# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0305/ # command:# Making conformation for sequence T0305 numbered 1 through 297 Created new target T0305 from T0305.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0305/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0305//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bzlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bzlA expands to /projects/compbio/data/pdb/2bzl.pdb.gz 2bzlA:Skipped atom 1123, because occupancy 0.3 <= existing 0.700 in 2bzlA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1137, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1139, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 2bzlA # T0305 read from 2bzlA/merged-good-all-a2m # 2bzlA read from 2bzlA/merged-good-all-a2m # adding 2bzlA to template set # found chain 2bzlA in template set Warning: unaligning (T0305)Y16 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)M908 Warning: unaligning (T0305)G22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bzlA)M908 Warning: unaligning (T0305)E143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bzlA)K1029 T0305 8 :FVKHIGEL 2bzlA 896 :RFRTLKKK # choosing archetypes in rotamer library T0305 23 :FSEDFEEVQRCTADM 2bzlA 909 :VFTEYEQIPKKKANG T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKD 2bzlA 924 :IFSTAALPENAERSRIREVVPYEENRVELIPTKENN T0305 79 :SDYINANYVDG 2bzlA 960 :TGYINASHIKV T0305 90 :YNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2bzlA 973 :GGAEWHYIATQGPLPHTCHDFWQMVWEQGVNVIAMVTAEEEGGRTKSHRYWP T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 2bzlA 1031 :SSATYGKFKVTTKFRTDSVCYATTGLKVKHLL T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bzlA 1063 :SGQERTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2bzlA 1112 :NRHPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 8 number of extra gaps= 0 total=8 Number of alignments=1 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set Warning: unaligning (T0305)Y16 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)M908 Warning: unaligning (T0305)G22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bzlA)M908 T0305 5 :MK 2bzlA 897 :FR T0305 11 :HIGEL 2bzlA 899 :TLKKK T0305 23 :FSEDFEEVQRCTAD 2bzlA 909 :VFTEYEQIPKKKAN T0305 39 :ITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKD 2bzlA 923 :GIFSTAALPENAERSRIREVVPYEENRVELIPTKENN T0305 79 :SDYINANYVDG 2bzlA 960 :TGYINASHIKV T0305 90 :YNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2bzlA 973 :GGAEWHYIATQGPLPHTCHDFWQMVWEQGVNVIAMVTAEEEGGRTKSHRYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 2bzlA 1030 :HSSATYGKFKVTTKFRTDSVCYATTGLKVKHLL T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bzlA 1063 :SGQERTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2bzlA 1112 :NRHPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 9 number of extra gaps= 0 total=17 Number of alignments=2 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set Warning: unaligning (T0305)H11 because first residue in template chain is (2bzlA)E895 Warning: unaligning (T0305)Q20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)M908 Warning: unaligning (T0305)S24 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bzlA)M908 Warning: unaligning (T0305)T142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)K1029 T0305 12 :IGELYSNN 2bzlA 896 :RFRTLKKK T0305 25 :EDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2bzlA 909 :VFTEYEQIPKKKANGIFSTAALPENAERSRIREVVPYEENRVELI T0305 73 :GKDSKHSDYINANYVD 2bzlA 954 :PTKENNTGYINASHIK T0305 89 :GYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2bzlA 972 :VGGAEWHYIATQGPLPHTCHDFWQMVWEQGVNVIAMVTAEEEGGRTKSHRYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bzlA 1030 :HSSATYGKFKVTTKFRTDSVCYATTGLKVKH T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bzlA 1061 :LLSGQERTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2bzlA 1112 :NRHPPIVVHCSAGVGRTGVLILSELMIYCLEHNEKVEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=24 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bzcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1bzcA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1bzcA/merged-good-all-a2m.gz for input Trying 1bzcA/merged-good-all-a2m Error: Couldn't open file 1bzcA/merged-good-all-a2m or 1bzcA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c83A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1c83A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1c83A/merged-good-all-a2m.gz for input Trying 1c83A/merged-good-all-a2m Error: Couldn't open file 1c83A/merged-good-all-a2m or 1c83A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bijA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bijA expands to /projects/compbio/data/pdb/2bij.pdb.gz 2bijA:Skipped atom 617, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 618, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 2bijA # T0305 read from 2bijA/merged-good-all-a2m # 2bijA read from 2bijA/merged-good-all-a2m # adding 2bijA to template set # found chain 2bijA in template set Warning: unaligning (T0305)Y81 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I330 Warning: unaligning (T0305)I82 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I330 Warning: unaligning (T0305)E130 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bijA)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)E423 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)E423 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0305 10 :KHIGELYS 2bijA 264 :EELHEKAL T0305 19 :NQHGFSEDFEEVQRCTA 2bijA 272 :DPFLLQAEFFEIPMNFV T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 2bijA 289 :DPKEYDIPGLVRKNRYKTILPNPHSRVCLT T0305 75 :DSKHSD 2bijA 319 :SPDPDD T0305 83 :NANYVDGYNKA 2bijA 331 :NANYIRGYGGE T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 2bijA 343 :KVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIE T0305 136 :CDQYWPT 2bijA 384 :CTEYWPE T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bijA 391 :EQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :R 2bijA 421 :G T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2bijA 424 :ERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEA T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bijA 461 :EGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAILG 2bijA 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 12 number of extra gaps= 3 total=36 Number of alignments=4 # 2bijA read from 2bijA/merged-good-all-a2m # found chain 2bijA in template set Warning: unaligning (T0305)Y81 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I330 Warning: unaligning (T0305)I82 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I330 Warning: unaligning (T0305)E130 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bijA)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)E423 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)E423 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0305 2 :FQSMKQFVKH 2bijA 260 :VLQAEELHEK T0305 17 :SNNQHGFSEDFEEV 2bijA 270 :ALDPFLLQAEFFEI T0305 35 :ADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRP 2bijA 284 :PMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTS T0305 76 :SKHSD 2bijA 320 :PDPDD T0305 83 :NANYVDGYNKA 2bijA 331 :NANYIRGYGGE T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 2bijA 343 :KVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIE T0305 136 :CDQYWP 2bijA 384 :CTEYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bijA 390 :EEQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :R 2bijA 421 :G T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bijA 424 :ERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bijA 463 :PHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAILG 2bijA 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 12 number of extra gaps= 3 total=48 Number of alignments=5 # 2bijA read from 2bijA/merged-good-all-a2m # found chain 2bijA in template set Warning: unaligning (T0305)Y81 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I330 Warning: unaligning (T0305)I82 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I330 Warning: unaligning (T0305)E130 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bijA)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)E423 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)E423 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0305 19 :NQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2bijA 268 :EKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLT T0305 75 :DSKHSD 2bijA 319 :SPDPDD T0305 83 :NANYVDGY 2bijA 331 :NANYIRGY T0305 91 :NKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 2bijA 340 :GEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIE T0305 136 :CDQYWPT 2bijA 384 :CTEYWPE T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bijA 391 :EQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :R 2bijA 421 :G T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bijA 424 :ERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bijA 463 :PHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAIL 2bijA 516 :QTCEQYQFVHHVMSLYEK Number of specific fragments extracted= 10 number of extra gaps= 3 total=58 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2f6fA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2f6fA/merged-good-all-a2m.gz for input Trying 2f6fA/merged-good-all-a2m Error: Couldn't open file 2f6fA/merged-good-all-a2m or 2f6fA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aax/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aax expands to /projects/compbio/data/pdb/1aax.pdb.gz 1aax:Warning: there is no chain 1aax will retry with 1aaxA # T0305 read from 1aax/merged-good-all-a2m # 1aax read from 1aax/merged-good-all-a2m # adding 1aax to template set # found chain 1aax in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1aax)E2 T0305 5 :MKQFVKHIG 1aax 3 :MEKEFEQID T0305 17 :SN 1aax 12 :KS T0305 21 :HGFSEDFEEVQRCTADM 1aax 14 :GSWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 1aax 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1aax 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1aax 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRN 1aax 140 :LKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1aax 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1aax 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=68 Number of alignments=7 # 1aax read from 1aax/merged-good-all-a2m # found chain 1aax in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1aax)E2 T0305 5 :MKQFVKHIGELY 1aax 3 :MEKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTA 1aax 15 :SWAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 1aax 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1aax 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1aax 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1aax 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1aax 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1aax 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=77 Number of alignments=8 # 1aax read from 1aax/merged-good-all-a2m # found chain 1aax in template set T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1aax 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1aax 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1aax 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1aax 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1aax 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1aax 206 :PEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=84 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wchA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wchA expands to /projects/compbio/data/pdb/1wch.pdb.gz 1wchA:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1921, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2200, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2202, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2204, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2206, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2371, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2373, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2375, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2377, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2379, because occupancy 0.500 <= existing 0.500 in 1wchA # T0305 read from 1wchA/merged-good-all-a2m # 1wchA read from 1wchA/merged-good-all-a2m # adding 1wchA to template set # found chain 1wchA in template set T0305 3 :QSMKQFVKHIGELYSNN 1wchA 2195 :ANLKSVIRVLRGLLDQG T0305 22 :GFSEDFEEVQRCTA 1wchA 2212 :IPSKELENLQELKP T0305 37 :MN 1wchA 2226 :LD T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKL 1wchA 2228 :QCLIGQTKENRRKNRYKNILPYDATRVPL T0305 76 :SKHSDYINANYV 1wchA 2257 :GDEGGYINASFI T0305 88 :DGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1wchA 2271 :PVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWP T0305 142 :TENSEE 1wchA 2327 :LGKTTM T0305 148 :YGNIIVTLKSTKIHACYTVRRFSIRN 1wchA 2334 :SNRLRLALVRMQQLKGFVVRAMTLED T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 1wchA 2360 :IQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIH T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTR Number of specific fragments extracted= 10 number of extra gaps= 0 total=94 Number of alignments=10 # 1wchA read from 1wchA/merged-good-all-a2m # found chain 1wchA in template set T0305 4 :SMKQFVKHIGELYSNNQ 1wchA 2196 :NLKSVIRVLRGLLDQGI T0305 23 :FSEDFEEVQRCTADM 1wchA 2213 :PSKELENLQELKPLD T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKL 1wchA 2228 :QCLIGQTKENRRKNRYKNILPYDATRVPL T0305 76 :SKHSDYINANYV 1wchA 2257 :GDEGGYINASFI T0305 88 :DGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1wchA 2271 :PVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWPN T0305 143 :ENSEEY 1wchA 2328 :GKTTMV T0305 149 :GNIIVTLKSTKIHACYTVRRFSIRNTK 1wchA 2335 :NRLRLALVRMQQLKGFVVRAMTLEDIQ T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 1wchA 2362 :TREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIH T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTR Number of specific fragments extracted= 9 number of extra gaps= 0 total=103 Number of alignments=11 # 1wchA read from 1wchA/merged-good-all-a2m # found chain 1wchA in template set T0305 7 :QFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1wchA 2195 :ANLKSVIRVLRGLLDQGIPSKELENLQELKPLDQCLIGQTKENRRKNRYKNILPYDATRVPLG T0305 77 :KHSDYINANYV 1wchA 2258 :DEGGYINASFI T0305 88 :DGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1wchA 2271 :PVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWPN T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1wchA 2329 :KTTMVSNRLRLALVRMQQLKGFVVRAMTLED T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 1wchA 2360 :IQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIH T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLT Number of specific fragments extracted= 6 number of extra gaps= 0 total=109 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rpmA expands to /projects/compbio/data/pdb/1rpm.pdb.gz 1rpmA:# T0305 read from 1rpmA/merged-good-all-a2m # 1rpmA read from 1rpmA/merged-good-all-a2m # adding 1rpmA to template set # found chain 1rpmA in template set T0305 5 :MKQFVKHIGELYSNNQHGFSEDFEE 1rpmA 882 :VADLLQHITQMKCAEGYGFKEEYES T0305 33 :CTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1rpmA 907 :FFEGQSAPWDSAKKDENRMKNRYGNIIAYDHSRVRLQTIEGDTN T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1rpmA 951 :SDYINGNYIDGYHRPNHYIATQGPMQETIYDFWRMVWHENTASIIMVTNLVEVGRVKCCKYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1rpmA 1014 :DDTEIYKDIKVTLIETELLAEYVIRTFAVEK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1rpmA 1045 :RGVHEIREIRQFHFTGWPDHGVPYHATGLLGFVRQVKSKSPPSAGPLVVHCSAGAGRTGCFIVIDIMLDMAEREGVVDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEAC Number of specific fragments extracted= 5 number of extra gaps= 0 total=114 Number of alignments=13 # 1rpmA read from 1rpmA/merged-good-all-a2m # found chain 1rpmA in template set T0305 3 :QSMKQFVKHIGELYSNNQHGFSEDFEEV 1rpmA 880 :IRVADLLQHITQMKCAEGYGFKEEYESF T0305 34 :TADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1rpmA 908 :FEGQSAPWDSAKKDENRMKNRYGNIIAYDHSRVRLQTIEGDTN T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1rpmA 951 :SDYINGNYIDGYHRPNHYIATQGPMQETIYDFWRMVWHENTASIIMVTNLVEVGRVKCCKYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 1rpmA 1014 :DDTEIYKDIKVTLIETELLAEYVIRTFAVEKRG T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1rpmA 1047 :VHEIREIRQFHFTGWPDHGVPYHATGLLGFVRQVKSKSPPSAGPLVVHCSAGAGRTGCFIVIDIMLDMAEREGVVDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEAC Number of specific fragments extracted= 5 number of extra gaps= 0 total=119 Number of alignments=14 # 1rpmA read from 1rpmA/merged-good-all-a2m # found chain 1rpmA in template set T0305 13 :GELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1rpmA 887 :QHITQMKCAEGYGFKEEYESFFEGQSAPWDSAKKDENRMKNRYGNIIAYDHSRVRLQ T0305 72 :PGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1rpmA 944 :TIEGDTNSDYINGNYIDGYHRPNHYIATQGPMQETIYDFWRMVWHENTASIIMVTNLVEVGRVKCCKYWPD T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1rpmA 1015 :DTEIYKDIKVTLIETELLAEYVIRTFAVEK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1rpmA 1045 :RGVHEIREIRQFHFTGWPDHGVPYHATGLLGFVRQVKSKSPPSAGPLVVHCSAGAGRTGCFIVIDIMLDMAEREGVVDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEAC Number of specific fragments extracted= 4 number of extra gaps= 0 total=123 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2ahsA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2ahsA/merged-good-all-a2m.gz for input Trying 2ahsA/merged-good-all-a2m Error: Couldn't open file 2ahsA/merged-good-all-a2m or 2ahsA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ygrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1ygrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1ygrA/merged-good-all-a2m.gz for input Trying 1ygrA/merged-good-all-a2m Error: Couldn't open file 1ygrA/merged-good-all-a2m or 1ygrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g59A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2g59A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2g59A/merged-good-all-a2m.gz for input Trying 2g59A/merged-good-all-a2m Error: Couldn't open file 2g59A/merged-good-all-a2m or 2g59A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rxdA expands to /projects/compbio/data/pdb/1rxd.pdb.gz 1rxdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0305 read from 1rxdA/merged-good-all-a2m # 1rxdA read from 1rxdA/merged-good-all-a2m # adding 1rxdA to template set # found chain 1rxdA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0305 92 :KAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 1rxdA 14 :KNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEAT T0305 130 :EK 1rxdA 58 :EK T0305 185 :KG 1rxdA 60 :EG T0305 196 :YHYTQWP 1rxdA 62 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1rxdA 94 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1rxdA 120 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFIH 1rxdA 141 :NSKQLLYLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=131 Number of alignments=16 # 1rxdA read from 1rxdA/merged-good-all-a2m # found chain 1rxdA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0305 92 :KAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1rxdA 14 :KNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATY T0305 175 :KVKKGQK 1rxdA 53 :DTTLVEK T0305 187 :RQ 1rxdA 60 :EG T0305 196 :YHYTQWP 1rxdA 62 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1rxdA 94 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1rxdA 120 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1rxdA 141 :NSKQLLYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=139 Number of alignments=17 # 1rxdA read from 1rxdA/merged-good-all-a2m # found chain 1rxdA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0305 65 :RVKLR 1rxdA 10 :EVTYK T0305 93 :AKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1rxdA 15 :NMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATY T0305 196 :YHYTQWP 1rxdA 62 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1rxdA 94 :EPGCCIAVHCVAGLGRAPVLVALALIE T0305 259 :STVNVLGFLKHIRTQRNYLV 1rxdA 121 :GGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1rxdA 141 :NSKQLLYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=146 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yfoA expands to /projects/compbio/data/pdb/1yfo.pdb.gz 1yfoA:# T0305 read from 1yfoA/merged-good-all-a2m # 1yfoA read from 1yfoA/merged-good-all-a2m # adding 1yfoA to template set # found chain 1yfoA in template set Warning: unaligning (T0305)N173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yfoA)Q388 Warning: unaligning (T0305)E190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yfoA)Q388 T0305 3 :Q 1yfoA 210 :P T0305 4 :SMKQFVKHIGELYSNNQHGFSEDFEEVQRCTADM 1yfoA 213 :PVDKLEEEINRRMADDNKLFREEFNALPACPIQA T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1yfoA 247 :TCEAASKEENKEKNRYVNILPYDHSRVHLTPVEGVPD T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIR 1yfoA 284 :SDYINASFINGYQEKNKFIAAQGPKEETVNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGCWTYGNVRVSVEDVTVLVDYTVRKFCIQ T0305 191 :RVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1yfoA 389 :RLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQYAGAIVVHCSAGVGRTGTFVVIDAMLDMMHSERKVDVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHYLY Number of specific fragments extracted= 5 number of extra gaps= 0 total=151 Number of alignments=19 # 1yfoA read from 1yfoA/merged-good-all-a2m # found chain 1yfoA in template set Warning: unaligning (T0305)N173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yfoA)Q388 Warning: unaligning (T0305)E190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yfoA)Q388 T0305 1 :YFQSMKQFVKHIGELYSNNQHGFSEDFEEVQ 1yfoA 210 :PPLPVDKLEEEINRRMADDNKLFREEFNALP T0305 34 :TADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1yfoA 241 :ACPIQATCEAASKEENKEKNRYVNILPYDHSRVHLTPVEGVPD T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIR 1yfoA 284 :SDYINASFINGYQEKNKFIAAQGPKEETVNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGCWTYGNVRVSVEDVTVLVDYTVRKFCIQ T0305 191 :RVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1yfoA 389 :RLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQYAGAIVVHCSAGVGRTGTFVVIDAMLDMMHSERKVDVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHYLY Number of specific fragments extracted= 4 number of extra gaps= 0 total=155 Number of alignments=20 # 1yfoA read from 1yfoA/merged-good-all-a2m # found chain 1yfoA in template set Warning: unaligning (T0305)N173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yfoA)Q388 Warning: unaligning (T0305)E190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yfoA)Q388 T0305 7 :QFVKHIGELY 1yfoA 216 :KLEEEINRRM T0305 21 :HGFSEDFEEVQR 1yfoA 226 :ADDNKLFREEFN T0305 33 :CTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1yfoA 240 :PACPIQATCEAASKEENKEKNRYVNILPYDHSRVHLT T0305 72 :PGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIR 1yfoA 277 :PVEGVPDSDYINASFINGYQEKNKFIAAQGPKEETVNDFWRMIWEQNTATIVMVTNLKERKECKCAQYWPDQGCWTYGNVRVSVEDVTVLVDYTVRKFCIQ T0305 191 :RVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1yfoA 389 :RLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQYAGAIVVHCSAGVGRTGTFVVIDAMLDMMHSERKVDVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHYL Number of specific fragments extracted= 5 number of extra gaps= 0 total=160 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fprA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1fprA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1fprA/merged-good-all-a2m.gz for input Trying 1fprA/merged-good-all-a2m Error: Couldn't open file 1fprA/merged-good-all-a2m or 1fprA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u24A expands to /projects/compbio/data/pdb/1u24.pdb.gz 1u24A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0305 read from 1u24A/merged-good-all-a2m # 1u24A read from 1u24A/merged-good-all-a2m # adding 1u24A to template set # found chain 1u24A in template set T0305 4 :SMKQFVKHIGELYSN 1u24A 149 :SQHEALADERHRLHA T0305 62 :DHSRVKLRPLPGK 1u24A 165 :LHKTVYIAPLGKH T0305 139 :YWPTE 1u24A 178 :KLPEG T0305 144 :NSEEYGNI 1u24A 184 :EVRRVQKV T0305 187 :RQN 1u24A 201 :AGM T0305 195 :QYHYTQWPDMGVP 1u24A 204 :RYFRIAATDHVWP T0305 209 :YALPVLTFVRRSSAA 1u24A 217 :TPENIDRFLAFYRTL T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1u24A 232 :PQDAWLHFHCEAGVGRTTAFMVMTDML T0305 257 :DKSTVNVLGFLKHIRTQRNYLVQT 1u24A 259 :KNPSVSLKDILYRQHEIGGFYYGE T0305 281 :EEQYIFIHDALLEAIL 1u24A 295 :TKYYREKIVMIEQFYR Number of specific fragments extracted= 10 number of extra gaps= 0 total=170 Number of alignments=22 # 1u24A read from 1u24A/merged-good-all-a2m # found chain 1u24A in template set T0305 3 :QSMKQFVKHIGELY 1u24A 148 :KSQHEALADERHRL T0305 28 :EEVQ 1u24A 162 :HAAL T0305 63 :HSRVKLRPLPGK 1u24A 166 :HKTVYIAPLGKH T0305 139 :YWPTENSEE 1u24A 178 :KLPEGGEVR T0305 148 :YGNII 1u24A 188 :VQKVQ T0305 187 :RQNE 1u24A 201 :AGMR T0305 196 :YHYTQWPDMGVP 1u24A 205 :YFRIAATDHVWP T0305 209 :YALPVLTFVRRSSA 1u24A 217 :TPENIDRFLAFYRT T0305 225 :MPETGPVLVHCSAGVGRTGTYIVIDSML 1u24A 231 :LPQDAWLHFHCEAGVGRTTAFMVMTDML T0305 257 :DKSTVNVLGFLKHIRTQRNYLVQT 1u24A 259 :KNPSVSLKDILYRQHEIGGFYYGE T0305 281 :EEQYIFIHDALLEAIL 1u24A 295 :TKYYREKIVMIEQFYR Number of specific fragments extracted= 11 number of extra gaps= 0 total=181 Number of alignments=23 # 1u24A read from 1u24A/merged-good-all-a2m # found chain 1u24A in template set Warning: unaligning (T0305)A35 because first residue in template chain is (1u24A)T23 T0305 36 :DMNITAEHSNHPENKHKNRYINILAYDH 1u24A 24 :VTEPVGSYARAERPQDFEGFVWRLDNDG T0305 72 :PGKDSKHSD 1u24A 79 :YVPSREGMD T0305 93 :AKAYIATQGPLKSTFEDFWRMIWEQ 1u24A 88 :ALHISGSSAFTPAQLKNVAAKLREK T0305 118 :NTGIIVMITNLVE 1u24A 115 :GPIYDVDLRQESH T0305 198 :YTQWPDMGVP 1u24A 207 :RIAATDHVWP T0305 209 :YALPVLTFVRRSSA 1u24A 217 :TPENIDRFLAFYRT T0305 225 :MPETGPVLVHCSAGVGRTGTYIVIDSMLQ 1u24A 231 :LPQDAWLHFHCEAGVGRTTAFMVMTDMLK T0305 258 :KSTVNVLGFLKHIRTQRNYLVQT 1u24A 260 :NPSVSLKDILYRQHEIGGFYYGE T0305 281 :EEQYIFIHDALLEAIL 1u24A 295 :TKYYREKIVMIEQFYR Number of specific fragments extracted= 9 number of extra gaps= 0 total=190 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pty/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pty expands to /projects/compbio/data/pdb/1pty.pdb.gz 1pty:Warning: there is no chain 1pty will retry with 1ptyA Skipped atom 397, because occupancy 0.490 <= existing 0.510 in 1pty Skipped atom 399, because occupancy 0.490 <= existing 0.510 in 1pty Skipped atom 401, because occupancy 0.490 <= existing 0.510 in 1pty # T0305 read from 1pty/merged-good-all-a2m # 1pty read from 1pty/merged-good-all-a2m # adding 1pty to template set # found chain 1pty in template set T0305 8 :FVKHIGELYSNN 1pty 3 :MEKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTADM 1pty 15 :SWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 1pty 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1pty 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYG 1pty 129 :EEKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1pty 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1pty 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pty 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pty 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=199 Number of alignments=25 # 1pty read from 1pty/merged-good-all-a2m # found chain 1pty in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1pty)E2 T0305 5 :MKQFVKHIGEL 1pty 3 :MEKEFEQIDKS T0305 21 :HGFSEDFEEVQRCTA 1pty 14 :GSWAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 1pty 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1pty 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1pty 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1pty 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1pty 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pty 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pty 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=208 Number of alignments=26 # 1pty read from 1pty/merged-good-all-a2m # found chain 1pty in template set T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1pty 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1pty 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1pty 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1pty 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1pty 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pty 206 :PEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pty 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=215 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zckA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zckA expands to /projects/compbio/data/pdb/1zck.pdb.gz 1zckA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0305 read from 1zckA/merged-good-all-a2m # 1zckA read from 1zckA/merged-good-all-a2m # adding 1zckA to template set # found chain 1zckA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0305 89 :GYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 1zckA 12 :VTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEAT T0305 130 :EK 1zckA 59 :EK T0305 185 :KG 1zckA 61 :EG T0305 196 :YHYTQWP 1zckA 63 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1zckA 95 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1zckA 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFIH 1zckA 142 :NSKQLLYLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=223 Number of alignments=28 # 1zckA read from 1zckA/merged-good-all-a2m # found chain 1zckA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0305 89 :GYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 1zckA 12 :VTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEAT T0305 174 :TKVKKGQK 1zckA 53 :YDTTLVEK T0305 187 :RQ 1zckA 61 :EG T0305 196 :YHYTQWP 1zckA 63 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1zckA 95 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1zckA 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1zckA 142 :NSKQLLYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=231 Number of alignments=29 # 1zckA read from 1zckA/merged-good-all-a2m # found chain 1zckA in template set Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0305 65 :RVKLR 1zckA 11 :EVTYK T0305 93 :AKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1zckA 16 :NMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATY T0305 196 :YHYTQWP 1zckA 63 :IHVLDWP T0305 206 :VPEYALPVLTFVRRSSAARM 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1zckA 95 :EPGCCIAVHCVAGLGRAPVLVALALIE T0305 259 :STVNVLGFLKHIRTQRNYLV 1zckA 122 :GGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1zckA 142 :NSKQLLYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=238 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ytn expands to /projects/compbio/data/pdb/1ytn.pdb.gz 1ytn:Warning: there is no chain 1ytn will retry with 1ytnA # T0305 read from 1ytn/merged-good-all-a2m # 1ytn read from 1ytn/merged-good-all-a2m # adding 1ytn to template set # found chain 1ytn in template set T0305 4 :SMKQFVKHIGELYS 1ytn 193 :ARAELSSRLTTLRN T0305 32 :RCTADMN 1ytn 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1ytn 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 79 :SD 1ytn 242 :AD T0305 82 :INANYVDGYNKA 1ytn 244 :LNANYIQVGNTR T0305 96 :YIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1ytn 256 :TIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1ytn 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIH 1ytn 303 :RQSGTYGSITVESKMTQQV T0305 162 :ACYTVRRFSIRNTK 1ytn 325 :DGIMADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVP 1ytn 339 :AGQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1ytn 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytn 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytn 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytn 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLEA 1ytn 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=253 Number of alignments=31 # 1ytn read from 1ytn/merged-good-all-a2m # found chain 1ytn in template set T0305 5 :MKQFVKHIGELYS 1ytn 194 :RAELSSRLTTLRN T0305 32 :RCTADMN 1ytn 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1ytn 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 79 :SD 1ytn 242 :AD T0305 82 :INANYVDGYNK 1ytn 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1ytn 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1ytn 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1ytn 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRNT 1ytn 329 :ADMYTLTIREA T0305 187 :RQNERVVIQYHYTQWPDMGVP 1ytn 340 :GQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1ytn 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytn 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytn 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytn 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLEA 1ytn 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=268 Number of alignments=32 # 1ytn read from 1ytn/merged-good-all-a2m # found chain 1ytn in template set T0305 23 :FSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1ytn 197 :LSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRAD T0305 82 :INANYVDGYN 1ytn 244 :LNANYIQVGN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHAC 1ytn 254 :TRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRN 1ytn 329 :ADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVPE 1ytn 339 :AGQKTISVPVVHVGNWPDQTAVS T0305 210 :ALPVLTFVRRSSAARM 1ytn 362 :SEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytn 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytn 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytn 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1ytn 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=278 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l8gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1l8gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1l8gA/merged-good-all-a2m.gz for input Trying 1l8gA/merged-good-all-a2m Error: Couldn't open file 1l8gA/merged-good-all-a2m or 1l8gA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1larA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1larA expands to /projects/compbio/data/pdb/1lar.pdb.gz 1larA:# T0305 read from 1larA/merged-good-all-a2m # 1larA read from 1larA/merged-good-all-a2m # adding 1larA to template set # found chain 1larA in template set T0305 5 :MKQFVKHIGELYSNNQHGFSEDFEEVQ 1larA 1308 :ITDLADNIERLKANDGLKFSQEYESID T0305 35 :ADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1larA 1335 :PGQQFTWENSNLEVNKPKNRYANVIAYDHSRVILTSIDGVPG T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1larA 1377 :SDYINANYIDGYRKQNAYIATQGPLPETMGDFWRMVWEQRTATVVMMTRLEEKSRVKCDQYWPARGTETCGLIQVTLLDTVELATYTVRTFALHK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1larA 1472 :SGSSEKRELRQFQFMAWPDHGVPEYPTPILAFLRRVKACNPLDAGPMVVHCSAGVGRTGCFIVIDAMLERMKHEKTVDIYGHVTCMRSQRNYMVQTEDQYVFIHEALLEAAT Number of specific fragments extracted= 4 number of extra gaps= 0 total=282 Number of alignments=34 # 1larA read from 1larA/merged-good-all-a2m # found chain 1larA in template set T0305 5 :MKQFVKHIGELYSNNQHGFSEDFEEV 1larA 1308 :ITDLADNIERLKANDGLKFSQEYESI T0305 34 :TADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1larA 1334 :DPGQQFTWENSNLEVNKPKNRYANVIAYDHSRVILTSIDGVPG T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 1larA 1377 :SDYINANYIDGYRKQNAYIATQGPLPETMGDFWRMVWEQRTATVVMMTRLEEKSRVKCDQYWPARGTETCGLIQVTLLDTVELATYTVRTFALHKSG T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1larA 1474 :SSEKRELRQFQFMAWPDHGVPEYPTPILAFLRRVKACNPLDAGPMVVHCSAGVGRTGCFIVIDAMLERMKHEKTVDIYGHVTCMRSQRNYMVQTEDQYVFIHEALLEAAT Number of specific fragments extracted= 4 number of extra gaps= 0 total=286 Number of alignments=35 # 1larA read from 1larA/merged-good-all-a2m # found chain 1larA in template set T0305 11 :HIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1larA 1311 :LADNIERLKANDGLKFSQEYESIDPGQQFTWENSNLEVNKPKNRYANVIAYDHSRVILT T0305 72 :PGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1larA 1370 :SIDGVPGSDYINANYIDGYRKQNAYIATQGPLPETMGDFWRMVWEQRTATVVMMTRLEEKSRVKCDQYWPARGTETCGLIQVTLLDTVELATYTVRTFALHK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1larA 1472 :SGSSEKRELRQFQFMAWPDHGVPEYPTPILAFLRRVKACNPLDAGPMVVHCSAGVGRTGCFIVIDAMLERMKHEKTVDIYGHVTCMRSQRNYMVQTEDQYVFIHEALLEAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=289 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yptA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yptA expands to /projects/compbio/data/pdb/1ypt.pdb.gz 1yptA:# T0305 read from 1yptA/merged-good-all-a2m # 1yptA read from 1yptA/merged-good-all-a2m # adding 1yptA to template set # found chain 1yptA in template set Warning: unaligning (T0305)F2 because first residue in template chain is (1yptA)P191 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (1yptA)V445 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (1yptA)V445 T0305 3 :QSMKQFVKHIGELYS 1yptA 192 :EARAELSSRLTTLRN T0305 32 :RCTADMN 1yptA 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1yptA 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 79 :SD 1yptA 242 :AD T0305 82 :INANYVDGYNK 1yptA 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1yptA 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1yptA 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIH 1yptA 303 :RQSGTYGSITVESKMTQQV T0305 162 :ACYTVRRFSIRNTK 1yptA 325 :DGIMADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVP 1yptA 339 :AGQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1yptA 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1yptA 394 :DSKLRPVIHCRAGVGRTAQLIGAMCMN T0305 258 :K 1yptA 421 :D T0305 259 :STVNVLGFLKHIRTQRNY 1yptA 425 :SQLSVEDMVSQMRVQRNG T0305 279 :QTEEQYIFIHDAL 1yptA 446 :QKDEQLDVLIKLA Number of specific fragments extracted= 15 number of extra gaps= 1 total=304 Number of alignments=37 # 1yptA read from 1yptA/merged-good-all-a2m # found chain 1yptA in template set Warning: unaligning (T0305)S17 because first residue in template chain is (1yptA)P191 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (1yptA)V445 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (1yptA)V445 T0305 18 :NNQHGFSEDFEEVQR 1yptA 192 :EARAELSSRLTTLRN T0305 33 :CTADMN 1yptA 208 :LAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1yptA 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 72 :PG 1yptA 242 :AD T0305 82 :INANYVDGYNK 1yptA 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1yptA 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1yptA 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1yptA 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRNT 1yptA 329 :ADMYTLTIREA T0305 187 :RQNERVVIQYHYTQWPDMGVP 1yptA 340 :GQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1yptA 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1yptA 394 :DSKLRPVIHCRAGVGRTAQLIGAMCMN T0305 258 :K 1yptA 421 :D T0305 259 :STVNVLGFLKHIRTQRNY 1yptA 425 :SQLSVEDMVSQMRVQRNG T0305 279 :QTEEQYIFIHDAL 1yptA 446 :QKDEQLDVLIKLA Number of specific fragments extracted= 15 number of extra gaps= 1 total=319 Number of alignments=38 # 1yptA read from 1yptA/merged-good-all-a2m # found chain 1yptA in template set Warning: unaligning (T0305)S17 because first residue in template chain is (1yptA)P191 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (1yptA)V445 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (1yptA)V445 T0305 18 :NNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1yptA 192 :EARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRAD T0305 82 :INANYVDGYN 1yptA 244 :LNANYIQVGN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCD 1yptA 254 :TRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFG T0305 140 :WPT 1yptA 298 :MPD T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1yptA 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRN 1yptA 329 :ADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVPE 1yptA 339 :AGQKTISVPVVHVGNWPDQTAVS T0305 210 :ALPVLTFVRRSSAARM 1yptA 362 :SEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQ 1yptA 394 :DSKLRPVIHCRAGVGRTAQLIGAMCMND T0305 258 :K 1yptA 422 :S T0305 259 :STVNVLGFLKHIRTQRNY 1yptA 425 :SQLSVEDMVSQMRVQRNG T0305 279 :QTEEQYIFIHDAL 1yptA 446 :QKDEQLDVLIKLA Number of specific fragments extracted= 12 number of extra gaps= 1 total=331 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yts/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yts expands to /projects/compbio/data/pdb/1yts.pdb.gz 1yts:Warning: there is no chain 1yts will retry with 1ytsA # T0305 read from 1yts/merged-good-all-a2m # 1yts read from 1yts/merged-good-all-a2m # adding 1yts to template set # found chain 1yts in template set Warning: unaligning (T0305)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P347 Warning: unaligning (T0305)I194 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P347 Warning: unaligning (T0305)W201 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P355 Warning: unaligning (T0305)P202 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P355 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)S395 Warning: unaligning (T0305)E227 because of BadResidue code BAD_PEPTIDE at template residue (1yts)S395 Warning: unaligning (T0305)P230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yts)P399 Warning: unaligning (T0305)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yts)P399 Warning: unaligning (T0305)V233 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)H402 Warning: unaligning (T0305)H234 because of BadResidue code BAD_PEPTIDE at template residue (1yts)H402 T0305 3 :QSMKQFVKHIGELYS 1yts 192 :EARAELSSRLTTLRN T0305 32 :RCTADMN 1yts 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1yts 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 72 :PG 1yts 242 :AD T0305 82 :INANYVDGYNKA 1yts 244 :LNANYIQVGNTR T0305 96 :YIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1yts 256 :TIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1yts 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIH 1yts 303 :RQSGTYGSITVESKMTQQV T0305 162 :ACYTVRRFSIRNTK 1yts 325 :DGIMADMYTLTIRE T0305 186 :GRQNERV 1yts 339 :AGQKTIS T0305 195 :QYHYTQ 1yts 348 :VVHVGN T0305 203 :DMGVP 1yts 356 :DQTAV T0305 209 :YALPVLTFVRRSSAARM 1yts 361 :SSEVTKALASLVDQTAE T0305 228 :TG 1yts 396 :KL T0305 232 :L 1yts 400 :V T0305 235 :CSAGVGRTGTYIVIDSM 1yts 403 :SRAGVGRTAQLIGAMCM T0305 257 :DKSTVNVLGFLKHIRTQRNY 1yts 423 :RNSQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1yts 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 18 number of extra gaps= 5 total=349 Number of alignments=40 # 1yts read from 1yts/merged-good-all-a2m # found chain 1yts in template set Warning: unaligning (T0305)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P347 Warning: unaligning (T0305)I194 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P347 Warning: unaligning (T0305)W201 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P355 Warning: unaligning (T0305)P202 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P355 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)S395 Warning: unaligning (T0305)E227 because of BadResidue code BAD_PEPTIDE at template residue (1yts)S395 Warning: unaligning (T0305)P230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yts)P399 Warning: unaligning (T0305)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yts)P399 Warning: unaligning (T0305)V233 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)H402 Warning: unaligning (T0305)H234 because of BadResidue code BAD_PEPTIDE at template residue (1yts)H402 T0305 5 :MKQFVKHIGELYS 1yts 194 :RAELSSRLTTLRN T0305 32 :RCTADMN 1yts 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1yts 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 72 :PG 1yts 242 :AD T0305 82 :INANYVDGYNK 1yts 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1yts 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1yts 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1yts 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRNT 1yts 329 :ADMYTLTIREA T0305 187 :RQNERV 1yts 340 :GQKTIS T0305 195 :QYHYTQ 1yts 348 :VVHVGN T0305 203 :DMGVP 1yts 356 :DQTAV T0305 209 :YALPVLTFVRRSSAARM 1yts 361 :SSEVTKALASLVDQTAE T0305 228 :TG 1yts 396 :KL T0305 232 :L 1yts 400 :V T0305 235 :CSAGVGRTGTYIVIDSM 1yts 403 :SRAGVGRTAQLIGAMCM T0305 257 :DKSTVNVLGFLKHIRTQRNY 1yts 423 :RNSQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1yts 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 18 number of extra gaps= 5 total=367 Number of alignments=41 # 1yts read from 1yts/merged-good-all-a2m # found chain 1yts in template set Warning: unaligning (T0305)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P347 Warning: unaligning (T0305)I194 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P347 Warning: unaligning (T0305)W201 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)P355 Warning: unaligning (T0305)P202 because of BadResidue code BAD_PEPTIDE at template residue (1yts)P355 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)S395 Warning: unaligning (T0305)E227 because of BadResidue code BAD_PEPTIDE at template residue (1yts)S395 Warning: unaligning (T0305)P230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yts)P399 Warning: unaligning (T0305)V231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yts)P399 Warning: unaligning (T0305)V233 because of BadResidue code BAD_PEPTIDE in next template residue (1yts)H402 Warning: unaligning (T0305)H234 because of BadResidue code BAD_PEPTIDE at template residue (1yts)H402 T0305 20 :QHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1yts 194 :RAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRAD T0305 82 :INANYVDGYN 1yts 244 :LNANYIQVGN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHAC 1yts 254 :TRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRN 1yts 329 :ADMYTLTIRE T0305 186 :GRQNERV 1yts 339 :AGQKTIS T0305 195 :QYHYTQ 1yts 348 :VVHVGN T0305 203 :DMGVPE 1yts 356 :DQTAVS T0305 210 :ALPVLTFVRRSSAARM 1yts 362 :SEVTKALASLVDQTAE T0305 228 :TG 1yts 396 :KL T0305 232 :L 1yts 400 :V T0305 235 :CSAGVGRTGTYIVIDSM 1yts 403 :SRAGVGRTAQLIGAMCM T0305 257 :DK 1yts 422 :SR T0305 259 :STVNVLGFLKHIRTQRNY 1yts 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1yts 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 14 number of extra gaps= 5 total=381 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p15A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p15A expands to /projects/compbio/data/pdb/1p15.pdb.gz 1p15A:# T0305 read from 1p15A/merged-good-all-a2m # 1p15A read from 1p15A/merged-good-all-a2m # adding 1p15A to template set # found chain 1p15A in template set Warning: unaligning (T0305)V129 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0305)E130 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0305)K131 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0305)G132 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0305)C136 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)A636 Warning: unaligning (T0305)D137 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)A636 Warning: unaligning (T0305)S157 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E657 Warning: unaligning (T0305)T158 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E657 Warning: unaligning (T0305)K185 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)R674 Warning: unaligning (T0305)G186 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)R674 Warning: unaligning (T0305)R187 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E675 T0305 43 :HSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1p15A 544 :TGNLPANMKKNRVLQIIPYEFNRVIIPVKRGEEN T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNL 1p15A 578 :TDYVNASFIDGYRQKDSYIASQGPLLHTIEDFWRMIWEWKSCSIVMLTEL T0305 133 :RRK 1p15A 632 :QEK T0305 138 :QYWPTENSEEYGNIIVTLK 1p15A 637 :QYWPSDGLVSYGDITVELK T0305 159 :KIHACYTVRRFSIRN 1p15A 658 :EECESYTVRDLLVTN T0305 188 :QNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMP 1p15A 676 :NKSRQIRQFHFHGWPEVGIPSDGKGMINIIAAVQKQQQQ T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1p15A 716 :GNHPITVHCSAGAGRTGTFCALSTVLERVKAEGILDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYI Number of specific fragments extracted= 7 number of extra gaps= 4 total=388 Number of alignments=43 # 1p15A read from 1p15A/merged-good-all-a2m # found chain 1p15A in template set Warning: unaligning (T0305)V129 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0305)E130 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0305)K131 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0305)G132 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0305)C136 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)A636 Warning: unaligning (T0305)D137 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)A636 Warning: unaligning (T0305)S157 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E657 Warning: unaligning (T0305)T158 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E657 Warning: unaligning (T0305)T174 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)R674 Warning: unaligning (T0305)K175 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)R674 Warning: unaligning (T0305)R187 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E675 T0305 43 :HSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 1p15A 544 :TGNLPANMKKNRVLQIIPYEFNRVIIPVKRGEEN T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNL 1p15A 578 :TDYVNASFIDGYRQKDSYIASQGPLLHTIEDFWRMIWEWKSCSIVMLTEL T0305 133 :RRK 1p15A 632 :QEK T0305 138 :QYWPTENSEEYGNIIVTLK 1p15A 637 :QYWPSDGLVSYGDITVELK T0305 159 :KIHACYTVRRFSIRN 1p15A 658 :EECESYTVRDLLVTN T0305 188 :QNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMP 1p15A 676 :NKSRQIRQFHFHGWPEVGIPSDGKGMINIIAAVQKQQQQ T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 1p15A 716 :GNHPITVHCSAGAGRTGTFCALSTVLERVKAEGILDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYI Number of specific fragments extracted= 7 number of extra gaps= 4 total=395 Number of alignments=44 # 1p15A read from 1p15A/merged-good-all-a2m # found chain 1p15A in template set Warning: unaligning (T0305)V129 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0305)E130 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0305)K131 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0305)G132 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0305)C136 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)A636 Warning: unaligning (T0305)D137 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)A636 Warning: unaligning (T0305)S157 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E657 Warning: unaligning (T0305)T158 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E657 Warning: unaligning (T0305)K185 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)R674 Warning: unaligning (T0305)G186 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)R674 Warning: unaligning (T0305)R187 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E675 T0305 43 :HSNHPENKHKNRYINILAYDHSRVKLR 1p15A 544 :TGNLPANMKKNRVLQIIPYEFNRVIIP T0305 72 :PGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNL 1p15A 571 :VKRGEENTDYVNASFIDGYRQKDSYIASQGPLLHTIEDFWRMIWEWKSCSIVMLTEL T0305 133 :RRK 1p15A 632 :QEK T0305 138 :QYWPTENSEEYGNIIVTLK 1p15A 637 :QYWPSDGLVSYGDITVELK T0305 159 :KIHACYTVRRFSIRN 1p15A 658 :EECESYTVRDLLVTN T0305 188 :QNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1p15A 676 :NKSRQIRQFHFHGWPEVGIPSDGKGMINIIAAVQKQQQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLE 1p15A 715 :SGNHPITVHCSAGAGRTGTFCALSTVLERVKAEGILDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQE Number of specific fragments extracted= 7 number of extra gaps= 4 total=402 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q6nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1q6nA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1q6nA/merged-good-all-a2m.gz for input Trying 1q6nA/merged-good-all-a2m Error: Couldn't open file 1q6nA/merged-good-all-a2m or 1q6nA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g7fA expands to /projects/compbio/data/pdb/1g7f.pdb.gz 1g7fA:# T0305 read from 1g7fA/merged-good-all-a2m # 1g7fA read from 1g7fA/merged-good-all-a2m # adding 1g7fA to template set # found chain 1g7fA in template set Warning: unaligning (T0305)Q7 because first residue in template chain is (1g7fA)E2 Warning: unaligning (T0305)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)C32 Warning: unaligning (T0305)A41 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)C32 Warning: unaligning (T0305)A162 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)Y152 Warning: unaligning (T0305)C163 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)Y152 Warning: unaligning (T0305)S259 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 Warning: unaligning (T0305)T260 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)D240 T0305 8 :FVKHIGELYS 1g7fA 3 :MEKEFEQIDK T0305 20 :QHGFSEDFEEVQRCTADM 1g7fA 13 :SGSWAAIYQDIRHEASDF T0305 42 :EHSNHPENKHKNRYINILAYDHSRVKLR 1g7fA 33 :RVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1g7fA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1g7fA 129 :EEKEMIFED T0305 151 :IIVTLKSTKIH 1g7fA 140 :LKLTLISEDIK T0305 164 :YTVRRFSIRN 1g7fA 153 :YTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1g7fA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDK 1g7fA 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKR T0305 261 :VNVLGFLK 1g7fA 244 :VDIKKVLL T0305 270 :IRTQRNYLVQTEEQYIFIHDALLEAIL 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 11 number of extra gaps= 3 total=413 Number of alignments=46 # 1g7fA read from 1g7fA/merged-good-all-a2m # found chain 1g7fA in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1g7fA)E2 Warning: unaligning (T0305)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)C32 Warning: unaligning (T0305)A41 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)C32 Warning: unaligning (T0305)A162 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)Y152 Warning: unaligning (T0305)C163 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)Y152 Warning: unaligning (T0305)S259 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 Warning: unaligning (T0305)T260 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)D240 T0305 5 :MKQFVKHIG 1g7fA 3 :MEKEFEQID T0305 17 :S 1g7fA 12 :K T0305 20 :QHGFSEDFEEVQRCTA 1g7fA 13 :SGSWAAIYQDIRHEAS T0305 38 :NI 1g7fA 29 :DF T0305 42 :EHSNHPENKHKNRYINILAYDHSRVKLRPLP 1g7fA 33 :RVAKLPKNKNRNRYRDVSPFDHSRIKLHQED T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1g7fA 64 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1g7fA 129 :EEKEMIFED T0305 151 :IIVTLKSTKIH 1g7fA 140 :LKLTLISEDIK T0305 164 :YTVRRFSIRNTK 1g7fA 153 :YTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1g7fA 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDK 1g7fA 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKR T0305 261 :VNVLGFLK 1g7fA 244 :VDIKKVLL T0305 270 :IRTQRNYLVQTEEQYIFIHDALLEAIL 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 13 number of extra gaps= 3 total=426 Number of alignments=47 # 1g7fA read from 1g7fA/merged-good-all-a2m # found chain 1g7fA in template set Warning: unaligning (T0305)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)C32 Warning: unaligning (T0305)A41 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)C32 Warning: unaligning (T0305)A162 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)Y152 Warning: unaligning (T0305)C163 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)Y152 Warning: unaligning (T0305)S259 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 Warning: unaligning (T0305)T260 because of BadResidue code BAD_PEPTIDE at template residue (1g7fA)D240 T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNI 1g7fA 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDF T0305 42 :EHSNHPENKHKNRYINILAYDHSRVKLR 1g7fA 33 :RVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1g7fA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1g7fA 130 :EKEMIFE T0305 150 :NIIVTLKSTKIH 1g7fA 139 :NLKLTLISEDIK T0305 164 :YTVRRFSIRN 1g7fA 153 :YTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1g7fA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDK 1g7fA 206 :PEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKR T0305 261 :VNVLGFLK 1g7fA 244 :VDIKKVLL T0305 270 :IRTQRNYLVQTEEQYIFIHDALLEAIL 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 3 total=436 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d5rA expands to /projects/compbio/data/pdb/1d5r.pdb.gz 1d5rA:# T0305 read from 1d5rA/merged-good-all-a2m # 1d5rA read from 1d5rA/merged-good-all-a2m # adding 1d5rA to template set # found chain 1d5rA in template set T0305 56 :INILAYDHSRVKLR 1d5rA 16 :YQEDGFDLDLTYIY T0305 75 :DS 1d5rA 30 :PN T0305 96 :YIATQGPLKST 1d5rA 32 :IIAMGFPAERL T0305 107 :FEDFWRMIWEQ 1d5rA 50 :IDDVVRFLDSK T0305 118 :NTGIIVMITNLVEKGR 1d5rA 63 :NHYKIYNLCAERHYDT T0305 185 :KGRQNERVV 1d5rA 79 :AKFNCRVAQ T0305 199 :TQWPDMGVP 1d5rA 88 :YPFEDHNPP T0305 209 :YALPVLTFVRRSSAARMPETG 1d5rA 97 :QLELIKPFCEDLDQWLSEDDN T0305 230 :PVLVHCSAGVGRTGTYIVIDSML 1d5rA 119 :VAAIHCKAGKGRTGVMICAYLLH T0305 257 :DKSTVNVLGFLKHIRTQRNY 1d5rA 142 :RGKFLKAQEALDFYGEVRTR T0305 277 :LVQTEEQYIFIHDALL 1d5rA 165 :GVTIPSQRRYVYYYSY T0305 294 :AIL 1d5rA 181 :LLK Number of specific fragments extracted= 12 number of extra gaps= 0 total=448 Number of alignments=49 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set Warning: unaligning (T0305)N57 because first residue in template chain is (1d5rA)R14 T0305 58 :ILAYDHSRVKLRPLPG 1d5rA 15 :RYQEDGFDLDLTYIYP T0305 95 :AYIATQGPLKS 1d5rA 31 :NIIAMGFPAER T0305 106 :TFEDFWRMIWEQ 1d5rA 49 :NIDDVVRFLDSK T0305 118 :NTGIIVMITNLVEKGRRK 1d5rA 63 :NHYKIYNLCAERHYDTAK T0305 187 :RQNERVVI 1d5rA 81 :FNCRVAQY T0305 200 :QWPDMGVP 1d5rA 89 :PFEDHNPP T0305 209 :YALPVLTFVRRSSAARMPET 1d5rA 97 :QLELIKPFCEDLDQWLSEDD T0305 229 :GPVLVHCSAGVGRTGTYIVIDSML 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLH T0305 257 :DKSTVNVLGFLKHIRTQRNY 1d5rA 142 :RGKFLKAQEALDFYGEVRTR T0305 277 :LVQTEEQYIFIHDALLEA 1d5rA 165 :GVTIPSQRRYVYYYSYLL T0305 296 :L 1d5rA 183 :K Number of specific fragments extracted= 11 number of extra gaps= 0 total=459 Number of alignments=50 # 1d5rA read from 1d5rA/merged-good-all-a2m # found chain 1d5rA in template set T0305 57 :NILAYDHSRVKLR 1d5rA 17 :QEDGFDLDLTYIY T0305 94 :KAYIATQGPL 1d5rA 30 :PNIIAMGFPA T0305 104 :KSTFEDFWRMIWEQ 1d5rA 47 :RNNIDDVVRFLDSK T0305 118 :NTGIIVMITNLVEKG 1d5rA 63 :NHYKIYNLCAERHYD T0305 184 :PKGRQNERVVI 1d5rA 78 :TAKFNCRVAQY T0305 200 :QW 1d5rA 89 :PF T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1d5rA 91 :EDHNPPQLELIKPFCEDLDQWLS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQ 1d5rA 115 :DDNHVAAIHCKAGKGRTGVMICAYLLHR T0305 258 :KSTVNVLGFLKHIRTQRNY 1d5rA 143 :GKFLKAQEALDFYGEVRTR T0305 277 :LVQTEEQYIFIHDALLEA 1d5rA 165 :GVTIPSQRRYVYYYSYLL Number of specific fragments extracted= 10 number of extra gaps= 0 total=469 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ytw expands to /projects/compbio/data/pdb/1ytw.pdb.gz 1ytw:Warning: there is no chain 1ytw will retry with 1ytwA Skipped atom 1776, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1778, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1780, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1782, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1784, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1786, because occupancy 0.450 <= existing 0.550 in 1ytw # T0305 read from 1ytw/merged-good-all-a2m # 1ytw read from 1ytw/merged-good-all-a2m # adding 1ytw to template set # found chain 1ytw in template set T0305 4 :SMKQFVKHIGELYS 1ytw 193 :ARAELSSRLTTLRN T0305 32 :RCTADMN 1ytw 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1ytw 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 72 :PG 1ytw 242 :AD T0305 82 :INANYVDGYNKA 1ytw 244 :LNANYIQVGNTR T0305 96 :YIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1ytw 256 :TIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1ytw 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHA 1ytw 303 :RQSGTYGSITVESKMTQQVG T0305 163 :CYTVRRFSIRNTK 1ytw 326 :GIMADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVP 1ytw 339 :AGQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1ytw 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytw 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytw 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytw 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1ytw 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 15 number of extra gaps= 0 total=484 Number of alignments=52 # 1ytw read from 1ytw/merged-good-all-a2m # found chain 1ytw in template set T0305 5 :MKQFVKHIGELYS 1ytw 194 :RAELSSRLTTLRN T0305 32 :RCTADMN 1ytw 207 :TLAPATN T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVK 1ytw 214 :DPRYLQACGGEKLNRFRDIQCRRQTAVR T0305 72 :PG 1ytw 242 :AD T0305 82 :INANYVDGYNK 1ytw 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1ytw 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1ytw 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1ytw 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRNT 1ytw 329 :ADMYTLTIREA T0305 187 :RQNERVVIQYHYTQWPDMGVP 1ytw 340 :GQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1ytw 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytw 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytw 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytw 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLEA 1ytw 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=499 Number of alignments=53 # 1ytw read from 1ytw/merged-good-all-a2m # found chain 1ytw in template set T0305 23 :FSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1ytw 197 :LSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRAD T0305 82 :INANYVDGYN 1ytw 244 :LNANYIQVGN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACY 1ytw 254 :TRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLG T0305 165 :TVRRFSIRN 1ytw 330 :DMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVPE 1ytw 339 :AGQKTISVPVVHVGNWPDQTAVS T0305 210 :ALPVLTFVRRSSAARM 1ytw 362 :SEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1ytw 394 :DSKLRPVIHCRAGVGRTAQLIGAMCM T0305 258 :K 1ytw 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1ytw 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1ytw 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=509 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4uS/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g4uS expands to /projects/compbio/data/pdb/1g4u.pdb.gz 1g4uS:# T0305 read from 1g4uS/merged-good-all-a2m # 1g4uS read from 1g4uS/merged-good-all-a2m # adding 1g4uS to template set # found chain 1g4uS in template set Warning: unaligning (T0305)A222 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0305)T228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0305 3 :QSMKQFVKHIGELYS 1g4uS 264 :HELTQAVKKIHVIAK T0305 22 :GFSEDFEEVQ 1g4uS 282 :NVTAELEKIE T0305 37 :MNITAEHSNHPENKHKNRYI 1g4uS 292 :AGAPMPQTMSGPTLGLARFA T0305 57 :NILAYDHSRVKLR 1g4uS 314 :SIPINQQTQVKLS T0305 78 :HSDYINANYVDGYNKA 1g4uS 327 :DGMPVPVNTLTFDGKP T0305 95 :AYIATQGPLKS 1g4uS 343 :VALAGSYPKNT T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYW 1g4uS 356 :ALEAHMKMLLEKECSCLVVLTSEDQMQAKQLPPYF T0305 143 :ENSEEYGNIIVTLKSTKIHA 1g4uS 391 :RGSYTFGEVHTNSQKVSSAS T0305 163 :CYTVRRFSIRN 1g4uS 414 :AIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSS 1g4uS 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVK T0305 229 :GPVLVHCSAGVGRTGTYIVIDSM 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVL T0305 256 :KDKSTVNVLGFLKHIRTQRNY 1g4uS 498 :KDNPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDALLEAI 1g4uS 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 13 number of extra gaps= 0 total=522 Number of alignments=55 # 1g4uS read from 1g4uS/merged-good-all-a2m # found chain 1g4uS in template set Warning: unaligning (T0305)A222 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0305)T228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0305 5 :MKQFVKHIGELYS 1g4uS 266 :LTQAVKKIHVIAK T0305 22 :GFSEDFEEVQ 1g4uS 282 :NVTAELEKIE T0305 35 :ADM 1g4uS 292 :AGA T0305 40 :TAEHSNHPENKHKNRYI 1g4uS 295 :PMPQTMSGPTLGLARFA T0305 57 :NILAYDHSRVKLR 1g4uS 314 :SIPINQQTQVKLS T0305 72 :P 1g4uS 327 :D T0305 79 :SDYINANYVDGYNKA 1g4uS 328 :GMPVPVNTLTFDGKP T0305 95 :AYIATQGPLKS 1g4uS 343 :VALAGSYPKNT T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYW 1g4uS 356 :ALEAHMKMLLEKECSCLVVLTSEDQMQAKQLPPYF T0305 143 :ENSEEYGNIIVTLKST 1g4uS 391 :RGSYTFGEVHTNSQKV T0305 159 :KIHACYTVRRFSIRN 1g4uS 410 :SQGEAIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSS 1g4uS 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVK T0305 229 :GPVLVHCSAGVGRTGTYIVIDSM 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVL T0305 256 :KDKSTVNVLGFLKHIRTQRNY 1g4uS 498 :KDNPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDALLEAI 1g4uS 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 15 number of extra gaps= 0 total=537 Number of alignments=56 # 1g4uS read from 1g4uS/merged-good-all-a2m # found chain 1g4uS in template set Warning: unaligning (T0305)A222 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0305)T228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0305 7 :QFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1g4uS 264 :HELTQAVKKIHVIAKELKNVTAELEKIEAGAPMPQTMSGPTLGLARFAVSSIPINQQTQVKLS T0305 78 :HSDYINANYVDGYN 1g4uS 327 :DGMPVPVNTLTFDG T0305 93 :AKAYIATQGPL 1g4uS 341 :KPVALAGSYPK T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKGR 1g4uS 354 :PDALEAHMKMLLEKECSCLVVLTSEDQMQA T0305 137 :DQYWPT 1g4uS 384 :KQLPPY T0305 143 :ENSEEYGNIIVTLKSTKI 1g4uS 391 :RGSYTFGEVHTNSQKVSS T0305 161 :HACYTVRRFSIRN 1g4uS 412 :GEAIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSS 1g4uS 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVK T0305 229 :GPVLVHCSAGVGRTGTYIVIDSML 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLK T0305 257 :DKSTVNVLGFLKHIRTQRNY 1g4uS 499 :DNPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDA 1g4uS 520 :MLEDASQFVQLKAM Number of specific fragments extracted= 11 number of extra gaps= 0 total=548 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2shpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2shpA expands to /projects/compbio/data/pdb/2shp.pdb.gz 2shpA:# T0305 read from 2shpA/merged-good-all-a2m # 2shpA read from 2shpA/merged-good-all-a2m # adding 2shpA to template set # found chain 2shpA in template set Warning: unaligning (T0305)E14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)G246 Warning: unaligning (T0305)G22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)G246 Warning: unaligning (T0305)L71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)S302 Warning: unaligning (T0305)S79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)S302 Warning: unaligning (T0305)D80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)D303 Warning: unaligning (T0305)A93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)K324 Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0305)P102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0305)L103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2shpA)T411 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2shpA)T411 T0305 3 :QSMKQFVKHIG 2shpA 224 :AEIESRVRELS T0305 23 :FSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2shpA 247 :FWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLH T0305 81 :YINANYV 2shpA 304 :YINANII T0305 94 :KA 2shpA 325 :KS T0305 98 :ATQG 2shpA 329 :ATQG T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTE 2shpA 335 :QNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDE T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRNT 2shpA 376 :ALKEYGVMRVRNVKESAAHDYTLRELKLSKV T0305 185 :KGR 2shpA 407 :GQG T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2shpA 412 :ERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2shpA 450 :MDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGV T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 11 number of extra gaps= 3 total=559 Number of alignments=58 # 2shpA read from 2shpA/merged-good-all-a2m # found chain 2shpA in template set Warning: unaligning (T0305)S17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)G246 Warning: unaligning (T0305)G22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)G246 Warning: unaligning (T0305)P70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)S302 Warning: unaligning (T0305)S79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)S302 Warning: unaligning (T0305)D80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)D303 Warning: unaligning (T0305)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)K324 Warning: unaligning (T0305)A93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)K324 Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0305)P102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0305)L103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2shpA)T411 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2shpA)T411 T0305 2 :FQSMKQFVKHIGELY 2shpA 220 :RINAAEIESRVRELS T0305 23 :FSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2shpA 247 :FWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLH T0305 81 :YINANYVD 2shpA 304 :YINANIIM T0305 94 :KA 2shpA 325 :KS T0305 98 :ATQG 2shpA 329 :ATQG T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2shpA 335 :QNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPD T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKV 2shpA 375 :YALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQ T0305 187 :R 2shpA 409 :G T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2shpA 412 :ERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2shpA 450 :MDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGV T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 11 number of extra gaps= 3 total=570 Number of alignments=59 # 2shpA read from 2shpA/merged-good-all-a2m # found chain 2shpA in template set Warning: unaligning (T0305)E14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)G246 Warning: unaligning (T0305)E25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)G246 Warning: unaligning (T0305)L71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2shpA)S302 Warning: unaligning (T0305)S79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)S302 Warning: unaligning (T0305)D80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)D303 Warning: unaligning (T0305)A93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)K324 Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0305)P102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0305)L103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 Warning: unaligning (T0305)Q188 because of BadResidue code BAD_PEPTIDE in next template residue (2shpA)T411 Warning: unaligning (T0305)N189 because of BadResidue code BAD_PEPTIDE at template residue (2shpA)T411 T0305 6 :KQFVKHIG 2shpA 227 :ESRVRELS T0305 26 :DFEEVQRC 2shpA 247 :FWEEFETL T0305 34 :TADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2shpA 258 :ECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLH T0305 81 :YINANYVD 2shpA 304 :YINANIIM T0305 94 :KA 2shpA 325 :KS T0305 98 :ATQG 2shpA 329 :ATQG T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2shpA 335 :QNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPD T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2shpA 375 :YALKEYGVMRVRNVKESAAHDYTLRELKLSK T0305 184 :PKGR 2shpA 406 :VGQG T0305 190 :ERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2shpA 412 :ERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKD 2shpA 450 :MDAGPVVVHCSAGIGRTGTFIVIDILIDIIRE T0305 258 :KSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2shpA 485 :DCDIDVPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 12 number of extra gaps= 3 total=582 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l8kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1l8kA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1l8kA/merged-good-all-a2m.gz for input Trying 1l8kA/merged-good-all-a2m Error: Couldn't open file 1l8kA/merged-good-all-a2m or 1l8kA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f71A expands to /projects/compbio/data/pdb/2f71.pdb.gz 2f71A:Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 166, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 170, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 172, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 174, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 176, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 178, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1977, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1981, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1983, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2352, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2481, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2493, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2503, because occupancy 0.500 <= existing 0.500 in 2f71A # T0305 read from 2f71A/merged-good-all-a2m # 2f71A read from 2f71A/merged-good-all-a2m # adding 2f71A to template set # found chain 2f71A in template set Warning: unaligning (T0305)Q7 because first residue in template chain is (2f71A)E2 Warning: unaligning (T0305)R69 because of BadResidue code BAD_PEPTIDE in next template residue (2f71A)Q61 Warning: unaligning (T0305)S76 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)Q61 Warning: unaligning (T0305)K77 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)E62 Warning: unaligning (T0305)H78 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)D63 T0305 8 :FVKHIGELYSNN 2f71A 3 :MEKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTADM 2f71A 15 :SWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKL 2f71A 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2f71A 64 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYG 2f71A 129 :EEKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 2f71A 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2f71A 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2f71A 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=591 Number of alignments=61 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set Warning: unaligning (T0305)S4 because first residue in template chain is (2f71A)E2 Warning: unaligning (T0305)R69 because of BadResidue code BAD_PEPTIDE in next template residue (2f71A)Q61 Warning: unaligning (T0305)S76 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)Q61 Warning: unaligning (T0305)K77 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)E62 Warning: unaligning (T0305)H78 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)D63 T0305 5 :MKQFVKHIGE 2f71A 3 :MEKEFEQIDK T0305 18 :N 2f71A 13 :S T0305 21 :HGFSEDFEEVQRCTA 2f71A 14 :GSWAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKL 2f71A 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2f71A 64 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 2f71A 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 2f71A 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2f71A 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2f71A 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 1 total=601 Number of alignments=62 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set Warning: unaligning (T0305)R69 because of BadResidue code BAD_PEPTIDE in next template residue (2f71A)Q61 Warning: unaligning (T0305)S76 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)Q61 Warning: unaligning (T0305)K77 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)E62 Warning: unaligning (T0305)H78 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)D63 T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKL 2f71A 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2f71A 64 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 2f71A 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 2f71A 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2f71A 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2f71A 206 :PEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 1 total=608 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4wR/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g4wR expands to /projects/compbio/data/pdb/1g4w.pdb.gz 1g4wR:# T0305 read from 1g4wR/merged-good-all-a2m # 1g4wR read from 1g4wR/merged-good-all-a2m # adding 1g4wR to template set # found chain 1g4wR in template set Warning: unaligning (T0305)M37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4wR)P297 Warning: unaligning (T0305)S44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4wR)P297 T0305 3 :QSMKQFVKHIGE 1g4wR 264 :HELTQAVKKIHV T0305 23 :FSEDFEEVQRCTAD 1g4wR 276 :IAKELKNVTAELEK T0305 45 :NHPEN 1g4wR 298 :QTMSG T0305 50 :KHKNRYI 1g4wR 305 :LGLARFA T0305 57 :NILAYDHSRVKLR 1g4wR 314 :SIPINQQTQVKLS T0305 78 :HSDYINANYVDGYNKA 1g4wR 327 :DGMPVPVNTLTFDGKP T0305 95 :AYIATQGPLKST 1g4wR 343 :VALAGSYPKNTP T0305 107 :FEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYW 1g4wR 357 :LEAHMKMLLEKECSCLVVLTSEDQMQAKQLPPYF T0305 143 :ENSEEYGNIIVTLKSTKIH 1g4wR 391 :RGSYTFGEVHTNSQKVSSA T0305 162 :ACYTVRRFSIRN 1g4wR 413 :EAIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1g4wR 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVKNSNQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1g4wR 472 :SDKHLPMIHCLGGVGRTGTMAAALVLK T0305 257 :DKSTVNVLGFLKHIRTQRNY 1g4wR 499 :DNPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDALLEAI 1g4wR 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 14 number of extra gaps= 0 total=622 Number of alignments=64 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set Warning: unaligning (T0305)A35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4wR)P297 Warning: unaligning (T0305)E42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4wR)P297 T0305 5 :MKQFVKHIGE 1g4wR 266 :LTQAVKKIHV T0305 23 :FSEDFEEVQRC 1g4wR 276 :IAKELKNVTAE T0305 34 :T 1g4wR 289 :K T0305 43 :HSNHPENKHKNRYI 1g4wR 298 :QTMSGPTLGLARFA T0305 57 :NILAYDHSRVKLR 1g4wR 314 :SIPINQQTQVKLS T0305 72 :P 1g4wR 327 :D T0305 79 :SDYINANYVDGYNKA 1g4wR 328 :GMPVPVNTLTFDGKP T0305 95 :AYIATQGPLKS 1g4wR 343 :VALAGSYPKNT T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYW 1g4wR 356 :ALEAHMKMLLEKECSCLVVLTSEDQMQAKQLPPYF T0305 143 :ENSEEYGNIIVTLKSTKI 1g4wR 391 :RGSYTFGEVHTNSQKVSS T0305 161 :HACYTVRRFSIRN 1g4wR 412 :GEAIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1g4wR 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVKNSNQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1g4wR 472 :SDKHLPMIHCLGGVGRTGTMAAALVL T0305 256 :KDKSTVNVLGFLKHIRTQRNY 1g4wR 498 :KDNPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDALLEAI 1g4wR 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 15 number of extra gaps= 0 total=637 Number of alignments=65 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set T0305 56 :INILAYDHSRVKLR 1g4wR 313 :SSIPINQQTQVKLS T0305 78 :HSDYINANYVDGYN 1g4wR 327 :DGMPVPVNTLTFDG T0305 93 :AKAYIATQGPL 1g4wR 341 :KPVALAGSYPK T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKG 1g4wR 354 :PDALEAHMKMLLEKECSCLVVLTSEDQMQ T0305 137 :DQYWPT 1g4wR 383 :AKQLPP T0305 143 :ENSEEYGNIIVTLKSTK 1g4wR 391 :RGSYTFGEVHTNSQKVS T0305 160 :IHACYTVRRFSIRN 1g4wR 411 :QGEAIDQYNMQLSC T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1g4wR 425 :GEKRYTIPVLHVKNWPDHQPLPSTDQLEYLADRVKNSNQ T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQ 1g4wR 472 :SDKHLPMIHCLGGVGRTGTMAAALVLKD T0305 258 :KSTVNVLGFLKHIRTQRNY 1g4wR 500 :NPHSNLEQVRADFRDSRNN T0305 277 :LVQTEEQYIFIHDALLEA 1g4wR 520 :MLEDASQFVQLKAMQAQL Number of specific fragments extracted= 11 number of extra gaps= 0 total=648 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fpzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fpzA expands to /projects/compbio/data/pdb/1fpz.pdb.gz 1fpzA:# T0305 read from 1fpzA/merged-good-all-a2m # 1fpzA read from 1fpzA/merged-good-all-a2m # adding 1fpzA to template set # found chain 1fpzA in template set Warning: unaligning (T0305)L59 because first residue in template chain is (1fpzA)T25 T0305 60 :AYDHSRVKLR 1fpzA 26 :PIHISWLSLS T0305 89 :GYNKAKAYIATQGPL 1fpzA 36 :RVNCSQFLGLCALPG T0305 104 :KS 1fpzA 54 :KD T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKG 1fpzA 59 :NVQKDTEELKSCGIQDIFVFCTRGELS T0305 138 :QYWPTE 1fpzA 86 :KYRVPN T0305 187 :RQN 1fpzA 99 :CGI T0305 195 :QYHYTQWPDMGVP 1fpzA 102 :ITHHHPIADGGTP T0305 209 :YALPVLTFVRRSSAARMPE 1fpzA 115 :DIASCCEIMEELTTCLKNY T0305 229 :GPVLVHCSAGVGRTGTYIVIDSML 1fpzA 134 :RKTLIHSYGGLGRSCLVAACLLLY T0305 257 :DKSTVNVLGFLKHIRTQR 1fpzA 158 :LSDTISPEQAIDSLRDLR T0305 275 :NYLVQTEEQYIFI 1fpzA 177 :SGAIQTIKQYNYL Number of specific fragments extracted= 11 number of extra gaps= 0 total=659 Number of alignments=67 # 1fpzA read from 1fpzA/merged-good-all-a2m # found chain 1fpzA in template set Warning: unaligning (T0305)L59 because first residue in template chain is (1fpzA)T25 T0305 60 :AYDHSRVKLR 1fpzA 26 :PIHISWLSLS T0305 89 :GYNKAKAYIATQGPL 1fpzA 36 :RVNCSQFLGLCALPG T0305 104 :KS 1fpzA 54 :KD T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKGR 1fpzA 59 :NVQKDTEELKSCGIQDIFVFCTRGELSK T0305 139 :Y 1fpzA 87 :Y T0305 140 :WPT 1fpzA 89 :VPN T0305 181 :KG 1fpzA 94 :DL T0305 187 :RQNE 1fpzA 99 :CGII T0305 196 :YHYTQWPDMGVP 1fpzA 103 :THHHPIADGGTP T0305 209 :YALPVLTFVRRSSAARM 1fpzA 115 :DIASCCEIMEELTTCLK T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSML 1fpzA 132 :NYRKTLIHSYGGLGRSCLVAACLLLY T0305 257 :DKSTVNVLGFLKHIRTQRNY 1fpzA 158 :LSDTISPEQAIDSLRDLRGS T0305 277 :LVQTEEQYIFI 1fpzA 179 :AIQTIKQYNYL Number of specific fragments extracted= 13 number of extra gaps= 0 total=672 Number of alignments=68 # 1fpzA read from 1fpzA/merged-good-all-a2m # found chain 1fpzA in template set Warning: unaligning (T0305)D80 because first residue in template chain is (1fpzA)T25 T0305 81 :YINANYVDGY 1fpzA 26 :PIHISWLSLS T0305 91 :NKAKAYIATQGPL 1fpzA 38 :NCSQFLGLCALPG T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVE 1fpzA 57 :RRNVQKDTEELKSCGIQDIFVFCTRGE T0305 196 :YHYTQWPDMGVP 1fpzA 103 :THHHPIADGGTP T0305 209 :YALPVLTFVRRSSAARM 1fpzA 115 :DIASCCEIMEELTTCLK T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQ 1fpzA 132 :NYRKTLIHSYGGLGRSCLVAACLLLYL T0305 258 :KSTVNVLGFLKHIRTQR 1fpzA 159 :SDTISPEQAIDSLRDLR T0305 275 :NYLVQTEEQYIFI 1fpzA 177 :SGAIQTIKQYNYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=680 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2cfvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2cfvA/merged-good-all-a2m.gz for input Trying 2cfvA/merged-good-all-a2m Error: Couldn't open file 2cfvA/merged-good-all-a2m or 2cfvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2hnp expands to /projects/compbio/data/pdb/2hnp.pdb.gz 2hnp:Warning: there is no chain 2hnp will retry with 2hnpA # T0305 read from 2hnp/merged-good-all-a2m # 2hnp read from 2hnp/merged-good-all-a2m # adding 2hnp to template set # found chain 2hnp in template set T0305 11 :HIGELYSNN 2hnp 6 :EFEQIDKSG T0305 22 :GFSEDFEEVQRCTADM 2hnp 15 :SWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 2hnp 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2hnp 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 2hnp 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRN 2hnp 140 :LKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2hnp 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2hnp 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=689 Number of alignments=70 # 2hnp read from 2hnp/merged-good-all-a2m # found chain 2hnp in template set T0305 11 :HIGELYSNNQ 2hnp 6 :EFEQIDKSGS T0305 23 :FSEDFEEVQRCTA 2hnp 16 :WAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 2hnp 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2hnp 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 2hnp 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 2hnp 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2hnp 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 2hnp 204 :LSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=698 Number of alignments=71 # 2hnp read from 2hnp/merged-good-all-a2m # found chain 2hnp in template set Warning: unaligning (T0305)E14 because first residue in template chain is (2hnp)K5 T0305 15 :LYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2hnp 6 :EFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2hnp 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 2hnp 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 2hnp 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2hnp 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDK 2hnp 206 :PEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKR T0305 259 :STVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2hnp 242 :SSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=705 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bv5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bv5A expands to /projects/compbio/data/pdb/2bv5.pdb.gz 2bv5A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 603, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 604, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bv5A Bad short name: OCD for alphabet: pdb_atoms Bad short name: OCD for alphabet: pdb_atoms Skipped atom 1796, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1797, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1798, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1799, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2141, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 2bv5A # T0305 read from 2bv5A/merged-good-all-a2m # 2bv5A read from 2bv5A/merged-good-all-a2m # adding 2bv5A to template set # found chain 2bv5A in template set Warning: unaligning (T0305)Y96 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0305)I97 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0305)R133 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv5A)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv5A)K383 Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0305 5 :MKQFVKHI 2bv5A 263 :AEELHEKA T0305 18 :NNQHGFSEDFEEVQRCTA 2bv5A 271 :LDPFLLQAEFFEIPMNFV T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLRPLP 2bv5A 289 :DPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPD T0305 74 :KDSKHSDYINANYVDGYNKA 2bv5A 322 :PDDPLSSYINANYIRGYGGE T0305 94 :KA 2bv5A 343 :KV T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 2bv5A 347 :ATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMN T0305 136 :CDQYWP 2bv5A 384 :CTEYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bv5A 390 :EEQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 2bv5A 421 :GTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEA T0305 224 :RMPETGPVLV 2bv5A 461 :EGPHCAPIIV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bv5A 474 :AGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAILG 2bv5A 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 12 number of extra gaps= 3 total=717 Number of alignments=73 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set Warning: unaligning (T0305)Y96 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0305)I97 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0305)R134 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv5A)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv5A)K383 Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0305 2 :FQSMKQFVKHI 2bv5A 260 :VLQAEELHEKA T0305 18 :NNQHGFSEDFEEV 2bv5A 271 :LDPFLLQAEFFEI T0305 35 :ADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPG 2bv5A 284 :PMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDP T0305 75 :DSKHSDYINANYVDGYNKA 2bv5A 323 :DDPLSSYINANYIRGYGGE T0305 94 :KA 2bv5A 343 :KV T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 2bv5A 347 :ATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMN T0305 136 :CDQYWP 2bv5A 384 :CTEYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bv5A 390 :EEQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bv5A 421 :GTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQ T0305 226 :PETGPVLV 2bv5A 463 :PHCAPIIV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bv5A 474 :AGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAIL 2bv5A 516 :QTCEQYQFVHHVMSLYEK Number of specific fragments extracted= 12 number of extra gaps= 3 total=729 Number of alignments=74 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set Warning: unaligning (T0305)Y96 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0305)I97 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0305)R133 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv5A)K383 Warning: unaligning (T0305)K135 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv5A)K383 Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0305)L277 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0305)V278 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0305 22 :GFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2bv5A 271 :LDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLT T0305 71 :LPGKDSKHSDYINANYVDGY 2bv5A 319 :SPDPDDPLSSYINANYIRGY T0305 91 :NKAKA 2bv5A 340 :GEEKV T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 2bv5A 347 :ATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMN T0305 136 :CDQYWPT 2bv5A 384 :CTEYWPE T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2bv5A 391 :EQVAYDGVEITVQKVIHTEDYRLRLISLKS T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2bv5A 421 :GTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQ T0305 226 :PETGPVLV 2bv5A 463 :PHCAPIIV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNY 2bv5A 474 :AGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGG T0305 279 :QTEEQYIFIHDALLEAIL 2bv5A 516 :QTCEQYQFVHHVMSLYEK Number of specific fragments extracted= 10 number of extra gaps= 3 total=739 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oheA expands to /projects/compbio/data/pdb/1ohe.pdb.gz 1oheA:# T0305 read from 1oheA/merged-good-all-a2m # 1oheA read from 1oheA/merged-good-all-a2m # adding 1oheA to template set # found chain 1oheA in template set T0305 5 :MKQFVKHIGELYSNN 1oheA 179 :LLDCFHAVKKAMQYG T0305 20 :QHGFSEDFEEVQRC 1oheA 198 :NSFNLDEYEHYEKA T0305 48 :E 1oheA 212 :E T0305 62 :DHSRVKLR 1oheA 213 :NGDLNWII T0305 93 :AKAYIATQGPLK 1oheA 221 :PDRFIAFCGPHS T0305 105 :STFEDFWRMIWEQNTGIIVMITNLVEKGR 1oheA 243 :HSPETYIQYFKNHNVTTIIRLNKRMYDAK T0305 142 :TENSE 1oheA 275 :DAGFD T0305 196 :YHYTQWPDMGVPEY 1oheA 280 :HHDLFFADGSTPTD T0305 211 :LPVLTFVRRSS 1oheA 294 :AIVKEFLDICE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1oheA 305 :NAEGAIAVHSKAGLGRTGTLIACYIMK T0305 258 :KSTVNVLGFLKHIRTQRNYLVQTE 1oheA 332 :HYRMTAAETIAWVRICRPGSVIGP T0305 283 :QYIFIHDALLEAIL 1oheA 356 :QQQFLVMKQTNLWL Number of specific fragments extracted= 12 number of extra gaps= 0 total=751 Number of alignments=76 # 1oheA read from 1oheA/merged-good-all-a2m # found chain 1oheA in template set T0305 1 :YFQSMKQFVKHIGELYSN 1oheA 175 :FYITLLDCFHAVKKAMQY T0305 19 :NQHGF 1oheA 196 :NFNSF T0305 24 :SEDFEEVQR 1oheA 202 :LDEYEHYEK T0305 47 :PE 1oheA 211 :AE T0305 62 :DHSRVKLR 1oheA 213 :NGDLNWII T0305 90 :YN 1oheA 221 :PD T0305 95 :AYIATQGPLKS 1oheA 223 :RFIAFCGPHSR T0305 106 :TFEDFWRMIWEQNTGIIVMITNLVEKGRR 1oheA 244 :SPETYIQYFKNHNVTTIIRLNKRMYDAKR T0305 179 :G 1oheA 273 :F T0305 187 :RQNER 1oheA 274 :TDAGF T0305 195 :QYHYTQWPDMGVPEY 1oheA 279 :DHHDLFFADGSTPTD T0305 215 :TFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSM 1oheA 294 :AIVKEFLDICENAEGAIAVHSKAGLGRTGTLIACYIM T0305 257 :DKSTVNVLGFLKHIRTQRNYLVQ 1oheA 331 :KHYRMTAAETIAWVRICRPGSVI T0305 281 :EEQYIFIHDALLEAIL 1oheA 354 :GPQQQFLVMKQTNLWL Number of specific fragments extracted= 14 number of extra gaps= 0 total=765 Number of alignments=77 # 1oheA read from 1oheA/merged-good-all-a2m # found chain 1oheA in template set T0305 24 :SEDFEEVQR 1oheA 202 :LDEYEHYEK T0305 60 :AYDHSRVKLR 1oheA 211 :AENGDLNWII T0305 93 :AKAYIATQGPL 1oheA 221 :PDRFIAFCGPH T0305 104 :KSTFEDFWRMIWEQNTGIIVMITNLVEKGR 1oheA 242 :QHSPETYIQYFKNHNVTTIIRLNKRMYDAK T0305 196 :YHYTQWPDMGVPEY 1oheA 280 :HHDLFFADGSTPTD T0305 215 :TFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQ 1oheA 294 :AIVKEFLDICENAEGAIAVHSKAGLGRTGTLIACYIMKHY T0305 260 :TVNVLGFLKHIRTQRNYLVQ 1oheA 334 :RMTAAETIAWVRICRPGSVI T0305 281 :EEQYIFIHDA 1oheA 354 :GPQQQFLVMK Number of specific fragments extracted= 8 number of extra gaps= 0 total=773 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lqfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1lqfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1lqfA/merged-good-all-a2m.gz for input Trying 1lqfA/merged-good-all-a2m Error: Couldn't open file 1lqfA/merged-good-all-a2m or 1lqfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fh7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fh7A expands to /projects/compbio/data/pdb/2fh7.pdb.gz 2fh7A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1796, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1798, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1800, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1802, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1804, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1806, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1808, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3718, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3720, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3722, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3724, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3726, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3728, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3730, because occupancy 0.500 <= existing 0.500 in 2fh7A # T0305 read from 2fh7A/merged-good-all-a2m # 2fh7A read from 2fh7A/merged-good-all-a2m # adding 2fh7A to template set # found chain 2fh7A in template set Warning: unaligning (T0305)M225 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)P1580 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)P1580 T0305 4 :SMKQFVKHIGELYSNNQHGFSEDFEEVQ 2fh7A 1374 :PIADMAEHTERLKANDSLKLSQEYESID T0305 35 :ADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 2fh7A 1402 :PGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVILQPIEGIMG T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2fh7A 1444 :SDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATIVMMTRLEEKSRIKCDQYWPNRGTETYGFIQVTLLDTIELATFCVRTFSLHK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 2fh7A 1539 :NGSSEKREVRQFQFTAWPDHGVPEYPTPFLAFLRRVKTCN T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2fh7A 1581 :DAGPIVVHCSAGVGRTGCFIVIDAMLERIKPEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVG Number of specific fragments extracted= 5 number of extra gaps= 1 total=778 Number of alignments=79 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0305)M225 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)P1580 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)P1580 T0305 1 :YFQSMKQFVKHIGELYSNNQHGFSEDFEEV 2fh7A 1371 :PPIPIADMAEHTERLKANDSLKLSQEYESI T0305 34 :TADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDS 2fh7A 1401 :DPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVILQPIEGIMG T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 2fh7A 1444 :SDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATIVMMTRLEEKSRIKCDQYWPNRGTETYGFIQVTLLDTIELATFCVRTFSLHKNG T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 2fh7A 1541 :SSEKREVRQFQFTAWPDHGVPEYPTPFLAFLRRVKTCN T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2fh7A 1581 :DAGPIVVHCSAGVGRTGCFIVIDAMLERIKPEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAVGC Number of specific fragments extracted= 5 number of extra gaps= 1 total=783 Number of alignments=80 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0305)M225 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)P1580 Warning: unaligning (T0305)P226 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)P1580 T0305 8 :F 2fh7A 1381 :H T0305 15 :LYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2fh7A 1382 :TERLKANDSLKLSQEYESIDPGQQFTWEHSNLEVNKPKNRYANVIAYDHSRVILQ T0305 72 :PGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2fh7A 1437 :PIEGIMGSDYINANYVDGYRRQNAYIATQGPLPETFGDFWRMVWEQRSATIVMMTRLEEKSRIKCDQYWPNRGTETYGFIQVTLLDTIELATFCVRTFSLHK T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAAR 2fh7A 1539 :NGSSEKREVRQFQFTAWPDHGVPEYPTPFLAFLRRVKTCN T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAI 2fh7A 1581 :DAGPIVVHCSAGVGRTGCFIVIDAMLERIKPEKTVDVYGHVTLMRSQRNYMVQTEDQYSFIHEALLEAV Number of specific fragments extracted= 5 number of extra gaps= 1 total=788 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bzhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1bzhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1bzhA/merged-good-all-a2m.gz for input Trying 1bzhA/merged-good-all-a2m Error: Couldn't open file 1bzhA/merged-good-all-a2m or 1bzhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jlnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jlnA expands to /projects/compbio/data/pdb/1jln.pdb.gz 1jlnA:# T0305 read from 1jlnA/merged-good-all-a2m # 1jlnA read from 1jlnA/merged-good-all-a2m # adding 1jlnA to template set # found chain 1jlnA in template set T0305 9 :VKHIGELYSN 1jlnA 272 :RSQLRDVVAS T0305 20 :QHGFSEDFEEVQRCTADM 1jlnA 282 :SHLLQSEFMEIPMNFVDP T0305 42 :EHSNHPENKHKNRYINILAYDHSRVKLR 1jlnA 300 :KEIDIPRHGTKNRYKTILPNPLSRVCLR T0305 71 :LPGKDSKHSDYINANYVDGYNKA 1jlnA 328 :PKNITDSLSTYINANYIRGYSGK T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 1jlnA 352 :KAFIATQGPMINTVNDFWQMVWQEDSPVIVMITKLKEKN T0305 134 :RKCDQYWP 1jlnA 391 :EKCVLYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1jlnA 399 :EKRGIYGKVEVLVTGVTECDNYTIRNLVLKQ T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1jlnA 430 :GSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRL T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1jlnA 471 :EGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESR Number of specific fragments extracted= 9 number of extra gaps= 0 total=797 Number of alignments=82 # 1jlnA read from 1jlnA/merged-good-all-a2m # found chain 1jlnA in template set T0305 2 :FQSMKQFVKHIG 1jlnA 269 :VLTRSQLRDVVA T0305 19 :NQHGFSEDFEEVQ 1jlnA 281 :SSHLLQSEFMEIP T0305 36 :DMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1jlnA 294 :MNFVDPKEIDIPRHGTKNRYKTILPNPLSRVCLR T0305 71 :LPGKDSKHSDYINANYVDGYNKA 1jlnA 328 :PKNITDSLSTYINANYIRGYSGK T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 1jlnA 352 :KAFIATQGPMINTVNDFWQMVWQEDSPVIVMITKLKEKN T0305 134 :RKCDQYWP 1jlnA 391 :EKCVLYWP T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1jlnA 399 :EKRGIYGKVEVLVTGVTECDNYTIRNLVLKQ T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1jlnA 430 :GSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRL T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1jlnA 471 :EGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESR Number of specific fragments extracted= 9 number of extra gaps= 0 total=806 Number of alignments=83 # 1jlnA read from 1jlnA/merged-good-all-a2m # found chain 1jlnA in template set T0305 11 :HIGELYSNN 1jlnA 274 :QLRDVVASS T0305 25 :EDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1jlnA 283 :HLLQSEFMEIPMNFVDPKEIDIPRHGTKNRYKTILPNPLSRVCLR T0305 71 :LPGKDSKHSDYINANYVDGY 1jlnA 328 :PKNITDSLSTYINANYIRGY T0305 91 :NKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 1jlnA 349 :GKEKAFIATQGPMINTVNDFWQMVWQEDSPVIVMITKLKEKN T0305 134 :RKCDQYWPT 1jlnA 391 :EKCVLYWPE T0305 144 :NSEEYGNIIVTLKSTKIHACYTVRRFSIRN 1jlnA 400 :KRGIYGKVEVLVTGVTECDNYTIRNLVLKQ T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1jlnA 430 :GSHTQHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRL T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 1jlnA 471 :EGRGPVVVHCSAGIGRTGCFIATSIGCQQLKEEGVVDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESR Number of specific fragments extracted= 8 number of extra gaps= 0 total=814 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c7sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2c7sA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2c7sA/merged-good-all-a2m.gz for input Trying 2c7sA/merged-good-all-a2m Error: Couldn't open file 2c7sA/merged-good-all-a2m or 2c7sA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bzjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1bzjA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1bzjA/merged-good-all-a2m.gz for input Trying 1bzjA/merged-good-all-a2m Error: Couldn't open file 1bzjA/merged-good-all-a2m or 1bzjA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eeoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eeoA expands to /projects/compbio/data/pdb/1eeo.pdb.gz 1eeoA:# T0305 read from 1eeoA/merged-good-all-a2m # 1eeoA read from 1eeoA/merged-good-all-a2m # adding 1eeoA to template set # found chain 1eeoA in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1eeoA)E2 T0305 5 :MKQFVKHIGE 1eeoA 3 :MEKEFEQIDK T0305 20 :QHGFSEDFEEVQRCTADM 1eeoA 13 :SGSWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 1eeoA 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1eeoA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1eeoA 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRN 1eeoA 140 :LKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1eeoA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1eeoA 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=823 Number of alignments=85 # 1eeoA read from 1eeoA/merged-good-all-a2m # found chain 1eeoA in template set Warning: unaligning (T0305)S4 because first residue in template chain is (1eeoA)E2 T0305 5 :MKQFVKHIGE 1eeoA 3 :MEKEFEQIDK T0305 20 :QHGFSEDFEEVQRCTA 1eeoA 13 :SGSWAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 1eeoA 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1eeoA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1eeoA 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1eeoA 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1eeoA 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1eeoA 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=832 Number of alignments=86 # 1eeoA read from 1eeoA/merged-good-all-a2m # found chain 1eeoA in template set T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1eeoA 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1eeoA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1eeoA 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1eeoA 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1eeoA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1eeoA 206 :PEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=839 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gjtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2gjtA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2gjtA/merged-good-all-a2m.gz for input Trying 2gjtA/merged-good-all-a2m Error: Couldn't open file 2gjtA/merged-good-all-a2m or 2gjtA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lyvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0305 read from 1lyvA/merged-good-all-a2m # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set Warning: unaligning (T0305)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1lyvA)G223 Warning: unaligning (T0305)N49 because of BadResidue code BAD_PEPTIDE at template residue (1lyvA)G223 T0305 3 :QSMKQFVKHIGELYSN 1lyvA 192 :EARAELSSRLTTLRNT T0305 31 :QRCTADMN 1lyvA 208 :LAPATNDP T0305 42 :EHSNHP 1lyvA 216 :RYLQAC T0305 50 :KHKNRYINILAYDHSRVK 1lyvA 224 :EKLNRFRDIQCRRQTAVR T0305 72 :PG 1lyvA 242 :AD T0305 82 :INANYVDGYNKA 1lyvA 244 :LNANYIQVGNTR T0305 96 :YIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1lyvA 256 :TIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1lyvA 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIH 1lyvA 303 :RQSGTYGSITVESKMTQQV T0305 162 :AC 1lyvA 325 :DG T0305 164 :YTVRRFSIRN 1lyvA 329 :ADMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVP 1lyvA 339 :AGQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1lyvA 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCM T0305 258 :K 1lyvA 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1lyvA 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1lyvA 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 17 number of extra gaps= 1 total=856 Number of alignments=88 # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set Warning: unaligning (T0305)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1lyvA)G223 Warning: unaligning (T0305)N49 because of BadResidue code BAD_PEPTIDE at template residue (1lyvA)G223 T0305 5 :MKQFVKHIGELYSN 1lyvA 194 :RAELSSRLTTLRNT T0305 33 :CTADMNIT 1lyvA 208 :LAPATNDP T0305 42 :EHSNHP 1lyvA 216 :RYLQAC T0305 50 :KHKNRYINILAYDHSRVK 1lyvA 224 :EKLNRFRDIQCRRQTAVR T0305 72 :PG 1lyvA 242 :AD T0305 82 :INANYVDGYNK 1lyvA 244 :LNANYIQVGNT T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1lyvA 255 :RTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSE T0305 131 :KGRRKCDQYW 1lyvA 293 :NQRFGMPDYF T0305 143 :ENSEEYGNIIVTLKSTKIHAC 1lyvA 303 :RQSGTYGSITVESKMTQQVGL T0305 164 :YTVRRFSIRNT 1lyvA 329 :ADMYTLTIREA T0305 187 :RQNERVVIQYHYTQWPDMGVP 1lyvA 340 :GQKTISVPVVHVGNWPDQTAV T0305 209 :YALPVLTFVRRSSAARM 1lyvA 361 :SSEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCM T0305 258 :K 1lyvA 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1lyvA 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLEA 1lyvA 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 16 number of extra gaps= 1 total=872 Number of alignments=89 # 1lyvA read from 1lyvA/merged-good-all-a2m # found chain 1lyvA in training set Warning: unaligning (T0305)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1lyvA)G223 Warning: unaligning (T0305)N49 because of BadResidue code BAD_PEPTIDE at template residue (1lyvA)G223 T0305 20 :QHGFSEDFEEVQRCTADMNITAEHSNHP 1lyvA 194 :RAELSSRLTTLRNTLAPATNDPRYLQAC T0305 50 :KHKNRYINILAYDHSRVKLR 1lyvA 224 :EKLNRFRDIQCRRQTAVRAD T0305 82 :INANYVDGYN 1lyvA 244 :LNANYIQVGN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACY 1lyvA 254 :TRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLG T0305 165 :TVRRFSIRN 1lyvA 330 :DMYTLTIRE T0305 186 :GRQNERVVIQYHYTQWPDMGVPE 1lyvA 339 :AGQKTISVPVVHVGNWPDQTAVS T0305 210 :ALPVLTFVRRSSAARM 1lyvA 362 :SEVTKALASLVDQTAE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCM T0305 258 :K 1lyvA 420 :N T0305 259 :STVNVLGFLKHIRTQRNY 1lyvA 425 :SQLSVEDMVSQMRVQRNG T0305 277 :LVQTEEQYIFIHDALLE 1lyvA 444 :MVQKDEQLDVLIKLAEG Number of specific fragments extracted= 11 number of extra gaps= 1 total=883 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fjmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2fjmA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2fjmA/merged-good-all-a2m.gz for input Trying 2fjmA/merged-good-all-a2m Error: Couldn't open file 2fjmA/merged-good-all-a2m or 2fjmA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gwz/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1gwz/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1gwz/merged-good-all-a2m.gz for input Trying 1gwz/merged-good-all-a2m Error: Couldn't open file 1gwz/merged-good-all-a2m or 1gwz/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b49A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b49A expands to /projects/compbio/data/pdb/2b49.pdb.gz 2b49A:Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1568, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1614, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1618, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2b49A # T0305 read from 2b49A/merged-good-all-a2m # 2b49A read from 2b49A/merged-good-all-a2m # adding 2b49A to template set # found chain 2b49A in template set Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b49A)I715 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b49A)I715 T0305 26 :DFEEVQRCTADM 2b49A 649 :QFEQLYRKKPGL T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 2b49A 661 :AITFAKLPQNLDKNRYKDVLPYDTTRVLLQ T0305 75 :DS 2b49A 691 :GN T0305 79 :SDYINANYVDG 2b49A 693 :EDYINASYVNM T0305 90 :YNKAKA 2b49A 708 :ANLVNK T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 2b49A 716 :ATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWP T0305 142 :TENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2b49A 761 :PPDVMNHGGFHIQCQSEDCTIAYVSREMLVTN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2b49A 793 :TQTGEEHTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRV T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2b49A 834 :DSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYEE Number of specific fragments extracted= 9 number of extra gaps= 1 total=892 Number of alignments=91 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b49A)I715 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b49A)I715 T0305 25 :EDFEEVQRCTADM 2b49A 648 :IQFEQLYRKKPGL T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 2b49A 661 :AITFAKLPQNLDKNRYKDVLPYDTTRVLLQ T0305 76 :SK 2b49A 691 :GN T0305 79 :SDYINANYVDG 2b49A 693 :EDYINASYVNM T0305 90 :YNKAKA 2b49A 708 :ANLVNK T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2b49A 716 :ATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPD T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 2b49A 762 :PDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQ T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2b49A 795 :TGEEHTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRV T0305 227 :ETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2b49A 834 :DSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYEE Number of specific fragments extracted= 9 number of extra gaps= 1 total=901 Number of alignments=92 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set Warning: unaligning (T0305)E25 because first residue in template chain is (2b49A)V646 Warning: unaligning (T0305)Y96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b49A)I715 Warning: unaligning (T0305)I97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b49A)I715 T0305 26 :DFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2b49A 647 :LIQFEQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQ T0305 77 :KHSDYINANYVDGY 2b49A 691 :GNEDYINASYVNME T0305 91 :NKAKA 2b49A 709 :NLVNK T0305 98 :ATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2b49A 716 :ATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPD T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2b49A 762 :PDVMNHGGFHIQCQSEDCTIAYVSREMLVTN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSA 2b49A 793 :TQTGEEHTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRS T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2b49A 831 :LRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 7 number of extra gaps= 1 total=908 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zclA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zclA expands to /projects/compbio/data/pdb/1zcl.pdb.gz 1zclA:# T0305 read from 1zclA/merged-good-all-a2m # 1zclA read from 1zclA/merged-good-all-a2m # adding 1zclA to template set # found chain 1zclA in template set T0305 87 :VDGYNK 1zclA 12 :VTYKNM T0305 95 :AYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 1zclA 18 :RFLITHNPTNATLNKFIEELKKYGVTTIVRVCEAT T0305 130 :EK 1zclA 59 :EK T0305 143 :EN 1zclA 61 :EG T0305 196 :YHYTQWP 1zclA 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1zclA 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1zclA 95 :EPGCCIAVHSVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFIHD 1zclA 142 :NSKQLLYLEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=917 Number of alignments=94 # 1zclA read from 1zclA/merged-good-all-a2m # found chain 1zclA in template set T0305 87 :VDGYN 1zclA 12 :VTYKN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKG 1zclA 17 :MRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDT T0305 177 :KKG 1zclA 56 :TLV T0305 187 :RQNE 1zclA 59 :EKEG T0305 196 :YHYTQWP 1zclA 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1zclA 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1zclA 95 :EPGCCIAVHSVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFIHD 1zclA 142 :NSKQLLYLEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=926 Number of alignments=95 # 1zclA read from 1zclA/merged-good-all-a2m # found chain 1zclA in template set T0305 91 :NKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGR 1zclA 14 :YKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTT T0305 196 :YHYTQWP 1zclA 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1zclA 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1zclA 95 :EPGCCIAVHSVAGLGRAPVLVALALIE T0305 259 :STVNVLGFLKHIRTQRNYLV 1zclA 122 :GGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1zclA 142 :NSKQLLYL Number of specific fragments extracted= 6 number of extra gaps= 0 total=932 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a5y/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a5y expands to /projects/compbio/data/pdb/1a5y.pdb.gz 1a5y:Warning: there is no chain 1a5y will retry with 1a5yA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0305 read from 1a5y/merged-good-all-a2m # 1a5y read from 1a5y/merged-good-all-a2m # adding 1a5y to template set # found chain 1a5y in template set Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 T0305 9 :VKHIGELYSNN 1a5y 4 :EKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTADM 1a5y 15 :SWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 1a5y 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1a5y 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1a5y 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRN 1a5y 140 :LKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1a5y 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLV 1a5y 204 :LSPEHGPVVV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKST 1a5y 217 :AGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=942 Number of alignments=97 # 1a5y read from 1a5y/merged-good-all-a2m # found chain 1a5y in template set Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 T0305 9 :VKHIGELYSNN 1a5y 4 :EKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTA 1a5y 15 :SWAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 1a5y 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1a5y 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1a5y 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1a5y 140 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1a5y 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLV 1a5y 204 :LSPEHGPVVV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKST 1a5y 217 :AGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=952 Number of alignments=98 # 1a5y read from 1a5y/merged-good-all-a2m # found chain 1a5y in template set Warning: unaligning (T0305)H234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0305)S236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 T0305 13 :GELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1a5y 4 :EKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1a5y 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1a5y 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1a5y 139 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1a5y 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLV 1a5y 206 :PEHGPVVV T0305 237 :AGVGRTGTYIVIDSMLQQIKDKST 1a5y 217 :AGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=960 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ptvA expands to /projects/compbio/data/pdb/1ptv.pdb.gz 1ptvA:# T0305 read from 1ptvA/merged-good-all-a2m # 1ptvA read from 1ptvA/merged-good-all-a2m # adding 1ptvA to template set # found chain 1ptvA in template set Warning: unaligning (T0305)Q7 because first residue in template chain is (1ptvA)E2 T0305 8 :FVKHIGELYSNN 1ptvA 3 :MEKEFEQIDKSG T0305 22 :GFSEDFEEVQRCTADM 1ptvA 15 :SWAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKLR 1ptvA 31 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1ptvA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYG 1ptvA 129 :EEKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1ptvA 139 :NLKLTLISEDIKTYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1ptvA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1ptvA 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=969 Number of alignments=100 # 1ptvA read from 1ptvA/merged-good-all-a2m # found chain 1ptvA in template set T0305 8 :FVKHIGELYSNNQ 1ptvA 3 :MEKEFEQIDKSGS T0305 23 :FSEDFEEVQRCTA 1ptvA 16 :WAAIYQDIRHEAS T0305 38 :NITAEHSNHPENKHKNRYINILAYDHSRVKLR 1ptvA 29 :DFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1ptvA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1ptvA 129 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1ptvA 140 :LKLTLISEDIKTYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAA 1ptvA 165 :TQETREILHFHYTTWPDFGVPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1ptvA 204 :LSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=978 Number of alignments=101 # 1ptvA read from 1ptvA/merged-good-all-a2m # found chain 1ptvA in template set T0305 12 :IGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 1ptvA 3 :MEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLH T0305 76 :SKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1ptvA 61 :QEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1ptvA 130 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1ptvA 139 :NLKLTLISEDIKTYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 1ptvA 163 :LTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1ptvA 206 :PEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=985 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2azrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/2azrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/2azrA/merged-good-all-a2m.gz for input Trying 2azrA/merged-good-all-a2m Error: Couldn't open file 2azrA/merged-good-all-a2m or 2azrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x24A expands to /projects/compbio/data/pdb/1x24.pdb.gz 1x24A:# T0305 read from 1x24A/merged-good-all-a2m # 1x24A read from 1x24A/merged-good-all-a2m # adding 1x24A to template set # found chain 1x24A in template set T0305 89 :GYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLV 1x24A 12 :VTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEAT T0305 130 :E 1x24A 59 :E T0305 142 :TEN 1x24A 60 :KEG T0305 196 :YHYTQWP 1x24A 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1x24A 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1x24A 95 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1x24A 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFIH 1x24A 142 :NSKQLLYLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=993 Number of alignments=103 # 1x24A read from 1x24A/merged-good-all-a2m # found chain 1x24A in template set T0305 89 :GYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1x24A 12 :VTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATY T0305 175 :KVKKGQK 1x24A 54 :DTTLVEK T0305 187 :RQ 1x24A 61 :EG T0305 196 :YHYTQWP 1x24A 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1x24A 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSM 1x24A 95 :EPGCCIAVHCVAGLGRAPVLVALALI T0305 258 :KSTVNVLGFLKHIRTQRNYLV 1x24A 121 :EGGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1x24A 142 :NSKQLLYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=1001 Number of alignments=104 # 1x24A read from 1x24A/merged-good-all-a2m # found chain 1x24A in template set T0305 65 :RVKLR 1x24A 11 :EVTYK T0305 93 :AKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVE 1x24A 16 :NMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATY T0305 196 :YHYTQWP 1x24A 63 :IHVLDWP T0305 203 :DMGVPEYALPVLTFVRRSSAARM 1x24A 71 :DDGAPPSNQIVDDWLSLVKIKFR T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSML 1x24A 95 :EPGCCIAVHCVAGLGRAPVLVALALIE T0305 259 :STVNVLGFLKHIRTQRNYLV 1x24A 122 :GGMKYEDAVQFIRQKRRGAF T0305 280 :TEEQYIFI 1x24A 142 :NSKQLLYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=1008 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pa1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0305 read from 1pa1A/merged-good-all-a2m # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0305)F2 because first residue in template chain is (1pa1A)K497 Warning: unaligning (T0305)R69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pa1A)Q561 Warning: unaligning (T0305)K74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pa1A)Q561 Warning: unaligning (T0305)D75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)E562 Warning: unaligning (T0305)S76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)D563 Warning: unaligning (T0305)M204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0305 3 :QSMKQFVKHIGELYSNNQ 1pa1A 498 :LEFMEMEKEFEQIDKSGS T0305 23 :FSEDFEEVQRCTADM 1pa1A 516 :WAAIYQDIRHEASDF T0305 40 :TAEHSNHPENKHKNRYINILAYDHSRVKL 1pa1A 531 :PCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1pa1A 564 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1pa1A 629 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRN 1pa1A 640 :LKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPD 1pa1A 663 :LTTQETREILHFHYTTWPD T0305 206 :VPEYALPVLTFVRRSSAA 1pa1A 684 :VPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pa1A 704 :LSPEHGPVVVHDSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 2 total=1018 Number of alignments=106 # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0305)F2 because first residue in template chain is (1pa1A)K497 Warning: unaligning (T0305)R69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pa1A)Q561 Warning: unaligning (T0305)S76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pa1A)Q561 Warning: unaligning (T0305)K77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)E562 Warning: unaligning (T0305)H78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)D563 Warning: unaligning (T0305)M204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0305 3 :QSMKQFVKHIGELYSNNQ 1pa1A 498 :LEFMEMEKEFEQIDKSGS T0305 23 :FSEDFEEVQRC 1pa1A 516 :WAAIYQDIRHE T0305 36 :DMNITAEHSNHPENKHKNRYINILAYDHSRVKL 1pa1A 527 :ASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWP 1pa1A 564 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWP T0305 142 :TENSEEYGN 1pa1A 629 :EEKEMIFED T0305 151 :IIVTLKSTKIHACYTVRRFSIRNTK 1pa1A 640 :LKLTLISEDIKSYYTVRQLELENLT T0305 187 :RQNERVVIQYHYTQWPD 1pa1A 665 :TQETREILHFHYTTWPD T0305 206 :VPEYALPVLTFVRRSSAA 1pa1A 684 :VPESPASFLNFLFKVRES T0305 224 :RMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pa1A 704 :LSPEHGPVVVHDSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 10 number of extra gaps= 2 total=1028 Number of alignments=107 # 1pa1A read from 1pa1A/merged-good-all-a2m # found chain 1pa1A in training set Warning: unaligning (T0305)R69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pa1A)Q561 Warning: unaligning (T0305)S76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pa1A)Q561 Warning: unaligning (T0305)K77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)E562 Warning: unaligning (T0305)H78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)D563 Warning: unaligning (T0305)M204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0305)G205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0305 11 :HIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKL 1pa1A 502 :EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKL T0305 79 :SDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 1pa1A 564 :NDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQ T0305 143 :ENSEEYG 1pa1A 630 :EKEMIFE T0305 150 :NIIVTLKSTKIHACYTVRRFSIRN 1pa1A 639 :NLKLTLISEDIKSYYTVRQLELEN T0305 185 :KGRQNERVVIQYHYTQWPD 1pa1A 663 :LTTQETREILHFHYTTWPD T0305 206 :VPEYALPVLTFVRRSSAARM 1pa1A 684 :VPESPASFLNFLFKVRESGS T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKST 1pa1A 706 :PEHGPVVVHDSAGIGRSGTFCLADTCLLLMDKRKD T0305 261 :VNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 2 total=1036 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oemX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305/1oemX/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0305/1oemX/merged-good-all-a2m.gz for input Trying 1oemX/merged-good-all-a2m Error: Couldn't open file 1oemX/merged-good-all-a2m or 1oemX/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b3oA expands to /projects/compbio/data/pdb/2b3o.pdb.gz 2b3oA:# T0305 read from 2b3oA/merged-good-all-a2m # 2b3oA read from 2b3oA/merged-good-all-a2m # adding 2b3oA to template set # found chain 2b3oA in template set Warning: unaligning (T0305)F23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b3oA)F244 T0305 24 :SEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLP 2b3oA 245 :WEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRD T0305 73 :GKDS 2b3oA 295 :NIPG T0305 79 :SDYINANYV 2b3oA 299 :SDYINANYI T0305 88 :DGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEE 2b3oA 313 :GPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQR T0305 148 :YGNIIVTLKSTKIHACYTVRRFSIRN 2b3oA 374 :YGPYSVTNCGEHDTTEYKLRTLQVSP T0305 184 :PKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2b3oA 400 :LDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIK 2b3oA 444 :PHAGPIIVHCSAGIGRTGTIIVIDMLMENIS T0305 257 :DKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2b3oA 478 :LDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIET Number of specific fragments extracted= 8 number of extra gaps= 0 total=1044 Number of alignments=109 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set Warning: unaligning (T0305)F23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b3oA)F244 T0305 24 :SEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLP 2b3oA 245 :WEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRD T0305 73 :GKDS 2b3oA 295 :NIPG T0305 79 :SDYINANYVDG 2b3oA 299 :SDYINANYIKN T0305 90 :YNKA 2b3oA 314 :PDEN T0305 94 :KAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2b3oA 319 :KTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPE T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTK 2b3oA 369 :GMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLD T0305 186 :GRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2b3oA 402 :NGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKS 2b3oA 444 :PHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKG T0305 260 :TVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILG 2b3oA 481 :DIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIET Number of specific fragments extracted= 9 number of extra gaps= 0 total=1053 Number of alignments=110 # 2b3oA read from 2b3oA/merged-good-all-a2m # found chain 2b3oA in template set Warning: unaligning (T0305)F23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b3oA)F244 T0305 24 :SEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLR 2b3oA 245 :WEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQ T0305 71 :LPGKDSKHSDYINANYVD 2b3oA 291 :GRDSNIPGSDYINANYIK T0305 91 :NKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPT 2b3oA 316 :ENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPE T0305 143 :ENSEEYGNIIVTLKSTKIHACYTVRRFSIRN 2b3oA 369 :GMQRAYGPYSVTNCGEHDTTEYKLRTLQVSP T0305 184 :PKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARM 2b3oA 400 :LDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0305 226 :PETGPVLVHCSAGVGRTGTYIVIDSMLQQIKD 2b3oA 444 :PHAGPIIVHCSAGIGRTGTIIVIDMLMENIST T0305 258 :KSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAIL 2b3oA 479 :DCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1060 Number of alignments=111 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 111 Adding 2202 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -509.5232, CN propb: -509.5232 weights: 0.5145 constraints: 681 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 681 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 681 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1521 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1521 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 2202 # command: