T0326)E122 because of BadResidue code BAD_PEPTIDE in next template residue (1t36B)Y250 Warning: unaligning (T0326)E123 because of BadResidue code BAD_PEPTIDE at template residue (1t36B)Y250 Warning: unaligning (T0326)R180 because of BadResidue code BAD_PEPTIDE in next template residue (1t36B)A309 Warning: unaligning (T0326)G181 because of BadResidue code BAD_PEPTIDE at template residue (1t36B)A309 T0326 47 :KIKTEIQLLRLLGNTPLQVNVTLLYTETHKPK 1t36B 185 :KKEDELPFHVVAYDFGAKRNILRMLVDRGCRL T0326 84 :HILKFYTTFSAVKDRKFDGFIITGAPVELL 1t36B 217 :TIVPAQTSAEDVLKMNPDGIFLSNGPGDPA T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHR 1t36B 251 :AITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK T0326 172 :VAKDSVLF 1t36B 300 :VEKNVVMI T0326 182 :HDDFFWA 1t36B 310 :QNHGFAV T0326 199 :ED 1t36B 317 :DE T0326 202 :DKVP 1t36B 319 :ATLP T0326 206 :ELEILAES 1t36B 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1t36B 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD Number of specific fragments extracted= 9 number of extra gaps= 2 total=1292 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6vB/T0326-1m6vB-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m6vB expands to /projects/compbio/data/pdb/1m6v.pdb.gz 1m6vB:Skipped atom 10131, because occupancy 0.500 <= existing 0.500 in 1m6vB Skipped atom 10133, because occupancy 0.500 <= existing 0.500 in 1m6vB Skipped atom 10135, because occupancy 0.500 <= existing 0.500 in 1m6vB Skipped atom 10137, because occupancy 0.500 <= existing 0.500 in 1m6vB Skipped atom 10139, because occupancy 0.500 <= existing 0.500 in 1m6vB # T0326 read from 1m6vB/T0326-1m6vB-t06-local-adpstyle5.a2m # 1m6vB read from 1m6vB/T0326-1m6vB-t06-local-adpstyle5.a2m # adding 1m6vB to template set # found chain 1m6vB in template set Warning: unaligning (T0326)R239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m6vB)A363 T0326 48 :IKTEIQLLRLLGNTPLQVNVTLLYT 1m6vB 186 :KEDELPFHVVAYDFGAKRNILRMLV T0326 81 :PIEH 1m6vB 211 :DRGC T0326 85 :ILKFYTTFSAVKDRKFDGFIITGAPVELLP 1m6vB 218 :IVPAQTSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMFICWAAQAGLYYFYGIPKYELPQKLSGVYKHR 1m6vB 248 :CDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK T0326 172 :VAKDSVLFRGHDDFFWA 1m6vB 300 :VEKNVVMITAQNHGFAV T0326 199 :ED 1m6vB 317 :DE T0326 202 :DKVP 1m6vB 319 :ATLP T0326 206 :ELEILAES 1m6vB 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYD 1m6vB 333 :FDGTLQGIHRTDKPAFSFQGHPEAS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1301 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keeB/T0326-1keeB-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1keeB expands to /projects/compbio/data/pdb/1kee.pdb.gz 1keeB:Skipped atom 9815, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9817, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9819, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9821, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9823, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9825, because occupancy 0.500 <= existing 0.500 in 1keeB Skipped atom 9827, because occupancy 0.500 <= existing 0.500 in 1keeB # T0326 read from 1keeB/T0326-1keeB-t06-local-adpstyle5.a2m # 1keeB read from 1keeB/T0326-1keeB-t06-local-adpstyle5.a2m # adding 1keeB to template set # found chain 1keeB in template set Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1keeB)L270 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1keeB)L270 T0326 47 :KIKTEIQLLRLLGNTPLQVNVTLLYTETHKPK 1keeB 185 :KKEDELPFHVVAYDFGAKRNILRMLVDRGCRL T0326 84 :HILKFYTTFSAVKDRKFDGFIITGAPVELLP 1keeB 217 :TIVPAQTSAEDVLKMNPDGIFLSNGPGDPAP T0326 121 :WEELTEIMEWSRHNVYSTMF 1keeB 248 :CDYAITAIQKFLETDIPVFG T0326 144 :AAQAGLYYFYGIPKYELPQKLSGVYKHR 1keeB 271 :GHQLLALASGAKTVKMKFGHHGGNHPVK T0326 172 :VAKDSVLFRGHDDFFWA 1keeB 300 :VEKNVVMITAQNHGFAV T0326 199 :ED 1keeB 317 :DE T0326 202 :DKVP 1keeB 319 :ATLP T0326 206 :ELEILAES 1keeB 324 :NLRVTHKS T0326 214 :DEAGVYVVANKSERQIFVTGHPEYDRYTLR 1keeB 333 :FDGTLQGIHRTDKPAFSFQGHPEASPGPHD Number of specific fragments extracted= 9 number of extra gaps= 0 total=1310 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rw7A/T0326-1rw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rw7A expands to /projects/compbio/data/pdb/1rw7.pdb.gz 1rw7A:# T0326 read from 1rw7A/T0326-1rw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rw7A read from 1rw7A/T0326-1rw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rw7A to template set # found chain 1rw7A in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1rw7A)A2 Warning: unaligning (T0326)F88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rw7A)I88 Warning: unaligning (T0326)Y89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)I88 Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)G107 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)G107 Warning: unaligning (T0326)S131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rw7A)Y128 Warning: unaligning (T0326)R132 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)Y128 Warning: unaligning (T0326)G233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)N220 Warning: unaligning (T0326)H234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)N220 Warning: unaligning (T0326)Y247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)A234 T0326 35 :PLEILILNLM 1rw7A 3 :PKKVLLALTS T0326 45 :PDKIKTE 1rw7A 19 :SDGAKTG T0326 52 :IQLLRLLG 1rw7A 35 :FNTFRKEG T0326 65 :VNVTLLYTET 1rw7A 43 :FEVDFVSETG T0326 78 :KHTPIEH 1rw7A 53 :KFGWDEH T0326 85 :ILK 1rw7A 84 :TLA T0326 90 :TTFSAVKDRKFDGFIIT 1rw7A 89 :KTPKEVNADDYQIFFAS T0326 117 :EVDYWEELTEIMEW 1rw7A 113 :DYPKAKDLQDIASE T0326 133 :HNVYSTMFICWA 1rw7A 129 :ANGGVVAAVCHG T0326 151 :YFYGIPKYE 1rw7A 143 :IFDGLTDKK T0326 175 :DS 1rw7A 152 :TG T0326 177 :VLFRG 1rw7A 155 :PLIEG T0326 184 :DFFWA 1rw7A 160 :KSITG T0326 189 :PHSRYTEVKKED 1rw7A 183 :NLATVEDVAKKY T0326 206 :ELEILAESDEAGVYVVANKS 1rw7A 195 :GAKYLAPVGPWDDYSITDGR T0326 229 :IFVT 1rw7A 215 :LVTG T0326 235 :PEYDRYTLRDEY 1rw7A 221 :PASAHSTAVRSI Number of specific fragments extracted= 17 number of extra gaps= 5 total=1327 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rw7A/T0326-1rw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1rw7A/T0326-1rw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rw7A read from 1rw7A/T0326-1rw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rw7A in template set Warning: unaligning (T0326)Y89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)I88 Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)G107 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)G107 Warning: unaligning (T0326)S131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rw7A)Y128 Warning: unaligning (T0326)R132 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)Y128 T0326 35 :PLEILILNLMPDKI 1rw7A 3 :PKKVLLALTSYNDV T0326 62 :PLQVNVT 1rw7A 17 :FYSDGAK T0326 69 :LLYTETHKPKHTPIEHI 1rw7A 32 :LHPFNTFRKEGFEVDFV T0326 87 :KF 1rw7A 49 :SE T0326 90 :TTFSAVKDRKFDGFIIT 1rw7A 89 :KTPKEVNADDYQIFFAS T0326 109 :PVE 1rw7A 108 :HGT T0326 115 :FEEVDYWEELTEIMEW 1rw7A 111 :LFDYPKAKDLQDIASE T0326 133 :HNVYSTMFICWA 1rw7A 129 :ANGGVVAAVCHG T0326 152 :FYGI 1rw7A 144 :FDGL T0326 157 :KYELPQKLSG 1rw7A 197 :KYLAPVGPWD Number of specific fragments extracted= 10 number of extra gaps= 3 total=1337 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rw7A/T0326-1rw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1rw7A/T0326-1rw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rw7A read from 1rw7A/T0326-1rw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rw7A in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1rw7A)A2 Warning: unaligning (T0326)F88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rw7A)I88 Warning: unaligning (T0326)Y89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)I88 Warning: unaligning (T0326)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)G107 Warning: unaligning (T0326)A108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)G107 Warning: unaligning (T0326)S131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rw7A)Y128 Warning: unaligning (T0326)R132 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rw7A)Y128 Warning: unaligning (T0326)Y237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)N220 Warning: unaligning (T0326)D238 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)N220 Warning: unaligning (T0326)G251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rw7A)A234 Warning: unaligning (T0326)R252 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rw7A)A234 Warning: unaligning (T0326)L254 because last residue in template chain is (1rw7A)K236 T0326 35 :PLEILILN 1rw7A 3 :PKKVLLAL T0326 43 :LMPDKI 1rw7A 17 :FYSDGA T0326 49 :KTEIQLLRLLGNTPLQVNVT 1rw7A 29 :VEALHPFNTFRKEGFEVDFV T0326 69 :LLYTETHK 1rw7A 54 :FGWDEHSL T0326 77 :PKHTPIEHILK 1rw7A 76 :NKDSDFNKTLA T0326 90 :TTFSAVKDRKFDGFIIT 1rw7A 89 :KTPKEVNADDYQIFFAS T0326 117 :EVDYWEELTEIMEW 1rw7A 113 :DYPKAKDLQDIASE T0326 133 :HNVYSTMFICWA 1rw7A 129 :ANGGVVAAVCHG T0326 151 :YFYGIPKY 1rw7A 143 :IFDGLTDK T0326 173 :AKDSVLFRGHD 1rw7A 151 :KTGRPLIEGKS T0326 188 :APHS 1rw7A 162 :ITGF T0326 193 :YTEV 1rw7A 172 :ILGV T0326 198 :KEDIDKVP 1rw7A 176 :DSILKAKN T0326 206 :ELEILAESDEAGVYVVANKS 1rw7A 195 :GAKYLAPVGPWDDYSITDGR T0326 230 :FVTG 1rw7A 215 :LVTG T0326 239 :RYTLRDEYYRDI 1rw7A 221 :PASAHSTAVRSI T0326 253 :N 1rw7A 235 :L Number of specific fragments extracted= 17 number of extra gaps= 5 total=1354 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qvzA/T0326-1qvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qvzA expands to /projects/compbio/data/pdb/1qvz.pdb.gz 1qvzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 589, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1qvzA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OD for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1731, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1773, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1775, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1777, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1779, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1781, because occupancy 0.500 <= existing 0.500 in 1qvzA Skipped atom 1783, because occupancy 0.500 <= existing 0.500 in 1qvzA # T0326 read from 1qvzA/T0326-1qvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qvzA read from 1qvzA/T0326-1qvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qvzA to template set # found chain 1qvzA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1qvzA)A2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qvzA)H139 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qvzA)H139 T0326 35 :PLEILILNLM 1qvzA 3 :PKKVLLALTS T0326 45 :PDKIKTE 1qvzA 19 :SDGMKTG T0326 52 :IQLLRLLGNTP 1qvzA 32 :LHPFNTFRKEG T0326 65 :VNVTLLYTET 1qvzA 43 :FEVDFVSETG T0326 78 :KHTPIEH 1qvzA 53 :KFGWDEH T0326 85 :ILKFYTTFSAVKDRKFDGFIITGA 1qvzA 84 :TLAKIKTPKEVNADDYQIFMASAG T0326 117 :EVDYWEELTEIMEWSRHNVYSTMF 1qvzA 113 :DYPKAKDLQDIASEIYANGGVVAA T0326 144 :A 1qvzA 140 :G T0326 151 :YFYGIPKYE 1qvzA 143 :MFDGLTDKK T0326 174 :KDSVLFR 1qvzA 152 :TGRPLIE T0326 183 :DDFFWA 1qvzA 159 :GKSITG T0326 189 :PHSRYTEVK 1qvzA 183 :NLATVEDVA T0326 202 :DKV 1qvzA 192 :KKY T0326 206 :ELEILAESDEAGVYVVANKS 1qvzA 195 :GAKYLAPVGPWDDYSITDGR T0326 229 :IFVTGHPEYDRYTLRDEYY 1qvzA 215 :LVTGVNPASAHSTAVRSID Number of specific fragments extracted= 15 number of extra gaps= 0 total=1369 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qvzA/T0326-1qvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1qvzA/T0326-1qvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qvzA read from 1qvzA/T0326-1qvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qvzA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1qvzA)A2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qvzA)H139 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qvzA)H139 T0326 35 :PLEILILNLMPDKI 1qvzA 3 :PKKVLLALTSYNDV T0326 62 :PLQVNVT 1qvzA 17 :FYSDGMK T0326 69 :LLYTETHKPKHTPIEHI 1qvzA 32 :LHPFNTFRKEGFEVDFV T0326 87 :KF 1qvzA 49 :SE T0326 89 :YTTFSAVKDRKFDGFIITGAPVE 1qvzA 88 :IKTPKEVNADDYQIFMASAGHGT T0326 115 :FEEVDYWEELTEIMEWSRHNVYSTMF 1qvzA 111 :LFDYPKAKDLQDIASEIYANGGVVAA T0326 144 :A 1qvzA 140 :G T0326 152 :FYGI 1qvzA 144 :FDGL T0326 157 :KYELPQKLSGV 1qvzA 197 :KYLAPVGPWDD T0326 169 :KHRVAKD 1qvzA 208 :YSITDGR Number of specific fragments extracted= 10 number of extra gaps= 0 total=1379 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qvzA/T0326-1qvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1qvzA/T0326-1qvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qvzA read from 1qvzA/T0326-1qvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qvzA in template set Warning: unaligning (T0326)R34 because first residue in template chain is (1qvzA)A2 Warning: unaligning (T0326)I141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qvzA)H139 Warning: unaligning (T0326)W143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qvzA)H139 T0326 35 :PLEILILNLMPDKI 1qvzA 3 :PKKVLLALTSYNDV T0326 49 :KTEIQLLRLLGNTPLQVNVT 1qvzA 29 :VEALHPFNTFRKEGFEVDFV T0326 69 :LLYTETHKPKHTPIEHILKFYTT 1qvzA 54 :FGWDEHSLAKDFLNGQDETDFKN T0326 92 :FSAVKDR 1qvzA 81 :FNKTLAK T0326 99 :KFDGFIITGA 1qvzA 98 :DYQIFMASAG T0326 115 :FEE 1qvzA 114 :YPK T0326 121 :WEELTEIMEWSRHNVYSTMF 1qvzA 117 :AKDLQDIASEIYANGGVVAA T0326 144 :A 1qvzA 140 :G T0326 151 :YFYGIPKY 1qvzA 143 :MFDGLTDK T0326 173 :AKDSVLFRGHD 1qvzA 151 :KTGRPLIEGKS T0326 188 :APHS 1qvzA 162 :ITGF T0326 193 :YTEV 1qvzA 172 :IMGV T0326 198 :KEDIDKVP 1qvzA 176 :DSILKAKN T0326 206 :ELEILAESDEAGVYVVANKS 1qvzA 195 :GAKYLAPVGPWDDYSITDGR T0326 230 :FVTG 1qvzA 215 :LVTG T0326 237 :YDRYTLRDEYYRDIG 1qvzA 219 :VNPASAHSTAVRSID Number of specific fragments extracted= 16 number of extra gaps= 0 total=1395 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpwB/T0326-1gpwB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gpwB expands to /projects/compbio/data/pdb/1gpw.pdb.gz 1gpwB:# T0326 read from 1gpwB/T0326-1gpwB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpwB read from 1gpwB/T0326-1gpwB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gpwB to template set # found chain 1gpwB in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1gpwB)M1 T0326 37 :EILILNLMPDKIKTEIQLLRLL 1gpwB 2 :RIGIISVGPGNIMNLYRGVKRA T0326 59 :GNTP 1gpwB 26 :NFED T0326 65 :VNVTLLYT 1gpwB 30 :VSIELVES T0326 95 :VKDRKFDGFIITGA 1gpwB 38 :PRNDLYDLLFIPGV T0326 109 :PV 1gpwB 53 :HF T0326 115 :FEEVDYWEE 1gpwB 55 :GEGMRRLRE T0326 124 :LTEIMEWSRHNVYSTMFICWAAQ 1gpwB 66 :LIDFVRKHVEDERYVVGVCLGMQ T0326 157 :KYELPQKLSGVYKHRVAKD 1gpwB 113 :LRSRRLPHMGWNEVIFKDT T0326 182 :H 1gpwB 132 :F T0326 183 :DDFFWAPHSRYTEVKKED 1gpwB 134 :NGYYYFVHTYRAVCEEEH T0326 209 :ILAES 1gpwB 152 :VLGTT T0326 214 :DEAG 1gpwB 159 :DGEI T0326 218 :VYVVAN 1gpwB 164 :PSAVRK T0326 226 :ERQIFVTGHPEYDRYTLRDEYYRDIGRNLK 1gpwB 170 :GRILGFQFHPEKSSKIGRKLLEKVIECSLS Number of specific fragments extracted= 14 number of extra gaps= 0 total=1409 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpwB/T0326-1gpwB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1gpwB/T0326-1gpwB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpwB read from 1gpwB/T0326-1gpwB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpwB in template set Warning: unaligning (T0326)L55 because first residue in template chain is (1gpwB)M1 T0326 56 :RLLGNTPLQVNVTLL 1gpwB 2 :RIGIISVGPGNIMNL T0326 71 :YTETHKPK 1gpwB 19 :GVKRASEN T0326 79 :HTPIEHILKFYTT 1gpwB 29 :DVSIELVESPRND T0326 99 :KFDGFII 1gpwB 42 :LYDLLFI T0326 107 :GAPVEL 1gpwB 49 :PGVGHF T0326 115 :FEEVDYWEE 1gpwB 55 :GEGMRRLRE T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAG 1gpwB 66 :LIDFVRKHVEDERYVVGVCLGMQLL T0326 155 :I 1gpwB 91 :F T0326 157 :KYEL 1gpwB 112 :KLRS T0326 161 :PQKLSGVYKHRVAKD 1gpwB 117 :RLPHMGWNEVIFKDT T0326 182 :H 1gpwB 132 :F T0326 184 :DFFWA 1gpwB 133 :PNGYY T0326 191 :SRYTEVK 1gpwB 138 :YFVHTYR T0326 199 :EDID 1gpwB 145 :AVCE T0326 205 :PE 1gpwB 149 :EE T0326 207 :LEILAESDEAG 1gpwB 152 :VLGTTEYDGEI T0326 218 :VYVVANKS 1gpwB 164 :PSAVRKGR T0326 228 :QIFVTGHPEYDR 1gpwB 172 :ILGFQFHPEKSS T0326 278 :SHAHLFFSNWLNY 1gpwB 184 :KIGRKLLEKVIEC Number of specific fragments extracted= 19 number of extra gaps= 0 total=1428 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpwB/T0326-1gpwB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 1gpwB/T0326-1gpwB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpwB read from 1gpwB/T0326-1gpwB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpwB in template set Warning: unaligning (T0326)L36 because first residue in template chain is (1gpwB)M1 Warning: unaligning (T0326)V256 because last residue in template chain is (1gpwB)R200 T0326 37 :EILILNLMPDKIKTEIQLLRLLGNTPLQVNVTLLYTETHK 1gpwB 2 :RIGIISVGPGNIMNLYRGVKRASENFEDVSIELVESPRND T0326 99 :KFDGFIITGAPV 1gpwB 42 :LYDLLFIPGVGH T0326 115 :FEEVDYWEELTEIM 1gpwB 61 :LRENDLIDFVRKHV T0326 133 :HNVYSTMFICWAAQ 1gpwB 75 :EDERYVVGVCLGMQ T0326 156 :PKYELPQKLSGVYKHRVAKDSV 1gpwB 112 :KLRSRRLPHMGWNEVIFKDTFP T0326 183 :DDFFWAPHSRYTEVKKED 1gpwB 134 :NGYYYFVHTYRAVCEEEH T0326 207 :LEI 1gpwB 152 :VLG T0326 210 :LAESDEAGVYVVANK 1gpwB 156 :TEYDGEIFPSAVRKG T0326 227 :RQIFVTGHPEYDRYTLRDEYYRDIGRNLK 1gpwB 171 :RILGFQFHPEKSSKIGRKLLEKVIECSLS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1437 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s1mA/T0326-1s1mA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s1mA expands to /projects/compbio/data/pdb/1s1m.pdb.gz 1s1mA:Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 1s1mA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 1s1mA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 1s1mA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 1s1mA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 1s1mA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 1s1mA # T0326 read from 1s1mA/T0326-1s1mA-t06-local-adpstyle5.a2m # 1s1mA read from 1s1mA/T0326-1s1mA-t06-local-adpstyle5.a2m # adding 1s1mA to template set # found chain 1s1mA in template set Warning: unaligning (T0326)I155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s1mA)T438 Warning: unaligning (T0326)N223 because of BadResidue code BAD_PEPTIDE in next template residue (1s1mA)P504 Warning: unaligning (T0326)K224 because of BadResidue code BAD_PEPTIDE at template residue (1s1mA)P504 T0326 56 :RLLGNTPLQVN 1s1mA 300 :ELPDAYKSVIE T0326 70 :LYTETHKPKHTPIEH 1s1mA 311 :ALKHGGLKNRVSVNI T0326 85 :ILKFYTTFSAVK 1s1mA 328 :IDSQDVETRGVE T0326 97 :DRKFDGFIITGAPV 1s1mA 341 :LKGLDAILVPGGFG T0326 112 :LLP 1s1mA 355 :YRG T0326 121 :WEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1s1mA 358 :VEGMITTARFARENNIPYLGICLGMQVALID T0326 163 :KLSGVYKHRVAKDSVLFRGHDDFFWAPHSRY 1s1mA 439 :MRLGAQQCQLVDDSLVRQLYNAPTIVERHRH T0326 194 :TEVKKEDIDKVP 1s1mA 471 :YEVNNMLLKQIE T0326 206 :ELEILAES 1s1mA 485 :GLRVAGRS T0326 214 :DEAGVYVVA 1s1mA 494 :DDQLVEIIE T0326 225 :SER 1s1mA 505 :NHP T0326 228 :QIFVTGHPEYDRYTL 1s1mA 509 :FVACQFHPEFTSTPR Number of specific fragments extracted= 12 number of extra gaps= 1 total=1449 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kxjA/T0326-1kxjA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kxjA expands to /projects/compbio/data/pdb/1kxj.pdb.gz 1kxjA:# T0326 read from 1kxjA/T0326-1kxjA-t06-local-adpstyle5.a2m # 1kxjA read from 1kxjA/T0326-1kxjA-t06-local-adpstyle5.a2m # adding 1kxjA to template set # found chain 1kxjA in template set T0326 36 :LEILILNLMPDK 1kxjA 1 :MRIGIISVGPGN T0326 48 :IKTEIQLLRLLGNT 1kxjA 14 :MNLYRGVKRASENF T0326 88 :FYTTFSAV 1kxjA 28 :EDVSIELV T0326 96 :KDRKFDGFIITGAPV 1kxjA 39 :RNDLYDLLFIPGVGH T0326 113 :L 1kxjA 54 :F T0326 115 :FEEVDYWEE 1kxjA 55 :GEGMRRLRE T0326 124 :LTEIMEWSRHNVYSTMFICWAAQAGLYY 1kxjA 66 :LIDFVRKHVEDERYVVGVCLGMQLLFEE T0326 152 :FYGIPK 1kxjA 107 :EGNVVK T0326 158 :YELPQKLSGVYKHRVAKD 1kxjA 114 :RSRRLPHMGWNEVIFKDT T0326 188 :APHSRYTEVKKEDI 1kxjA 132 :FPNGYYYFVHTYRA T0326 203 :KVPELEILAESDEAG 1kxjA 146 :VCEEEHVLGTTEYDG T0326 218 :VYVVANKSERQIFVTGHPEYDRYTLRDEYYR 1kxjA 162 :IFPSAVRKGRILGFQFHPEKSSKIGRKLLEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=1461 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcnA/T0326-1vcnA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vcnA expands to /projects/compbio/data/pdb/1vcn.pdb.gz 1vcnA:# T0326 read from 1vcnA/T0326-1vcnA-t06-local-adpstyle5.a2m # 1vcnA read from 1vcnA/T0326-1vcnA-t06-local-adpstyle5.a2m # adding 1vcnA to template set # found chain 1vcnA in template set Warning: unaligning (T0326)H30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcnA)H296 Warning: unaligning (T0326)D32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcnA)H296 Warning: unaligning (T0326)L43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcnA)P313 Warning: unaligning (T0326)P45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcnA)P313 Warning: unaligning (T0326)T72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcnA)A346 Warning: unaligning (T0326)P77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcnA)A346 Warning: unaligning (T0326)A108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcnA)V367 Warning: unaligning (T0326)V118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcnA)V367 Warning: unaligning (T0326)Q162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcnA)T440 Warning: unaligning (T0326)A216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcnA)G501 T0326 33 :I 1vcnA 297 :P T0326 34 :RPLEILILN 1vcnA 299 :RTVKIAIAG T0326 46 :DKIKTEIQLLRLLGNTP 1vcnA 314 :DAYLSLLEALRHAGIKN T0326 63 :LQVNVTLLY 1vcnA 332 :ARVEVKWVD T0326 88 :FYTTF 1vcnA 347 :ADLDE T0326 96 :KDRKFDGFIITG 1vcnA 352 :AFRDVSGILVPG T0326 119 :DYWEELTEIMEWSRHNVYSTMFICWAAQAGLYY 1vcnA 368 :RGIEGKVRAAQYARERKIPYLGICLGLQIAVIE T0326 163 :KLSGVYKHRVAKDSVLFRGHDDFFWAPHSRY 1vcnA 441 :MRLGDWPMRIKPGTLLHRLYGKEEVLERHRH T0326 194 :TEVKKEDIDKVP 1vcnA 473 :YEVNPLYVDGLE T0326 206 :ELEILAESDE 1vcnA 487 :GLVVSATTPG T0326 218 :VYVVANKSER 1vcnA 505 :VEAIELKDHP T0326 228 :QIFVTGHPEYDRYTL 1vcnA 516 :FLGLQSHPEFKSRPM Number of specific fragments extracted= 12 number of extra gaps= 0 total=1473 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cmd/T0326-2cmd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cmd expands to /projects/compbio/data/pdb/2cmd.pdb.gz 2cmd:Warning: there is no chain 2cmd will retry with 2cmdA # T0326 read from 2cmd/T0326-2cmd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cmd read from 2cmd/T0326-2cmd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cmd to template set # found chain 2cmd in template set T0326 34 :RPLEILILNLMPD 2cmd 26 :SGSELSLYDIAPV T0326 51 :EIQLLRLLGNTPLQVNVTLLYTET 2cmd 39 :TPGVAVDLSHIPTAVKIKGFSGED T0326 92 :FSAV 2cmd 63 :ATPA T0326 97 :DRKFDGFIITGA 2cmd 67 :LEGADVVLISAG T0326 109 :PVELLPFEEV 2cmd 81 :RKPGMDRSDL T0326 121 :WEE 2cmd 91 :FNV T0326 124 :LTEIMEWSRHN 2cmd 98 :VKNLVQQVAKT T0326 135 :VYSTMFI 2cmd 110 :PKACIGI T0326 144 :AAQAGLYY 2cmd 124 :TVAIAAEV T0326 152 :FYGIPKYELPQKLSGVY 2cmd 161 :LKGKQPGEVEVPVIGGH T0326 183 :DDFFWAP 2cmd 178 :SGVTILP T0326 200 :DIDKVPELE 2cmd 185 :LLSQVPGVS T0326 237 :YDRYTLRDEYYR 2cmd 194 :FTEQEVADLTKR T0326 250 :I 2cmd 213 :V T0326 251 :GRN 2cmd 216 :AKA T0326 268 :PTKTPILTWWSHAHLFFSNWLNYCI 2cmd 219 :GGGSATLSMGQAAARFGLSLVRALQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1489 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cmd/T0326-2cmd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2cmd/T0326-2cmd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cmd read from 2cmd/T0326-2cmd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cmd in template set Warning: unaligning (T0326)G154 because of BadResidue code BAD_PEPTIDE in next template residue (2cmd)V137 Warning: unaligning (T0326)I155 because of BadResidue code BAD_PEPTIDE at template residue (2cmd)V137 T0326 12 :VKVLAKE 2cmd 17 :ALLLKTQ T0326 44 :MPD 2cmd 24 :LPS T0326 55 :LRLLGNTPLQVNVTLLYTET 2cmd 27 :GSELSLYDIAPVTPGVAVDL T0326 75 :HKPKHTPIEHI 2cmd 48 :HIPTAVKIKGF T0326 88 :FYTTFSAVK 2cmd 59 :SGEDATPAL T0326 98 :RKFDGFIITGAPVEL 2cmd 68 :EGADVVLISAGVRRK T0326 113 :LPFEEV 2cmd 85 :MDRSDL T0326 121 :WEE 2cmd 91 :FNV T0326 124 :LTEIMEWSRHN 2cmd 98 :VKNLVQQVAKT T0326 135 :VYSTMFI 2cmd 110 :PKACIGI T0326 144 :AAQAGLYYF 2cmd 124 :TVAIAAEVL T0326 153 :Y 2cmd 135 :A T0326 182 :HDDFFWAP 2cmd 165 :QPGEVEVP T0326 190 :HSRYTEVK 2cmd 177 :HSGVTILP T0326 200 :DIDKVPE 2cmd 185 :LLSQVPG T0326 237 :YDRYTLRD 2cmd 194 :FTEQEVAD T0326 245 :EYYRDIGRNL 2cmd 212 :EVVEAKAGGG T0326 271 :TPILTWWSHAHLFFSNWLNYCI 2cmd 222 :SATLSMGQAAARFGLSLVRALQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=1507 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cmd/T0326-2cmd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0326 read from 2cmd/T0326-2cmd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cmd read from 2cmd/T0326-2cmd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cmd in template set Warning: unaligning (T0326)G154 because of BadResidue code BAD_PEPTIDE in next template residue (2cmd)V137 Warning: unaligning (T0326)I155 because of BadResidue code BAD_PEPTIDE at template residue (2cmd)V137 T0326 36 :LEILILNLMPDKIKTEIQ 2cmd 28 :SELSLYDIAPVTPGVAVD T0326 58 :LGNTPLQVNVTLLY 2cmd 46 :LSHIPTAVKIKGFS T0326 78 :KHTPIEHI 2cmd 60 :GEDATPAL T0326 98 :RKFDGFIITGAPVEL 2cmd 68 :EGADVVLISAGVRRK T0326 113 :LPFEEV 2cmd 85 :MDRSDL T0326 119 :DYWEELTEIMEWSRHNV 2cmd 93 :VNAGIVKNLVQQVAKTC T0326 136 :YSTMFICWAAQAGLYYFY 2cmd 118 :TNPVNTTVAIAAEVLKKA T0326 159 :ELPQKLSGVY 2cmd 138 :YDKNKLFGVT T0326 177 :VLFRGHDDFFWAP 2cmd 160 :ELKGKQPGEVEVP T0326 190 :HSRYT 2cmd 177 :HSGVT T0326 201 :IDKVPELE 2cmd 186 :LSQVPGVS T0326 237 :YDRYTLRDEYYRDIGRN 2cmd 194 :FTEQEVADLTKRIQNAG T0326 267 :DPTKTPILTWWSHAHLFFSNWLNYC 2cmd 218 :AGGGSATLSMGQAAARFGLSLVRAL Number of specific fragments extracted= 13 number of extra gaps= 1 total=1520 Will force an alignment to be made, even if fragment is small Number of alignments=110 # command:CPU_time= 43.437 sec, elapsed time= 46.626 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 110 Adding 46056 constraints to all_contacts Done adding distance constraints # command:CPU_time= 43.651 sec, elapsed time= 46.851 sec. # command:Reading probabilities from T0326.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 29.218 Optimizing... Probability sum: -548.409, CN propb: -548.409 weights: 0.261 constraints: 876 # command:CPU_time= 712.427 sec, elapsed time= 716.049 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 876 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 876 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 5391 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 5391 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 37393 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 37393 # command:CPU_time= 713.238 sec, elapsed time= 717.410 sec. # command: