# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0305//projects/compbio/experiments/protein-predict/casp7/T0305/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0305//projects/compbio/experiments/protein-predict/casp7/T0305/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0305/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0305/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0305)S250.CB, (T0305)F266.CB) [> 3.2779 = 5.4632 < 7.1022] w=1.0000 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)I270.CB) [> 3.8513 = 6.4188 < 8.3445] w=1.0000 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)L267.CB) [> 3.6564 = 6.0939 < 7.9221] w=1.0000 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)F266.CB) [> 3.3074 = 5.5123 < 7.1660] w=1.0000 to align # Constraint # added constraint: constraint((T0305)I246.CB, (T0305)I270.CB) [> 3.8352 = 6.3920 < 8.3096] w=1.0000 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)I287.CB) [> 3.6096 = 6.0160 < 7.8208] w=1.0000 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)I270.CB) [> 3.8314 = 6.3856 < 8.3013] w=1.0000 to align # Constraint # added constraint: constraint((T0305)V239.CB, (T0305)R274.CB) [> 3.9119 = 6.5198 < 8.4757] w=1.0000 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)T242.CB) [> 2.9940 = 4.9900 < 6.4870] w=0.9843 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)G243.CA) [> 4.0221 = 6.7036 < 8.7146] w=0.9843 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)I246.CB) [> 3.9720 = 6.6200 < 8.6060] w=0.9843 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)R274.CB) [> 3.2910 = 5.4850 < 7.1304] w=0.9843 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)L232.CB) [> 3.8023 = 6.3372 < 8.2383] w=0.9843 to align # Constraint # added constraint: constraint((T0305)Q100.CB, (T0305)G238.CA) [> 3.1854 = 5.3091 < 6.9018] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)L232.CB) [> 3.6907 = 6.1512 < 7.9966] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)L232.CB) [> 4.2894 = 7.1490 < 9.2937] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)L232.CB) [> 2.7866 = 4.6444 < 6.0377] w=0.9843 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)L232.CB) [> 4.2097 = 7.0162 < 9.1211] w=0.9843 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)Y245.CB) [> 3.8946 = 6.4910 < 8.4383] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)R241.CB) [> 2.6305 = 4.3841 < 5.6993] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)T242.CB) [> 3.6216 = 6.0360 < 7.8469] w=0.9843 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)Y245.CB) [> 3.6817 = 6.1362 < 7.9770] w=0.9843 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)T126.CB) [> 4.3023 = 7.1705 < 9.3217] w=0.9765 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)G238.CA) [> 4.1696 = 6.9493 < 9.0341] w=0.9765 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)I248.CB) [> 3.4910 = 5.8184 < 7.5639] w=0.9765 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)Q283.CB) [> 2.9738 = 4.9563 < 6.4432] w=0.9765 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)I287.CB) [> 3.0778 = 5.1297 < 6.6686] w=0.9765 to align # Constraint # added constraint: constraint((T0305)V263.CB, (T0305)I287.CB) [> 3.4438 = 5.7396 < 7.4615] w=0.9765 to align # Constraint # added constraint: constraint((T0305)L267.CB, (T0305)Y284.CB) [> 4.3755 = 7.2924 < 9.4802] w=0.9765 to align # Constraint # added constraint: constraint((T0305)R241.CB, (T0305)Q283.CB) [> 4.4586 = 7.4310 < 9.6603] w=0.9736 to align # Constraint # added constraint: constraint((T0305)V233.CB, (T0305)I246.CB) [> 3.6531 = 6.0884 < 7.9150] w=0.9711 to align # Constraint # added constraint: constraint((T0305)V233.CB, (T0305)Y245.CB) [> 3.4392 = 5.7320 < 7.4517] w=0.9711 to align # Constraint # added constraint: constraint((T0305)V233.CB, (T0305)T242.CB) [> 2.8528 = 4.7548 < 6.1812] w=0.9711 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)Y198.CB) [> 3.9817 = 6.6361 < 8.6270] w=0.9602 to align # Constraint # added constraint: constraint((T0305)I248.CB, (T0305)I287.CB) [> 3.6469 = 6.0781 < 7.9015] w=0.9592 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)F286.CB) [> 3.8044 = 6.3407 < 8.2429] w=0.9592 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)D249.CB) [> 3.4219 = 5.7031 < 7.4141] w=0.9572 to align # Constraint # added constraint: constraint((T0305)T119.CB, (T0305)G229.CA) [> 3.5101 = 5.8502 < 7.6053] w=0.9558 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)V233.CB) [> 4.0995 = 6.8326 < 8.8823] w=0.9554 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)W201.CB) [> 3.6637 = 6.1061 < 7.9380] w=0.9554 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)V233.CB) [> 2.7290 = 4.5483 < 5.9128] w=0.9554 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)V231.CB) [> 3.7771 = 6.2951 < 8.1837] w=0.9554 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)V231.CB) [> 2.8349 = 4.7249 < 6.1424] w=0.9554 to align # Constraint # added constraint: constraint((T0305)T119.CB, (T0305)P230.CB) [> 3.4920 = 5.8199 < 7.5659] w=0.9554 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)V233.CB) [> 3.2985 = 5.4975 < 7.1467] w=0.9554 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)G229.CA) [> 3.8548 = 6.4246 < 8.3520] w=0.9554 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)Y196.CB) [> 4.2064 = 7.0107 < 9.1139] w=0.9523 to align # Constraint # added constraint: constraint((T0305)T119.CB, (T0305)L232.CB) [> 2.9883 = 4.9804 < 6.4745] w=0.9523 to align # Constraint # added constraint: constraint((T0305)V213.CB, (T0305)I248.CB) [> 3.9272 = 6.5453 < 8.5089] w=0.9519 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)V263.CB) [> 4.1636 = 6.9393 < 9.0211] w=0.9476 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)V231.CB) [> 4.4766 = 7.4610 < 9.6993] w=0.9476 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)A223.CB) [> 3.4873 = 5.8121 < 7.5558] w=0.9400 to align # Constraint # added constraint: constraint((T0305)Q117.CB, (T0305)P230.CB) [> 3.5043 = 5.8406 < 7.5928] w=0.9313 to align # Constraint # added constraint: constraint((T0305)S220.CB, (T0305)V231.CB) [> 4.1243 = 6.8738 < 8.9360] w=0.9283 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)C235.CB) [> 4.1597 = 6.9328 < 9.0127] w=0.9265 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)S236.CB) [> 3.5492 = 5.9154 < 7.6901] w=0.9265 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)C235.CB) [> 2.7630 = 4.6050 < 5.9865] w=0.9265 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)C235.CB) [> 2.9640 = 4.9399 < 6.4219] w=0.9265 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)S236.CB) [> 3.1966 = 5.3276 < 6.9259] w=0.9265 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)F266.CB) [> 3.6514 = 6.0857 < 7.9113] w=0.9250 to align # Constraint # added constraint: constraint((T0305)T119.CB, (T0305)V231.CB) [> 3.9716 = 6.6193 < 8.6052] w=0.9234 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)Y196.CB) [> 4.0039 = 6.6732 < 8.6751] w=0.9234 to align # Constraint # added constraint: constraint((T0305)Q100.CB, (T0305)A237.CB) [> 3.4084 = 5.6807 < 7.3850] w=0.9154 to align # Constraint # added constraint: constraint((T0305)V233.CB, (T0305)G243.CA) [> 4.4690 = 7.4483 < 9.6828] w=0.9137 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)V278.CB) [> 3.3404 = 5.5673 < 7.2375] w=0.9133 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)V278.CB) [> 3.7011 = 6.1685 < 8.0190] w=0.9133 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)V278.CB) [> 3.9117 = 6.5195 < 8.4754] w=0.9133 to align # Constraint # added constraint: constraint((T0305)L267.CB, (T0305)V278.CB) [> 3.3632 = 5.6053 < 7.2869] w=0.9133 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)V239.CB) [> 4.2930 = 7.1549 < 9.3014] w=0.9112 to align # Constraint # added constraint: constraint((T0305)G240.CA, (T0305)Q283.CB) [> 3.6119 = 6.0199 < 7.8258] w=0.9105 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)G238.CA) [> 3.7308 = 6.2180 < 8.0834] w=0.9105 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)G238.CA) [> 3.3113 = 5.5189 < 7.1745] w=0.9105 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)S220.CB) [> 3.5795 = 5.9658 < 7.7555] w=0.9076 to align # Constraint # added constraint: constraint((T0305)V263.CB, (T0305)H288.CB) [> 3.6417 = 6.0694 < 7.8903] w=0.9030 to align # Constraint # added constraint: constraint((T0305)N118.CB, (T0305)G229.CA) [> 2.8301 = 4.7169 < 6.1319] w=0.9027 to align # Constraint # added constraint: constraint((T0305)W201.CB, (T0305)R241.CB) [> 3.5633 = 5.9389 < 7.7206] w=0.9022 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)I287.CB) [> 4.4324 = 7.3873 < 9.6034] w=0.9015 to align # Constraint # added constraint: constraint((T0305)S221.CB, (T0305)D249.CB) [> 4.2349 = 7.0582 < 9.1757] w=0.8979 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)H234.CB) [> 4.1796 = 6.9660 < 9.0558] w=0.8977 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)H234.CB) [> 2.8440 = 4.7400 < 6.1619] w=0.8977 to align # Constraint # added constraint: constraint((T0305)Q100.CB, (T0305)H234.CB) [> 3.7519 = 6.2532 < 8.1291] w=0.8977 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)H234.CB) [> 2.8819 = 4.8031 < 6.2440] w=0.8977 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)V231.CB) [> 4.2356 = 7.0593 < 9.1770] w=0.8977 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)H234.CB) [> 3.6989 = 6.1648 < 8.0142] w=0.8977 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)H234.CB) [> 4.1489 = 6.9148 < 8.9892] w=0.8977 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)L232.CB) [> 2.7429 = 4.5715 < 5.9429] w=0.8977 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)I246.CB) [> 3.1764 = 5.2939 < 6.8821] w=0.8977 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)H234.CB) [> 4.4529 = 7.4214 < 9.6479] w=0.8948 to align # Constraint # added constraint: constraint((T0305)L267.CB, (T0305)L277.CB) [> 4.2183 = 7.0304 < 9.1396] w=0.8906 to align # Constraint # added constraint: constraint((T0305)P207.CB, (T0305)F286.CB) [> 4.0182 = 6.6970 < 8.7061] w=0.8902 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)P230.CB) [> 3.0620 = 5.1034 < 6.6344] w=0.8900 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)L277.CB) [> 2.6176 = 4.3627 < 5.6715] w=0.8898 to align # Constraint # added constraint: constraint((T0305)V239.CB, (T0305)L277.CB) [> 2.8975 = 4.8292 < 6.2779] w=0.8898 to align # Constraint # added constraint: constraint((T0305)G205.CA, (T0305)E282.CB) [> 3.5279 = 5.8799 < 7.6438] w=0.8838 to align # Constraint # added constraint: constraint((T0305)V239.CB, (T0305)Q279.CB) [> 3.4462 = 5.7436 < 7.4667] w=0.8834 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)H197.CB) [> 2.7783 = 4.6305 < 6.0197] w=0.8834 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)Y196.CB) [> 4.2052 = 7.0087 < 9.1113] w=0.8834 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)T99.CB) [> 4.4564 = 7.4273 < 9.6554] w=0.8790 to align # Constraint # added constraint: constraint((T0305)I248.CB, (T0305)A290.CB) [> 3.1483 = 5.2472 < 6.8214] w=0.8790 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)Y198.CB) [> 4.4501 = 7.4169 < 9.6419] w=0.8744 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)V231.CB) [> 4.2574 = 7.0957 < 9.2244] w=0.8688 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)P230.CB) [> 3.1221 = 5.2035 < 6.7646] w=0.8688 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)V233.CB) [> 3.4219 = 5.7032 < 7.4142] w=0.8688 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)V231.CB) [> 3.2244 = 5.3741 < 6.9863] w=0.8688 to align # Constraint # added constraint: constraint((T0305)V278.CB, (T0305)I287.CB) [> 4.1241 = 6.8735 < 8.9356] w=0.8672 to align # Constraint # added constraint: constraint((T0305)V206.CB, (T0305)F286.CB) [> 2.6537 = 4.4227 < 5.7496] w=0.8653 to align # Constraint # added constraint: constraint((T0305)V263.CB, (T0305)L291.CB) [> 3.7627 = 6.2711 < 8.1524] w=0.8637 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)L291.CB) [> 3.2095 = 5.3491 < 6.9538] w=0.8637 to align # Constraint # added constraint: constraint((T0305)V213.CB, (T0305)A290.CB) [> 3.6710 = 6.1184 < 7.9539] w=0.8598 to align # Constraint # added constraint: constraint((T0305)Q100.CB, (T0305)S236.CB) [> 4.1775 = 6.9624 < 9.0511] w=0.8576 to align # Constraint # added constraint: constraint((T0305)G240.CA, (T0305)T280.CB) [> 4.4198 = 7.3663 < 9.5761] w=0.8530 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)Y245.CB) [> 4.1141 = 6.8568 < 8.9138] w=0.8522 to align # Constraint # added constraint: constraint((T0305)A210.CB, (T0305)D289.CB) [> 3.0616 = 5.1027 < 6.6335] w=0.8501 to align # Constraint # added constraint: constraint((T0305)A210.CB, (T0305)A290.CB) [> 2.8932 = 4.8219 < 6.2685] w=0.8501 to align # Constraint # added constraint: constraint((T0305)L214.CB, (T0305)A290.CB) [> 3.7236 = 6.2060 < 8.0678] w=0.8501 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)Q195.CB) [> 2.9168 = 4.8614 < 6.3198] w=0.8451 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)Q195.CB) [> 4.5479 = 7.5798 < 9.8538] w=0.8451 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)Q273.CB) [> 2.7570 = 4.5950 < 5.9734] w=0.8450 to align # Constraint # added constraint: constraint((T0305)G240.CA, (T0305)L277.CB) [> 3.6327 = 6.0545 < 7.8709] w=0.8437 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)P230.CB) [> 3.5032 = 5.8386 < 7.5902] w=0.8402 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)I246.CB) [> 3.6447 = 6.0745 < 7.8969] w=0.8374 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)I270.CB) [> 3.5670 = 5.9450 < 7.7285] w=0.8374 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)Q117.CB) [> 3.8979 = 6.4964 < 8.4453] w=0.8371 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)S220.CB) [> 3.6912 = 6.1520 < 7.9976] w=0.8356 to align # Constraint # added constraint: constraint((T0305)N83.CB, (T0305)T99.CB) [> 3.7279 = 6.2132 < 8.0772] w=0.8355 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)A98.CB) [> 4.1036 = 6.8393 < 8.8911] w=0.8355 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)T99.CB) [> 2.1502 = 3.5836 < 4.6586] w=0.8355 to align # Constraint # added constraint: constraint((T0305)N85.CB, (T0305)A98.CB) [> 3.2976 = 5.4960 < 7.1448] w=0.8355 to align # Constraint # added constraint: constraint((T0305)N85.CB, (T0305)Q273.CB) [> 3.3613 = 5.6022 < 7.2829] w=0.8355 to align # Constraint # added constraint: constraint((T0305)N85.CB, (T0305)R274.CB) [> 2.4683 = 4.1139 < 5.3481] w=0.8355 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)M113.CB) [> 3.4781 = 5.7969 < 7.5359] w=0.8340 to align # Constraint # added constraint: constraint((T0305)L59.CB, (T0305)N275.CB) [> 3.9603 = 6.6006 < 8.5807] w=0.8340 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)N275.CB) [> 3.8170 = 6.3616 < 8.2701] w=0.8340 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)V263.CB) [> 3.6257 = 6.0428 < 7.8557] w=0.8321 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)V261.CB) [> 3.2412 = 5.4021 < 7.0227] w=0.8321 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)Y86.CB) [> 2.9670 = 4.9450 < 6.4285] w=0.8260 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)A84.CB) [> 4.0901 = 6.8168 < 8.8619] w=0.8260 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)N85.CB) [> 3.4931 = 5.8218 < 7.5684] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)A84.CB) [> 2.5252 = 4.2087 < 5.4713] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)N85.CB) [> 3.9750 = 6.6250 < 8.6125] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)Y86.CB) [> 3.6451 = 6.0751 < 7.8976] w=0.8260 to align # Constraint # added constraint: constraint((T0305)N83.CB, (T0305)Q100.CB) [> 2.8169 = 4.6948 < 6.1032] w=0.8260 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)M113.CB) [> 3.8052 = 6.3421 < 8.2447] w=0.8260 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)Q273.CB) [> 3.9626 = 6.6044 < 8.5857] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)R274.CB) [> 3.7699 = 6.2832 < 8.1681] w=0.8260 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)N85.CB) [> 2.7646 = 4.6076 < 5.9899] w=0.8260 to align # Constraint # added constraint: constraint((T0305)Y61.CB, (T0305)R274.CB) [> 3.8560 = 6.4266 < 8.3546] w=0.8260 to align # Constraint # added constraint: constraint((T0305)Y61.CB, (T0305)N85.CB) [> 3.7296 = 6.2160 < 8.0808] w=0.8260 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)R274.CB) [> 4.0229 = 6.7049 < 8.7163] w=0.8260 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)N85.CB) [> 2.9755 = 4.9591 < 6.4469] w=0.8260 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)N83.CB) [> 3.2240 = 5.3734 < 6.9854] w=0.8260 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)V239.CB) [> 3.5681 = 5.9469 < 7.7309] w=0.8260 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)A237.CB) [> 2.9504 = 4.9173 < 6.3925] w=0.8260 to align # Constraint # added constraint: constraint((T0305)Y196.CB, (T0305)S220.CB) [> 3.3837 = 5.6396 < 7.3314] w=0.8260 to align # Constraint # added constraint: constraint((T0305)Y196.CB, (T0305)R219.CB) [> 3.9634 = 6.6056 < 8.5873] w=0.8260 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)V192.CB) [> 3.5090 = 5.8483 < 7.6028] w=0.8260 to align # Constraint # added constraint: constraint((T0305)F169.CB, (T0305)Q195.CB) [> 3.4914 = 5.8191 < 7.5648] w=0.8260 to align # Constraint # added constraint: constraint((T0305)R167.CB, (T0305)H197.CB) [> 4.0873 = 6.8122 < 8.8559] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)Y196.CB) [> 3.3286 = 5.5476 < 7.2119] w=0.8260 to align # Constraint # added constraint: constraint((T0305)T165.CB, (T0305)T199.CB) [> 3.8208 = 6.3679 < 8.2783] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)I171.CB) [> 3.3063 = 5.5105 < 7.1637] w=0.8260 to align # Constraint # added constraint: constraint((T0305)S145.CB, (T0305)T154.CB) [> 2.7821 = 4.6369 < 6.0279] w=0.8260 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)T199.CB) [> 3.4816 = 5.8026 < 7.5434] w=0.8260 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)Y198.CB) [> 2.9929 = 4.9882 < 6.4847] w=0.8260 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)Q195.CB) [> 3.9264 = 6.5441 < 8.5073] w=0.8260 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)Y196.CB) [> 3.0981 = 5.1636 < 6.7126] w=0.8260 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)I171.CB) [> 4.1275 = 6.8792 < 8.9429] w=0.8260 to align # Constraint # added constraint: constraint((T0305)W111.CB, (T0305)V153.CB) [> 3.8199 = 6.3665 < 8.2764] w=0.8260 to align # Constraint # added constraint: constraint((T0305)W111.CB, (T0305)I151.CB) [> 2.8539 = 4.7566 < 6.1835] w=0.8260 to align # Constraint # added constraint: constraint((T0305)W111.CB, (T0305)Y148.CB) [> 3.2867 = 5.4779 < 7.1213] w=0.8260 to align # Constraint # added constraint: constraint((T0305)G240.CA, (T0305)V278.CB) [> 3.5323 = 5.8872 < 7.6534] w=0.8238 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)F110.CB) [> 4.3983 = 7.3304 < 9.5296] w=0.8230 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)R241.CB) [> 4.2139 = 7.0232 < 9.1301] w=0.8230 to align # Constraint # added constraint: constraint((T0305)P102.CB, (T0305)H234.CB) [> 4.5371 = 7.5619 < 9.8305] w=0.8200 to align # Constraint # added constraint: constraint((T0305)N53.CB, (T0305)Q100.CB) [> 4.3784 = 7.2973 < 9.4865] w=0.8164 to align # Constraint # added constraint: constraint((T0305)K52.CB, (T0305)N83.CB) [> 3.6756 = 6.1260 < 7.9638] w=0.8164 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)R274.CB) [> 4.0851 = 6.8085 < 8.8510] w=0.8161 to align # Constraint # added constraint: constraint((T0305)N53.CB, (T0305)N83.CB) [> 3.1774 = 5.2956 < 6.8843] w=0.8106 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)N83.CB) [> 4.1589 = 6.9316 < 9.0110] w=0.8106 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)Q100.CB) [> 2.8073 = 4.6788 < 6.0824] w=0.8106 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)G101.CA) [> 3.8184 = 6.3640 < 8.2733] w=0.8106 to align # Constraint # added constraint: constraint((T0305)Y55.CB, (T0305)A237.CB) [> 3.2357 = 5.3928 < 7.0106] w=0.8106 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)A84.CB) [> 3.7577 = 6.2629 < 8.1417] w=0.8088 to align # Constraint # added constraint: constraint((T0305)G89.CA, (T0305)S250.CB) [> 3.6124 = 6.0207 < 7.8269] w=0.8083 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)Y198.CB) [> 3.0110 = 5.0183 < 6.5238] w=0.8067 to align # Constraint # added constraint: constraint((T0305)F107.CB, (T0305)Y148.CB) [> 3.3791 = 5.6318 < 7.3214] w=0.8067 to align # Constraint # added constraint: constraint((T0305)I82.CB, (T0305)M113.CB) [> 3.4375 = 5.7291 < 7.4478] w=0.8066 to align # Constraint # added constraint: constraint((T0305)I82.CB, (T0305)F110.CB) [> 4.1781 = 6.9635 < 9.0526] w=0.8066 to align # Constraint # added constraint: constraint((T0305)I82.CB, (T0305)T99.CB) [> 4.0868 = 6.8114 < 8.8548] w=0.8066 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)I97.CB) [> 3.6518 = 6.0863 < 7.9122] w=0.8034 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)V233.CB) [> 4.5938 = 7.6564 < 9.9533] w=0.8032 to align # Constraint # added constraint: constraint((T0305)F107.CB, (T0305)Y139.CB) [> 2.7790 = 4.6317 < 6.0212] w=0.8010 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)A237.CB) [> 3.8892 = 6.4819 < 8.4265] w=0.7991 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)P230.CB) [> 4.1369 = 6.8948 < 8.9633] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)V193.CB) [> 3.7882 = 6.3136 < 8.2077] w=0.7971 to align # Constraint # added constraint: constraint((T0305)T119.CB, (T0305)V193.CB) [> 4.0255 = 6.7091 < 8.7218] w=0.7971 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)V193.CB) [> 3.2571 = 5.4284 < 7.0570] w=0.7971 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)I194.CB) [> 3.8199 = 6.3665 < 8.2764] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)V193.CB) [> 4.3233 = 7.2055 < 9.3671] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)I194.CB) [> 3.0142 = 5.0236 < 6.5307] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)V193.CB) [> 3.7694 = 6.2822 < 8.1669] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)I194.CB) [> 4.3705 = 7.2842 < 9.4695] w=0.7971 to align # Constraint # added constraint: constraint((T0305)R168.CB, (T0305)I194.CB) [> 3.6846 = 6.1411 < 7.9834] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I171.CB, (T0305)V193.CB) [> 3.3659 = 5.6098 < 7.2927] w=0.7971 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)F216.CB) [> 3.4299 = 5.7165 < 7.4315] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)Q100.CB) [> 4.3580 = 7.2634 < 9.4424] w=0.7971 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)V87.CB) [> 4.4656 = 7.4427 < 9.6756] w=0.7971 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)I82.CB) [> 3.4335 = 5.7224 < 7.4392] w=0.7971 to align # Constraint # added constraint: constraint((T0305)R112.CB, (T0305)I151.CB) [> 4.0254 = 6.7089 < 8.7216] w=0.7971 to align # Constraint # added constraint: constraint((T0305)W115.CB, (T0305)N173.CB) [> 3.8035 = 6.3392 < 8.2409] w=0.7971 to align # Constraint # added constraint: constraint((T0305)I151.CB, (T0305)N173.CB) [> 3.4301 = 5.7168 < 7.4319] w=0.7971 to align # Constraint # added constraint: constraint((T0305)L155.CB, (T0305)F169.CB) [> 3.4887 = 5.8144 < 7.5588] w=0.7971 to align # Constraint # added constraint: constraint((T0305)S157.CB, (T0305)R167.CB) [> 4.1356 = 6.8927 < 8.9605] w=0.7971 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)H197.CB) [> 4.5037 = 7.5062 < 9.7580] w=0.7971 to align # Constraint # added constraint: constraint((T0305)R172.CB, (T0305)E190.CB) [> 3.0529 = 5.0881 < 6.6146] w=0.7971 to align # Constraint # added constraint: constraint((T0305)V239.CB, (T0305)V278.CB) [> 4.5494 = 7.5823 < 9.8570] w=0.7953 to align # Constraint # added constraint: constraint((T0305)S44.CB, (T0305)L59.CB) [> 2.7729 = 4.6215 < 6.0079] w=0.7952 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)H234.CB) [> 4.4401 = 7.4002 < 9.6202] w=0.7938 to align # Constraint # added constraint: constraint((T0305)A210.CB, (T0305)F286.CB) [> 4.0616 = 6.7693 < 8.8001] w=0.7924 to align # Constraint # added constraint: constraint((T0305)A210.CB, (T0305)E293.CB) [> 3.0835 = 5.1392 < 6.6809] w=0.7914 to align # Constraint # added constraint: constraint((T0305)W115.CB, (T0305)I171.CB) [> 3.6527 = 6.0879 < 7.9142] w=0.7875 to align # Constraint # added constraint: constraint((T0305)I151.CB, (T0305)I171.CB) [> 3.6392 = 6.0654 < 7.8850] w=0.7875 to align # Constraint # added constraint: constraint((T0305)I151.CB, (T0305)R172.CB) [> 4.1594 = 6.9324 < 9.0121] w=0.7875 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)R172.CB) [> 2.5999 = 4.3332 < 5.6332] w=0.7875 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)F169.CB) [> 3.4928 = 5.8213 < 7.5677] w=0.7875 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)S170.CB) [> 4.3950 = 7.3250 < 9.5225] w=0.7875 to align # Constraint # added constraint: constraint((T0305)T154.CB, (T0305)F169.CB) [> 4.0607 = 6.7678 < 8.7982] w=0.7875 to align # Constraint # added constraint: constraint((T0305)T154.CB, (T0305)S170.CB) [> 2.8474 = 4.7457 < 6.1694] w=0.7875 to align # Constraint # added constraint: constraint((T0305)K156.CB, (T0305)R168.CB) [> 2.9000 = 4.8333 < 6.2832] w=0.7875 to align # Constraint # added constraint: constraint((T0305)T165.CB, (T0305)H197.CB) [> 2.8540 = 4.7567 < 6.1837] w=0.7875 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)Q195.CB) [> 4.2124 = 7.0207 < 9.1270] w=0.7875 to align # Constraint # added constraint: constraint((T0305)R167.CB, (T0305)Q195.CB) [> 2.5136 = 4.1893 < 5.4461] w=0.7875 to align # Constraint # added constraint: constraint((T0305)F169.CB, (T0305)V192.CB) [> 4.2750 = 7.1251 < 9.2626] w=0.7875 to align # Constraint # added constraint: constraint((T0305)I171.CB, (T0305)R191.CB) [> 3.0457 = 5.0762 < 6.5990] w=0.7875 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)L232.CB) [> 4.4834 = 7.4723 < 9.7140] w=0.7872 to align # Constraint # added constraint: constraint((T0305)H43.CB, (T0305)D62.CB) [> 3.4286 = 5.7144 < 7.4287] w=0.7856 to align # Constraint # added constraint: constraint((T0305)K52.CB, (T0305)I82.CB) [> 4.2145 = 7.0242 < 9.1314] w=0.7817 to align # Constraint # added constraint: constraint((T0305)K104.CB, (T0305)D137.CB) [> 3.1812 = 5.3021 < 6.8927] w=0.7817 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)L103.CB) [> 3.5923 = 5.9872 < 7.7834] w=0.7817 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)Q100.CB) [> 4.4214 = 7.3690 < 9.5797] w=0.7799 to align # Constraint # added constraint: constraint((T0305)L59.CB, (T0305)N83.CB) [> 4.1493 = 6.9155 < 8.9902] w=0.7799 to align # Constraint # added constraint: constraint((T0305)N85.CB, (T0305)T99.CB) [> 4.3902 = 7.3170 < 9.5120] w=0.7777 to align # Constraint # added constraint: constraint((T0305)P102.CB, (T0305)Y139.CB) [> 3.0257 = 5.0429 < 6.5557] w=0.7721 to align # Constraint # added constraint: constraint((T0305)I194.CB, (T0305)A223.CB) [> 3.2495 = 5.4158 < 7.0406] w=0.7702 to align # Constraint # added constraint: constraint((T0305)F169.CB, (T0305)V193.CB) [> 2.6856 = 4.4761 < 5.8189] w=0.7682 to align # Constraint # added constraint: constraint((T0305)R167.CB, (T0305)I194.CB) [> 4.3941 = 7.3236 < 9.5206] w=0.7682 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)I194.CB) [> 3.9413 = 6.5688 < 8.5395] w=0.7682 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)H197.CB) [> 3.6491 = 6.0818 < 7.9064] w=0.7682 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)Y196.CB) [> 3.6307 = 6.0511 < 7.8665] w=0.7682 to align # Constraint # added constraint: constraint((T0305)T242.CB, (T0305)L277.CB) [> 4.1072 = 6.8453 < 8.8989] w=0.7682 to align # Constraint # added constraint: constraint((T0305)T158.CB, (T0305)R168.CB) [> 4.2078 = 7.0131 < 9.1170] w=0.7682 to align # Constraint # added constraint: constraint((T0305)E108.CB, (T0305)I151.CB) [> 4.0140 = 6.6900 < 8.6969] w=0.7682 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)G238.CA) [> 4.4417 = 7.4028 < 9.6236] w=0.7682 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)H234.CB) [> 4.4693 = 7.4489 < 9.6835] w=0.7649 to align # Constraint # added constraint: constraint((T0305)W140.CB, (T0305)F169.CB) [> 3.8349 = 6.3915 < 8.3090] w=0.7625 to align # Constraint # added constraint: constraint((T0305)F110.CB, (T0305)Y139.CB) [> 3.6386 = 6.0644 < 7.8837] w=0.7625 to align # Constraint # added constraint: constraint((T0305)K156.CB, (T0305)S170.CB) [> 3.4961 = 5.8268 < 7.5749] w=0.7606 to align # Constraint # added constraint: constraint((T0305)L155.CB, (T0305)R167.CB) [> 3.5617 = 5.9362 < 7.7170] w=0.7586 to align # Constraint # added constraint: constraint((T0305)T158.CB, (T0305)R167.CB) [> 3.0959 = 5.1598 < 6.7077] w=0.7586 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)E190.CB) [> 3.6065 = 6.0108 < 7.8140] w=0.7586 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)R191.CB) [> 4.3475 = 7.2458 < 9.4195] w=0.7586 to align # Constraint # added constraint: constraint((T0305)L267.CB, (T0305)I287.CB) [> 4.4349 = 7.3915 < 9.6090] w=0.7570 to align # Constraint # added constraint: constraint((T0305)S44.CB, (T0305)A60.CB) [> 3.2123 = 5.3538 < 6.9599] w=0.7567 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)S236.CB) [> 4.1535 = 6.9224 < 8.9992] w=0.7529 to align # Constraint # added constraint: constraint((T0305)W115.CB, (T0305)I151.CB) [> 3.7653 = 6.2755 < 8.1581] w=0.7510 to align # Constraint # added constraint: constraint((T0305)I82.CB, (T0305)T106.CB) [> 3.9339 = 6.5564 < 8.5234] w=0.7510 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)Y96.CB) [> 2.7041 = 4.5068 < 5.8589] w=0.7508 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)I97.CB) [> 4.2623 = 7.1039 < 9.2351] w=0.7508 to align # Constraint # added constraint: constraint((T0305)N118.CB, (T0305)T228.CB) [> 3.6490 = 6.0817 < 7.9062] w=0.7491 to align # Constraint # added constraint: constraint((T0305)F169.CB, (T0305)I194.CB) [> 4.4743 = 7.4571 < 9.6943] w=0.7490 to align # Constraint # added constraint: constraint((T0305)C163.CB, (T0305)P212.CB) [> 2.8402 = 4.7336 < 6.1537] w=0.7490 to align # Constraint # added constraint: constraint((T0305)N85.CB, (T0305)I97.CB) [> 4.2447 = 7.0745 < 9.1968] w=0.7489 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)I97.CB) [> 3.5710 = 5.9517 < 7.7373] w=0.7489 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)L252.CB) [> 4.0328 = 6.7213 < 8.7377] w=0.7458 to align # Constraint # added constraint: constraint((T0305)K156.CB, (T0305)F169.CB) [> 4.1209 = 6.8682 < 8.9286] w=0.7414 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)R224.CB) [> 3.4106 = 5.6843 < 7.3896] w=0.7414 to align # Constraint # added constraint: constraint((T0305)R168.CB, (T0305)Q195.CB) [> 4.5228 = 7.5379 < 9.7993] w=0.7393 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)C136.CB) [> 2.7676 = 4.6126 < 5.9964] w=0.7336 to align # Constraint # added constraint: constraint((T0305)F107.CB, (T0305)D137.CB) [> 3.6570 = 6.0950 < 7.9236] w=0.7336 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)C136.CB) [> 3.3222 = 5.5370 < 7.1982] w=0.7336 to align # Constraint # added constraint: constraint((T0305)W140.CB, (T0305)L155.CB) [> 3.8872 = 6.4787 < 8.4223] w=0.7336 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)I171.CB) [> 4.2367 = 7.0612 < 9.1795] w=0.7318 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)T199.CB) [> 3.7008 = 6.1680 < 8.0183] w=0.7297 to align # Constraint # added constraint: constraint((T0305)R168.CB, (T0305)V192.CB) [> 3.8121 = 6.3536 < 8.2596] w=0.7297 to align # Constraint # added constraint: constraint((T0305)L155.CB, (T0305)R168.CB) [> 4.4846 = 7.4743 < 9.7166] w=0.7297 to align # Constraint # added constraint: constraint((T0305)W111.CB, (T0305)I171.CB) [> 3.8421 = 6.4036 < 8.3246] w=0.7297 to align # Constraint # added constraint: constraint((T0305)W140.CB, (T0305)R167.CB) [> 3.9751 = 6.6252 < 8.6128] w=0.7240 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)V193.CB) [> 4.4829 = 7.4715 < 9.7130] w=0.7221 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)T119.CB) [> 4.0611 = 6.7686 < 8.7991] w=0.7213 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)Q283.CB) [> 4.5996 = 7.6661 < 9.9659] w=0.7174 to align # Constraint # added constraint: constraint((T0305)W111.CB, (T0305)Y139.CB) [> 4.4153 = 7.3589 < 9.5666] w=0.7125 to align # Constraint # added constraint: constraint((T0305)T154.CB, (T0305)R172.CB) [> 4.4496 = 7.4160 < 9.6408] w=0.7125 to align # Constraint # added constraint: constraint((T0305)S220.CB, (T0305)D249.CB) [> 4.0708 = 6.7846 < 8.8200] w=0.7111 to align # Constraint # added constraint: constraint((T0305)W115.CB, (T0305)R191.CB) [> 3.9143 = 6.5239 < 8.4810] w=0.7105 to align # Constraint # added constraint: constraint((T0305)P102.CB, (T0305)D137.CB) [> 3.3067 = 5.5112 < 7.1645] w=0.7047 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)Q200.CB) [> 4.1045 = 6.8408 < 8.8930] w=0.7029 to align # Constraint # added constraint: constraint((T0305)C163.CB, (T0305)F216.CB) [> 3.9595 = 6.5991 < 8.5789] w=0.7029 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)I82.CB) [> 3.5545 = 5.9242 < 7.7015] w=0.7009 to align # Constraint # added constraint: constraint((T0305)T165.CB, (T0305)Y196.CB) [> 4.6490 = 7.7483 < 10.0728] w=0.7008 to align # Constraint # added constraint: constraint((T0305)N83.CB, (T0305)T106.CB) [> 4.5614 = 7.6024 < 9.8831] w=0.7008 to align # Constraint # added constraint: constraint((T0305)V206.CB, (T0305)I285.CB) [> 4.4902 = 7.4836 < 9.7287] w=0.6977 to align # Constraint # added constraint: constraint((T0305)Y55.CB, (T0305)Q100.CB) [> 4.3450 = 7.2417 < 9.4142] w=0.6951 to align # Constraint # added constraint: constraint((T0305)I246.CB, (T0305)L277.CB) [> 4.3660 = 7.2768 < 9.4598] w=0.6932 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)Y86.CB) [> 4.6645 = 7.7741 < 10.1063] w=0.6932 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)Y96.CB) [> 4.5356 = 7.5593 < 9.8271] w=0.6911 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)M113.CB) [> 3.7902 = 6.3170 < 8.2121] w=0.6897 to align # Constraint # added constraint: constraint((T0305)V213.CB, (T0305)Y245.CB) [> 4.4169 = 7.3614 < 9.5699] w=0.6861 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)E116.CB) [> 4.0373 = 6.7288 < 8.7474] w=0.6816 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)Q117.CB) [> 4.1565 = 6.9274 < 9.0056] w=0.6816 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)I82.CB) [> 4.5269 = 7.5448 < 9.8082] w=0.6816 to align # Constraint # added constraint: constraint((T0305)L214.CB, (T0305)I248.CB) [> 4.4283 = 7.3804 < 9.5946] w=0.6816 to align # Constraint # added constraint: constraint((T0305)S145.CB, (T0305)L155.CB) [> 4.2808 = 7.1346 < 9.2750] w=0.6816 to align # Constraint # added constraint: constraint((T0305)L214.CB, (T0305)A294.CB) [> 3.4367 = 5.7279 < 7.4463] w=0.6743 to align # Constraint # added constraint: constraint((T0305)P141.CB, (T0305)V153.CB) [> 3.6075 = 6.0124 < 7.8162] w=0.6740 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)W201.CB) [> 4.3314 = 7.2189 < 9.3846] w=0.6722 to align # Constraint # added constraint: constraint((T0305)K52.CB, (T0305)L103.CB) [> 4.3024 = 7.1706 < 9.3218] w=0.6720 to align # Constraint # added constraint: constraint((T0305)L252.CB, (T0305)A294.CB) [> 3.3094 = 5.5156 < 7.1703] w=0.6708 to align # Constraint # added constraint: constraint((T0305)E42.CB, (T0305)D62.CB) [> 3.4818 = 5.8030 < 7.5438] w=0.6643 to align # Constraint # added constraint: constraint((T0305)V206.CB, (T0305)T244.CB) [> 4.3852 = 7.3086 < 9.5012] w=0.6631 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)C235.CB) [> 4.5303 = 7.5505 < 9.8156] w=0.6591 to align # Constraint # added constraint: constraint((T0305)Y196.CB, (T0305)A223.CB) [> 4.2593 = 7.0989 < 9.2286] w=0.6547 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)Y81.CB) [> 4.2341 = 7.0568 < 9.1738] w=0.6527 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)D80.CB) [> 2.9785 = 4.9641 < 6.4533] w=0.6527 to align # Constraint # added constraint: constraint((T0305)Y164.CB, (T0305)R219.CB) [> 4.3673 = 7.2789 < 9.4625] w=0.6527 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)R191.CB) [> 4.2478 = 7.0797 < 9.2036] w=0.6451 to align # Constraint # added constraint: constraint((T0305)S157.CB, (T0305)R168.CB) [> 2.9172 = 4.8620 < 6.3206] w=0.6451 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)Y276.CB) [> 3.4360 = 5.7267 < 7.4447] w=0.6435 to align # Constraint # added constraint: constraint((T0305)K52.CB, (T0305)S105.CB) [> 4.2231 = 7.0385 < 9.1501] w=0.6373 to align # Constraint # added constraint: constraint((T0305)P141.CB, (T0305)T154.CB) [> 3.9973 = 6.6621 < 8.6608] w=0.6355 to align # Constraint # added constraint: constraint((T0305)P141.CB, (T0305)L155.CB) [> 2.9501 = 4.9168 < 6.3919] w=0.6355 to align # Constraint # added constraint: constraint((T0305)I248.CB, (T0305)L291.CB) [> 3.7819 = 6.3031 < 8.1941] w=0.6355 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)N83.CB) [> 4.6044 = 7.6740 < 9.9762] w=0.6354 to align # Constraint # added constraint: constraint((T0305)I255.CB, (T0305)I295.CB) [> 3.7872 = 6.3120 < 8.2056] w=0.6259 to align # Constraint # added constraint: constraint((T0305)N49.CB, (T0305)Y81.CB) [> 2.8875 = 4.8125 < 6.2562] w=0.6259 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)D80.CB) [> 2.7210 = 4.5350 < 5.8955] w=0.6238 to align # Constraint # added constraint: constraint((T0305)A162.CB, (T0305)Q200.CB) [> 4.4910 = 7.4850 < 9.7304] w=0.6181 to align # Constraint # added constraint: constraint((T0305)N150.CB, (T0305)N173.CB) [> 3.5417 = 5.9029 < 7.6737] w=0.6142 to align # Constraint # added constraint: constraint((T0305)N144.CB, (T0305)L155.CB) [> 3.8154 = 6.3590 < 8.2668] w=0.6142 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)C136.CB) [> 4.4526 = 7.4211 < 9.6474] w=0.6066 to align # Constraint # added constraint: constraint((T0305)L252.CB, (T0305)L291.CB) [> 4.0266 = 6.7111 < 8.7244] w=0.6066 to align # Constraint # added constraint: constraint((T0305)I255.CB, (T0305)L291.CB) [> 4.3814 = 7.3023 < 9.4930] w=0.6066 to align # Constraint # added constraint: constraint((T0305)H43.CB, (T0305)A60.CB) [> 4.3758 = 7.2929 < 9.4808] w=0.6066 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)E116.CB) [> 3.4475 = 5.7458 < 7.4695] w=0.6046 to align # Constraint # added constraint: constraint((T0305)R172.CB, (T0305)R191.CB) [> 4.5779 = 7.6298 < 9.9187] w=0.6046 to align # Constraint # added constraint: constraint((T0305)R172.CB, (T0305)N189.CB) [> 4.1086 = 6.8476 < 8.9019] w=0.5950 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)S79.CB) [> 4.2840 = 7.1401 < 9.2821] w=0.5950 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)Y81.CB) [> 4.4159 = 7.3599 < 9.5679] w=0.5950 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)Y198.CB) [> 4.6479 = 7.7465 < 10.0704] w=0.5946 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)R219.CB) [> 4.2705 = 7.1176 < 9.2528] w=0.5873 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)Q138.CB) [> 3.4564 = 5.7606 < 7.4888] w=0.5777 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)K135.CB) [> 3.0348 = 5.0580 < 6.5754] w=0.5777 to align # Constraint # added constraint: constraint((T0305)P102.CB, (T0305)C136.CB) [> 3.9248 = 6.5413 < 8.5036] w=0.5777 to align # Constraint # added constraint: constraint((T0305)S44.CB, (T0305)Y81.CB) [> 4.2304 = 7.0507 < 9.1660] w=0.5777 to align # Constraint # added constraint: constraint((T0305)R168.CB, (T0305)V193.CB) [> 4.5548 = 7.5913 < 9.8687] w=0.5777 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)I82.CB) [> 4.6602 = 7.7670 < 10.0970] w=0.5777 to align # Constraint # added constraint: constraint((T0305)A41.CB, (T0305)L59.CB) [> 2.7125 = 4.5208 < 5.8771] w=0.5681 to align # Constraint # added constraint: constraint((T0305)G89.CA, (T0305)H269.CB) [> 3.7598 = 6.2663 < 8.1462] w=0.5677 to align # Constraint # added constraint: constraint((T0305)N173.CB, (T0305)N189.CB) [> 3.2071 = 5.3452 < 6.9488] w=0.5661 to align # Constraint # added constraint: constraint((T0305)V213.CB, (T0305)T244.CB) [> 4.3821 = 7.3034 < 9.4945] w=0.5613 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)D249.CB) [> 4.3962 = 7.3270 < 9.5251] w=0.5510 to align # Constraint # added constraint: constraint((T0305)C136.CB, (T0305)H234.CB) [> 4.5019 = 7.5032 < 9.7542] w=0.5488 to align # Constraint # added constraint: constraint((T0305)N45.CB, (T0305)L59.CB) [> 4.0461 = 6.7436 < 8.7666] w=0.5488 to align # Constraint # added constraint: constraint((T0305)H43.CB, (T0305)Y81.CB) [> 3.3979 = 5.6631 < 7.3621] w=0.5488 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)L277.CB) [> 4.3658 = 7.2764 < 9.4593] w=0.5485 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)G229.CA) [> 4.1631 = 6.9384 < 9.0200] w=0.5454 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)Y81.CB) [> 4.5032 = 7.5054 < 9.7570] w=0.5372 to align # Constraint # added constraint: constraint((T0305)V213.CB, (T0305)F286.CB) [> 4.1812 = 6.9687 < 9.0594] w=0.5324 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)V231.CB) [> 4.2900 = 7.1501 < 9.2951] w=0.5261 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)A95.CB) [> 4.0009 = 6.6682 < 8.6687] w=0.5198 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)L232.CB) [> 4.6193 = 7.6989 < 10.0086] w=0.5178 to align # Constraint # added constraint: constraint((T0305)F27.CB, (T0305)Y284.CB) [> 3.1465 = 5.2442 < 6.8175] w=0.5103 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)D80.CB) [> 4.2176 = 7.0294 < 9.1382] w=0.5007 to align # Constraint # added constraint: constraint((T0305)C163.CB, (T0305)T215.CB) [> 3.8187 = 6.3644 < 8.2738] w=0.5007 to align # Constraint # added constraint: constraint((T0305)V263.CB, (T0305)Y284.CB) [> 4.6124 = 7.6873 < 9.9935] w=0.4948 to align # Constraint # added constraint: constraint((T0305)A41.CB, (T0305)Y61.CB) [> 3.4361 = 5.7269 < 7.4449] w=0.4911 to align # Constraint # added constraint: constraint((T0305)A41.CB, (T0305)A60.CB) [> 3.8666 = 6.4443 < 8.3776] w=0.4911 to align # Constraint # added constraint: constraint((T0305)D203.CB, (T0305)R241.CB) [> 4.3661 = 7.2769 < 9.4600] w=0.4898 to align # Constraint # added constraint: constraint((T0305)E130.CB, (T0305)S236.CB) [> 4.1344 = 6.8907 < 8.9580] w=0.4869 to align # Constraint # added constraint: constraint((T0305)A210.CB, (T0305)A294.CB) [> 4.5810 = 7.6351 < 9.9256] w=0.4814 to align # Constraint # added constraint: constraint((T0305)S24.CB, (T0305)E281.CB) [> 3.3776 = 5.6294 < 7.3182] w=0.4814 to align # Constraint # added constraint: constraint((T0305)F216.CB, (T0305)Y245.CB) [> 3.9067 = 6.5112 < 8.4645] w=0.4801 to align # Constraint # added constraint: constraint((T0305)D26.CB, (T0305)L264.CB) [> 3.9263 = 6.5438 < 8.5070] w=0.4718 to align # Constraint # added constraint: constraint((T0305)S250.CB, (T0305)I270.CB) [> 4.3820 = 7.3033 < 9.4943] w=0.4632 to align # Constraint # added constraint: constraint((T0305)Y198.CB, (T0305)R241.CB) [> 4.7132 = 7.8553 < 10.2118] w=0.4622 to align # Constraint # added constraint: constraint((T0305)V30.CB, (T0305)K268.CB) [> 3.7318 = 6.2197 < 8.0856] w=0.4622 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)T242.CB) [> 4.6469 = 7.7448 < 10.0683] w=0.4565 to align # Constraint # added constraint: constraint((T0305)T34.CB, (T0305)R271.CB) [> 3.5681 = 5.9469 < 7.7309] w=0.4525 to align # Constraint # added constraint: constraint((T0305)Y198.CB, (T0305)V213.CB) [> 4.2863 = 7.1438 < 9.2870] w=0.4333 to align # Constraint # added constraint: constraint((T0305)I39.CB, (T0305)Y61.CB) [> 2.5272 = 4.2119 < 5.4755] w=0.4333 to align # Constraint # added constraint: constraint((T0305)V30.CB, (T0305)L264.CB) [> 3.7811 = 6.3019 < 8.1925] w=0.4333 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)C136.CB) [> 4.5880 = 7.6468 < 9.9408] w=0.4333 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)G238.CA) [> 4.6521 = 7.7535 < 10.0795] w=0.4332 to align # Constraint # added constraint: constraint((T0305)V30.CB, (T0305)L267.CB) [> 3.7070 = 6.1784 < 8.0319] w=0.4236 to align # Constraint # added constraint: constraint((T0305)N173.CB, (T0305)E190.CB) [> 4.5729 = 7.6215 < 9.9079] w=0.4236 to align # Constraint # added constraint: constraint((T0305)N118.CB, (T0305)R191.CB) [> 4.1427 = 6.9045 < 8.9759] w=0.4216 to align # Constraint # added constraint: constraint((T0305)D88.CB, (T0305)H269.CB) [> 3.9012 = 6.5019 < 8.4525] w=0.4216 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)A290.CB) [> 4.6875 = 7.8125 < 10.1562] w=0.4189 to align # Constraint # added constraint: constraint((T0305)M204.CB, (T0305)T280.CB) [> 3.5794 = 5.9656 < 7.7553] w=0.4181 to align # Constraint # added constraint: constraint((T0305)P207.CB, (T0305)F216.CB) [> 4.4542 = 7.4236 < 9.6507] w=0.4159 to align # Constraint # added constraint: constraint((T0305)I39.CB, (T0305)D62.CB) [> 4.1866 = 6.9777 < 9.0710] w=0.4140 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)N173.CB) [> 4.3003 = 7.1671 < 9.3172] w=0.4140 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)H288.CB) [> 3.3497 = 5.5829 < 7.2577] w=0.4044 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)D203.CB) [> 4.4661 = 7.4435 < 9.6765] w=0.4006 to align # Constraint # added constraint: constraint((T0305)F23.CB, (T0305)I285.CB) [> 3.1944 = 5.3239 < 6.9211] w=0.3948 to align # Constraint # added constraint: constraint((T0305)F23.CB, (T0305)Y284.CB) [> 3.9283 = 6.5472 < 8.5114] w=0.3948 to align # Constraint # added constraint: constraint((T0305)Y90.CB, (T0305)S250.CB) [> 3.2788 = 5.4646 < 7.1040] w=0.3945 to align # Constraint # added constraint: constraint((T0305)I248.CB, (T0305)A294.CB) [> 4.0956 = 6.8260 < 8.8738] w=0.3894 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)R112.CB) [> 4.5534 = 7.5890 < 9.8656] w=0.3851 to align # Constraint # added constraint: constraint((T0305)I39.CB, (T0305)N275.CB) [> 4.3138 = 7.1897 < 9.3466] w=0.3851 to align # Constraint # added constraint: constraint((T0305)T154.CB, (T0305)I171.CB) [> 4.6521 = 7.7535 < 10.0796] w=0.3851 to align # Constraint # added constraint: constraint((T0305)N173.CB, (T0305)G186.CA) [> 3.2806 = 5.4677 < 7.1080] w=0.3851 to align # Constraint # added constraint: constraint((T0305)K92.CB, (T0305)Q253.CB) [> 3.1697 = 5.2829 < 6.8677] w=0.3850 to align # Constraint # added constraint: constraint((T0305)Q100.CB, (T0305)C235.CB) [> 4.4966 = 7.4943 < 9.7426] w=0.3830 to align # Constraint # added constraint: constraint((T0305)C136.CB, (T0305)C235.CB) [> 4.6076 = 7.6793 < 9.9831] w=0.3755 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)L292.CB) [> 3.5043 = 5.8405 < 7.5926] w=0.3755 to align # Constraint # added constraint: constraint((T0305)M204.CB, (T0305)Q279.CB) [> 3.8905 = 6.4841 < 8.4294] w=0.3751 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)T242.CB) [> 4.7055 = 7.8426 < 10.1953] w=0.3665 to align # Constraint # added constraint: constraint((T0305)F23.CB, (T0305)E281.CB) [> 3.2877 = 5.4796 < 7.1234] w=0.3659 to align # Constraint # added constraint: constraint((T0305)F8.CB, (T0305)H288.CB) [> 4.4134 = 7.3556 < 9.5623] w=0.3659 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)F216.CB) [> 4.4523 = 7.4205 < 9.6466] w=0.3623 to align # Constraint # added constraint: constraint((T0305)K92.CB, (T0305)S250.CB) [> 2.8113 = 4.6855 < 6.0912] w=0.3572 to align # Constraint # added constraint: constraint((T0305)D26.CB, (T0305)Y284.CB) [> 4.3172 = 7.1954 < 9.3540] w=0.3563 to align # Constraint # added constraint: constraint((T0305)I39.CB, (T0305)H63.CB) [> 3.7619 = 6.2699 < 8.1508] w=0.3563 to align # Constraint # added constraint: constraint((T0305)A162.CB, (T0305)P212.CB) [> 3.9851 = 6.6419 < 8.6344] w=0.3562 to align # Constraint # added constraint: constraint((T0305)N91.CB, (T0305)Q254.CB) [> 4.1209 = 6.8682 < 8.9287] w=0.3466 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)A290.CB) [> 4.6119 = 7.6865 < 9.9924] w=0.3466 to align # Constraint # added constraint: constraint((T0305)W201.CB, (T0305)V213.CB) [> 4.6105 = 7.6841 < 9.9893] w=0.3466 to align # Constraint # added constraint: constraint((T0305)K135.CB, (T0305)C235.CB) [> 4.3776 = 7.2959 < 9.4847] w=0.3466 to align # Constraint # added constraint: constraint((T0305)T40.CB, (T0305)H63.CB) [> 4.5322 = 7.5537 < 9.8199] w=0.3466 to align # Constraint # added constraint: constraint((T0305)Y139.CB, (T0305)Y148.CB) [> 4.4272 = 7.3787 < 9.5923] w=0.3466 to align # Constraint # added constraint: constraint((T0305)R167.CB, (T0305)Y196.CB) [> 4.6776 = 7.7959 < 10.1347] w=0.3446 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)A294.CB) [> 4.2420 = 7.0700 < 9.1910] w=0.3399 to align # Constraint # added constraint: constraint((T0305)A35.CB, (T0305)K268.CB) [> 4.1536 = 6.9227 < 8.9995] w=0.3370 to align # Constraint # added constraint: constraint((T0305)V9.CB, (T0305)L292.CB) [> 3.5057 = 5.8429 < 7.5958] w=0.3370 to align # Constraint # added constraint: constraint((T0305)I255.CB, (T0305)A294.CB) [> 4.0739 = 6.7899 < 8.8268] w=0.3370 to align # Constraint # added constraint: constraint((T0305)A35.CB, (T0305)N275.CB) [> 4.0927 = 6.8212 < 8.8675] w=0.3370 to align # Constraint # added constraint: constraint((T0305)M251.CB, (T0305)N262.CB) [> 4.4326 = 7.3876 < 9.6039] w=0.3289 to align # Constraint # added constraint: constraint((T0305)D26.CB, (T0305)E281.CB) [> 3.8080 = 6.3466 < 8.2506] w=0.3274 to align # Constraint # added constraint: constraint((T0305)Y16.CB, (T0305)I285.CB) [> 4.5164 = 7.5273 < 9.7855] w=0.3274 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)D88.CB) [> 4.3920 = 7.3200 < 9.5160] w=0.3254 to align # Constraint # added constraint: constraint((T0305)G120.CA, (T0305)P230.CB) [> 4.0660 = 6.7767 < 8.8097] w=0.3200 to align # Constraint # added constraint: constraint((T0305)N49.CB, (T0305)S79.CB) [> 4.3866 = 7.3110 < 9.5043] w=0.3177 to align # Constraint # added constraint: constraint((T0305)K156.CB, (T0305)V192.CB) [> 4.6490 = 7.7482 < 10.0727] w=0.3177 to align # Constraint # added constraint: constraint((T0305)C33.CB, (T0305)K268.CB) [> 3.6844 = 6.1406 < 7.9828] w=0.3177 to align # Constraint # added constraint: constraint((T0305)A35.CB, (T0305)R271.CB) [> 3.3880 = 5.6467 < 7.3407] w=0.3177 to align # Constraint # added constraint: constraint((T0305)G89.CA, (T0305)I246.CB) [> 4.4497 = 7.4162 < 9.6411] w=0.3136 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)Q200.CB) [> 3.5289 = 5.8814 < 7.6458] w=0.3088 to align # Constraint # added constraint: constraint((T0305)V30.CB, (T0305)Y284.CB) [> 4.3026 = 7.1711 < 9.3224] w=0.3081 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)Q195.CB) [> 4.7030 = 7.8383 < 10.1897] w=0.3061 to align # Constraint # added constraint: constraint((T0305)K94.CB, (T0305)P230.CB) [> 3.5214 = 5.8690 < 7.6296] w=0.3027 to align # Constraint # added constraint: constraint((T0305)F266.CB, (T0305)I287.CB) [> 4.3081 = 7.1802 < 9.3343] w=0.2949 to align # Constraint # added constraint: constraint((T0305)S221.CB, (T0305)L252.CB) [> 4.1389 = 6.8982 < 8.9677] w=0.2895 to align # Constraint # added constraint: constraint((T0305)M37.CB, (T0305)Y61.CB) [> 3.5433 = 5.9055 < 7.6771] w=0.2889 to align # Constraint # added constraint: constraint((T0305)G101.CA, (T0305)M124.CB) [> 4.7327 = 7.8879 < 10.2542] w=0.2888 to align # Constraint # added constraint: constraint((T0305)F27.CB, (T0305)V278.CB) [> 4.6046 = 7.6743 < 9.9766] w=0.2888 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)P202.CB) [> 3.9837 = 6.6396 < 8.6314] w=0.2830 to align # Constraint # added constraint: constraint((T0305)Y90.CB, (T0305)Q254.CB) [> 3.3814 = 5.6357 < 7.3264] w=0.2792 to align # Constraint # added constraint: constraint((T0305)P207.CB, (T0305)T244.CB) [> 4.3305 = 7.2175 < 9.3828] w=0.2784 to align # Constraint # added constraint: constraint((T0305)L252.CB, (T0305)I295.CB) [> 4.2831 = 7.1385 < 9.2801] w=0.2776 to align # Constraint # added constraint: constraint((T0305)Y81.CB, (T0305)D109.CB) [> 4.6262 = 7.7103 < 10.0233] w=0.2695 to align # Constraint # added constraint: constraint((T0305)S220.CB, (T0305)Y245.CB) [> 4.2593 = 7.0989 < 9.2286] w=0.2672 to align # Constraint # added constraint: constraint((T0305)L15.CB, (T0305)H288.CB) [> 4.1413 = 6.9022 < 8.9729] w=0.2600 to align # Constraint # added constraint: constraint((T0305)N150.CB, (T0305)G186.CA) [> 3.5419 = 5.9031 < 7.6740] w=0.2599 to align # Constraint # added constraint: constraint((T0305)G89.CA, (T0305)F266.CB) [> 3.9674 = 6.6123 < 8.5959] w=0.2579 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)R191.CB) [> 4.4493 = 7.4154 < 9.6400] w=0.2579 to align # Constraint # added constraint: constraint((T0305)V231.CB, (T0305)D249.CB) [> 4.4026 = 7.3377 < 9.5390] w=0.2429 to align # Constraint # added constraint: constraint((T0305)T34.CB, (T0305)K268.CB) [> 3.9874 = 6.6457 < 8.6394] w=0.2407 to align # Constraint # added constraint: constraint((T0305)K159.CB, (T0305)R168.CB) [> 4.2802 = 7.1336 < 9.2737] w=0.2407 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)T244.CB) [> 4.6123 = 7.6871 < 9.9932] w=0.2393 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)F169.CB) [> 4.5237 = 7.5395 < 9.8014] w=0.2387 to align # Constraint # added constraint: constraint((T0305)Y198.CB, (T0305)P207.CB) [> 4.6754 = 7.7924 < 10.1301] w=0.2311 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)D289.CB) [> 4.2880 = 7.1466 < 9.2906] w=0.2311 to align # Constraint # added constraint: constraint((T0305)Y55.CB, (T0305)S236.CB) [> 4.6610 = 7.7683 < 10.0988] w=0.2311 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)H197.CB) [> 4.6366 = 7.7277 < 10.0460] w=0.2311 to align # Constraint # added constraint: constraint((T0305)F110.CB, (T0305)Y148.CB) [> 4.6380 = 7.7299 < 10.0489] w=0.2311 to align # Constraint # added constraint: constraint((T0305)C163.CB, (T0305)V213.CB) [> 4.4584 = 7.4307 < 9.6599] w=0.2311 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)L277.CB) [> 4.6255 = 7.7092 < 10.0220] w=0.2311 to align # Constraint # added constraint: constraint((T0305)E29.CB, (T0305)L264.CB) [> 4.4128 = 7.3547 < 9.5611] w=0.2215 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)I285.CB) [> 4.6404 = 7.7340 < 10.0541] w=0.2215 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)T174.CB) [> 3.1957 = 5.3261 < 6.9239] w=0.2214 to align # Constraint # added constraint: constraint((T0305)Y139.CB, (T0305)V153.CB) [> 4.5386 = 7.5643 < 9.8336] w=0.2137 to align # Constraint # added constraint: constraint((T0305)I151.CB, (T0305)T174.CB) [> 3.9747 = 6.6245 < 8.6118] w=0.2118 to align # Constraint # added constraint: constraint((T0305)Y90.CB, (T0305)V261.CB) [> 3.3865 = 5.6441 < 7.3374] w=0.2096 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)P230.CB) [> 4.6910 = 7.8183 < 10.1638] w=0.2022 to align # Constraint # added constraint: constraint((T0305)F8.CB, (T0305)V261.CB) [> 3.8563 = 6.4272 < 8.3554] w=0.2022 to align # Constraint # added constraint: constraint((T0305)F8.CB, (T0305)L291.CB) [> 3.9351 = 6.5585 < 8.5260] w=0.2022 to align # Constraint # added constraint: constraint((T0305)F8.CB, (T0305)L292.CB) [> 3.4422 = 5.7369 < 7.4580] w=0.2022 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)R274.CB) [> 4.4580 = 7.4300 < 9.6590] w=0.1910 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)Y198.CB) [> 4.4751 = 7.4585 < 9.6961] w=0.1905 to align # Constraint # added constraint: constraint((T0305)K94.CB, (T0305)V231.CB) [> 4.4704 = 7.4506 < 9.6858] w=0.1835 to align # Constraint # added constraint: constraint((T0305)M5.CB, (T0305)I295.CB) [> 3.3821 = 5.6368 < 7.3278] w=0.1829 to align # Constraint # added constraint: constraint((T0305)F8.CB, (T0305)V263.CB) [> 3.8866 = 6.4776 < 8.4209] w=0.1829 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)Q279.CB) [> 4.7337 = 7.8895 < 10.2563] w=0.1733 to align # Constraint # added constraint: constraint((T0305)I39.CB, (T0305)S64.CB) [> 4.6476 = 7.7460 < 10.0698] w=0.1733 to align # Constraint # added constraint: constraint((T0305)E147.CB, (T0305)T174.CB) [> 4.2501 = 7.0835 < 9.2086] w=0.1733 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)S170.CB) [> 4.6895 = 7.8159 < 10.1607] w=0.1733 to align # Constraint # added constraint: constraint((T0305)W201.CB, (T0305)C235.CB) [> 4.7227 = 7.8712 < 10.2325] w=0.1679 to align # Constraint # added constraint: constraint((T0305)R218.CB, (T0305)L252.CB) [> 4.2812 = 7.1353 < 9.2759] w=0.1647 to align # Constraint # added constraint: constraint((T0305)M5.CB, (T0305)H288.CB) [> 3.8316 = 6.3860 < 8.3019] w=0.1637 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)G243.CA) [> 4.6503 = 7.7506 < 10.0757] w=0.1617 to align # Constraint # added constraint: constraint((T0305)L155.CB, (T0305)S170.CB) [> 4.4897 = 7.4828 < 9.7276] w=0.1617 to align # Constraint # added constraint: constraint((T0305)M37.CB, (T0305)K268.CB) [> 4.6260 = 7.7101 < 10.0231] w=0.1541 to align # Constraint # added constraint: constraint((T0305)I82.CB, (T0305)P102.CB) [> 4.3919 = 7.3198 < 9.5157] w=0.1539 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)R274.CB) [> 4.6273 = 7.7122 < 10.0258] w=0.1525 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)V233.CB) [> 4.6966 = 7.8277 < 10.1760] w=0.1523 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)Q200.CB) [> 3.6774 = 6.1289 < 7.9676] w=0.1505 to align # Constraint # added constraint: constraint((T0305)D36.CB, (T0305)K268.CB) [> 4.0572 = 6.7620 < 8.7906] w=0.1444 to align # Constraint # added constraint: constraint((T0305)M5.CB, (T0305)V261.CB) [> 3.9925 = 6.6542 < 8.6505] w=0.1444 to align # Constraint # added constraint: constraint((T0305)V87.CB, (T0305)V233.CB) [> 4.7300 = 7.8834 < 10.2484] w=0.1444 to align # Constraint # added constraint: constraint((T0305)V261.CB, (T0305)I295.CB) [> 4.5756 = 7.6260 < 9.9138] w=0.1444 to align # Constraint # added constraint: constraint((T0305)Y86.CB, (T0305)E227.CB) [> 4.0479 = 6.7465 < 8.7704] w=0.1444 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)A84.CB) [> 3.8078 = 6.3463 < 8.2501] w=0.1444 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)D109.CB) [> 3.4488 = 5.7480 < 7.4724] w=0.1444 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)T199.CB) [> 4.3464 = 7.2441 < 9.4173] w=0.1422 to align # Constraint # added constraint: constraint((T0305)M37.CB, (T0305)H63.CB) [> 3.6034 = 6.0057 < 7.8074] w=0.1348 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)F169.CB) [> 4.5845 = 7.6408 < 9.9330] w=0.1348 to align # Constraint # added constraint: constraint((T0305)G89.CA, (T0305)G265.CA) [> 4.7059 = 7.8431 < 10.1960] w=0.1328 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)H197.CB) [> 3.6160 = 6.0267 < 7.8347] w=0.1263 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)F23.CB) [> 3.7766 = 6.2944 < 8.1827] w=0.1252 to align # Constraint # added constraint: constraint((T0305)V9.CB, (T0305)I295.CB) [> 3.9964 = 6.6606 < 8.6588] w=0.1252 to align # Constraint # added constraint: constraint((T0305)P70.CB, (T0305)S79.CB) [> 3.2017 = 5.3361 < 6.9370] w=0.1252 to align # Constraint # added constraint: constraint((T0305)P70.CB, (T0305)D80.CB) [> 2.8626 = 4.7710 < 6.2023] w=0.1252 to align # Constraint # added constraint: constraint((T0305)F110.CB, (T0305)L232.CB) [> 4.6343 = 7.7238 < 10.0410] w=0.1186 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)H234.CB) [> 4.7020 = 7.8366 < 10.1876] w=0.1155 to align # Constraint # added constraint: constraint((T0305)D88.CB, (T0305)S250.CB) [> 4.6449 = 7.7415 < 10.0640] w=0.1155 to align # Constraint # added constraint: constraint((T0305)F107.CB, (T0305)G149.CA) [> 4.6761 = 7.7934 < 10.1314] w=0.1155 to align # Constraint # added constraint: constraint((T0305)I114.CB, (T0305)I151.CB) [> 4.6590 = 7.7650 < 10.0945] w=0.1155 to align # Constraint # added constraint: constraint((T0305)V247.CB, (T0305)A290.CB) [> 4.6129 = 7.6882 < 9.9946] w=0.1155 to align # Constraint # added constraint: constraint((T0305)V9.CB, (T0305)L296.CB) [> 4.3393 = 7.2322 < 9.4019] w=0.1059 to align # Constraint # added constraint: constraint((T0305)K94.CB, (T0305)G229.CA) [> 4.2878 = 7.1464 < 9.2903] w=0.1059 to align # Constraint # added constraint: constraint((T0305)I97.CB, (T0305)I114.CB) [> 4.4583 = 7.4305 < 9.6596] w=0.1056 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)S79.CB) [> 3.1704 = 5.2840 < 6.8692] w=0.1039 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)G229.CA) [> 4.2545 = 7.0908 < 9.2180] w=0.1022 to align # Constraint # added constraint: constraint((T0305)P207.CB, (T0305)Y245.CB) [> 4.2314 = 7.0523 < 9.1680] w=0.0971 to align # Constraint # added constraint: constraint((T0305)G13.CA, (T0305)F23.CB) [> 3.8770 = 6.4616 < 8.4001] w=0.0963 to align # Constraint # added constraint: constraint((T0305)K94.CB, (T0305)I246.CB) [> 4.5884 = 7.6473 < 9.9414] w=0.0963 to align # Constraint # added constraint: constraint((T0305)A162.CB, (T0305)L211.CB) [> 4.5019 = 7.5033 < 9.7542] w=0.0963 to align # Constraint # added constraint: constraint((T0305)F27.CB, (T0305)L264.CB) [> 4.2867 = 7.1444 < 9.2878] w=0.0963 to align # Constraint # added constraint: constraint((T0305)L103.CB, (T0305)K135.CB) [> 3.9980 = 6.6633 < 8.6623] w=0.0963 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)P230.CB) [> 4.4462 = 7.4104 < 9.6335] w=0.0923 to align # Constraint # added constraint: constraint((T0305)V129.CB, (T0305)S236.CB) [> 3.8052 = 6.3419 < 8.2445] w=0.0911 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)H78.CB) [> 3.9855 = 6.6426 < 8.6354] w=0.0885 to align # Constraint # added constraint: constraint((T0305)N57.CB, (T0305)Y276.CB) [> 4.4011 = 7.3351 < 9.5356] w=0.0867 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)N83.CB) [> 4.7479 = 7.9132 < 10.2871] w=0.0867 to align # Constraint # added constraint: constraint((T0305)I125.CB, (T0305)F216.CB) [> 4.6990 = 7.8317 < 10.1812] w=0.0867 to align # Constraint # added constraint: constraint((T0305)Y198.CB, (T0305)Y245.CB) [> 4.6744 = 7.7908 < 10.1280] w=0.0867 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)V193.CB) [> 4.6424 = 7.7374 < 10.0586] w=0.0867 to align # Constraint # added constraint: constraint((T0305)A60.CB, (T0305)Y81.CB) [> 4.7127 = 7.8545 < 10.2108] w=0.0867 to align # Constraint # added constraint: constraint((T0305)Q31.CB, (T0305)K268.CB) [> 4.3124 = 7.1873 < 9.3435] w=0.0867 to align # Constraint # added constraint: constraint((T0305)K104.CB, (T0305)Y139.CB) [> 3.9446 = 6.5744 < 8.5467] w=0.0866 to align # Constraint # added constraint: constraint((T0305)I12.CB, (T0305)K268.CB) [> 4.5515 = 7.5859 < 9.8617] w=0.0866 to align # Constraint # added constraint: constraint((T0305)L15.CB, (T0305)K268.CB) [> 3.7145 = 6.1908 < 8.0481] w=0.0866 to align # Constraint # added constraint: constraint((T0305)Y16.CB, (T0305)Y276.CB) [> 2.3941 = 3.9901 < 5.1871] w=0.0866 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)A98.CB) [> 3.6478 = 6.0797 < 7.9036] w=0.0860 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)I97.CB) [> 3.2829 = 5.4715 < 7.1130] w=0.0860 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)R224.CB) [> 4.3252 = 7.2086 < 9.3712] w=0.0850 to align # Constraint # added constraint: constraint((T0305)L103.CB, (T0305)V129.CB) [> 4.0684 = 6.7807 < 8.8149] w=0.0831 to align # Constraint # added constraint: constraint((T0305)S4.CB, (T0305)T260.CB) [> 3.3521 = 5.5868 < 7.2628] w=0.0770 to align # Constraint # added constraint: constraint((T0305)M5.CB, (T0305)I255.CB) [> 3.5091 = 5.8485 < 7.6031] w=0.0770 to align # Constraint # added constraint: constraint((T0305)A41.CB, (T0305)N57.CB) [> 4.1158 = 6.8597 < 8.9176] w=0.0770 to align # Constraint # added constraint: constraint((T0305)L15.CB, (T0305)C33.CB) [> 3.7812 = 6.3020 < 8.1925] w=0.0770 to align # Constraint # added constraint: constraint((T0305)E208.CB, (T0305)T244.CB) [> 3.8762 = 6.4603 < 8.3984] w=0.0769 to align # Constraint # added constraint: constraint((T0305)E208.CB, (T0305)Y245.CB) [> 4.0127 = 6.6879 < 8.6943] w=0.0769 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)I246.CB) [> 3.8106 = 6.3510 < 8.2564] w=0.0750 to align # Constraint # added constraint: constraint((T0305)L155.CB, (T0305)Q195.CB) [> 3.9974 = 6.6624 < 8.6611] w=0.0750 to align # Constraint # added constraint: constraint((T0305)I246.CB, (T0305)F266.CB) [> 4.7394 = 7.8991 < 10.2688] w=0.0750 to align # Constraint # added constraint: constraint((T0305)T260.CB, (T0305)I295.CB) [> 4.1233 = 6.8722 < 8.9339] w=0.0693 to align # Constraint # added constraint: constraint((T0305)L103.CB, (T0305)E130.CB) [> 3.9481 = 6.5802 < 8.5542] w=0.0691 to align # Constraint # added constraint: constraint((T0305)F107.CB, (T0305)E130.CB) [> 3.6100 = 6.0166 < 7.8216] w=0.0691 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)I114.CB) [> 4.6124 = 7.6874 < 9.9936] w=0.0689 to align # Constraint # added constraint: constraint((T0305)I121.CB, (T0305)Y198.CB) [> 4.7356 = 7.8927 < 10.2606] w=0.0689 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)Y198.CB) [> 2.8763 = 4.7939 < 6.2320] w=0.0689 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)P202.CB) [> 4.4790 = 7.4649 < 9.7044] w=0.0689 to align # Constraint # added constraint: constraint((T0305)M5.CB, (T0305)V263.CB) [> 3.4732 = 5.7888 < 7.5254] w=0.0674 to align # Constraint # added constraint: constraint((T0305)L71.CB, (T0305)D80.CB) [> 3.9885 = 6.6475 < 8.6418] w=0.0674 to align # Constraint # added constraint: constraint((T0305)P72.CB, (T0305)I82.CB) [> 4.5138 = 7.5230 < 9.7799] w=0.0674 to align # Constraint # added constraint: constraint((T0305)H11.CB, (T0305)K268.CB) [> 4.0832 = 6.8053 < 8.8469] w=0.0674 to align # Constraint # added constraint: constraint((T0305)A162.CB, (T0305)Y209.CB) [> 3.8838 = 6.4730 < 8.4149] w=0.0674 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)G240.CA) [> 4.6382 = 7.7303 < 10.0494] w=0.0660 to align # Constraint # added constraint: constraint((T0305)Y196.CB, (T0305)L232.CB) [> 4.7017 = 7.8362 < 10.1870] w=0.0660 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)Y96.CB) [> 3.1100 = 5.1834 < 6.7385] w=0.0640 to align # Constraint # added constraint: constraint((T0305)H63.CB, (T0305)T99.CB) [> 3.6005 = 6.0008 < 7.8011] w=0.0640 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)A93.CB) [> 3.4675 = 5.7791 < 7.5129] w=0.0603 to align # Constraint # added constraint: constraint((T0305)R54.CB, (T0305)P102.CB) [> 4.3397 = 7.2328 < 9.4026] w=0.0596 to align # Constraint # added constraint: constraint((T0305)A41.CB, (T0305)I56.CB) [> 3.7067 = 6.1779 < 8.0312] w=0.0578 to align # Constraint # added constraint: constraint((T0305)F2.CB, (T0305)N262.CB) [> 2.6378 = 4.3964 < 5.7153] w=0.0578 to align # Constraint # added constraint: constraint((T0305)A84.CB, (T0305)F110.CB) [> 4.7871 = 7.9785 < 10.3720] w=0.0578 to align # Constraint # added constraint: constraint((T0305)Y96.CB, (T0305)T242.CB) [> 4.7078 = 7.8464 < 10.2003] w=0.0578 to align # Constraint # added constraint: constraint((T0305)F27.CB, (T0305)K268.CB) [> 4.4459 = 7.4098 < 9.6328] w=0.0578 to align # Constraint # added constraint: constraint((T0305)P212.CB, (T0305)Y245.CB) [> 4.6846 = 7.8077 < 10.1501] w=0.0558 to align # Constraint # added constraint: constraint((T0305)L59.CB, (T0305)Y276.CB) [> 4.0706 = 6.7844 < 8.8197] w=0.0542 to align # Constraint # added constraint: constraint((T0305)S250.CB, (T0305)T260.CB) [> 3.9397 = 6.5661 < 8.5360] w=0.0530 to align # Constraint # added constraint: constraint((T0305)T242.CB, (T0305)R274.CB) [> 4.7410 = 7.9017 < 10.2722] w=0.0527 to align # Constraint # added constraint: constraint((T0305)P102.CB, (T0305)W111.CB) [> 4.3729 = 7.2882 < 9.4747] w=0.0527 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)Y276.CB) [> 4.0508 = 6.7514 < 8.7768] w=0.0524 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)T242.CB) [> 4.6344 = 7.7239 < 10.0411] w=0.0490 to align # Constraint # added constraint: constraint((T0305)F2.CB, (T0305)T260.CB) [> 2.9600 = 4.9334 < 6.4134] w=0.0481 to align # Constraint # added constraint: constraint((T0305)P70.CB, (T0305)E116.CB) [> 4.3205 = 7.2008 < 9.3610] w=0.0481 to align # Constraint # added constraint: constraint((T0305)L71.CB, (T0305)N150.CB) [> 4.5578 = 7.5964 < 9.8753] w=0.0481 to align # Constraint # added constraint: constraint((T0305)Q138.CB, (T0305)S236.CB) [> 3.9448 = 6.5747 < 8.5471] w=0.0481 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)T106.CB) [> 4.2407 = 7.0678 < 9.1882] w=0.0481 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)Y81.CB) [> 4.2104 = 7.0173 < 9.1225] w=0.0461 to align # Constraint # added constraint: constraint((T0305)N127.CB, (T0305)C235.CB) [> 4.7623 = 7.9371 < 10.3183] w=0.0461 to align # Constraint # added constraint: constraint((T0305)H63.CB, (T0305)Q100.CB) [> 4.1640 = 6.9400 < 9.0220] w=0.0450 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)F110.CB) [> 4.4899 = 7.4832 < 9.7281] w=0.0450 to align # Constraint # added constraint: constraint((T0305)V66.CB, (T0305)R274.CB) [> 2.6298 = 4.3830 < 5.6979] w=0.0450 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)I246.CB) [> 3.3871 = 5.6452 < 7.3388] w=0.0450 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)R274.CB) [> 3.9384 = 6.5640 < 8.5331] w=0.0450 to align # Constraint # added constraint: constraint((T0305)R69.CB, (T0305)Y96.CB) [> 2.6065 = 4.3442 < 5.6475] w=0.0450 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)A95.CB) [> 2.9678 = 4.9464 < 6.4303] w=0.0410 to align # Constraint # added constraint: constraint((T0305)H11.CB, (T0305)G22.CA) [> 4.7598 = 7.9331 < 10.3130] w=0.0385 to align # Constraint # added constraint: constraint((T0305)W115.CB, (T0305)E190.CB) [> 4.2118 = 7.0196 < 9.1255] w=0.0385 to align # Constraint # added constraint: constraint((T0305)T158.CB, (T0305)S170.CB) [> 3.5831 = 5.9718 < 7.7634] w=0.0385 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)T174.CB) [> 4.3768 = 7.2947 < 9.4831] w=0.0385 to align # Constraint # added constraint: constraint((T0305)V153.CB, (T0305)N173.CB) [> 3.1858 = 5.3098 < 6.9027] w=0.0385 to align # Constraint # added constraint: constraint((T0305)I152.CB, (T0305)K175.CB) [> 4.4493 = 7.4155 < 9.6401] w=0.0385 to align # Constraint # added constraint: constraint((T0305)N173.CB, (T0305)V192.CB) [> 4.5008 = 7.5013 < 9.7517] w=0.0385 to align # Constraint # added constraint: constraint((T0305)R172.CB, (T0305)V192.CB) [> 3.1270 = 5.2117 < 6.7752] w=0.0385 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)Q195.CB) [> 4.1985 = 6.9975 < 9.0967] w=0.0385 to align # Constraint # added constraint: constraint((T0305)F169.CB, (T0305)H197.CB) [> 3.9901 = 6.6502 < 8.6452] w=0.0385 to align # Constraint # added constraint: constraint((T0305)R167.CB, (T0305)T199.CB) [> 3.4826 = 5.8043 < 7.5456] w=0.0385 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)Y198.CB) [> 3.2133 = 5.3556 < 6.9622] w=0.0385 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)S236.CB) [> 4.5999 = 7.6665 < 9.9664] w=0.0320 to align # Constraint # added constraint: constraint((T0305)T199.CB, (T0305)Y245.CB) [> 4.5563 = 7.5938 < 9.8720] w=0.0316 to align # Constraint # added constraint: constraint((T0305)N49.CB, (T0305)A60.CB) [> 3.7700 = 6.2833 < 8.1683] w=0.0308 to align # Constraint # added constraint: constraint((T0305)C33.CB, (T0305)Y61.CB) [> 4.1708 = 6.9513 < 9.0367] w=0.0289 to align # Constraint # added constraint: constraint((T0305)A95.CB, (T0305)I270.CB) [> 4.7994 = 7.9990 < 10.3987] w=0.0289 to align # Constraint # added constraint: constraint((T0305)V231.CB, (T0305)I246.CB) [> 4.7484 = 7.9139 < 10.2881] w=0.0289 to align # Constraint # added constraint: constraint((T0305)L15.CB, (T0305)L292.CB) [> 3.4746 = 5.7910 < 7.5283] w=0.0289 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)N189.CB) [> 3.6336 = 6.0559 < 7.8727] w=0.0289 to align # Constraint # added constraint: constraint((T0305)Y55.CB, (T0305)V239.CB) [> 4.7945 = 7.9908 < 10.3880] w=0.0289 to align # Constraint # added constraint: constraint((T0305)K67.CB, (T0305)H78.CB) [> 4.0946 = 6.8244 < 8.8717] w=0.0289 to align # Constraint # added constraint: constraint((T0305)A98.CB, (T0305)C235.CB) [> 4.7463 = 7.9105 < 10.2836] w=0.0289 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)Y198.CB) [> 4.3068 = 7.1780 < 9.3314] w=0.0289 to align # Constraint # added constraint: constraint((T0305)L68.CB, (T0305)G243.CA) [> 4.6559 = 7.7599 < 10.0878] w=0.0289 to align # Constraint # added constraint: constraint((T0305)V166.CB, (T0305)T199.CB) [> 4.7375 = 7.8958 < 10.2645] w=0.0289 to align # Constraint # added constraint: constraint((T0305)D26.CB, (T0305)K268.CB) [> 4.7481 = 7.9135 < 10.2876] w=0.0289 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)H197.CB) [> 4.7943 = 7.9905 < 10.3877] w=0.0289 to align # Constraint # added constraint: constraint((T0305)S170.CB, (T0305)I194.CB) [> 3.4744 = 5.7907 < 7.5279] w=0.0289 to align # Constraint # added constraint: constraint((T0305)I171.CB, (T0305)I194.CB) [> 4.6809 = 7.8014 < 10.1419] w=0.0289 to align # Constraint # added constraint: constraint((T0305)D80.CB, (T0305)T106.CB) [> 4.1634 = 6.9390 < 9.0206] w=0.0289 to align # Constraint # added constraint: constraint((T0305)G240.CA, (T0305)R274.CB) [> 4.6031 = 7.6718 < 9.9733] w=0.0285 to align # Constraint # added constraint: constraint((T0305)Y61.CB, (T0305)Q100.CB) [> 4.4249 = 7.3749 < 9.5873] w=0.0269 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)V192.CB) [> 4.3296 = 7.2161 < 9.3809] w=0.0241 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)V193.CB) [> 4.6324 = 7.7206 < 10.0368] w=0.0241 to align # Constraint # added constraint: constraint((T0305)M124.CB, (T0305)V193.CB) [> 3.3143 = 5.5239 < 7.1810] w=0.0241 to align # Constraint # added constraint: constraint((T0305)T242.CB, (T0305)N275.CB) [> 4.5335 = 7.5558 < 9.8225] w=0.0235 to align # Constraint # added constraint: constraint((T0305)G243.CA, (T0305)N275.CB) [> 2.8992 = 4.8319 < 6.2815] w=0.0235 to align # Constraint # added constraint: constraint((T0305)T244.CB, (T0305)L291.CB) [> 4.2914 = 7.1523 < 9.2980] w=0.0235 to align # Constraint # added constraint: constraint((T0305)K268.CB, (T0305)L277.CB) [> 4.7015 = 7.8358 < 10.1866] w=0.0235 to align # Constraint # added constraint: constraint((T0305)V176.CB, (T0305)Y198.CB) [> 2.6448 = 4.4079 < 5.7303] w=0.0220 to align # Constraint # added constraint: constraint((T0305)V217.CB, (T0305)K256.CB) [> 2.9165 = 4.8609 < 6.3192] w=0.0211 to align # Constraint # added constraint: constraint((T0305)T126.CB, (T0305)A237.CB) [> 4.7816 = 7.9693 < 10.3602] w=0.0199 to align # Constraint # added constraint: constraint((T0305)Y1.CB, (T0305)N262.CB) [> 4.5124 = 7.5206 < 9.7768] w=0.0193 to align # Constraint # added constraint: constraint((T0305)A93.CB, (T0305)Q254.CB) [> 4.4100 = 7.3499 < 9.5549] w=0.0193 to align # Constraint # added constraint: constraint((T0305)L71.CB, (T0305)G149.CA) [> 4.4524 = 7.4206 < 9.6468] w=0.0193 to align # Constraint # added constraint: constraint((T0305)T154.CB, (T0305)T174.CB) [> 4.5634 = 7.6057 < 9.8874] w=0.0192 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)M113.CB) [> 4.4146 = 7.3576 < 9.5649] w=0.0161 to align # Constraint # added constraint: constraint((T0305)S64.CB, (T0305)A237.CB) [> 4.5148 = 7.5246 < 9.7820] w=0.0161 to align # Constraint # added constraint: constraint((T0305)I122.CB, (T0305)R133.CB) [> 4.2743 = 7.1238 < 9.2610] w=0.0161 to align # Constraint # added constraint: constraint((T0305)V123.CB, (T0305)I194.CB) [> 3.8799 = 6.4665 < 8.4064] w=0.0161 to align # Constraint # added constraint: constraint((T0305)R133.CB, (T0305)N189.CB) [> 4.6907 = 7.8179 < 10.1633] w=0.0161 to align # Constraint # added constraint: constraint((T0305)R65.CB, (T0305)Y148.CB) [> 4.7294 = 7.8823 < 10.2469] w=0.0157 to align # Constraint # added constraint: constraint((T0305)H63.CB, (T0305)G149.CA) [> 3.7970 = 6.3283 < 8.2268] w=0.0157 to align # Constraint # added constraint: constraint((T0305)L128.CB, (T0305)V176.CB) [> 4.7035 = 7.8391 < 10.1908] w=0.0124 to align # Constraint # added constraint: constraint((T0305)M204.CB, (T0305)C235.CB) [> 4.5798 = 7.6330 < 9.9228] w=0.0109 to align # Constraint # added constraint: constraint((T0305)C33.CB, (T0305)N57.CB) [> 3.7670 = 6.2784 < 8.1619] w=0.0096 to align # Constraint # added constraint: constraint((T0305)N57.CB, (T0305)A237.CB) [> 4.7628 = 7.9379 < 10.3193] w=0.0096 to align # Constraint # added constraint: constraint((T0305)Y1.CB, (T0305)H288.CB) [> 3.7133 = 6.1889 < 8.0456] w=0.0096 to align # Constraint # added constraint: constraint((T0305)Y1.CB, (T0305)L264.CB) [> 4.7731 = 7.9552 < 10.3418] w=0.0096 to align # Constraint # added constraint: constraint((T0305)P70.CB, (T0305)Y96.CB) [> 4.2991 = 7.1651 < 9.3147] w=0.0080 to align # Constraint # added constraint: constraint((T0305)P70.CB, (T0305)I97.CB) [> 3.0733 = 5.1221 < 6.6588] w=0.0080 to align # Constraint # added constraint: constraint((T0305)L71.CB, (T0305)I246.CB) [> 3.6533 = 6.0889 < 7.9155] w=0.0080 to align # Constraint # added constraint: constraint((T0305)I56.CB, (T0305)V66.CB) [> 4.0597 = 6.7661 < 8.7959] w=0.0080 to align # Constraint # added constraint: constraint((T0305)I56.CB, (T0305)R274.CB) [> 4.7015 = 7.8358 < 10.1865] w=0.0080 to align # Constraint # added constraint: constraint((T0305)I58.CB, (T0305)R69.CB) [> 2.6216 = 4.3694 < 5.6802] w=0.0080 to align # Constraint # added constraint: constraint((T0305)D80.CB, (T0305)A93.CB) [> 3.0508 = 5.0847 < 6.6101] w=0.0078 to align # Constraint # added constraint: constraint((T0305)D62.CB, (T0305)N150.CB) [> 4.6780 = 7.7967 < 10.1357] w=0.0078 to align # Constraint # added constraint: constraint((T0305)S44.CB, (T0305)Y55.CB) [> 2.4694 = 4.1157 < 5.3505] w=0.0057 to align # Constraint # added constraint: constraint((T0305)N53.CB, (T0305)A237.CB) [> 3.9775 = 6.6291 < 8.6179] w=0.0057 to align # Constraint # added constraint: constraint((T0305)T99.CB, (T0305)I122.CB) [> 4.7300 = 7.8834 < 10.2484] w=0.0029 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0305/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0305/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 286 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 290 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 266 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 269 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 188 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 284 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 283 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 290 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 276 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 678, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 680, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 682, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 684, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 954, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 956, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 958, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 960, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 978, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 980, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 982, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 984, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1002, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1004, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1006, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1008, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1074, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1076, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1078, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1080, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1109, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1110, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1112, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1113, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1115, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 1116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 280 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 289 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 224 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 286 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 295 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 290 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 296 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 290 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 284 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 271 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 174 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 174 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 277 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 914, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 916, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 918, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 920, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 634, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 636, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 638, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 640, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 926, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 928, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 930, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 932, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 283 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 258 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)T174.CA and (T0305)K185.CA only 0.000 apart, marking (T0305)K185.CA as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 1049, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 987, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 279 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 254, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 256, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 454, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 516, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 518, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 520, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 522, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 524, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 662, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 664, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 746, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 748, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 750, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 752, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 754, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 756, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 758, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 760, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 772, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 782, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 784, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 946, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 948, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 950, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 952, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 970, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 972, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 974, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 976, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 994, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 996, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 998, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1000, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1066, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1068, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1070, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1072, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1098, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1099, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1101, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1105, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1107, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 1108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 626, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 628, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 Skipped atom 585, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz Skipped atom 770, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL3.pdb.gz # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 275 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 174 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 294 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)S157.O and (T0305)T158.N only 0.000 apart, marking (T0305)T158.N as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)V129.O and (T0305)E130.N only 0.000 apart, marking (T0305)E130.N as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0305)Q3.O and (T0305)S4.N only 0.000 apart, marking (T0305)S4.N as missing WARNING: atoms too close: (T0305)L68.O and (T0305)R69.N only 0.000 apart, marking (T0305)R69.N as missing # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 274 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0305 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 278 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5152 model score -0.5204 model score -0.5316 model score -0.6373 model score -0.5339 model score -0.5901 model score -0.5879 model score -0.5158 model score -0.5707 model score -0.5696 model score -0.5256 model score -0.6695 model score -0.5872 model score -0.6630 model score -0.5677 model score -0.7262 model score 1.6250 model score 1.9722 model score 1.9983 model score 1.7134 model score 1.7505 model score 2.0541 model score 1.9237 model score 1.8956 model score 1.8599 model score -0.7442 model score -0.5767 model score -0.6114 model score -0.7342 model score -0.6532 model score -0.7195 model score -0.7137 model score -0.6745 model score -0.7080 model score -0.6955 model score -0.6953 model score -0.6923 model score -0.7199 model score -0.7098 model score -0.7046 model score -0.6689 model score -0.7140 model score 1.2680 model score 1.2669 model score 1.2670 model score 1.2644 model score 1.2670 model score -0.7192 model score -0.6932 model score -0.6590 model score -0.7013 model score -0.7136 model score -0.7495 model score -0.7174 model score -0.6745 model score -0.7191 model score -0.7080 model score -0.7352 model score 1.3130 model score 1.8618 model score 1.3734 model score 2.1428 model score 1.2871 model score 1.2648 model score 1.2651 model score 1.2647 model score 1.2645 model score 1.2647 model score 1.2871 model score 1.2648 model score 1.2645 model score 1.2710 model score 2.4617 model score 2.3742 model score 2.5177 model score 2.3573 model score 2.3701 model score -0.7178 model score -0.6709 model score 0.0316 model score -0.0821 model score 2.0035 model score 1.2650 model score 1.2690 model score 1.2695 model score 1.2661 model score 1.2830 model score -0.7122 model score -0.7174 model score -0.7172 model score -0.6718 model score -0.7191 model score -0.6552 model score -0.6640 model score -0.7155 model score -0.6786 model score -0.7040 model score -0.7257 model score -0.7478 model score -0.7549 model score -0.6377 model score -0.6743 model score -0.6723 model score -0.6108 model score -0.6634 model score -0.6886 model score -0.6342 model score -0.6344 model score -0.6587 model score -0.6292 model score -0.7038 model score -0.7314 model score -0.6726 model score -0.6816 model score -0.6626 model score -0.3606 model score -0.3868 model score -0.4390 model score -0.4901 model score -0.4349 model score -0.6886 model score -0.6841 model score -0.6841 model score -0.6870 model score -0.6916 model score -0.6889 model score -0.7272 model score -0.7075 model score -0.6841 model score 1.0466 model score -0.5886 model score -0.7335 model score -0.7335 model score -0.7122 model score -0.7192 model score -0.7110 model score -0.7049 model score -0.7164 model score -0.6949 model score -0.6949 model score -0.6969 model score -0.7184 model score -0.6827 model score -0.6827 model score -0.6813 model score -0.7188 model score -0.7192 model score -0.6824 model score -0.7267 model score -0.7102 model score -0.7045 model score -0.7210 model score -0.6652 model score -0.6477 model score -0.5890 model score -0.6750 model score -0.6393 model score -0.7251 model score -0.6996 model score -0.6609 model score -0.7124 model score -0.7124 model score -0.7121 model score -0.7289 model score -0.7224 model score -0.7244 model score -0.7266 model score -0.7291 model score 2.4701 model score -0.7348 model score -0.7014 model score -0.6668 model score 1.2647 model score 1.2648 model score 1.2651 model score 1.2649 model score 1.2652 model score 1.2649 model score 1.2646 model score 1.2648 model score 1.2652 model score 1.2643 model score -0.6142 model score -0.3737 model score -0.6457 model score -0.7009 model score -0.6879 model score -0.7085 model score -0.6634 model score -0.6231 model score -0.7384 model score -0.6609 model score -0.6892 model score -0.6725 model score -0.6284 model score -0.7384 model score -0.6697 model score -0.7085 model score -0.6730 model score -0.6272 model score -0.6636 model score -0.7253 model score 1.2650 model score 1.2651 model score 1.2648 model score 1.2656 model score 1.2646 model score -0.7138 model score 1.2650 model score 1.2651 model score 1.2648 model score 1.2656 model score 1.2646 model score -0.7282 model score -0.7275 model score -0.7125 model score -0.7392 model score -0.6895 model score -0.6836 model score -0.6367 model score 1.2651 model score 1.2648 model score 1.2646 model score 1.2649 model score 1.2645 model score 1.2656 model score 1.2662 model score 1.2646 model score 1.2646 model score 1.2649 model score -0.7139 model score -0.7199 model score -0.7304 model score -0.6708 model score -0.7374 model score 2.3160 model score 2.1252 model score 2.5530 model score 2.3839 model score 2.2445 model score -0.7223 model score -0.6690 model score -0.5976 model score -0.5772 model score -0.6372 model score -0.6388 model score -0.6549 model score -0.6422 model score -0.6160 model score -0.6349 model score -0.3995 model score -0.6857 model score -0.7281 model score -0.2366 model score -0.2445 model score 0.0047 model score -0.6136 USE_META, weight: 0.9348 cost: -0.5152 min: -0.7549 max: 2.5530 USE_META, weight: 0.9362 cost: -0.5204 min: -0.7549 max: 2.5530 USE_META, weight: 0.9393 cost: -0.5316 min: -0.7549 max: 2.5530 USE_META, weight: 0.9680 cost: -0.6373 min: -0.7549 max: 2.5530 USE_META, weight: 0.9399 cost: -0.5339 min: -0.7549 max: 2.5530 USE_META, weight: 0.9551 cost: -0.5901 min: -0.7549 max: 2.5530 USE_META, weight: 0.9546 cost: -0.5879 min: -0.7549 max: 2.5530 USE_META, weight: 0.9349 cost: -0.5158 min: -0.7549 max: 2.5530 USE_META, weight: 0.9499 cost: -0.5707 min: -0.7549 max: 2.5530 USE_META, weight: 0.9496 cost: -0.5696 min: -0.7549 max: 2.5530 USE_META, weight: 0.9376 cost: -0.5256 min: -0.7549 max: 2.5530 USE_META, weight: 0.9768 cost: -0.6695 min: -0.7549 max: 2.5530 USE_META, weight: 0.9544 cost: -0.5872 min: -0.7549 max: 2.5530 USE_META, weight: 0.9750 cost: -0.6630 min: -0.7549 max: 2.5530 USE_META, weight: 0.9491 cost: -0.5677 min: -0.7549 max: 2.5530 USE_META, weight: 0.9922 cost: -0.7262 min: -0.7549 max: 2.5530 USE_META, weight: 0.3525 cost: 1.6250 min: -0.7549 max: 2.5530 USE_META, weight: 0.2580 cost: 1.9722 min: -0.7549 max: 2.5530 USE_META, weight: 0.2509 cost: 1.9983 min: -0.7549 max: 2.5530 USE_META, weight: 0.3284 cost: 1.7134 min: -0.7549 max: 2.5530 USE_META, weight: 0.3183 cost: 1.7505 min: -0.7549 max: 2.5530 USE_META, weight: 0.2357 cost: 2.0541 min: -0.7549 max: 2.5530 USE_META, weight: 0.2712 cost: 1.9237 min: -0.7549 max: 2.5530 USE_META, weight: 0.2789 cost: 1.8956 min: -0.7549 max: 2.5530 USE_META, weight: 0.2886 cost: 1.8599 min: -0.7549 max: 2.5530 USE_META, weight: 0.9971 cost: -0.7442 min: -0.7549 max: 2.5530 USE_META, weight: 0.9515 cost: -0.5767 min: -0.7549 max: 2.5530 USE_META, weight: 0.9609 cost: -0.6114 min: -0.7549 max: 2.5530 USE_META, weight: 0.9944 cost: -0.7342 min: -0.7549 max: 2.5530 USE_META, weight: 0.9723 cost: -0.6532 min: -0.7549 max: 2.5530 USE_META, weight: 0.9904 cost: -0.7195 min: -0.7549 max: 2.5530 USE_META, weight: 0.9888 cost: -0.7137 min: -0.7549 max: 2.5530 USE_META, weight: 0.9781 cost: -0.6745 min: -0.7549 max: 2.5530 USE_META, weight: 0.9872 cost: -0.7080 min: -0.7549 max: 2.5530 USE_META, weight: 0.9838 cost: -0.6955 min: -0.7549 max: 2.5530 USE_META, weight: 0.9838 cost: -0.6953 min: -0.7549 max: 2.5530 USE_META, weight: 0.9830 cost: -0.6923 min: -0.7549 max: 2.5530 USE_META, weight: 0.9905 cost: -0.7199 min: -0.7549 max: 2.5530 USE_META, weight: 0.9877 cost: -0.7098 min: -0.7549 max: 2.5530 USE_META, weight: 0.9863 cost: -0.7046 min: -0.7549 max: 2.5530 USE_META, weight: 0.9766 cost: -0.6689 min: -0.7549 max: 2.5530 USE_META, weight: 0.9889 cost: -0.7140 min: -0.7549 max: 2.5530 USE_META, weight: 0.4496 cost: 1.2680 min: -0.7549 max: 2.5530 USE_META, weight: 0.4499 cost: 1.2669 min: -0.7549 max: 2.5530 USE_META, weight: 0.4499 cost: 1.2670 min: -0.7549 max: 2.5530 USE_META, weight: 0.4506 cost: 1.2644 min: -0.7549 max: 2.5530 USE_META, weight: 0.4499 cost: 1.2670 min: -0.7549 max: 2.5530 USE_META, weight: 0.9903 cost: -0.7192 min: -0.7549 max: 2.5530 USE_META, weight: 0.9832 cost: -0.6932 min: -0.7549 max: 2.5530 USE_META, weight: 0.9739 cost: -0.6590 min: -0.7549 max: 2.5530 USE_META, weight: 0.9854 cost: -0.7013 min: -0.7549 max: 2.5530 USE_META, weight: 0.9888 cost: -0.7136 min: -0.7549 max: 2.5530 USE_META, weight: 0.9985 cost: -0.7495 min: -0.7549 max: 2.5530 USE_META, weight: 0.9898 cost: -0.7174 min: -0.7549 max: 2.5530 USE_META, weight: 0.9781 cost: -0.6745 min: -0.7549 max: 2.5530 USE_META, weight: 0.9903 cost: -0.7191 min: 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1.2710 min: -0.7549 max: 2.5530 USE_META, weight: 0.1248 cost: 2.4617 min: -0.7549 max: 2.5530 USE_META, weight: 0.1486 cost: 2.3742 min: -0.7549 max: 2.5530 USE_META, weight: 0.1096 cost: 2.5177 min: -0.7549 max: 2.5530 USE_META, weight: 0.1532 cost: 2.3573 min: -0.7549 max: 2.5530 USE_META, weight: 0.1497 cost: 2.3701 min: -0.7549 max: 2.5530 USE_META, weight: 0.9899 cost: -0.7178 min: -0.7549 max: 2.5530 USE_META, weight: 0.9771 cost: -0.6709 min: -0.7549 max: 2.5530 USE_META, weight: 0.7860 cost: 0.0316 min: -0.7549 max: 2.5530 USE_META, weight: 0.8169 cost: -0.0821 min: -0.7549 max: 2.5530 USE_META, weight: 0.2495 cost: 2.0035 min: -0.7549 max: 2.5530 USE_META, weight: 0.4504 cost: 1.2650 min: -0.7549 max: 2.5530 USE_META, weight: 0.4494 cost: 1.2690 min: -0.7549 max: 2.5530 USE_META, weight: 0.4492 cost: 1.2695 min: -0.7549 max: 2.5530 USE_META, weight: 0.4501 cost: 1.2661 min: -0.7549 max: 2.5530 USE_META, weight: 0.4455 cost: 1.2830 min: -0.7549 max: 2.5530 USE_META, weight: 0.9884 cost: -0.7122 min: -0.7549 max: 2.5530 USE_META, weight: 0.9898 cost: -0.7174 min: -0.7549 max: 2.5530 USE_META, weight: 0.9897 cost: -0.7172 min: -0.7549 max: 2.5530 USE_META, weight: 0.9774 cost: -0.6718 min: -0.7549 max: 2.5530 USE_META, weight: 0.9903 cost: -0.7191 min: -0.7549 max: 2.5530 USE_META, weight: 0.9729 cost: -0.6552 min: -0.7549 max: 2.5530 USE_META, weight: 0.9753 cost: -0.6640 min: -0.7549 max: 2.5530 USE_META, weight: 0.9893 cost: -0.7155 min: -0.7549 max: 2.5530 USE_META, weight: 0.9792 cost: -0.6786 min: -0.7549 max: 2.5530 USE_META, weight: 0.9862 cost: -0.7040 min: -0.7549 max: 2.5530 USE_META, weight: 0.9921 cost: -0.7257 min: -0.7549 max: 2.5530 USE_META, weight: 0.9981 cost: -0.7478 min: -0.7549 max: 2.5530 USE_META, weight: 1.0000 cost: -0.7549 min: -0.7549 max: 2.5530 USE_META, weight: 0.9681 cost: -0.6377 min: -0.7549 max: 2.5530 USE_META, weight: 0.9781 cost: -0.6743 min: -0.7549 max: 2.5530 USE_META, weight: 0.9775 cost: -0.6723 min: -0.7549 max: 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max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.8939 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.8939 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 0.8939 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 Number of contacts in models: 257 Number of contacts in alignments: 111 NUMB_ALIGNS: 111 Adding 12366 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -518.7411, CN propb: -518.7411 weights: 0.4205 constraints: 921 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 921 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 921 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 11445 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 11445 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 12366 # command: