# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0441 numbered 1 through 342 Created new target T0441 from T0441.a2m # command:CPU_time= 6.555 sec, elapsed time= 6.756 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jftA/T0441-1jftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jftA expands to /projects/compbio/data/pdb/1jft.pdb.gz 1jftA:# T0441 read from 1jftA/T0441-1jftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jftA read from 1jftA/T0441-1jftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jftA to template set # found chain 1jftA in template set Warning: unaligning (T0441)V13 because first residue in template chain is (1jftA)A2 T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY # choosing archetypes in rotamer library T0441 149 :NTPVLEIAELSSKAS 1jftA 139 :HIPMVVMDAGEAKAD T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1jftA 155 :TDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRAST 1jftA 317 :QSIEVHPRLIERRSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jftA/T0441-1jftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jftA/T0441-1jftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jftA read from 1jftA/T0441-1jftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jftA in template set Warning: unaligning (T0441)V13 because first residue in template chain is (1jftA)A2 T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSKASYLNIGVDH 1jftA 139 :HIPMVVMDAGEAKADFTDAVIDN T0441 172 :FEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1jftA 163 :FEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRASTAI 1jftA 317 :QSIEVHPRLIERRSVAD Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jftA/T0441-1jftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jftA/T0441-1jftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jftA read from 1jftA/T0441-1jftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jftA in template set Warning: unaligning (T0441)V13 because first residue in template chain is (1jftA)A2 T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSK 1jftA 139 :HIPMVVMDAGEAK T0441 162 :ASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 1jftA 153 :DFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVAD Number of specific fragments extracted= 3 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bblA/T0441-3bblA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bblA expands to /projects/compbio/data/pdb/3bbl.pdb.gz 3bblA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 3bblA/T0441-3bblA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bblA read from 3bblA/T0441-3bblA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bblA to template set # found chain 3bblA in template set Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (3bblA)D283 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (3bblA)D283 T0441 70 :SYSIALIIPS 3bblA 63 :SFMIGYSWTQ T0441 80 :LFEKACAHFLPSFQ 3bblA 81 :ILDQFLSSMVREAG T0441 98 :KAGYQLLLGYSDYSIE 3bblA 95 :AVNYFVLPFPFSEDRS T0441 117 :KLLSTFLESR 3bblA 113 :DIYRDLIRSG T0441 127 :PAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSS 3bblA 124 :VDGFVLSSINYNDPRVQFLLKQKFPFVAFGRSNPDWDFAWVDIDGTAGTRQAVEYLIGRGHRRIAILAWPEDSRVGNDRLQGYLEAMQTAQLPIETGYILRGEGTFEVGRAMTLHLLDLSPE T0441 249 :LNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3bblA 248 :PTAIMTLNDTMAIGAMAAARERGLTIGTDLAIIG T0441 285 :GSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 3bblA 284 :DAPMVQYLFPPLSSVRQPIAEAGRKCIELLVAIVEGREPE T0441 325 :RPTSMGFKLKRRASTAIN 3bblA 325 :KHILLQPSLIIRASEGHH Number of specific fragments extracted= 8 number of extra gaps= 1 total=19 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bblA/T0441-3bblA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3bblA/T0441-3bblA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bblA read from 3bblA/T0441-3bblA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bblA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (3bblA)L62 Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (3bblA)D283 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (3bblA)D283 T0441 70 :SYSIALII 3bblA 63 :SFMIGYSW T0441 78 :PSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLR 3bblA 75 :PGQVNHILDQFLSSMVREAGAVNYFVLPFPFSEDRSQIDIYRDLIRSGNVDGFVLSSINYNDPRVQFLLKQKFPFVAFGRSNPDWDFAWVDIDGTAGTRQAVEYLIGRGHRRIAILAWPEDSRVGNDRLQGYLEAMQTAQLPIETGYILRGEGTFEVGRAMTLHLLDL T0441 246 :DSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3bblA 245 :ERRPTAIMTLNDTMAIGAMAAARERGLTIGTDLAIIG T0441 285 :GSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 3bblA 284 :DAPMVQYLFPPLSSVRQPIAEAGRKCIELLVAIVEGREPE T0441 325 :RPTSMGFKLKRRASTAIN 3bblA 325 :KHILLQPSLIIRASEGHH Number of specific fragments extracted= 5 number of extra gaps= 1 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bblA/T0441-3bblA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3bblA/T0441-3bblA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bblA read from 3bblA/T0441-3bblA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bblA in template set Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (3bblA)D283 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (3bblA)D283 T0441 74 :ALIIPS 3bblA 65 :MIGYSW T0441 80 :LFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLR 3bblA 77 :QVNHILDQFLSSMVREAGAVNYFVLPFPFSEDRSQIDIYRDLIRSGNVDGFVLSSINYNDPRVQFLLKQKFPFVAFGRSNPDWDFAWVDIDGTAGTRQAVEYLIGRGHRRIAILAWPEDSRVGNDRLQGYLEAMQTAQLPIETGYILRGEGTFEVGRAMTLHLLDL T0441 246 :DSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3bblA 245 :ERRPTAIMTLNDTMAIGAMAAARERGLTIGTDLAIIG T0441 285 :GSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAI 3bblA 284 :DAPMVQYLFPPLSSVRQPIAEAGRKCIELLVAIVEGREPEQKHILLQPSLIIRASEG Number of specific fragments extracted= 4 number of extra gaps= 1 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cs3A/T0441-3cs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cs3A expands to /projects/compbio/data/pdb/3cs3.pdb.gz 3cs3A:Skipped atom 50, because occupancy 0.5 <= existing 0.500 in 3cs3A Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1577, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1579, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1851, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1853, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1856, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1870, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1978, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1982, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 3cs3A Skipped atom 2136, because occupancy 0.500 <= existing 0.500 in 3cs3A # T0441 read from 3cs3A/T0441-3cs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cs3A read from 3cs3A/T0441-3cs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cs3A to template set # found chain 3cs3A in template set Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)Y69 Warning: unaligning (T0441)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)Y69 Warning: unaligning (T0441)S248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)P229 Warning: unaligning (T0441)L249 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)P229 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)N236 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)N236 T0441 67 :SAESYSIALIIP 3cs3A 56 :RRQTNIIGVYLA T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDY 3cs3A 70 :GGSFYGELLEGIKKGLALFDYEMIVCSGKK T0441 124 :ESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 3cs3A 106 :EKMVDGAIILDWTFPTKEIEKFAERGHSIVVLDRTTEHRNIRQVLLDNRGGATQAIEQFVNVGSKKVLLLSGPEKGYDSQERLAVSTRELTRFGIPYE T0441 225 :TTHEAPSSQLGAEGLAKLLLRDS 3cs3A 204 :IIQGDFTEPSGYAAAKKILSQPQ T0441 250 :NALVC 3cs3A 230 :VDVFA T0441 257 :EEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEER 3cs3A 237 :DEMAIGVYKYVAETNYQMGKDIRIIGFDNSELGAFVQPRLATIAYSKHRWGMVAAEKIIHLMRGEAAES T0441 327 :TSMGFKLKRRASTA 3cs3A 306 :EHIYTRFIEGESFP Number of specific fragments extracted= 7 number of extra gaps= 3 total=35 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cs3A/T0441-3cs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3cs3A/T0441-3cs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cs3A read from 3cs3A/T0441-3cs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cs3A in template set Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)Y69 Warning: unaligning (T0441)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)Y69 Warning: unaligning (T0441)S248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)P229 Warning: unaligning (T0441)L249 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)P229 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)N236 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)N236 Warning: unaligning (T0441)I341 because last residue in template chain is (3cs3A)S320 T0441 67 :SAESYSIALIIP 3cs3A 56 :RRQTNIIGVYLA T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDY 3cs3A 70 :GGSFYGELLEGIKKGLALFDYEMIVCSGKK T0441 124 :ESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 3cs3A 106 :EKMVDGAIILDWTFPTKEIEKFAERGHSIVVLDRTTEHRNIRQVLLDNRGGATQAIEQFVNVGSKKVLLLSGPEKGYDSQERLAVSTRELTRFGIPYE T0441 225 :TTHEAPSSQLGAEGLAKLLLRD 3cs3A 204 :IIQGDFTEPSGYAAAKKILSQP T0441 247 :S 3cs3A 227 :T T0441 250 :NALVC 3cs3A 230 :VDVFA T0441 257 :EEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 3cs3A 237 :DEMAIGVYKYVAETNYQMGKDIRIIGFDNSELGAFVQPRLATIAYSKHRWGMVAAEKIIHLMRGEAAE T0441 326 :PTSMGFKLKRRASTA 3cs3A 305 :SEHIYTRFIEGESFP Number of specific fragments extracted= 8 number of extra gaps= 3 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cs3A/T0441-3cs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3cs3A/T0441-3cs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cs3A read from 3cs3A/T0441-3cs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cs3A in template set Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)Y69 Warning: unaligning (T0441)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)Y69 Warning: unaligning (T0441)S248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)P229 Warning: unaligning (T0441)L249 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)P229 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3cs3A)N236 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3cs3A)N236 Warning: unaligning (T0441)A340 because last residue in template chain is (3cs3A)S320 T0441 67 :SAESYSIALIIP 3cs3A 56 :RRQTNIIGVYLA T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDY 3cs3A 70 :GGSFYGELLEGIKKGLALFDYEMIVCSGKK T0441 123 :LESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 3cs3A 105 :PEKMVDGAIILDWTFPTKEIEKFAERGHSIVVLDRTTEHRNIRQVLLDNRGGATQAIEQFVNVGSKKVLLLSGPEKGYDSQERLAVSTRELTRFGIPYE T0441 224 :LTTHEAPS 3cs3A 204 :IIQGDFTE T0441 233 :QLGAEGLAKLLLRD 3cs3A 212 :PSGYAAAKKILSQP T0441 247 :S 3cs3A 227 :T T0441 250 :NALVC 3cs3A 230 :VDVFA T0441 257 :EEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 3cs3A 237 :DEMAIGVYKYVAETNYQMGKDIRIIGFDNSELGAFVQPRLATIAYSKHRWGMVAAEKIIHLMRGEAAESEHIYTRFIEGESFP Number of specific fragments extracted= 8 number of extra gaps= 3 total=51 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o20A/T0441-2o20A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2o20A expands to /projects/compbio/data/pdb/2o20.pdb.gz 2o20A:Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1509, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 1983, because occupancy 0.400 <= existing 0.600 in 2o20A Skipped atom 1985, because occupancy 0.400 <= existing 0.600 in 2o20A Skipped atom 1987, because occupancy 0.400 <= existing 0.600 in 2o20A Skipped atom 1989, because occupancy 0.400 <= existing 0.600 in 2o20A Skipped atom 1991, because occupancy 0.400 <= existing 0.600 in 2o20A Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2074, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2076, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2078, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2080, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2082, because occupancy 0.500 <= existing 0.500 in 2o20A Skipped atom 2084, because occupancy 0.500 <= existing 0.500 in 2o20A # T0441 read from 2o20A/T0441-2o20A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o20A read from 2o20A/T0441-2o20A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o20A to template set # found chain 2o20A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2o20A)R62 Warning: unaligning (T0441)G168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)I162 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)I162 Warning: unaligning (T0441)L252 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V244 Warning: unaligning (T0441)V253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V244 Warning: unaligning (T0441)S298 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V290 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V290 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNI 2o20A 63 :TTTVGVILPTITSTYFAAITRGVDDIASMYKYNMILANSDNDVEKEEKVLETFLSKQVDGIVYMGSSLDEKIRTSLKNSRTPVVLVGTIDGDKEIPSV T0441 170 :DHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLR 2o20A 163 :DYHLAAYQSTKKLIDSGNKKIAYIMGSLKDVENTERMVGYQEALLEANIEFDENLVFEGNYSYEQGKALAERLLER T0441 248 :SLNA 2o20A 239 :GATS T0441 254 :CSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLT 2o20A 245 :VSHDTVAVGLLSAMMDKGVKVPEDFEIISGANSPITQYTYPTLT T0441 300 :EFDYERMGTKAAEKLLHAIKGEPEE 2o20A 291 :NQPLYDLGAVAMRLLTKLMLKEDVE T0441 325 :RPTSMGFKLKRRAST 2o20A 317 :NQLVLDHEIFSRRST Number of specific fragments extracted= 6 number of extra gaps= 3 total=57 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o20A/T0441-2o20A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2o20A/T0441-2o20A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o20A read from 2o20A/T0441-2o20A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o20A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2o20A)R62 Warning: unaligning (T0441)G168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)I162 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)I162 Warning: unaligning (T0441)L252 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V244 Warning: unaligning (T0441)V253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V244 Warning: unaligning (T0441)S298 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V290 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V290 Warning: unaligning (T0441)A340 because last residue in template chain is (2o20A)K332 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNI 2o20A 63 :TTTVGVILPTITSTYFAAITRGVDDIASMYKYNMILANSDNDVEKEEKVLETFLSKQVDGIVYMGSSLDEKIRTSLKNSRTPVVLVGTIDGDKEIPSV T0441 170 :DHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRD 2o20A 163 :DYHLAAYQSTKKLIDSGNKKIAYIMGSLKDVENTERMVGYQEALLEANIEFDENLVFEGNYSYEQGKALAERLLERG T0441 249 :LNA 2o20A 240 :ATS T0441 254 :CSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLT 2o20A 245 :VSHDTVAVGLLSAMMDKGVKVPEDFEIISGANSPITQYTYPTLT T0441 300 :EFDYERMGTKAAEKLLHAIKGEPEE 2o20A 291 :NQPLYDLGAVAMRLLTKLMLKEDVE T0441 325 :RPTSMGFKLKRRAST 2o20A 317 :NQLVLDHEIFSRRST Number of specific fragments extracted= 6 number of extra gaps= 3 total=63 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o20A/T0441-2o20A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2o20A/T0441-2o20A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o20A read from 2o20A/T0441-2o20A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o20A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2o20A)R62 Warning: unaligning (T0441)G168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)I162 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)I162 Warning: unaligning (T0441)L252 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V244 Warning: unaligning (T0441)V253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V244 Warning: unaligning (T0441)S298 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2o20A)V290 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2o20A)V290 Warning: unaligning (T0441)I341 because last residue in template chain is (2o20A)K332 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNI 2o20A 63 :TTTVGVILPTITSTYFAAITRGVDDIASMYKYNMILANSDNDVEKEEKVLETFLSKQVDGIVYMGSSLDEKIRTSLKNSRTPVVLVGTIDGDKEIPSV T0441 170 :DHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLL 2o20A 163 :DYHLAAYQSTKKLIDSGNKKIAYIMGSLKDVENTERMVGYQEALLEANIEFDENLVFEGNYSYEQGKALAERLL T0441 246 :DSSLNA 2o20A 237 :ERGATS T0441 254 :CSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLT 2o20A 245 :VSHDTVAVGLLSAMMDKGVKVPEDFEIISGANSPITQYTYPTLT T0441 300 :EFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 2o20A 291 :NQPLYDLGAVAMRLLTKLMLKEDVEQNQLVLDHEIFSRRST Number of specific fragments extracted= 5 number of extra gaps= 3 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgyA/T0441-2rgyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rgyA expands to /projects/compbio/data/pdb/2rgy.pdb.gz 2rgyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 2rgyA/T0441-2rgyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgyA read from 2rgyA/T0441-2rgyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rgyA to template set # found chain 2rgyA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2rgyA)L85 Warning: unaligning (T0441)A340 because last residue in template chain is (2rgyA)R359 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYS 2rgyA 86 :GIIGLFVPTFFGSYYGTILKQTDLELRAVHRHVVVATGCGE T0441 112 :IEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 2rgyA 130 :REQALEAVRFLIGRDCDGVVVISHDLHDEDLDELHRMHPKMVFLNRAFDALPDASFCPDHRRGGELAAATLIEHGHRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLIESDFSPEGGYAATCQLLESKAPFTGLFCANDTMAVSALARFQQLGISVPGDVSVIGYDDDYSAAYAAPALTSVHIPTAELTQNAVRWLINQCYGTKWEIFREFPVTVSMRASV Number of specific fragments extracted= 2 number of extra gaps= 0 total=70 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgyA/T0441-2rgyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2rgyA/T0441-2rgyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgyA read from 2rgyA/T0441-2rgyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rgyA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2rgyA)L85 Warning: unaligning (T0441)I341 because last residue in template chain is (2rgyA)R359 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYS 2rgyA 86 :GIIGLFVPTFFGSYYGTILKQTDLELRAVHRHVVVATGCGE T0441 112 :IEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 2rgyA 130 :REQALEAVRFLIGRDCDGVVVISHDLHDEDLDELHRMHPKMVFLNRAFDALPDASFCPDHRRGGELAAATLIEHGHRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLIESDFSPEGGYAATCQLLESKAPFTGLFCANDTMAVSALARFQQLGISVPGDVSVIGYDDDYSAAYAAPALTSVHIPTAELTQNAVRWLINQCYGTKWEIFREFPVTVSMRASVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgyA/T0441-2rgyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2rgyA/T0441-2rgyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgyA read from 2rgyA/T0441-2rgyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rgyA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2rgyA)L85 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 2rgyA 86 :GIIGLFVPTFFGSYYGTILKQTDLELRAVHRHVVVATGCG T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEER 2rgyA 129 :PREQALEAVRFLIGRDCDGVVVISHDLHDEDLDELHRMHPKMVFLNRAFDALPDASFCPDHRRGGELAAATLIEHGHRKLAVISGPFTASDNVERLDGFFDELARHGIARDSVPLIESDFSPEGGYAATCQLLESKAPFTGLFCANDTMAVSALARFQQLGISVPGDVSVIGYDDDYSAAYAAPALTSVHIPTAELTQNAVRWLINQCYGTKWEI T0441 327 :TSMGFKLKRRASTAIN 2rgyA 344 :FREFPVTVSMRASVAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=75 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2iksA/T0441-2iksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2iksA expands to /projects/compbio/data/pdb/2iks.pdb.gz 2iksA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 2iksA/T0441-2iksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2iksA read from 2iksA/T0441-2iksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2iksA to template set # found chain 2iksA in template set Warning: unaligning (T0441)A68 because first residue in template chain is (2iksA)G59 Warning: unaligning (T0441)L132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)S124 Warning: unaligning (T0441)F133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)S124 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)F273 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)F273 T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVV 2iksA 60 :RTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLLQRQVDAII T0441 134 :GSEHS 2iksA 125 :TSLPP T0441 139 :QRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMI 2iksA 131 :HPFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWK T0441 217 :YLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAII 2iksA 207 :DDPREVHFLYANSYEREAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIA T0441 284 :EGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2iksA 274 :GDNELLDFLQCPVLAVAQRHRDVAERVLEIVLASLDEPRKP T0441 325 :RPTSMGFKLKRRAST 2iksA 317 :GLTRIKRNLYRRGVL Number of specific fragments extracted= 6 number of extra gaps= 2 total=81 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2iksA/T0441-2iksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2iksA/T0441-2iksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2iksA read from 2iksA/T0441-2iksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2iksA in template set Warning: unaligning (T0441)A68 because first residue in template chain is (2iksA)G59 Warning: unaligning (T0441)L132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)S124 Warning: unaligning (T0441)F133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)S124 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)F273 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)F273 T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVV 2iksA 60 :RTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLLQRQVDAII T0441 134 :GSEHSQ 2iksA 125 :TSLPPE T0441 140 :RTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2iksA 132 :PFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWKDDPREV T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAII 2iksA 213 :HFLYANSYEREAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIA T0441 284 :EGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2iksA 274 :GDNELLDFLQCPVLAVAQRHRDVAERVLEIVLASLDEPRKP T0441 325 :RPTSMGFKLKRRASTA 2iksA 317 :GLTRIKRNLYRRGVLS Number of specific fragments extracted= 6 number of extra gaps= 2 total=87 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2iksA/T0441-2iksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2iksA/T0441-2iksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2iksA read from 2iksA/T0441-2iksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2iksA in template set Warning: unaligning (T0441)A68 because first residue in template chain is (2iksA)G59 Warning: unaligning (T0441)L132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)S124 Warning: unaligning (T0441)F133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)S124 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2iksA)F273 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2iksA)F273 T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVV 2iksA 60 :RTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLLQRQVDAII T0441 134 :GSEHSQ 2iksA 125 :TSLPPE T0441 140 :RTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLT 2iksA 132 :PFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAEELRKFPAETVLYLGALPELSVSFLREQGFRTAWKDDPRE T0441 222 :HFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAII 2iksA 212 :VHFLYANSYEREAAAQLFEKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIA T0441 284 :EGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 2iksA 274 :GDNELLDFLQCPVLAVAQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNLYRRG Number of specific fragments extracted= 5 number of extra gaps= 2 total=92 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qu7A/T0441-2qu7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qu7A expands to /projects/compbio/data/pdb/2qu7.pdb.gz 2qu7A:Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2qu7A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2qu7A # T0441 read from 2qu7A/T0441-2qu7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qu7A read from 2qu7A/T0441-2qu7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qu7A to template set # found chain 2qu7A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qu7A)R63 Warning: unaligning (T0441)V271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qu7A)K267 Warning: unaligning (T0441)L272 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qu7A)K267 T0441 70 :SYSIALIIPS 2qu7A 64 :SNIIAFIVPD T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2qu7A 74 :QNPFFTEVLTEISHECQKHHLHVAVASSEENEDKQQDLIETFVSQNVSAIILVPVKSK T0441 139 :QRT 2qu7A 136 :REW T0441 148 :SNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLT 2qu7A 139 :LKIPIMTLDRELESTSLPSITVDNEEAAYIATKRVLESTCKEVGLLLANPNISTTIGRKNGYNKAISEFDLN T0441 220 :PDHFLTTHEA 2qu7A 213 :PSLIHYSDQQ T0441 230 :PSSQLGAEGLAKLLLR 2qu7A 227 :AQIYSGYEATKTLLSK T0441 248 :SLNALVCSHEEIAIGALFECHRR 2qu7A 243 :GIKGIVATNHLLLLGALQAIKES T0441 273 :KVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEER 2qu7A 268 :EIKKDVIIVGFDDSYWNEIYTPKLTVISQPVKEMGQVAAKMIYKLIKGKDVTS T0441 327 :TSMGFKLKRRASTA 2qu7A 321 :IKLSTKLIIRESCS Number of specific fragments extracted= 9 number of extra gaps= 1 total=101 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qu7A/T0441-2qu7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qu7A/T0441-2qu7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qu7A read from 2qu7A/T0441-2qu7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qu7A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qu7A)R63 Warning: unaligning (T0441)V271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qu7A)K267 Warning: unaligning (T0441)L272 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qu7A)K267 T0441 70 :SYSIALIIPS 2qu7A 64 :SNIIAFIVPD T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2qu7A 74 :QNPFFTEVLTEISHECQKHHLHVAVASSEENEDKQQDLIETFVSQNVSAIILVPVKSK T0441 139 :QR 2qu7A 136 :RE T0441 147 :ASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPS 2qu7A 138 :WLKIPIMTLDRELESTSLPSITVDNEEAAYIATKRVLESTCKEVGLLLANPNISTTIGRKNGYNKAISEFDLNVNPSLIHYSDQQ T0441 232 :SQLGAEGLAKLLLRD 2qu7A 229 :IYSGYEATKTLLSKG T0441 249 :LNALVCSHEEIAIGALFECHRR 2qu7A 244 :IKGIVATNHLLLLGALQAIKES T0441 273 :KVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2qu7A 268 :EIKKDVIIVGFDDSYWNEIYTPKLTVISQPVKEMGQVAAKMIYKLIKGKDVT T0441 326 :PTSMGFKLKRRASTAIN 2qu7A 320 :SIKLSTKLIIRESCSFN Number of specific fragments extracted= 8 number of extra gaps= 1 total=109 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qu7A/T0441-2qu7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qu7A/T0441-2qu7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qu7A read from 2qu7A/T0441-2qu7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qu7A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qu7A)R63 Warning: unaligning (T0441)V271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qu7A)K267 Warning: unaligning (T0441)L272 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qu7A)K267 Warning: unaligning (T0441)I341 because last residue in template chain is (2qu7A)N336 T0441 70 :SYSIALIIPS 2qu7A 64 :SNIIAFIVPD T0441 81 :FEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2qu7A 74 :QNPFFTEVLTEISHECQKHHLHVAVASSEENEDKQQDLIETFVSQNVSAIILVPVKSK T0441 139 :QR 2qu7A 136 :RE T0441 147 :ASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTT 2qu7A 138 :WLKIPIMTLDRELESTSLPSITVDNEEAAYIATKRVLESTCKEVGLLLANPNISTTIGRKNGYNKAISEFDLNVNPSLIH T0441 227 :HEAPSSQLGAEGLAKLLLR 2qu7A 220 :DQQLGTNAQIYSGYEATKT T0441 246 :DSSLNALVCSHEEIAIGALFECHRR 2qu7A 241 :SKGIKGIVATNHLLLLGALQAIKES T0441 273 :KVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 2qu7A 268 :EIKKDVIIVGFDDSYWNEIYTPKLTVISQPVKEMGQVAAKMIYKLIKGKDVTSIKLSTKLIIRESCSF Number of specific fragments extracted= 7 number of extra gaps= 1 total=116 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fepA/T0441-2fepA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fepA expands to /projects/compbio/data/pdb/2fep.pdb.gz 2fepA:# T0441 read from 2fepA/T0441-2fepA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fepA read from 2fepA/T0441-2fepA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fepA to template set # found chain 2fepA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2fepA)T61 Warning: unaligning (T0441)A340 because last residue in template chain is (2fepA)K333 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGAR 2fepA 62 :TTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGP T0441 197 :GNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2fepA 189 :AEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVE T0441 325 :RPTSMGFKLKRRAST 2fepA 318 :HIVELPHRIELRKST Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fepA/T0441-2fepA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fepA/T0441-2fepA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fepA read from 2fepA/T0441-2fepA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fepA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2fepA)T61 Warning: unaligning (T0441)A340 because last residue in template chain is (2fepA)K333 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQR 2fepA 62 :TTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRS T0441 205 :QLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2fepA 197 :KLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVE T0441 325 :RPTSMGFKLKRRAST 2fepA 318 :HIVELPHRIELRKST Number of specific fragments extracted= 3 number of extra gaps= 0 total=122 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fepA/T0441-2fepA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fepA/T0441-2fepA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fepA read from 2fepA/T0441-2fepA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fepA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2fepA)T61 Warning: unaligning (T0441)I341 because last residue in template chain is (2fepA)K333 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQR 2fepA 62 :TTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRS T0441 205 :QLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 2fepA 197 :KLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKST Number of specific fragments extracted= 2 number of extra gaps= 0 total=124 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bilA/T0441-3bilA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bilA expands to /projects/compbio/data/pdb/3bil.pdb.gz 3bilA:Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1851, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1853, because occupancy 0.500 <= existing 0.500 in 3bilA Skipped atom 1855, because occupancy 0.500 <= existing 0.500 in 3bilA # T0441 read from 3bilA/T0441-3bilA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bilA read from 3bilA/T0441-3bilA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bilA to template set # found chain 3bilA in template set Warning: unaligning (T0441)S72 because first residue in template chain is (3bilA)T67 Warning: unaligning (T0441)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)N130 Warning: unaligning (T0441)S135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)N130 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)M145 Warning: unaligning (T0441)T150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)M145 Warning: unaligning (T0441)A162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)T159 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)T277 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)T277 Warning: unaligning (T0441)A317 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)T320 Warning: unaligning (T0441)T327 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)T320 Warning: unaligning (T0441)I341 because last residue in template chain is (3bilA)S335 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLF 3bilA 68 :IGVIVPSLINHYFAAMVTEIQSTASKAGLATIITNSNEDATTMSGSLEFLTSHGVDGIICV T0441 136 :EHSQRTHQLLEA 3bilA 131 :EECANQLEDLQK T0441 151 :PVLEIAELSSK 3bilA 146 :PVVLVDRELPG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYL 3bilA 160 :IPTATSNPQPGIAAAVELLAHNNALPIGYLSGPMDTSTGRERLEDFKAACANSKI T0441 221 :DHFLTTHEAPSSQLGAEGLAKLLLR 3bilA 215 :GEQLVFLGGYEQSVGFEGATKLLDQ T0441 248 :SLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3bilA 240 :GAKTLFAGDSMMTIGVIEACHKAGLVIGKDVSVIGF T0441 286 :SSMGEHAYPSLTSAEFDYERMGTKAAEKLLH 3bilA 278 :HPLFALQPHPLTVIDQNVEQLAQRAVSILTE T0441 328 :SMGFKLKRRAST 3bilA 321 :TIPTALIHRESI T0441 340 :A 3bilA 334 :N Number of specific fragments extracted= 9 number of extra gaps= 2 total=133 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bilA/T0441-3bilA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3bilA/T0441-3bilA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bilA read from 3bilA/T0441-3bilA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bilA in template set Warning: unaligning (T0441)S72 because first residue in template chain is (3bilA)T67 Warning: unaligning (T0441)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)N130 Warning: unaligning (T0441)S135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)N130 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)M145 Warning: unaligning (T0441)T150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)M145 Warning: unaligning (T0441)A162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)T159 Warning: unaligning (T0441)S163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)T159 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)T277 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)T277 Warning: unaligning (T0441)A317 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)T320 Warning: unaligning (T0441)T327 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)T320 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLF 3bilA 68 :IGVIVPSLINHYFAAMVTEIQSTASKAGLATIITNSNEDATTMSGSLEFLTSHGVDGIICV T0441 136 :EHSQRTHQLLEA 3bilA 131 :EECANQLEDLQK T0441 151 :PVLEIAELSSK 3bilA 146 :PVVLVDRELPG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLT 3bilA 160 :IPTATSNPQPGIAAAVELLAHNNALPIGYLSGPMDTSTGRERLEDFKAACANSKIG T0441 222 :HFLTTHEAPSSQLGAEGLAKLLLRD 3bilA 216 :EQLVFLGGYEQSVGFEGATKLLDQG T0441 249 :LNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3bilA 241 :AKTLFAGDSMMTIGVIEACHKAGLVIGKDVSVIGF T0441 286 :SSMGEHAYPSLTSAEFDYERMGTKAAEKLLH 3bilA 278 :HPLFALQPHPLTVIDQNVEQLAQRAVSILTE T0441 328 :SMGFKLKRRASTAIN 3bilA 321 :TIPTALIHRESIINS Number of specific fragments extracted= 8 number of extra gaps= 2 total=141 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bilA/T0441-3bilA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3bilA/T0441-3bilA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bilA read from 3bilA/T0441-3bilA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bilA in template set Warning: unaligning (T0441)S72 because first residue in template chain is (3bilA)T67 Warning: unaligning (T0441)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)N130 Warning: unaligning (T0441)S135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)N130 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bilA)M145 Warning: unaligning (T0441)T150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)M145 Warning: unaligning (T0441)S163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bilA)T159 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3bilA)T277 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3bilA)T277 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLF 3bilA 68 :IGVIVPSLINHYFAAMVTEIQSTASKAGLATIITNSNEDATTMSGSLEFLTSHGVDGIICV T0441 136 :EHSQRTHQLLEA 3bilA 131 :EECANQLEDLQK T0441 151 :PVLEIAELSSK 3bilA 146 :PVVLVDRELPG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 3bilA 160 :IPTATSNPQPGIAAAVELLAHNNALPIGYLSGPMDTSTGRERLEDFKAACANSKIGE T0441 223 :FLTTHEAPSSQLGAEGLAKLLL 3bilA 217 :QLVFLGGYEQSVGFEGATKLLD T0441 247 :SSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3bilA 239 :QGAKTLFAGDSMMTIGVIEACHKAGLVIGKDVSVIGF T0441 286 :SSMGEHAYPSLTSAEFDYERMGTKAAEKLL 3bilA 278 :HPLFALQPHPLTVIDQNVEQLAQRAVSILT Number of specific fragments extracted= 7 number of extra gaps= 2 total=148 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brqA/T0441-3brqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3brqA expands to /projects/compbio/data/pdb/3brq.pdb.gz 3brqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 3brqA/T0441-3brqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brqA read from 3brqA/T0441-3brqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3brqA to template set # found chain 3brqA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3brqA)T17 Warning: unaligning (T0441)E82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)Y33 Warning: unaligning (T0441)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)Y33 Warning: unaligning (T0441)N216 because of BadResidue code BAD_PEPTIDE in next template residue (3brqA)G167 Warning: unaligning (T0441)Y217 because of BadResidue code BAD_PEPTIDE at template residue (3brqA)G167 Warning: unaligning (T0441)R245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)K198 Warning: unaligning (T0441)S248 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)K198 Warning: unaligning (T0441)I341 because last residue in template chain is (3brqA)A291 T0441 71 :YSIALIIPS 3brqA 18 :QTLGLVVTN T0441 80 :LF 3brqA 28 :LY T0441 85 :CAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 3brqA 34 :FSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLS T0441 139 :QRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIE 3brqA 89 :DEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQ T0441 218 :LTPDHFLTTHEAPSSQLGAEGLAKLLL 3brqA 168 :IALNEKLIANGKWTPASGAEGVEMLLE T0441 249 :LNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 3brqA 199 :FSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=154 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brqA/T0441-3brqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3brqA/T0441-3brqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brqA read from 3brqA/T0441-3brqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3brqA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3brqA)T17 Warning: unaligning (T0441)K83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)Y33 Warning: unaligning (T0441)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)Y33 Warning: unaligning (T0441)N216 because of BadResidue code BAD_PEPTIDE in next template residue (3brqA)G167 Warning: unaligning (T0441)Y217 because of BadResidue code BAD_PEPTIDE at template residue (3brqA)G167 Warning: unaligning (T0441)R245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)K198 Warning: unaligning (T0441)S248 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)K198 Warning: unaligning (T0441)I341 because last residue in template chain is (3brqA)A291 T0441 71 :YSIALIIPSLFE 3brqA 18 :QTLGLVVTNTLY T0441 85 :CAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 3brqA 34 :FSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLS T0441 139 :QRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIE 3brqA 89 :DEIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQ T0441 218 :LTPDHFLTTHEAPSSQLGAEGLAKLLL 3brqA 168 :IALNEKLIANGKWTPASGAEGVEMLLE T0441 249 :LNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTA 3brqA 199 :FSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSPPKTFSGKLIRRDSLI Number of specific fragments extracted= 5 number of extra gaps= 1 total=159 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brqA/T0441-3brqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3brqA/T0441-3brqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brqA read from 3brqA/T0441-3brqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3brqA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3brqA)T17 Warning: unaligning (T0441)K83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)Y33 Warning: unaligning (T0441)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)Y33 Warning: unaligning (T0441)N216 because of BadResidue code BAD_PEPTIDE in next template residue (3brqA)G167 Warning: unaligning (T0441)Y217 because of BadResidue code BAD_PEPTIDE at template residue (3brqA)G167 Warning: unaligning (T0441)R245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brqA)K198 Warning: unaligning (T0441)S248 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brqA)K198 T0441 71 :YSIALIIPSLFE 3brqA 18 :QTLGLVVTNTLY T0441 85 :CAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 3brqA 34 :FSELLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSV T0441 140 :RTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIE 3brqA 90 :EIDDIIDAHSQPIMVLNRRLRKNSSHSVWCDHKQTSFNAVAELINAGHQEIAFLTGSMDSPTSIERLAGYKDALAQ T0441 218 :LTPDHFLTTHEAPSSQLGAEGLAKLLL 3brqA 168 :IALNEKLIANGKWTPASGAEGVEMLLE T0441 249 :LNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEER 3brqA 199 :FSALVASNDDMAIGAMKALHERGVAVPEQVSVIGFDDIAIAPYTVPALSSVKIPVTEMIQEIIGRLIFMLDGGDFSP T0441 327 :TSMGFKLKRRASTAIN 3brqA 276 :PKTFSGKLIRRDSLIA Number of specific fragments extracted= 6 number of extra gaps= 1 total=165 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jyeA/T0441-1jyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jyeA expands to /projects/compbio/data/pdb/1jye.pdb.gz 1jyeA:# T0441 read from 1jyeA/T0441-1jyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jyeA read from 1jyeA/T0441-1jyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jyeA to template set # found chain 1jyeA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1jyeA)L62 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYS 1jyeA 63 :LIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMV T0441 109 :DYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1jyeA 101 :RSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAAC T0441 149 :NTPVLEIAEL 1jyeA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDH 1jyeA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIA T0441 225 :TTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 1jyeA 215 :EREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT T0441 340 :A 1jyeA 331 :A Number of specific fragments extracted= 6 number of extra gaps= 0 total=171 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jyeA/T0441-1jyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jyeA/T0441-1jyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jyeA read from 1jyeA/T0441-1jyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jyeA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1jyeA)L62 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYS 1jyeA 63 :LIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVERS T0441 112 :IEQEEKLLSTFLESRPAGVVLFGS 1jyeA 104 :VEACKTAVHNLLAQRVSGLIINYP T0441 137 :HSQRTHQLLEAS 1jyeA 128 :LDDQDAIAVEAA T0441 149 :NTPVLEIAEL 1jyeA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 1jyeA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI T0441 224 :LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 1jyeA 214 :AEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAP Number of specific fragments extracted= 6 number of extra gaps= 0 total=177 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jyeA/T0441-1jyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jyeA/T0441-1jyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jyeA read from 1jyeA/T0441-1jyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jyeA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1jyeA)L62 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1jyeA 63 :LIGVATSSLALHAPSQIVAAILSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1jyeA 103 :GVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAAC T0441 149 :NTPVLEIAEL 1jyeA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 1jyeA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI T0441 224 :LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERP 1jyeA 214 :AEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGN T0441 328 :SMGFKLKRRASTAIN 1jyeA 317 :QLLPVSLVKRKTTLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=183 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ctpA/T0441-3ctpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ctpA expands to /projects/compbio/data/pdb/3ctp.pdb.gz 3ctpA:Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 3ctpA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 3ctpA # T0441 read from 3ctpA/T0441-3ctpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ctpA read from 3ctpA/T0441-3ctpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ctpA to template set # found chain 3ctpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3ctpA)S60 Warning: unaligning (T0441)P78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ctpA)N69 Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ctpA)N69 Warning: unaligning (T0441)S138 because of BadResidue code BAD_PEPTIDE in next template residue (3ctpA)D129 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)N268 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)N268 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)Q284 Warning: unaligning (T0441)F301 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)Q284 Warning: unaligning (T0441)I341 because last residue in template chain is (3ctpA)S325 T0441 71 :YSIALII 3ctpA 61 :KTIGLMV T0441 80 :LFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEH 3ctpA 70 :ISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQC T0441 145 :LEASNTPVLEIAELSSK 3ctpA 131 :YANIDIPVVAFENHILD T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHF 3ctpA 148 :NIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFI T0441 225 :TTHEAPSSQ 3ctpA 209 :EFQHDFQVK T0441 245 :RDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3ctpA 228 :DIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGF T0441 286 :SSMGEHAYPSLTSA 3ctpA 269 :SFIGELLYPSLTTI T0441 302 :DYERMGTKAAEKLLHAIKGEPEE 3ctpA 285 :PIEALAYTIIELLIKIINGEGVL T0441 325 :RPTSMGFKLKRRASTA 3ctpA 309 :EDYIMEVKLIERETTI Number of specific fragments extracted= 9 number of extra gaps= 4 total=192 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ctpA/T0441-3ctpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3ctpA/T0441-3ctpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ctpA read from 3ctpA/T0441-3ctpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ctpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3ctpA)S60 Warning: unaligning (T0441)P78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ctpA)N69 Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ctpA)N69 Warning: unaligning (T0441)S138 because of BadResidue code BAD_PEPTIDE in next template residue (3ctpA)D129 Warning: unaligning (T0441)Q139 because of BadResidue code BAD_PEPTIDE at template residue (3ctpA)D129 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)N268 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)N268 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)Q284 Warning: unaligning (T0441)F301 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)Q284 Warning: unaligning (T0441)I341 because last residue in template chain is (3ctpA)S325 T0441 71 :YSIALII 3ctpA 61 :KTIGLMV T0441 80 :LFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEH 3ctpA 70 :ISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQC T0441 144 :LLEASNTPVLEIAELSSK 3ctpA 130 :EYANIDIPVVAFENHILD T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 3ctpA 148 :NIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEID T0441 223 :FLTTHEAPSSQL 3ctpA 207 :FIEFQHDFQVKM T0441 247 :SSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3ctpA 230 :VNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGF T0441 286 :SSMGEHAYPSLTSA 3ctpA 269 :SFIGELLYPSLTTI T0441 302 :DYERMGTKAAEKLLHAIKGEPEE 3ctpA 285 :PIEALAYTIIELLIKIINGEGVL T0441 325 :RPTSMGFKLKRRASTA 3ctpA 309 :EDYIMEVKLIERETTI Number of specific fragments extracted= 9 number of extra gaps= 4 total=201 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ctpA/T0441-3ctpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3ctpA/T0441-3ctpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ctpA read from 3ctpA/T0441-3ctpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ctpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3ctpA)S60 Warning: unaligning (T0441)P78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ctpA)N69 Warning: unaligning (T0441)S79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ctpA)N69 Warning: unaligning (T0441)S138 because of BadResidue code BAD_PEPTIDE in next template residue (3ctpA)D129 Warning: unaligning (T0441)Q139 because of BadResidue code BAD_PEPTIDE at template residue (3ctpA)D129 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)N268 Warning: unaligning (T0441)G285 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)N268 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3ctpA)Q284 Warning: unaligning (T0441)F301 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3ctpA)Q284 T0441 71 :YSIALII 3ctpA 61 :KTIGLMV T0441 80 :LFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEH 3ctpA 70 :ISNPFFNQMASVIEEYAKNKGYTLFLCNTDDDKEKEKTYLEVLQSHRVAGIIASRSQC T0441 144 :LLEASNTPVLEIAELSSK 3ctpA 130 :EYANIDIPVVAFENHILD T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTT 3ctpA 148 :NIITISSDNYNGGRMAFDHLYEKGCRKILHIKGPEVFEATELRYKGFLDGARAKDLEIDFIEFQ T0441 227 :HEAPSSQ 3ctpA 221 :EDINSMK T0441 245 :RDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICL 3ctpA 228 :DIVNYDGIFVFNDIAAATVMRALKKRGVSIPQEVQIIGF T0441 286 :SSMGEHAYPSLTSA 3ctpA 269 :SFIGELLYPSLTTI T0441 302 :DYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 3ctpA 285 :PIEALAYTIIELLIKIINGEGVLIEDYIMEVKLIERETTIS Number of specific fragments extracted= 8 number of extra gaps= 4 total=209 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3kA/T0441-3c3kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3c3kA expands to /projects/compbio/data/pdb/3c3k.pdb.gz 3c3kA:# T0441 read from 3c3kA/T0441-3c3kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3kA read from 3c3kA/T0441-3c3kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3c3kA to template set # found chain 3c3kA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (3c3kA)K7 Warning: unaligning (T0441)S108 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)E47 Warning: unaligning (T0441)D109 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)E47 Warning: unaligning (T0441)L218 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D156 Warning: unaligning (T0441)T219 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D156 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c3kA)D220 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c3kA)D220 Warning: unaligning (T0441)S295 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)L232 Warning: unaligning (T0441)L296 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)L232 Warning: unaligning (T0441)G320 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D257 Warning: unaligning (T0441)E321 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D257 Warning: unaligning (T0441)P322 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c3kA)V263 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGY 3c3kA 8 :TGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCN T0441 110 :YSIEQEEKLLSTFLESRPAGVVLFGSEHS 3c3kA 48 :SDLARSRSCLTLLSGKMVDGVITMDALSE T0441 139 :QRTHQLL 3c3kA 78 :PELQNII T0441 148 :SNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 3c3kA 85 :GAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHG T0441 220 :PDHF 3c3kA 157 :YSRI T0441 225 :TTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3c3kA 161 :SYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVG T0441 285 :GSSMGEHAYP 3c3kA 221 :GVDISQITVP T0441 297 :TSAEFDYERMGTKAAEKLLHAIK 3c3kA 233 :TTVQQPSEQIGMKAVSLLLEQIH T0441 326 :PTSMGFKLKRRAST 3c3kA 264 :HHLLPWKFVRRQSS Number of specific fragments extracted= 9 number of extra gaps= 5 total=218 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3kA/T0441-3c3kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3c3kA/T0441-3c3kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3kA read from 3c3kA/T0441-3c3kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c3kA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (3c3kA)K7 Warning: unaligning (T0441)S108 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)E47 Warning: unaligning (T0441)D109 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)E47 Warning: unaligning (T0441)L218 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D156 Warning: unaligning (T0441)T219 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D156 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c3kA)D220 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c3kA)D220 Warning: unaligning (T0441)S295 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)L232 Warning: unaligning (T0441)L296 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)L232 Warning: unaligning (T0441)G320 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D257 Warning: unaligning (T0441)E321 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D257 Warning: unaligning (T0441)P322 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c3kA)V263 Warning: unaligning (T0441)A340 because last residue in template chain is (3c3kA)E278 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGY 3c3kA 8 :TGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCN T0441 110 :YSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEA 3c3kA 48 :SDLARSRSCLTLLSGKMVDGVITMDALSELPELQNIIG T0441 149 :NTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 3c3kA 86 :AFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHG T0441 220 :PD 3c3kA 157 :YS T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3c3kA 159 :RISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVG T0441 285 :GSSMGEHAYP 3c3kA 221 :GVDISQITVP T0441 297 :TSAEFDYERMGTKAAEKLLHAIK 3c3kA 233 :TTVQQPSEQIGMKAVSLLLEQIH T0441 326 :PTSMGFKLKRRAST 3c3kA 264 :HHLLPWKFVRRQSS Number of specific fragments extracted= 8 number of extra gaps= 5 total=226 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3c3kA/T0441-3c3kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3c3kA/T0441-3c3kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c3kA read from 3c3kA/T0441-3c3kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c3kA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (3c3kA)K7 Warning: unaligning (T0441)S108 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)E47 Warning: unaligning (T0441)D109 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)E47 Warning: unaligning (T0441)L218 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D156 Warning: unaligning (T0441)T219 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D156 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c3kA)D220 Warning: unaligning (T0441)E284 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c3kA)D220 Warning: unaligning (T0441)S295 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)L232 Warning: unaligning (T0441)L296 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)L232 Warning: unaligning (T0441)G320 because of BadResidue code BAD_PEPTIDE in next template residue (3c3kA)D257 Warning: unaligning (T0441)E321 because of BadResidue code BAD_PEPTIDE at template residue (3c3kA)D257 Warning: unaligning (T0441)P322 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c3kA)V263 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGY 3c3kA 8 :TGMLLVMVSNIANPFCAAVVKGIEKTAEKNGYRILLCN T0441 110 :YSIEQEEKLLSTFLESRPAGVVLFGSEHS 3c3kA 48 :SDLARSRSCLTLLSGKMVDGVITMDALSE T0441 139 :QRTHQLL 3c3kA 78 :PELQNII T0441 148 :SNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 3c3kA 85 :GAFPWVQCAEYDPLSTVSSVSIDDVAASEYVVDQLVKSGKKRIALINHDLAYQYAQHRESGYLNRLKFHG T0441 220 :PD 3c3kA 157 :YS T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIIC 3c3kA 159 :RISYAENLDYMAGKLATFSLLKSAVKPDAIFAISDVLAAGAIQALTESGLSIPQDVAVVG T0441 285 :GSSMGEHAYP 3c3kA 221 :GVDISQITVP T0441 297 :TSAEFDYERMGTKAAEKLLHAIK 3c3kA 233 :TTVQQPSEQIGMKAVSLLLEQIH T0441 328 :SMGFKLKRRA 3c3kA 264 :HHLLPWKFVR Number of specific fragments extracted= 9 number of extra gaps= 5 total=235 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ioyA/T0441-2ioyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ioyA expands to /projects/compbio/data/pdb/2ioy.pdb.gz 2ioyA:Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 376, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 378, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 380, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 382, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 384, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 386, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 501, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 503, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 505, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 507, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 509, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 511, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 513, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 515, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 840, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 844, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 846, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 848, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 850, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 852, because occupancy 0.400 <= existing 0.600 in 2ioyA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1235, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1333, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1335, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1339, because occupancy 0.500 <= existing 0.500 in 2ioyA Skipped atom 1341, because occupancy 0.500 <= existing 0.500 in 2ioyA # T0441 read from 2ioyA/T0441-2ioyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ioyA read from 2ioyA/T0441-2ioyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ioyA to template set # found chain 2ioyA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2ioyA)K2 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)N191 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)N191 Warning: unaligning (T0441)L272 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q208 Warning: unaligning (T0441)T276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q208 Warning: unaligning (T0441)D277 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)G209 Warning: unaligning (T0441)T339 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q275 Warning: unaligning (T0441)A340 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q275 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2ioyA 3 :TIGLVISTLNNPFFVTLKNGAEEKAKELGYKIIVEDSQNDSSKELSNVEDLIQQKVDVLLINPVDSD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2ioyA 72 :VTAIKEANSKNIPVITIDRSANGGD T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2ioyA 98 :VCHIASDNVKGGEMAAEFIAKA T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2ioyA 122 :GKGNVVELEGIPGASAARDRGKGFDEAIAKYP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVC 2ioyA 154 :DIKIVAKQAADFDRSKGLSVMENILQAQPKIDAVFA T0441 257 :EEIAIGALFECHRRV 2ioyA 192 :DEMALGAIKAIEAAN T0441 278 :IAIICLEGSSMG 2ioyA 210 :IIVVGFDGTEDA T0441 290 :EHAYPS 2ioyA 223 :KAIKEG T0441 296 :L 2ioyA 230 :M T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAS 2ioyA 232 :ATIAQQPALMGSLGVEMADKYLKGEKIPNFIPAELKLITKEN Number of specific fragments extracted= 10 number of extra gaps= 3 total=245 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ioyA/T0441-2ioyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2ioyA/T0441-2ioyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ioyA read from 2ioyA/T0441-2ioyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ioyA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2ioyA)K2 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)N191 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)N191 Warning: unaligning (T0441)P275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q208 Warning: unaligning (T0441)T276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q208 Warning: unaligning (T0441)D277 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)G209 Warning: unaligning (T0441)T339 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q275 Warning: unaligning (T0441)A340 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q275 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2ioyA 3 :TIGLVISTLNNPFFVTLKNGAEEKAKELGYKIIVEDSQNDSSKELSNVEDLIQQKVDVLLINPVDSD T0441 140 :RTHQLLEASNTPVLEIAELSSKASY 2ioyA 73 :TAIKEANSKNIPVITIDRSANGGDV T0441 165 :LNIGVDHFEVGKACTRHLIEQ 2ioyA 99 :CHIASDNVKGGEMAAEFIAKA T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2ioyA 122 :GKGNVVELEGIPGASAARDRGKGFDEAIAKYP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVC 2ioyA 154 :DIKIVAKQAADFDRSKGLSVMENILQAQPKIDAVFA T0441 257 :EEIAIGALFECHRRV 2ioyA 192 :DEMALGAIKAIEAAN T0441 278 :IAIICLEGSSMGEHA 2ioyA 210 :IIVVGFDGTEDALKA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAS 2ioyA 228 :GKMAATIAQQPALMGSLGVEMADKYLKGEKIPNFIPAELKLITKEN Number of specific fragments extracted= 8 number of extra gaps= 3 total=253 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ioyA/T0441-2ioyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2ioyA/T0441-2ioyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ioyA read from 2ioyA/T0441-2ioyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ioyA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2ioyA)K2 Warning: unaligning (T0441)S255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)N191 Warning: unaligning (T0441)H256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)N191 Warning: unaligning (T0441)P275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q208 Warning: unaligning (T0441)T276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q208 Warning: unaligning (T0441)D277 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)G209 Warning: unaligning (T0441)A340 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ioyA)Q275 Warning: unaligning (T0441)I341 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ioyA)Q275 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2ioyA 3 :TIGLVISTLNNPFFVTLKNGAEEKAKELGYKIIVEDSQNDSSKELSNVEDLIQQKVDVLLINPVDSDA T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2ioyA 73 :TAIKEANSKNIPVITIDRSANGGD T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2ioyA 98 :VCHIASDNVKGGEMAAEFIAKA T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYL 2ioyA 122 :GKGNVVELEGIPGASAARDRGKGFDEAIAKYPD T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVC 2ioyA 155 :IKIVAKQAADFDRSKGLSVMENILQAQPKIDAVFA T0441 257 :EEIAIGALFECHRRV 2ioyA 192 :DEMALGAIKAIEAAN T0441 278 :IAIICLEGSSMGEHA 2ioyA 210 :IIVVGFDGTEDALKA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEER 2ioyA 228 :GKMAATIAQQPALMGSLGVEMADKYLKGEKIPN T0441 327 :TSMGFKLKRRAST 2ioyA 261 :FIPAELKLITKEN Number of specific fragments extracted= 9 number of extra gaps= 3 total=262 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h0aA/T0441-2h0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h0aA expands to /projects/compbio/data/pdb/2h0a.pdb.gz 2h0aA:# T0441 read from 2h0aA/T0441-2h0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h0aA read from 2h0aA/T0441-2h0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h0aA to template set # found chain 2h0aA in template set Warning: unaligning (T0441)S125 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)Y118 Warning: unaligning (T0441)S138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2h0aA)R138 Warning: unaligning (T0441)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)R195 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYS 2h0aA 66 :VSVLLPFVATEFYRRLVEGIEGVLLEQRYDLALFPILSL T0441 126 :RPAGVVLFGSEH 2h0aA 119 :LTDGLILASYDL T0441 147 :ASNTPVLEIAELSSK 2h0aA 140 :PTERPVVLVDAQNPR T0441 164 :YLNIGVDHFEVGKACTRHLIEQG 2h0aA 155 :YDSVYLDNRLGGRLAGAYLARFP T0441 188 :KNVGFIGA 2h0aA 178 :GPIFAIAV T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHA 2h0aA 196 :TVFAERMAGFQEALKEAGRPFSPDRLYITRHSQEGGRLALRHFLEKASPPLNVFAGADQVALGVLEEAVRLGLTPGRDVRVLGFDGHPFAEEA T0441 295 :SLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2h0aA 289 :GLSTIAQPVEAMGARAAQLLLERMRGYQGP T0441 325 :RPTSMGFKLKRRAST 2h0aA 320 :REVRFEPVLVERAST T0441 340 :AIN 2h0aA 336 :TPP Number of specific fragments extracted= 9 number of extra gaps= 0 total=271 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h0aA/T0441-2h0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2h0aA/T0441-2h0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h0aA read from 2h0aA/T0441-2h0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h0aA in template set Warning: unaligning (T0441)E115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2h0aA)Y118 Warning: unaligning (T0441)S125 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)Y118 Warning: unaligning (T0441)S138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2h0aA)R138 Warning: unaligning (T0441)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)R195 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYS 2h0aA 66 :VSVLLPFVATEFYRRLVEGIEGVLLEQRYDLALFPILSL T0441 126 :RPAGVVLFGSEH 2h0aA 119 :LTDGLILASYDL T0441 147 :ASNTPVLEIAELSSK 2h0aA 140 :PTERPVVLVDAQNPR T0441 164 :YLNIGVDHFEVGKACTRHLIE 2h0aA 155 :YDSVYLDNRLGGRLAGAYLAR T0441 188 :KNVGFIGARG 2h0aA 178 :GPIFAIAVEE T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEH 2h0aA 196 :TVFAERMAGFQEALKEAGRPFSPDRLYITRHSQEGGRLALRHFLEKASPPLNVFAGADQVALGVLEEAVRLGLTPGRDVRVLGFDGHPFAEE T0441 294 :PSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2h0aA 288 :AGLSTIAQPVEAMGARAAQLLLERMRGYQGP T0441 325 :RPTSMGFKLKRRASTAIN 2h0aA 320 :REVRFEPVLVERASTGTP Number of specific fragments extracted= 8 number of extra gaps= 0 total=279 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h0aA/T0441-2h0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2h0aA/T0441-2h0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h0aA read from 2h0aA/T0441-2h0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h0aA in template set Warning: unaligning (T0441)E115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2h0aA)Y118 Warning: unaligning (T0441)S125 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)Y118 Warning: unaligning (T0441)S138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2h0aA)R138 Warning: unaligning (T0441)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2h0aA)R195 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQ 2h0aA 66 :VSVLLPFVATEFYRRLVEGIEGVLLEQRYDLALFPILSLARL T0441 126 :RPAGVVLFGSEH 2h0aA 119 :LTDGLILASYDL T0441 147 :ASNTPVLEIAELSSK 2h0aA 140 :PTERPVVLVDAQNPR T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARG 2h0aA 155 :YDSVYLDNRLGGRLAGAYLARFPGPIFAIAVEEE T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHA 2h0aA 196 :TVFAERMAGFQEALKEAGRPFSPDRLYITRHSQEGGRLALRHFLEKASPPLNVFAGADQVALGVLEEAVRLGLTPGRDVRVLGFDGHPFAEEA T0441 295 :SLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 2h0aA 289 :GLSTIAQPVEAMGARAAQLLLERMRGYQGPPREVRFEPVLVERASTGT Number of specific fragments extracted= 6 number of extra gaps= 0 total=285 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bykA/T0441-1bykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bykA expands to /projects/compbio/data/pdb/1byk.pdb.gz 1bykA:# T0441 read from 1bykA/T0441-1bykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bykA read from 1bykA/T0441-1bykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bykA to template set # found chain 1bykA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (1bykA)S61 Warning: unaligning (T0441)I155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bykA)A146 Warning: unaligning (T0441)A156 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bykA)A146 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 1bykA 62 :DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTGI T0441 145 :LEASNTPVLE 1bykA 135 :LAHWQSSLVL T0441 157 :ELSSK 1bykA 147 :RDAKG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNH 1bykA 152 :FASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHSD T0441 200 :STLQRQLHGWQSAMIENYLTP 1bykA 189 :TTGKRRHEAYLAFCKAHKLHP T0441 224 :LTTHEAPSSQLGAEGLAKL 1bykA 210 :VAALPGLAMKQGYENVAKV T0441 245 :RDSSLNALVCSHEEIAIGALFECHRRVL 1bykA 229 :ITPETTALLCATDTLALGASKYLQEQRI T0441 276 :TDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFK 1bykA 257 :DTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPAT Number of specific fragments extracted= 8 number of extra gaps= 1 total=293 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bykA/T0441-1bykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1bykA/T0441-1bykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bykA read from 1bykA/T0441-1bykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bykA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (1bykA)S61 Warning: unaligning (T0441)I155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bykA)A146 Warning: unaligning (T0441)A156 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bykA)A146 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEH 1bykA 62 :DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTG T0441 138 :SQR 1bykA 131 :TEE T0441 144 :LLEASNTPVLE 1bykA 134 :MLAHWQSSLVL T0441 157 :ELSSK 1bykA 147 :RDAKG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHST 1bykA 152 :FASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHSDVT T0441 202 :LQRQLHGWQSAMIENYLT 1bykA 191 :GKRRHEAYLAFCKAHKLH T0441 223 :FLTTHEAPSSQLGAEGLAKL 1bykA 209 :PVAALPGLAMKQGYENVAKV T0441 245 :RDSSLNALVCSHEEIAIGALFECHRRVL 1bykA 229 :ITPETTALLCATDTLALGASKYLQEQRI T0441 276 :TDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFK 1bykA 257 :DTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPAT Number of specific fragments extracted= 9 number of extra gaps= 1 total=302 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bykA/T0441-1bykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1bykA/T0441-1bykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bykA read from 1bykA/T0441-1bykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bykA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (1bykA)S61 Warning: unaligning (T0441)I155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bykA)A146 Warning: unaligning (T0441)A156 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bykA)A146 T0441 70 :SYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 1bykA 62 :DKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTGIT T0441 145 :LEASNTPVLE 1bykA 135 :LAHWQSSLVL T0441 157 :ELSSK 1bykA 147 :RDAKG T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGN 1bykA 152 :FASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHS T0441 199 :HSTLQRQLHGWQSAMIENYLTP 1bykA 188 :VTTGKRRHEAYLAFCKAHKLHP T0441 224 :LTTHEAPSSQLGAEGLAKLL 1bykA 210 :VAALPGLAMKQGYENVAKVI T0441 246 :DSSLNALVCSHEEIAIGALFECHRRVL 1bykA 230 :TPETTALLCATDTLALGASKYLQEQRI T0441 276 :TDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFK 1bykA 257 :DTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPAT Number of specific fragments extracted= 8 number of extra gaps= 1 total=310 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jx6A/T0441-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jx6A expands to /projects/compbio/data/pdb/1jx6.pdb.gz 1jx6A:# T0441 read from 1jx6A/T0441-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0441-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jx6A to template set # found chain 1jx6A in template set Warning: unaligning (T0441)G25 because first residue in template chain is (1jx6A)G27 T0441 26 :TMTVSRALRT 1jx6A 28 :YWGYQEFLDE T0441 40 :SDKLRE 1jx6A 38 :FPEQRN T0441 46 :KIQQVVD 1jx6A 47 :ALSEAVR T0441 58 :PNKAAGALASAESYSIALIIPS 1jx6A 54 :AQPVPLSKPTQRPIKISVVYPG T0441 80 :LFEKACAHFLPSFQQALNKAG 1jx6A 77 :QVSDYWVRNIASFEKRLYKLN T0441 101 :YQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 1jx6A 102 :LNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTR T0441 139 :QRTHQLLEAS 1jx6A 141 :RKFVEHVLDS T0441 149 :NTPVLEIAELS 1jx6A 152 :NTKLILQNITT T0441 160 :SKAS 1jx6A 165 :REWD T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 1jx6A 173 :FLYVGFDHAEGSRELATEFGKF T0441 186 :GFKNVGFIGARGN 1jx6A 197 :KHTYYSVLYFSEG T0441 200 :STLQRQLHGWQSAMIENY 1jx6A 210 :YISDVRGDTFIHQVNRDN T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGR T0441 276 :TDIAIICLEGSSMG 1jx6A 282 :EDIMINGWGGGSAE T0441 290 :EHAYPS 1jx6A 297 :DAIQKG T0441 296 :L 1jx6A 304 :L T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 1jx6A 306 :ITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADS Number of specific fragments extracted= 17 number of extra gaps= 0 total=327 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jx6A/T0441-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jx6A/T0441-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0441-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0441 40 :SDKLREKIQQV 1jx6A 38 :FPEQRNLTNAL T0441 65 :LAS 1jx6A 52 :VRA T0441 68 :AESYSIALIIPS 1jx6A 64 :QRPIKISVVYPG T0441 80 :LFEKACAHFLPSFQQALNKAGYQLLLGYS 1jx6A 77 :QVSDYWVRNIASFEKRLYKLNINYQLNQV T0441 109 :DYSIEQEEKLLSTFLESRPAGVVLFG 1jx6A 110 :NADIKQQSLSLMEALKSKSDYLIFTL T0441 135 :SEHSQRTHQLLEA 1jx6A 137 :TTRHRKFVEHVLD T0441 148 :SNTPVLEIAE 1jx6A 151 :TNTKLILQNI T0441 158 :LSSKASYLNIGVDHFEVGKACTRHLIEQGFK 1jx6A 167 :WDKHQPFLYVGFDHAEGSRELATEFGKFFPK T0441 189 :NVGFIGARGNH 1jx6A 200 :YYSVLYFSEGY T0441 201 :TLQRQLHGWQSAMIENY 1jx6A 211 :ISDVRGDTFIHQVNRDN T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGR T0441 276 :TDIAIICLEGSSMG 1jx6A 282 :EDIMINGWGGGSAE T0441 291 :HAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 1jx6A 300 :QKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADS Number of specific fragments extracted= 13 number of extra gaps= 0 total=340 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jx6A/T0441-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1jx6A/T0441-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0441-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0441 40 :SDKLREKIQQ 1jx6A 38 :FPEQRNLTNA T0441 51 :VDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYS 1jx6A 48 :LSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQV T0441 109 :DYSIEQEEKLLSTFLESRPAGVVLFGSEHS 1jx6A 110 :NADIKQQSLSLMEALKSKSDYLIFTLDTTR T0441 140 :RTHQLLEASNTPVLEIAELS 1jx6A 142 :KFVEHVLDSTNTKLILQNIT T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQ 1jx6A 169 :KHQPFLYVGFDHAEGSRELATEFGKF T0441 186 :GFKNVGFIGARGN 1jx6A 197 :KHTYYSVLYFSEG T0441 200 :STLQRQLHGWQSAMIENY 1jx6A 210 :YISDVRGDTFIHQVNRDN T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGR T0441 276 :TDIAIICLEGSSMGEHA 1jx6A 282 :EDIMINGWGGGSAELDA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1jx6A 302 :GDLDITVMRMNDDTGIAMAEAIKWDLEDKPVP T0441 326 :PTSMGFKLKRRAS 1jx6A 334 :TVYSGDFEIVTKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=351 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dri/T0441-2dri-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dri expands to /projects/compbio/data/pdb/2dri.pdb.gz 2dri:Warning: there is no chain 2dri will retry with 2driA # T0441 read from 2dri/T0441-2dri-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dri read from 2dri/T0441-2dri-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dri to template set # found chain 2dri in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2dri)K1 Warning: unaligning (T0441)A337 because last residue in template chain is (2dri)Q271 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2dri 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2dri 72 :GNAVKMANQANIPVITLDRQATKGE T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2dri 98 :VSHIASDNVLGGKIAGDYIAKK T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYL 2dri 122 :EGAKVIELQGIAGTSAARERGEGFQQAVAAHKF T0441 221 :DHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2dri 155 :NVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK T0441 276 :TDIAIICLEGSSMG 2dri 207 :SDVMVVGFDGTPDG T0441 290 :EHAYPSL 2dri 223 :AVNDGKL T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRR 2dri 231 :ATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=359 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dri/T0441-2dri-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2dri/T0441-2dri-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dri read from 2dri/T0441-2dri-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dri in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2dri)K1 Warning: unaligning (T0441)A337 because last residue in template chain is (2dri)Q271 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2dri 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2dri 72 :GNAVKMANQANIPVITLDRQATKGE T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFK 2dri 98 :VSHIASDNVLGGKIAGDYIAKKAGE T0441 189 :NVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2dri 125 :KVIELQGIAGTSAARERGEGFQQAVAAHKFNV T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRV 2dri 157 :LASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAG T0441 275 :PTDIAIICLEGSSMGEHA 2dri 206 :KSDVMVVGFDGTPDGEKA T0441 294 :PSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRR 2dri 228 :KLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=366 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dri/T0441-2dri-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2dri/T0441-2dri-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dri read from 2dri/T0441-2dri-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dri in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2dri)K1 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2dri 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDA T0441 140 :RTHQLLEASNTPVLEIAELSSK 2dri 73 :NAVKMANQANIPVITLDRQATK T0441 162 :ASYLNIGVDHFEVGKACTRHLIEQ 2dri 96 :EVVSHIASDNVLGGKIAGDYIAKK T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2dri 122 :EGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNV T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2dri 157 :LASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK T0441 276 :TDIAIICLEGSSMGEHA 2dri 207 :SDVMVVGFDGTPDGEKA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSM 2dri 227 :GKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPV T0441 331 :FKLKRRA 2dri 264 :DLKLVVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=374 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbqA/T0441-1dbqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dbqA expands to /projects/compbio/data/pdb/1dbq.pdb.gz 1dbqA:# T0441 read from 1dbqA/T0441-1dbqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbqA read from 1dbqA/T0441-1dbqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dbqA to template set # found chain 1dbqA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1dbqA)K60 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)G148 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G148 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)E149 Warning: unaligning (T0441)V169 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)N161 Warning: unaligning (T0441)D170 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)N161 Warning: unaligning (T0441)R196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbqA)A194 Warning: unaligning (T0441)Q203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbqA)A194 Warning: unaligning (T0441)R204 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G195 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1dbqA 61 :SIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIA 1dbqA 139 :HIPMVVMD T0441 160 :SKAS 1dbqA 150 :AKAD T0441 164 :YLNIG 1dbqA 155 :TDAVI T0441 171 :HFEVGKACTRHLIEQGFKNVGFIGA 1dbqA 162 :AFEGGYMAGRYLIERGHREIGVIPG T0441 205 :QLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1dbqA 196 :RLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRAST 1dbqA 317 :QSIEVHPRLIERRSV T0441 340 :A 1dbqA 333 :D Number of specific fragments extracted= 8 number of extra gaps= 2 total=382 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbqA/T0441-1dbqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1dbqA/T0441-1dbqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbqA read from 1dbqA/T0441-1dbqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dbqA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1dbqA)K60 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)G148 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G148 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)E149 Warning: unaligning (T0441)D170 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)N161 Warning: unaligning (T0441)H171 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)N161 Warning: unaligning (T0441)R196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbqA)A194 Warning: unaligning (T0441)Q203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbqA)A194 Warning: unaligning (T0441)R204 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G195 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1dbqA 61 :SIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIA 1dbqA 139 :HIPMVVMD T0441 160 :SKASYLNIGV 1dbqA 150 :AKADFTDAVI T0441 172 :FEVGKACTRHLIEQGFKNVGFIGA 1dbqA 163 :FEGGYMAGRYLIERGHREIGVIPG T0441 205 :QLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1dbqA 196 :RLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRASTAI 1dbqA 317 :QSIEVHPRLIERRSVAD Number of specific fragments extracted= 6 number of extra gaps= 2 total=388 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbqA/T0441-1dbqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1dbqA/T0441-1dbqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dbqA read from 1dbqA/T0441-1dbqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dbqA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (1dbqA)K60 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)G148 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G148 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)E149 Warning: unaligning (T0441)V169 because of BadResidue code BAD_PEPTIDE in next template residue (1dbqA)N161 Warning: unaligning (T0441)D170 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)N161 Warning: unaligning (T0441)R196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbqA)A194 Warning: unaligning (T0441)Q203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbqA)A194 Warning: unaligning (T0441)R204 because of BadResidue code BAD_PEPTIDE at template residue (1dbqA)G195 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1dbqA 61 :SIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIA 1dbqA 139 :HIPMVVMD T0441 160 :SKAS 1dbqA 150 :AKAD T0441 164 :YLNIG 1dbqA 155 :TDAVI T0441 171 :HFEVGKACTRHLIEQGFKNVGFIGA 1dbqA 162 :AFEGGYMAGRYLIERGHREIGVIPG T0441 205 :QLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 1dbqA 196 :RLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVAD Number of specific fragments extracted= 6 number of extra gaps= 2 total=394 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fn9A/T0441-2fn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fn9A expands to /projects/compbio/data/pdb/2fn9.pdb.gz 2fn9A:# T0441 read from 2fn9A/T0441-2fn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn9A read from 2fn9A/T0441-2fn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fn9A to template set # found chain 2fn9A in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2fn9A)G2 Warning: unaligning (T0441)A337 because last residue in template chain is (2fn9A)E281 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2fn9A 3 :KMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDAD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2fn9A 72 :IANVKRAKEAGIPVFCVDRGINARG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2fn9A 99 :VAQIYSDNYYGGVLAGEYFVKF T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2fn9A 129 :KEIPYAELLGILSAQPTWDRSNGFHSVVDQYP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2fn9A 161 :EFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGR T0441 276 :TDIAIICLEGSSMG 2fn9A 215 :TDIYIFGFDGAEDV T0441 290 :EHAYPS 2fn9A 230 :NAIKEG T0441 296 :LTSAEFDYERMGTKAAEKLLHAIKGEPE 2fn9A 239 :VATIMQFPKLMARLAVEWADQYLRGERS T0441 324 :ERPTSMGFKLKRR 2fn9A 268 :PEIVPVTVELVTR Number of specific fragments extracted= 9 number of extra gaps= 0 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fn9A/T0441-2fn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fn9A/T0441-2fn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn9A read from 2fn9A/T0441-2fn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fn9A in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2fn9A)G2 Warning: unaligning (T0441)A337 because last residue in template chain is (2fn9A)E281 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2fn9A 3 :KMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADG T0441 140 :RTHQLLEASNTPVLEIAELSS 2fn9A 73 :ANVKRAKEAGIPVFCVDRGIN T0441 161 :KASYLNIGVDHFEVGKACTRHLIEQ 2fn9A 96 :GLAVAQIYSDNYYGGVLAGEYFVKF T0441 186 :GFK 2fn9A 127 :DAK T0441 189 :NVGFIGARGNHSTLQRQLHGWQSAMIENY 2fn9A 132 :PYAELLGILSAQPTWDRSNGFHSVVDQYP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRV 2fn9A 161 :EFKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAG T0441 275 :PTDIAIICLEGSSMGEHA 2fn9A 214 :RTDIYIFGFDGAEDVINA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPE 2fn9A 236 :KQIVATIMQFPKLMARLAVEWADQYLRGERS T0441 324 :ERPTSMGFKLKRR 2fn9A 268 :PEIVPVTVELVTR Number of specific fragments extracted= 9 number of extra gaps= 0 total=412 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fn9A/T0441-2fn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fn9A/T0441-2fn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fn9A read from 2fn9A/T0441-2fn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fn9A in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2fn9A)G2 Warning: unaligning (T0441)S338 because last residue in template chain is (2fn9A)E281 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2fn9A 3 :KMAIVISTLNNPWFVVLAETAKQRAEQLGYEATIFDSQNDTAKESAHFDAIIAAGYDAIIFNPTDADG T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2fn9A 73 :ANVKRAKEAGIPVFCVDRGINARG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2fn9A 99 :VAQIYSDNYYGGVLAGEYFVKF T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYL 2fn9A 129 :KEIPYAELLGILSAQPTWDRSNGFHSVVDQYPE T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2fn9A 162 :FKMVAQQSAEFDRDTAYKVTEQILQAHPEIKAIWCGNDAMALGAMKACEAAGR T0441 276 :TDIAIICLEGSSMGEHA 2fn9A 215 :TDIYIFGFDGAEDVINA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRA 2fn9A 236 :KQIVATIMQFPKLMARLAVEWADQYLRGERSFPEIVPVTVELVTR Number of specific fragments extracted= 7 number of extra gaps= 0 total=419 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2driA/T0441-2driA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2driA expands to /projects/compbio/data/pdb/2dri.pdb.gz 2driA:# T0441 read from 2driA/T0441-2driA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2driA read from 2driA/T0441-2driA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2driA to template set # found chain 2driA in template set Warning: unaligning (T0441)A337 because last residue in template chain is (2driA)Q271 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2driA 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2driA 72 :GNAVKMANQANIPVITLDRQATKGE T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2driA 98 :VSHIASDNVLGGKIAGDYIAKK T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYL 2driA 122 :EGAKVIELQGIAGTSAARERGEGFQQAVAAHKF T0441 221 :DHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2driA 155 :NVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGK T0441 276 :TDIAIICLEGSSMG 2driA 207 :SDVMVVGFDGTPDG T0441 290 :EHAYPSL 2driA 223 :AVNDGKL T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRR 2driA 231 :ATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=427 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2driA/T0441-2driA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2driA/T0441-2driA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2driA read from 2driA/T0441-2driA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2driA in template set Warning: unaligning (T0441)A337 because last residue in template chain is (2driA)Q271 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2driA 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSD T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2driA 72 :GNAVKMANQANIPVITLDRQATKGE T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2driA 98 :VSHIASDNVLGGKIAGDYIAKK T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2driA 122 :EGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNV T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRV 2driA 157 :LASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAG T0441 275 :PTDIAIICLEGSSMGEHAYPS 2driA 206 :KSDVMVVGFDGTPDGEKAVND T0441 296 :LTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRR 2driA 230 :AATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=434 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2driA/T0441-2driA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2driA/T0441-2driA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2driA read from 2driA/T0441-2driA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2driA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2driA)K1 Warning: unaligning (T0441)A337 because last residue in template chain is (2driA)Q271 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2driA 2 :DTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDA T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2driA 73 :NAVKMANQANIPVITLDRQATKGE T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFK 2driA 98 :VSHIASDNVLGGKIAGDYIAKKAGE T0441 189 :NVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2driA 125 :KVIELQGIAGTSAARERGEGFQQAVAAHKFNV T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRV 2driA 157 :LASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAG T0441 275 :PTDIAIICLEGSSMGEHA 2driA 206 :KSDVMVVGFDGTPDGEKA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRR 2driA 227 :GKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=441 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3clkA/T0441-3clkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3clkA expands to /projects/compbio/data/pdb/3clk.pdb.gz 3clkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 3clkA/T0441-3clkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3clkA read from 3clkA/T0441-3clkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3clkA to template set # found chain 3clkA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3clkA)S61 Warning: unaligning (T0441)Y107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)H109 Warning: unaligning (T0441)E136 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)N133 Warning: unaligning (T0441)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)N133 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)P143 Warning: unaligning (T0441)P151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)P143 Warning: unaligning (T0441)L158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)D153 Warning: unaligning (T0441)K161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)D153 Warning: unaligning (T0441)N198 because of BadResidue code BAD_PEPTIDE in next template residue (3clkA)P190 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE at template residue (3clkA)P190 Warning: unaligning (T0441)E323 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)I315 Warning: unaligning (T0441)I341 because last residue in template chain is (3clkA)L334 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLG 3clkA 62 :NVIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIV T0441 118 :LLSTFLESRPAGVVLFGS 3clkA 110 :ALLTAIERPVMGILLLSI T0441 142 :HQLLEA 3clkA 134 :LQLLQS T0441 152 :VLEIAE 3clkA 144 :YCFLSM T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARG 3clkA 154 :DRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQ T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAK 3clkA 191 :YTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAMKA T0441 243 :LLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAI 3clkA 233 :FGKNTDLTGIIAASDMTAIGILNQASSFGIEVPKDLSIVSIDGTEMCKITRPQLTSISQDFFQMGVTGVQQIHQSV T0441 324 :ERPTSMGFKLKRRAST 3clkA 316 :VSQQFIPVNPVIRKST T0441 340 :A 3clkA 333 :R Number of specific fragments extracted= 9 number of extra gaps= 1 total=450 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3clkA/T0441-3clkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3clkA/T0441-3clkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3clkA read from 3clkA/T0441-3clkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3clkA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3clkA)S61 Warning: unaligning (T0441)Y107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)H109 Warning: unaligning (T0441)E136 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)N133 Warning: unaligning (T0441)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)N133 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)P143 Warning: unaligning (T0441)P151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)P143 Warning: unaligning (T0441)L158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)D153 Warning: unaligning (T0441)A162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)D153 Warning: unaligning (T0441)N198 because of BadResidue code BAD_PEPTIDE in next template residue (3clkA)P190 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE at template residue (3clkA)P190 Warning: unaligning (T0441)K319 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)I315 Warning: unaligning (T0441)E323 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)I315 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLG 3clkA 62 :NVIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIV T0441 118 :LLSTFLESRPAGVVLFGS 3clkA 110 :ALLTAIERPVMGILLLSI T0441 142 :HQLLEA 3clkA 134 :LQLLQS T0441 152 :VLEIAE 3clkA 144 :YCFLSM T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARG 3clkA 154 :DRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQ T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAK 3clkA 191 :YTGRKRLAGYKKALKEANIAINQEWIKPGDYSYTSGEQAMKA T0441 243 :LLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAI 3clkA 233 :FGKNTDLTGIIAASDMTAIGILNQASSFGIEVPKDLSIVSIDGTEMCKITRPQLTSISQDFFQMGVTGVQQIHQSV T0441 324 :ERPTSMGFKLKRRASTAIN 3clkA 316 :VSQQFIPVNPVIRKSTARL Number of specific fragments extracted= 8 number of extra gaps= 1 total=458 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3clkA/T0441-3clkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3clkA/T0441-3clkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3clkA read from 3clkA/T0441-3clkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3clkA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3clkA)S61 Warning: unaligning (T0441)Y107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)H109 Warning: unaligning (T0441)E136 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)N133 Warning: unaligning (T0441)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)N133 Warning: unaligning (T0441)S148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)P143 Warning: unaligning (T0441)P151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)P143 Warning: unaligning (T0441)L158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)D153 Warning: unaligning (T0441)K161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3clkA)D153 Warning: unaligning (T0441)N198 because of BadResidue code BAD_PEPTIDE in next template residue (3clkA)P190 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE at template residue (3clkA)P190 Warning: unaligning (T0441)K319 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3clkA)I315 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLG 3clkA 62 :NVIAAVVSSVRTNFAQQILDGIQEEAHKNGYNLIIV T0441 118 :LLSTFLESRPAGVVLFGS 3clkA 110 :ALLTAIERPVMGILLLSI T0441 142 :HQLLEA 3clkA 134 :LQLLQS T0441 152 :VLEIAE 3clkA 144 :YCFLSM T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARG 3clkA 154 :DRPFISSDDEDIGYQATNLLINEGHRQIGIAGIDQ T0441 200 :STLQRQLHGWQSAMIENYLTPDHFLTT 3clkA 191 :YTGRKRLAGYKKALKEANIAINQEWIK T0441 228 :EAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAI 3clkA 218 :PGDYSYTSGEQAMKAFGKNTDLTGIIAASDMTAIGILNQASSFGIEVPKDLSIVSIDGTEMCKITRPQLTSISQDFFQMGVTGVQQIHQSV T0441 321 :EPEERPTSMGFKLKRRAS 3clkA 316 :VSQQFIPVNPVIRKSTAR Number of specific fragments extracted= 8 number of extra gaps= 1 total=466 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qvcA/T0441-2qvcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qvcA expands to /projects/compbio/data/pdb/2qvc.pdb.gz 2qvcA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 2qvcA/T0441-2qvcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qvcA read from 2qvcA/T0441-2qvcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qvcA to template set # found chain 2qvcA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2qvcA)L32 T0441 72 :SIALIIPSL 2qvcA 33 :TIGVIGKSV T0441 82 :EKACAHFLPSFQQALNKAGYQLLLGYSDY 2qvcA 42 :HPYWSQVEQGVKAAGKALGVDTKFFVPQK T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHS 2qvcA 72 :DINAQLQMLESFIAEGVNGIAIAPSDPT T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 2qvcA 102 :IPTIKKALEMGIPVVTLDTDSPDSG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2qvcA 128 :YVYIGTDNYQAGYTAGLIMKEL T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMI 2qvcA 152 :GKGKVVIGTGSLTAMNSLQRIQGFKDAIK T0441 217 :YLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 2qvcA 181 :DSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKV T0441 276 :TDIAIICLEGSSMG 2qvcA 238 :GKVKIVCFDTTPDI T0441 290 :EHAYPS 2qvcA 253 :QYVKEG T0441 296 :L 2qvcA 260 :I T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGE 2qvcA 262 :ATMGQRPYMMGYLSVTVLYLMNKIG T0441 325 :RPTSMGFKLKRRAS 2qvcA 305 :YVIDTGVDVVTPEN Number of specific fragments extracted= 12 number of extra gaps= 0 total=478 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qvcA/T0441-2qvcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qvcA/T0441-2qvcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qvcA read from 2qvcA/T0441-2qvcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qvcA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2qvcA)L32 T0441 72 :SIALIIPSL 2qvcA 33 :TIGVIGKSV T0441 82 :EKACAHFLPSFQQALNKAGYQLLLGYSDY 2qvcA 42 :HPYWSQVEQGVKAAGKALGVDTKFFVPQK T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2qvcA 72 :DINAQLQMLESFIAEGVNGIAIAPSDPTA T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2qvcA 103 :PTIKKALEMGIPVVTLDTDSPDSG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2qvcA 128 :YVYIGTDNYQAGYTAGLIMKEL T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2qvcA 152 :GKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEI T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2qvcA 187 :VDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGK T0441 275 :PTDIAIICLEGSSMG 2qvcA 237 :VGKVKIVCFDTTPDI T0441 290 :EHAYPSLT 2qvcA 254 :YVKEGVIQ T0441 298 :SAEFDYERMGTKAAEKLLHAIKGE 2qvcA 263 :TMGQRPYMMGYLSVTVLYLMNKIG T0441 325 :RPTSMGFKLKR 2qvcA 295 :PKVKVDGKVDY Number of specific fragments extracted= 11 number of extra gaps= 0 total=489 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qvcA/T0441-2qvcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qvcA/T0441-2qvcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qvcA read from 2qvcA/T0441-2qvcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qvcA in template set Warning: unaligning (T0441)S72 because first residue in template chain is (2qvcA)L32 T0441 73 :IALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 2qvcA 33 :TIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQK T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2qvcA 72 :DINAQLQMLESFIAEGVNGIAIAPSDPTA T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2qvcA 103 :PTIKKALEMGIPVVTLDTDSPDSG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2qvcA 128 :YVYIGTDNYQAGYTAGLIMKEL T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAM 2qvcA 152 :GKGKVVIGTGSLTAMNSLQRIQGFKDAI T0441 216 :NYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2qvcA 180 :KDSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGK T0441 275 :PTDIAIICLEGSSMGEHA 2qvcA 237 :VGKVKIVCFDTTPDILQY T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPE 2qvcA 258 :GVIQATMGQRPYMMGYLSVTVLYLMNKIGVQ T0441 324 :ERPTSMGFKLKRRA 2qvcA 293 :MLPKVKVDGKVDYV Number of specific fragments extracted= 9 number of extra gaps= 0 total=498 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjoA/T0441-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rjoA expands to /projects/compbio/data/pdb/2rjo.pdb.gz 2rjoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 2rjoA/T0441-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0441-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rjoA to template set # found chain 2rjoA in template set Warning: unaligning (T0441)A68 because first residue in template chain is (2rjoA)L38 T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLES 2rjoA 39 :GQTTLACSFRSLTNPYYTAFNKGAQSFAKSVGLPYVPLTTEGSSEKGIADIRALLQK T0441 126 :RPAGVVLFGSEHS 2rjoA 97 :GGNLVLNVDPNDS T0441 139 :QRTHQLLEASNTPVLEIAELSSKA 2rjoA 113 :RVIVEACSKAGAYVTTIWNKPKDL T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2rjoA 146 :VAHLSYDGVAYGEETATQLFKS T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2rjoA 170 :GKGGVVALGGIFSNVPAIERKAGLDAALKKFP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLLRDS 2rjoA 202 :GIQLLDFQVADWNSQKAFPIMQAWMTRFN T0441 248 :SLNALVCSHEEIAIGALFECHRRVLK 2rjoA 232 :KIKGVWAANDDMALGAIEALRAEGLA T0441 276 :TDIAIICLEGSSMG 2rjoA 258 :GQIPVTGMDGTQPG T0441 290 :EHAYPS 2rjoA 273 :VAIKSG T0441 296 :LTSAEFDYERMGTKAAEKLLHAIKGEPE 2rjoA 281 :VASVDWDPFWLGGIGLSMGLQAKEKKID T0441 325 :RPTSMGFKLKRRAS 2rjoA 317 :RESFCTATFVTKTN Number of specific fragments extracted= 11 number of extra gaps= 0 total=509 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjoA/T0441-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2rjoA/T0441-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0441-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjoA in template set T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2rjoA 39 :GQTTLACSFRSLTNPYYTAFNKGAQSFAKSVGLPYVPLTTEGSSEKGIADIRALLQKTGGNLVLNVDPND T0441 139 :Q 2rjoA 110 :A T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2rjoA 114 :VIVEACSKAGAYVTTIWNKPKDLH T0441 164 :YLNIGVDHFEVGKACTRHLIE 2rjoA 146 :VAHLSYDGVAYGEETATQLFK T0441 185 :QGFKNVGFIGARGNHSTLQRQLHGWQSAMIEN 2rjoA 169 :GGKGGVVALGGIFSNVPAIERKAGLDAALKKF T0441 217 :YLTP 2rjoA 202 :GIQL T0441 223 :FLTTHEAPSSQLGAEGLAKLLLR 2rjoA 206 :LDFQVADWNSQKAFPIMQAWMTR T0441 246 :DSSLNALVCSHEEIAIGALFECHRRVL 2rjoA 230 :NSKIKGVWAANDDMALGAIEALRAEGL T0441 275 :PTDIAIICLEGSS 2rjoA 257 :AGQIPVTGMDGTQ T0441 288 :MGEHAYPSLT 2rjoA 272 :LVAIKSGELV T0441 298 :SAEFDYERMGTKAAEKLLHAIKGEPE 2rjoA 283 :SVDWDPFWLGGIGLSMGLQAKEKKID T0441 325 :RPTSMGFKLKRRAS 2rjoA 317 :RESFCTATFVTKTN Number of specific fragments extracted= 12 number of extra gaps= 0 total=521 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rjoA/T0441-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2rjoA/T0441-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0441-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjoA in template set Warning: unaligning (T0441)A68 because first residue in template chain is (2rjoA)L38 T0441 69 :ESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPA 2rjoA 39 :GQTTLACSFRSLTNPYYTAFNKGAQSFAKSVGLPYVPLTTEGSSEKGIADIRALLQKTGG T0441 129 :GVVLFGSEHSQ 2rjoA 100 :LVLNVDPNDSA T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 2rjoA 114 :VIVEACSKAGAYVTTIWNKPKDLH T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2rjoA 146 :VAHLSYDGVAYGEETATQLFKS T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2rjoA 170 :GKGGVVALGGIFSNVPAIERKAGLDAALKKFP T0441 219 :TPDHFLTTHEAPSSQLGAEGLAKLLL 2rjoA 202 :GIQLLDFQVADWNSQKAFPIMQAWMT T0441 245 :RDSSLNALVCSHEEIAIGALFECHRRVL 2rjoA 229 :FNSKIKGVWAANDDMALGAIEALRAEGL T0441 275 :PTDIAIICLEGSS 2rjoA 257 :AGQIPVTGMDGTQ T0441 289 :GEHA 2rjoA 271 :GLVA T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRA 2rjoA 278 :GELVASVDWDPFWLGGIGLSMGLQAKEKKIDLATLPKDRRESFCT Number of specific fragments extracted= 10 number of extra gaps= 0 total=531 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brsA/T0441-3brsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3brsA expands to /projects/compbio/data/pdb/3brs.pdb.gz 3brsA:Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 3brsA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 3brsA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 3brsA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 3brsA # T0441 read from 3brsA/T0441-3brsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brsA read from 3brsA/T0441-3brsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3brsA to template set # found chain 3brsA in template set Warning: unaligning (T0441)E69 because first residue in template chain is (3brsA)Q5 Warning: unaligning (T0441)F81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)S18 Warning: unaligning (T0441)V131 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)L71 Warning: unaligning (T0441)L132 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)L71 Warning: unaligning (T0441)A156 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)S98 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)S98 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3brsA)D112 Warning: unaligning (T0441)D170 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3brsA)D112 Warning: unaligning (T0441)N189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I134 Warning: unaligning (T0441)V190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I134 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I223 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I223 Warning: unaligning (T0441)G289 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brsA)E235 Warning: unaligning (T0441)Y293 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brsA)E235 Warning: unaligning (T0441)P294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I237 Warning: unaligning (T0441)S295 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I237 Warning: unaligning (T0441)L296 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)E239 Warning: unaligning (T0441)T297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)A240 Warning: unaligning (T0441)K334 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)T278 Warning: unaligning (T0441)R335 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)T278 Warning: unaligning (T0441)R336 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)D280 Warning: unaligning (T0441)A337 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)D280 T0441 70 :SYSIALIIPSL 3brsA 6 :YYMICIPKVLD T0441 82 :EKACAHFLPSFQQALNKAGYQLLLGYSDY 3brsA 19 :SDFWSVLVEGAQMAAKEYEIKLEFMAPEK T0441 111 :SIEQEEKLLSTFLESRPAGV 3brsA 50 :DYLVQNELIEEAIKRKPDVI T0441 133 :FGSEHS 3brsA 72 :AAADYE T0441 139 :QRTHQLLEASNTPVLEI 3brsA 80 :YDAAKEIKDAGIKLIVI T0441 158 :LSSKAS 3brsA 99 :GMKQDI T0441 164 :YLNIG 3brsA 106 :DITVA T0441 171 :HFEVGKACTRHLIEQ 3brsA 113 :NIQAGIRIGAVTKNL T0441 186 :GFK 3brsA 130 :KSG T0441 191 :GFIGARGNHSTLQRQLHGWQSAMIENY 3brsA 135 :GVISFVKNSKTAMDREEGLKIGLSDDS T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 3brsA 162 :NKIEAIYYCDSNYDKAYDGTVELLTKYPDISVMVGLNQYSATGAARAIKDMSLE T0441 276 :TDIAII 3brsA 216 :AKVKLV T0441 284 :EGSSM 3brsA 224 :DSSME T0441 298 :SAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKL 3brsA 241 :MVVQKPFNIGYLGVEKALKLLKKEYVPKQLDSGCAL Number of specific fragments extracted= 14 number of extra gaps= 8 total=545 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brsA/T0441-3brsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3brsA/T0441-3brsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brsA read from 3brsA/T0441-3brsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3brsA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3brsA)Q5 Warning: unaligning (T0441)E82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)S18 Warning: unaligning (T0441)V131 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)L71 Warning: unaligning (T0441)L132 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)L71 Warning: unaligning (T0441)A156 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)S98 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)S98 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3brsA)D112 Warning: unaligning (T0441)D170 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3brsA)D112 Warning: unaligning (T0441)N189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I134 Warning: unaligning (T0441)V190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I134 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I223 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I223 Warning: unaligning (T0441)G289 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3brsA)E235 Warning: unaligning (T0441)Y293 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brsA)E235 Warning: unaligning (T0441)P294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I237 Warning: unaligning (T0441)S295 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I237 Warning: unaligning (T0441)L296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)F238 Warning: unaligning (T0441)T297 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)E239 Warning: unaligning (T0441)K334 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)T278 Warning: unaligning (T0441)R335 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)T278 Warning: unaligning (T0441)R336 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)D280 Warning: unaligning (T0441)A337 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)D280 T0441 71 :YSIALIIPSLF 3brsA 6 :YYMICIPKVLD T0441 83 :KACAHFLPSFQQALNKAGYQLLLGYSDY 3brsA 20 :DFWSVLVEGAQMAAKEYEIKLEFMAPEK T0441 111 :SIEQEEKLLSTFLESRPAGV 3brsA 50 :DYLVQNELIEEAIKRKPDVI T0441 133 :FGSEHSQ 3brsA 72 :AAADYEK T0441 140 :RTHQLLEASNTPVLEI 3brsA 81 :DAAKEIKDAGIKLIVI T0441 158 :LSSKAS 3brsA 99 :GMKQDI T0441 164 :YLNIG 3brsA 106 :DITVA T0441 171 :HFEVGKACTRHLIEQ 3brsA 113 :NIQAGIRIGAVTKNL T0441 186 :GFK 3brsA 130 :KSG T0441 191 :GFIGARGNHSTLQRQLHGWQSAMIENY 3brsA 135 :GVISFVKNSKTAMDREEGLKIGLSDDS T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 3brsA 162 :NKIEAIYYCDSNYDKAYDGTVELLTKYPDISVMVGLNQYSATGAARAIKDMSLE T0441 276 :TDIAII 3brsA 216 :AKVKLV T0441 284 :EGSSM 3brsA 224 :DSSME T0441 298 :SAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKL 3brsA 241 :MVVQKPFNIGYLGVEKALKLLKKEYVPKQLDSGCAL Number of specific fragments extracted= 14 number of extra gaps= 7 total=559 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3brsA/T0441-3brsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3brsA/T0441-3brsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3brsA read from 3brsA/T0441-3brsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3brsA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3brsA)Q5 Warning: unaligning (T0441)L80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)S18 Warning: unaligning (T0441)F81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)S18 Warning: unaligning (T0441)V131 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)L71 Warning: unaligning (T0441)L132 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)L71 Warning: unaligning (T0441)A156 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)S98 Warning: unaligning (T0441)E157 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)S98 Warning: unaligning (T0441)V169 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (3brsA)D112 Warning: unaligning (T0441)D170 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (3brsA)D112 Warning: unaligning (T0441)N189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I134 Warning: unaligning (T0441)V190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I134 Warning: unaligning (T0441)C282 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I223 Warning: unaligning (T0441)L283 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I223 Warning: unaligning (T0441)A292 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3brsA)E235 Warning: unaligning (T0441)Y293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)I237 Warning: unaligning (T0441)P294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)I237 Warning: unaligning (T0441)S295 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)F238 Warning: unaligning (T0441)L296 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)E239 Warning: unaligning (T0441)T297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)A240 Warning: unaligning (T0441)R335 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3brsA)T278 Warning: unaligning (T0441)R336 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3brsA)T278 Warning: unaligning (T0441)A337 because of BadResidue code BAD_PEPTIDE in next template residue (3brsA)D280 Warning: unaligning (T0441)S338 because of BadResidue code BAD_PEPTIDE at template residue (3brsA)D280 T0441 71 :YSIALIIPS 3brsA 6 :YYMICIPKV T0441 82 :EKACAHFLPSFQQALNKAGYQLLLGYSDY 3brsA 19 :SDFWSVLVEGAQMAAKEYEIKLEFMAPEK T0441 111 :SIEQEEKLLSTFLESRPAGV 3brsA 50 :DYLVQNELIEEAIKRKPDVI T0441 133 :FGSEHSQ 3brsA 72 :AAADYEK T0441 140 :RTHQLLEASNTPVLEI 3brsA 81 :DAAKEIKDAGIKLIVI T0441 158 :LSSKAS 3brsA 99 :GMKQDI T0441 164 :YLNIG 3brsA 106 :DITVA T0441 171 :HFEVGKACTRHLIEQ 3brsA 113 :NIQAGIRIGAVTKNL T0441 186 :GFK 3brsA 130 :KSG T0441 191 :GFIGARGNHSTLQRQLHGWQSAMIENY 3brsA 135 :GVISFVKNSKTAMDREEGLKIGLSDDS T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 3brsA 162 :NKIEAIYYCDSNYDKAYDGTVELLTKYPDISVMVGLNQYSATGAARAIKDMSL T0441 275 :PTDIAII 3brsA 215 :EAKVKLV T0441 284 :EGSS 3brsA 224 :DSSM T0441 298 :SAEFDYERMGTKAAEKLLHAIKGEPEER 3brsA 241 :MVVQKPFNIGYLGVEKALKLLKKEYVPK T0441 327 :TSMGFKLK 3brsA 269 :QLDSGCAL Number of specific fragments extracted= 15 number of extra gaps= 7 total=574 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3hA/T0441-2h3hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h3hA expands to /projects/compbio/data/pdb/2h3h.pdb.gz 2h3hA:Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1179, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1181, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1183, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1185, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1187, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1189, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1191, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1193, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 2h3hA Skipped atom 1983, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1985, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1987, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1989, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1991, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1993, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1995, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 1997, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2179, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2181, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2183, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2185, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2187, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2189, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2191, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2193, because occupancy 0.300 <= existing 0.700 in 2h3hA Skipped atom 2195, because occupancy 0.300 <= existing 0.700 in 2h3hA # T0441 read from 2h3hA/T0441-2h3hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3hA read from 2h3hA/T0441-2h3hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h3hA to template set # found chain 2h3hA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2h3hA)M1 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE in next template residue (2h3hA)S92 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (2h3hA)S92 T0441 71 :YSIALIIPSL 2h3hA 2 :LTIGVIGKSV T0441 82 :EKACAHFLPSFQQALNKAGYQLLLG 2h3hA 12 :HPYWSQVEQGVKAAGKALGVDTKFF T0441 107 :YSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2h3hA 38 :PQKEDINAQLQMLESFIAEGVNGIAIAPSDPT T0441 139 :QRTHQLLEASNTPVLEIAE 2h3hA 72 :IPTIKKALEMGIPVVTLDT T0441 160 :SKAS 2h3hA 93 :PDSG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2h3hA 98 :YVYIGTDNYQAGYTAGLIMKEL T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMI 2h3hA 122 :GKGKVVIGTGSLTAMNSLQRIQGFKDAIK T0441 217 :YLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 2h3hA 151 :DSEIEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGKV T0441 276 :TDIAIICLEGSSMG 2h3hA 208 :GKVKIVCFDTTPDI T0441 290 :EHAYPS 2h3hA 223 :QYVKEG T0441 296 :L 2h3hA 230 :I T0441 297 :TSAEFDYERMGTKAAEKLLHAIKGE 2h3hA 232 :ATMGQRPYMMGYLSVTVLYLMNKIG T0441 324 :E 2h3hA 271 :G T0441 325 :RPTSMGFKLKRRAS 2h3hA 275 :YVIDTGVDVVTPEN Number of specific fragments extracted= 14 number of extra gaps= 1 total=588 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3hA/T0441-2h3hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2h3hA/T0441-2h3hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3hA read from 2h3hA/T0441-2h3hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h3hA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (2h3hA)M1 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE in next template residue (2h3hA)S92 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (2h3hA)S92 T0441 71 :YSIALIIPSL 2h3hA 2 :LTIGVIGKSV T0441 82 :EKACAHFLPSFQQALNKAGYQLLLGYSDY 2h3hA 12 :HPYWSQVEQGVKAAGKALGVDTKFFVPQK T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHS 2h3hA 42 :DINAQLQMLESFIAEGVNGIAIAPSDPT T0441 139 :QRTHQLLEASNTPVLEIAE 2h3hA 72 :IPTIKKALEMGIPVVTLDT T0441 160 :SKAS 2h3hA 93 :PDSG T0441 164 :YLNIGVDHFEVGKACTRHLIE 2h3hA 98 :YVYIGTDNYQAGYTAGLIMKE T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 2h3hA 122 :GKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSEIEI T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2h3hA 157 :VDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGK T0441 275 :PTDIAIICLEGSS 2h3hA 207 :VGKVKIVCFDTTP T0441 288 :MGEHAYPSLT 2h3hA 222 :LQYVKEGVIQ T0441 298 :SAEFDYERMGTKAAEKLLHAIKGE 2h3hA 233 :TMGQRPYMMGYLSVTVLYLMNKIG T0441 325 :RPTSMGFKLKR 2h3hA 265 :PKVKVDGKVDY Number of specific fragments extracted= 12 number of extra gaps= 1 total=600 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3hA/T0441-2h3hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2h3hA/T0441-2h3hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3hA read from 2h3hA/T0441-2h3hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h3hA in template set Warning: unaligning (T0441)Y71 because first residue in template chain is (2h3hA)M1 Warning: unaligning (T0441)L158 because of BadResidue code BAD_PEPTIDE in next template residue (2h3hA)S92 Warning: unaligning (T0441)S159 because of BadResidue code BAD_PEPTIDE at template residue (2h3hA)S92 T0441 72 :SIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 2h3hA 2 :LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQK T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2h3hA 42 :DINAQLQMLESFIAEGVNGIAIAPSDPTA T0441 140 :RTHQLLEASNTPVLEIAE 2h3hA 73 :PTIKKALEMGIPVVTLDT T0441 160 :SKAS 2h3hA 93 :PDSG T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 2h3hA 98 :YVYIGTDNYQAGYTAGLIMKEL T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENY 2h3hA 122 :GKGKVVIGTGSLTAMNSLQRIQGFKDAIKDSE T0441 220 :PDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 2h3hA 154 :IEIVDILNDEEDGARAVSLAEAALNAHPDLDAFFGVYAYNGPAQALVVKNAGK T0441 275 :PTDIAIICLEGSS 2h3hA 207 :VGKVKIVCFDTTP T0441 289 :GEHA 2h3hA 221 :ILQY T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPE 2h3hA 228 :GVIQATMGQRPYMMGYLSVTVLYLMNKIGVQ T0441 324 :ERPTSMGFKLKRRA 2h3hA 263 :MLPKVKVDGKVDYV Number of specific fragments extracted= 11 number of extra gaps= 1 total=611 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 8abpA/T0441-8abpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 8abpA expands to /projects/compbio/data/pdb/8abp.pdb.gz 8abpA:# T0441 read from 8abpA/T0441-8abpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8abpA read from 8abpA/T0441-8abpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 8abpA to template set # found chain 8abpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (8abpA)N2 Warning: unaligning (T0441)E321 because of BadResidue code BAD_PEPTIDE in next template residue (8abpA)E276 Warning: unaligning (T0441)P322 because of BadResidue code BAD_PEPTIDE at template residue (8abpA)E276 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYS 8abpA 3 :LKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAV T0441 110 :YSIEQEEKLLSTFLESRPAGVVLFGSEHS 8abpA 41 :PDGEKTLNAIDSLAASGAKGFVICTPDPK T0441 139 :QRTHQLLEASNTPVLEIAELSSKA 8abpA 72 :SAIVAKARGYDMKVIAVDDQFVNA T0441 163 :SYLNIGVDHFEVGKACTRHLIEQ 8abpA 102 :TVPLVMLAATKIGERQGQELYKE T0441 186 :GFK 8abpA 129 :GWD T0441 189 :NVGFIGAR 8abpA 134 :ESAVMAIT T0441 197 :GNHSTLQRQLHGWQSAMIENYLTPDHF 8abpA 143 :NELDTARRRTTGSMDALKAAGFPEKQI T0441 224 :LTTHEAPSSQLGAEGLAKLLLRDSSLN 8abpA 171 :QVPTKSNDIPGAFDAANSMLVQHPEVK T0441 251 :ALVCSHEEIAIGALFECHRRVLK 8abpA 200 :LIVGMNDSTVLGGVRATEGQGFK T0441 275 :PTDIAIICLEGSSMG 8abpA 223 :AADIIGIGINGVDAV T0441 290 :EHAYPSL 8abpA 242 :KAQATGF T0441 297 :TSAEFDYERMGTKAAEKLLHAI 8abpA 250 :GSLLPSPDVHGYKSSEMLYNWV T0441 319 :KG 8abpA 273 :KD T0441 323 :EE 8abpA 277 :PP T0441 325 :RPTSMGFKLKRRAS 8abpA 280 :FTEVTDVVLITRDN Number of specific fragments extracted= 15 number of extra gaps= 1 total=626 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 8abpA/T0441-8abpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 8abpA/T0441-8abpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8abpA read from 8abpA/T0441-8abpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 8abpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (8abpA)N2 Warning: unaligning (T0441)E321 because of BadResidue code BAD_PEPTIDE in next template residue (8abpA)E276 Warning: unaligning (T0441)P322 because of BadResidue code BAD_PEPTIDE at template residue (8abpA)E276 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSD 8abpA 3 :LKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHS 8abpA 42 :DGEKTLNAIDSLAASGAKGFVICTPDPK T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 8abpA 72 :SAIVAKARGYDMKVIAVDDQFVNAK T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 8abpA 103 :VPLVMLAATKIGERQGQELYKE T0441 186 :GFK 8abpA 129 :GWD T0441 189 :NVGFIG 8abpA 134 :ESAVMA T0441 195 :ARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTH 8abpA 141 :TANELDTARRRTTGSMDALKAAGFPEKQIYQVP T0441 228 :EAPSSQLGAEGLAKLLLRDSSLN 8abpA 175 :KSNDIPGAFDAANSMLVQHPEVK T0441 251 :ALVCSHEEIAIGALFECHRRVLKV 8abpA 200 :LIVGMNDSTVLGGVRATEGQGFKA T0441 276 :TDIAIICLEGSSMGEHA 8abpA 224 :ADIIGIGINGVDAVSEL T0441 293 :YPSLT 8abpA 245 :ATGFY T0441 298 :SAEFDYERMGTKAAEKLLHAI 8abpA 251 :SLLPSPDVHGYKSSEMLYNWV T0441 319 :KG 8abpA 273 :KD T0441 323 :EERPTSM 8abpA 277 :PPKFTEV T0441 330 :GFKLKRRAS 8abpA 285 :DVVLITRDN Number of specific fragments extracted= 15 number of extra gaps= 1 total=641 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 8abpA/T0441-8abpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 8abpA/T0441-8abpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8abpA read from 8abpA/T0441-8abpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 8abpA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (8abpA)N2 Warning: unaligning (T0441)P322 because of BadResidue code BAD_PEPTIDE in next template residue (8abpA)E276 Warning: unaligning (T0441)E323 because of BadResidue code BAD_PEPTIDE at template residue (8abpA)E276 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSD 8abpA 3 :LKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQ 8abpA 42 :DGEKTLNAIDSLAASGAKGFVICTPDPKL T0441 140 :RTHQLLEASNTPVLEIAELSSKAS 8abpA 73 :AIVAKARGYDMKVIAVDDQFVNAK T0441 164 :YLNIGVDHFEVGKACTRHLIEQ 8abpA 103 :VPLVMLAATKIGERQGQELYKE T0441 186 :GFK 8abpA 129 :GWD T0441 189 :NVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTT 8abpA 135 :SAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQV T0441 227 :HEAPSSQLGAEGLAKLLLRDS 8abpA 174 :TKSNDIPGAFDAANSMLVQHP T0441 248 :SLNALVCSHEEIAIGALFECHRRVLK 8abpA 197 :KHWLIVGMNDSTVLGGVRATEGQGFK T0441 275 :PTDIAIICLEGSSMGEHA 8abpA 223 :AADIIGIGINGVDAVSEL T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGE 8abpA 246 :TGFYGSLLPSPDVHGYKSSEMLYNWVAKD T0441 324 :ERPTSMGFKLKRRAST 8abpA 277 :PPKFTEVTDVVLITRD Number of specific fragments extracted= 11 number of extra gaps= 1 total=652 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvyA/T0441-2fvyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fvyA/T0441-2fvyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvyA read from 2fvyA/T0441-2fvyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fvyA in training set Warning: unaligning (T0441)S70 because first residue in template chain is (2fvyA)D2 Warning: unaligning (T0441)F81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2fvyA)D14 Warning: unaligning (T0441)E82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2fvyA)D14 Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (2fvyA)D236 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (2fvyA)D236 T0441 71 :YSIALIIPSL 2fvyA 3 :TRIGVTIYKY T0441 83 :KACAHFLPSFQQALNKA 2fvyA 15 :NFMSVVRKAIEQDAKAA T0441 100 :GYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2fvyA 33 :DVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPA T0441 139 :QRTHQLLEASNTPVLEIAELSSKA 2fvyA 74 :GTVIEKARGQNVPVVFFNKEPSRK T0441 163 :SYLNIGVDHFEVGKACTRHLIEQ 2fvyA 104 :KAYYVGTDSKESGIIQGDLIAKH T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDS 2fvyA 139 :GQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPN T0441 248 :SLNALVCSHEEIAIGALFECHRRVL 2fvyA 203 :KIEVVIANNDAMAMGAVEALKAHNK T0441 276 :TDIAIIC 2fvyA 228 :SSIPVFG T0441 285 :GSSMG 2fvyA 237 :ALPEA T0441 290 :EHAYPS 2fvyA 243 :ALVKSG T0441 296 :LTSAEFDYERMGTKAAEKLLHAIKGEPE 2fvyA 251 :AGTVLNDANNQAKATFDLAKNLADGKGA T0441 324 :ERPTSMGFKLKRRAST 2fvyA 288 :NKVVRVPYVGVDKDNL Number of specific fragments extracted= 12 number of extra gaps= 2 total=664 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvyA/T0441-2fvyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fvyA/T0441-2fvyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvyA read from 2fvyA/T0441-2fvyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fvyA in training set Warning: unaligning (T0441)S70 because first residue in template chain is (2fvyA)D2 Warning: unaligning (T0441)F81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2fvyA)D14 Warning: unaligning (T0441)E82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2fvyA)D14 Warning: unaligning (T0441)D246 because of BadResidue code BAD_PEPTIDE in next template residue (2fvyA)N202 Warning: unaligning (T0441)S247 because of BadResidue code BAD_PEPTIDE at template residue (2fvyA)N202 Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (2fvyA)D236 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (2fvyA)D236 Warning: unaligning (T0441)I341 because of BadResidue code BAD_PEPTIDE in next template residue (2fvyA)F306 T0441 71 :YSIALIIPSL 2fvyA 3 :TRIGVTIYKY T0441 83 :KACAHFLPSFQQALNK 2fvyA 15 :NFMSVVRKAIEQDAKA T0441 99 :AGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHS 2fvyA 32 :PDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPA T0441 139 :QRTHQLLEASNTPVLEIAELSSK 2fvyA 74 :GTVIEKARGQNVPVVFFNKEPSR T0441 162 :ASYLNIGVDHFEVGKACTRHLIEQ 2fvyA 103 :DKAYYVGTDSKESGIIQGDLIAKH T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLL 2fvyA 139 :GQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLS T0441 245 :R 2fvyA 200 :N T0441 248 :SLNALVCSHEEIAIGALFECHRRVL 2fvyA 203 :KIEVVIANNDAMAMGAVEALKAHNK T0441 276 :TDIAIIC 2fvyA 228 :SSIPVFG T0441 285 :GSSMG 2fvyA 237 :ALPEA T0441 290 :EHAYPSLT 2fvyA 244 :LVKSGALA T0441 298 :SAEFDYERMGTKAAEKLLHAIKGEP 2fvyA 253 :TVLNDANNQAKATFDLAKNLADGKG T0441 323 :EERPTSMGFKLKRRASTA 2fvyA 287 :DNKVVRVPYVGVDKDNLA Number of specific fragments extracted= 13 number of extra gaps= 4 total=677 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvyA/T0441-2fvyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2fvyA/T0441-2fvyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvyA read from 2fvyA/T0441-2fvyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fvyA in training set Warning: unaligning (T0441)S70 because first residue in template chain is (2fvyA)D2 Warning: unaligning (T0441)F81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2fvyA)D14 Warning: unaligning (T0441)E82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2fvyA)D14 Warning: unaligning (T0441)S247 because of BadResidue code BAD_PEPTIDE at template residue (2fvyA)N202 Warning: unaligning (T0441)L283 because of BadResidue code BAD_PEPTIDE in next template residue (2fvyA)D236 Warning: unaligning (T0441)E284 because of BadResidue code BAD_PEPTIDE at template residue (2fvyA)D236 T0441 71 :YSIALIIPSL 2fvyA 3 :TRIGVTIYKY T0441 83 :KACAHFLPSFQQALNKAG 2fvyA 15 :NFMSVVRKAIEQDAKAAP T0441 101 :YQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 2fvyA 34 :VQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAA T0441 140 :RTHQLLEASNTPVLEIAELSSK 2fvyA 75 :TVIEKARGQNVPVVFFNKEPSR T0441 162 :ASYLNIGVDHFEVGKACTRHLIEQ 2fvyA 103 :DKAYYVGTDSKESGIIQGDLIAKH T0441 186 :GFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRD 2fvyA 139 :GQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGP T0441 248 :SLNALVCSHEEIAIGALFECHRRVL 2fvyA 203 :KIEVVIANNDAMAMGAVEALKAHNK T0441 276 :TDIAIIC 2fvyA 228 :SSIPVFG T0441 285 :GSSMGEHA 2fvyA 237 :ALPEALAL T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRA 2fvyA 248 :GALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVR Number of specific fragments extracted= 10 number of extra gaps= 3 total=687 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3d02A/T0441-3d02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3d02A expands to /projects/compbio/data/pdb/3d02.pdb.gz 3d02A:Skipped atom 20, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 22, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 24, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 26, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 28, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 42, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 44, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 46, because occupancy 0.300 <= existing 0.700 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 184, because occupancy 0.370 <= existing 0.380 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 318, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 320, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 322, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 324, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 326, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 328, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 330, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 362, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 364, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 366, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 368, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 370, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 372, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 374, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 376, because occupancy 0.100 <= existing 0.900 in 3d02A Skipped atom 415, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 417, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 419, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 421, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 423, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 425, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 427, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 445, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 447, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 449, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 451, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 453, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 455, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 457, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 459, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 461, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 524, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 528, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 530, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 532, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 534, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 536, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 538, because occupancy 0.400 <= existing 0.600 in 3d02A Skipped atom 633, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 635, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 637, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 639, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 641, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 643, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 645, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 647, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 683, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 685, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 687, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 689, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 691, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 693, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 695, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 793, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 795, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 797, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 799, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 801, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 803, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 805, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 807, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 809, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 917, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 919, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 921, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 923, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 925, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 927, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 929, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 931, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 967, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 969, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 971, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 973, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 975, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 977, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 979, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 981, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 983, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1062, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1064, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1066, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1068, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1070, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1072, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1074, because occupancy 0.150 <= existing 0.600 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1076, because occupancy 0.200 <= existing 0.800 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1105, because occupancy 0.300 <= existing 0.700 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1107, because occupancy 0.300 <= existing 0.700 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1113, because occupancy 0.370 <= existing 0.380 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1115, because occupancy 0.300 <= existing 0.500 in 3d02A Skipped atom 1125, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1292, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1294, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1296, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1298, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1300, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1302, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1304, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1306, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1333, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1335, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1500, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1502, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1504, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1510, because occupancy 0.370 <= existing 0.380 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1571, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1573, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1575, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1577, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1579, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1581, because occupancy 0.300 <= existing 0.700 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1686, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1688, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1690, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1694, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1837, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1839, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1841, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1843, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1845, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1847, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1849, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1851, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1853, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 1855, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1859, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1861, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1863, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1865, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1902, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1904, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1906, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1910, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 3d02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2247, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2249, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2251, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2253, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2255, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2257, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2259, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2367, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2369, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2371, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2373, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2375, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2377, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2424, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2426, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2428, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2430, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2432, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2434, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2436, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2438, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2440, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2470, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2472, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2474, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2476, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2478, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2480, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2482, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2507, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2509, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2511, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2513, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2515, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2517, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2519, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2521, because occupancy 0.300 <= existing 0.700 in 3d02A Skipped atom 2567, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in 3d02A Skipped atom 2581, because occupancy 0.500 <= existing 0.500 in 3d02A # T0441 read from 3d02A/T0441-3d02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d02A read from 3d02A/T0441-3d02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3d02A to template set # found chain 3d02A in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3d02A)E28 Warning: unaligning (T0441)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3d02A)N133 Warning: unaligning (T0441)H171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3d02A)N133 Warning: unaligning (T0441)F172 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3d02A)E134 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE in next template residue (3d02A)P164 Warning: unaligning (T0441)S200 because of BadResidue code BAD_PEPTIDE at template residue (3d02A)P164 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3d02A)T266 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3d02A)T266 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 3d02A 29 :KTVVNISKVDGMPWFNRMGEGVVQAGKEFNLNASQVGPSS T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHS 3d02A 70 :DAPQQVKIIEDLIARKVDAITIVPNDAN T0441 139 :QRTHQLLEASNTPVLEIAELSSKAS 3d02A 100 :EPVFKKARDAGIVVLTNESPGQPSA T0441 164 :YLNIGV 3d02A 126 :WDVEII T0441 173 :EVGKACTRHLIEQ 3d02A 135 :KFAAEYVEHMAKR T0441 186 :GFKNVGFIGARGN 3d02A 150 :GKGGYVIYVGSLT T0441 201 :TLQRQLHGWQSAMIENYLTPDHFLTTHEA 3d02A 165 :QHNLWADLLVKYQKEHYPDMHEVTRRMPV T0441 230 :PSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 3d02A 195 :ESVDDSRRTTLDLMKTYPDLKAVVSFGSNGPIGAGRAVKEKRAK T0441 276 :TDIAIICLEGSSMG 3d02A 239 :NKVAVYGMMIPSQA T0441 290 :EHAYPS 3d02A 254 :SLIKSG T0441 296 :LTS 3d02A 262 :TEG T0441 301 :FDYERMGTKAAEKLLHAIKGEPEERPTSM 3d02A 267 :YDPATAGYALAAVASTLLNGKTIEPGFEL Number of specific fragments extracted= 12 number of extra gaps= 3 total=699 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3d02A/T0441-3d02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3d02A/T0441-3d02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d02A read from 3d02A/T0441-3d02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d02A in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3d02A)E28 Warning: unaligning (T0441)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3d02A)N133 Warning: unaligning (T0441)H171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3d02A)N133 Warning: unaligning (T0441)F172 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3d02A)E134 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE in next template residue (3d02A)P164 Warning: unaligning (T0441)S200 because of BadResidue code BAD_PEPTIDE at template residue (3d02A)P164 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3d02A)T266 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3d02A)T266 Warning: unaligning (T0441)R335 because of BadResidue code BAD_PEPTIDE in next template residue (3d02A)E302 Warning: unaligning (T0441)R336 because of BadResidue code BAD_PEPTIDE at template residue (3d02A)E302 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYS 3d02A 29 :KTVVNISKVDGMPWFNRMGEGVVQAGKEFNLNASQVGP T0441 109 :DYSIEQEEKLLSTFLESRPAGVVLFGSEHSQ 3d02A 68 :STDAPQQVKIIEDLIARKVDAITIVPNDANV T0441 140 :RTHQLLEASNTPVLEIAELS 3d02A 101 :PVFKKARDAGIVVLTNESPG T0441 160 :SKASYLNIGV 3d02A 122 :PSANWDVEII T0441 173 :EVGKACTRHLIEQ 3d02A 135 :KFAAEYVEHMAKR T0441 186 :GFKNVGFIGARGN 3d02A 150 :GKGGYVIYVGSLT T0441 201 :TLQRQLHGWQSAMIENYLTPDHFLTTHE 3d02A 165 :QHNLWADLLVKYQKEHYPDMHEVTRRMP T0441 230 :PSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVL 3d02A 195 :ESVDDSRRTTLDLMKTYPDLKAVVSFGSNGPIGAGRAVKEKRA T0441 275 :PTDIAIICLEGSSMGEHA 3d02A 238 :KNKVAVYGMMIPSQAASL T0441 293 :YPSLT 3d02A 258 :SGDIT T0441 298 :S 3d02A 264 :G T0441 301 :FDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLK 3d02A 267 :YDPATAGYALAAVASTLLNGKTIEPGFELKELGK T0441 337 :AST 3d02A 303 :VDS Number of specific fragments extracted= 13 number of extra gaps= 4 total=712 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3d02A/T0441-3d02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 3d02A/T0441-3d02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d02A read from 3d02A/T0441-3d02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d02A in template set Warning: unaligning (T0441)S70 because first residue in template chain is (3d02A)E28 Warning: unaligning (T0441)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3d02A)N133 Warning: unaligning (T0441)H171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3d02A)N133 Warning: unaligning (T0441)F172 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3d02A)E134 Warning: unaligning (T0441)H199 because of BadResidue code BAD_PEPTIDE in next template residue (3d02A)P164 Warning: unaligning (T0441)S200 because of BadResidue code BAD_PEPTIDE at template residue (3d02A)P164 Warning: unaligning (T0441)A299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3d02A)T266 Warning: unaligning (T0441)E300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3d02A)T266 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 3d02A 29 :KTVVNISKVDGMPWFNRMGEGVVQAGKEFNLNASQVGPSS T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQ 3d02A 70 :DAPQQVKIIEDLIARKVDAITIVPNDANV T0441 140 :RTHQLLEASNTPVLEIAELSSK 3d02A 101 :PVFKKARDAGIVVLTNESPGQP T0441 162 :ASYLNIGV 3d02A 124 :ANWDVEII T0441 173 :EVGKACTRHLIEQ 3d02A 135 :KFAAEYVEHMAKR T0441 186 :GFKNVGFIGARGN 3d02A 150 :GKGGYVIYVGSLT T0441 201 :TLQRQLHGWQSAMIENYLTPDHFLTT 3d02A 165 :QHNLWADLLVKYQKEHYPDMHEVTRR T0441 227 :HEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLK 3d02A 192 :PVAESVDDSRRTTLDLMKTYPDLKAVVSFGSNGPIGAGRAVKEKRAK T0441 276 :TDIAIICLEGSSMGEHA 3d02A 239 :NKVAVYGMMIPSQAASL T0441 293 :YPSLTS 3d02A 259 :GDITEG T0441 301 :FDYERMGTKAAEKLLHAIKGEPEERP 3d02A 267 :YDPATAGYALAAVASTLLNGKTIEPG T0441 328 :SMGFKLKR 3d02A 293 :FELKELGK Number of specific fragments extracted= 12 number of extra gaps= 3 total=724 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qh8A/T0441-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qh8A expands to /projects/compbio/data/pdb/2qh8.pdb.gz 2qh8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0441 read from 2qh8A/T0441-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0441-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qh8A to template set # found chain 2qh8A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0441)F81 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0441)E82 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0441 70 :SYSIALIIP 2qh8A 27 :TAKVAVSQI T0441 80 :L 2qh8A 36 :V T0441 83 :KACAHFLPSFQQALNKAGY 2qh8A 39 :PALDATRQGLLDGLKAKGY T0441 102 :QLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGS 2qh8A 64 :EFDYKTAQGNPAIAVQIARQFVGENPDVLVGIAT T0441 140 :RTHQLLEAS 2qh8A 98 :PTAQALVSA T0441 149 :NTPVLEIAELSSKA 2qh8A 109 :TIPIVFTAVTDPVG T0441 163 :SYLNIGVDHFEVGKACTRHLIEQ 2qh8A 133 :GKNVTGLSDLSPVEQHVELIKEI T0441 186 :GFKNVGFIGA 2qh8A 158 :NVKSIGVVYN T0441 197 :GNHSTLQRQLHGWQSAMIENYL 2qh8A 168 :PGEANAVSLMELLKLSAAKHGI T0441 221 :DHFLTTHE 2qh8A 190 :KLVEATAL T0441 231 :SSQLGAEGLAKLL 2qh8A 198 :KSADVQSATQAIA T0441 247 :SSLNALVCSHEEIAIGALFECHRRVLKVP 2qh8A 211 :EKSDVIYALIDNTVASAIEGMIVAANQAK T0441 278 :IAIICLEGSSMGE 2qh8A 240 :TPVFGAATSYVER T0441 295 :S 2qh8A 253 :G T0441 296 :LTSAEFDYERMGTKAAEKLLHAIKGEPE 2qh8A 255 :IASLGFDYYQIGVQTADYVAAILEGKEP T0441 324 :ERPTSMGFKLKRRAS 2qh8A 286 :DVQVAKGSDLVINKT Number of specific fragments extracted= 16 number of extra gaps= 1 total=740 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qh8A/T0441-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qh8A/T0441-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0441-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qh8A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0441)F81 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0441)E82 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0441 70 :SYSIALIIP 2qh8A 27 :TAKVAVSQI T0441 80 :L 2qh8A 36 :V T0441 83 :KACAHFLPSFQQALNKAGY 2qh8A 39 :PALDATRQGLLDGLKAKGY T0441 102 :QLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGS 2qh8A 64 :EFDYKTAQGNPAIAVQIARQFVGENPDVLVGIAT T0441 140 :RTHQLLEAS 2qh8A 98 :PTAQALVSA T0441 149 :NTPVLEIAEL 2qh8A 109 :TIPIVFTAVT T0441 159 :SSKASYLNIGVDHFEVGKACTRHLIE 2qh8A 129 :LEQPGKNVTGLSDLSPVEQHVELIKE T0441 185 :QGFKNVGFIGAR 2qh8A 157 :PNVKSIGVVYNP T0441 198 :NHSTLQRQLHGWQSAMIENYL 2qh8A 169 :GEANAVSLMELLKLSAAKHGI T0441 223 :FLTTHEAPSSQLGAEGLAKLL 2qh8A 190 :KLVEATALKSADVQSATQAIA T0441 247 :SSLNALVCSHEEIAIGALFECHRRVLKVP 2qh8A 211 :EKSDVIYALIDNTVASAIEGMIVAANQAK T0441 278 :IAIICLEGSSMG 2qh8A 240 :TPVFGAATSYVE T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 2qh8A 252 :RGAIASLGFDYYQIGVQTADYVAAILEGKEPG T0441 325 :RPTSMGFKLKRRAST 2qh8A 285 :LDVQVAKGSDLVINK Number of specific fragments extracted= 14 number of extra gaps= 1 total=754 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qh8A/T0441-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 2qh8A/T0441-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0441-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qh8A in template set Warning: unaligning (T0441)E69 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0441)F81 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0441)E82 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0441 70 :SYSIALII 2qh8A 27 :TAKVAVSQ T0441 79 :SL 2qh8A 35 :IV T0441 83 :KACAHFLPSFQQALNKAGY 2qh8A 39 :PALDATRQGLLDGLKAKGY T0441 102 :QLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGS 2qh8A 64 :EFDYKTAQGNPAIAVQIARQFVGENPDVLVGIAT T0441 140 :RTHQLLEAS 2qh8A 98 :PTAQALVSA T0441 149 :NTPVLEIAELSSK 2qh8A 109 :TIPIVFTAVTDPV T0441 162 :ASYLNIGVDH 2qh8A 133 :GKNVTGLSDL T0441 175 :GKACTRHLIEQ 2qh8A 145 :VEQHVELIKEI T0441 186 :GFKNVGFIGARGN 2qh8A 158 :NVKSIGVVYNPGE T0441 200 :STLQRQLHGWQSAMIENYLT 2qh8A 171 :ANAVSLMELLKLSAAKHGIK T0441 224 :LTTHEAPSSQLGAEGLAKLL 2qh8A 191 :LVEATALKSADVQSATQAIA T0441 247 :SSLNALVCSHEEIAI 2qh8A 211 :EKSDVIYALIDNTVA T0441 262 :GALFECHRRVL 2qh8A 230 :GMIVAANQAKT T0441 279 :AIICLEGS 2qh8A 241 :PVFGAATS T0441 288 :MGE 2qh8A 249 :YVE T0441 293 :YPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKR 2qh8A 252 :RGAIASLGFDYYQIGVQTADYVAAILEGKEPGSLDVQVAKGSD Number of specific fragments extracted= 16 number of extra gaps= 1 total=770 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tlfA/T0441-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tlfA expands to /projects/compbio/data/pdb/1tlf.pdb.gz 1tlfA:# T0441 read from 1tlfA/T0441-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0441-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tlfA to template set # found chain 1tlfA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (1tlfA)S61 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1tlfA 62 :LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGS 1tlfA 103 :GVEACKAAVHNLLAQRVSGLIINYP T0441 137 :HSQRTHQLLEAS 1tlfA 128 :LDDQDAIAVEAA T0441 149 :NTPVLEIAEL 1tlfA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDH 1tlfA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIA T0441 225 :TTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAST 1tlfA 215 :EREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTT T0441 340 :A 1tlfA 333 :N Number of specific fragments extracted= 7 number of extra gaps= 0 total=777 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tlfA/T0441-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1tlfA/T0441-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0441-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tlfA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (1tlfA)S61 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1tlfA 62 :LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGS 1tlfA 103 :GVEACKAAVHNLLAQRVSGLIINYP T0441 137 :HSQRTHQLLEAS 1tlfA 128 :LDDQDAIAVEAA T0441 149 :NTPVLEIAEL 1tlfA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 1tlfA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI T0441 224 :LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAI 1tlfA 214 :AEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=783 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tlfA/T0441-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1tlfA/T0441-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0441-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tlfA in template set Warning: unaligning (T0441)S70 because first residue in template chain is (1tlfA)S61 T0441 71 :YSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1tlfA 62 :LLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1tlfA 103 :GVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAAC T0441 149 :NTPVLEIAEL 1tlfA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 1tlfA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQP T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLK 1tlfA 213 :IAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLV Number of specific fragments extracted= 5 number of extra gaps= 0 total=788 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efaA/T0441-1efaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1efaA expands to /projects/compbio/data/pdb/1efa.pdb.gz 1efaA:# T0441 read from 1efaA/T0441-1efaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efaA read from 1efaA/T0441-1efaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1efaA to template set # found chain 1efaA in template set Warning: unaligning (T0441)G11 because first residue in template chain is (1efaA)K2 Warning: unaligning (T0441)T339 because last residue in template chain is (1efaA)T329 T0441 12 :NVTLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1efaA 3 :PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGS 1efaA 103 :GVEACKTAVHNLLAQRVSGLIINYP T0441 137 :HSQRTHQLLEAS 1efaA 128 :LDDQDAIAVEAA T0441 149 :NTPVLEIAEL 1efaA 142 :NVPALFLDVS T0441 160 :SKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDH 1efaA 152 :DQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIA T0441 225 :TTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAS 1efaA 215 :EREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKT Number of specific fragments extracted= 6 number of extra gaps= 0 total=794 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efaA/T0441-1efaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1efaA/T0441-1efaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efaA read from 1efaA/T0441-1efaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1efaA in template set Warning: unaligning (T0441)G11 because first residue in template chain is (1efaA)K2 Warning: unaligning (T0441)T339 because last residue in template chain is (1efaA)T329 T0441 12 :NVTLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDY 1efaA 3 :PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVER T0441 111 :SIEQEEKLLSTFLESRPAGVVLFGS 1efaA 103 :GVEACKTAVHNLLAQRVSGLIINYP T0441 137 :HSQRTHQLLEAS 1efaA 128 :LDDQDAIAVEAA T0441 149 :NTPVLEIA 1efaA 142 :NVPALFLD T0441 158 :LSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTP 1efaA 150 :VSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQP T0441 223 :FLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRAS 1efaA 213 :IAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKT Number of specific fragments extracted= 6 number of extra gaps= 0 total=800 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efaA/T0441-1efaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1efaA/T0441-1efaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efaA read from 1efaA/T0441-1efaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1efaA in template set Warning: unaligning (T0441)G11 because first residue in template chain is (1efaA)K2 T0441 12 :NVTLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYS 1efaA 3 :PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMV T0441 109 :DYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAELSSKASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPD 1efaA 101 :RSGVEACKTAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPI T0441 224 :LTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRA 1efaA 214 :AEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRK Number of specific fragments extracted= 3 number of extra gaps= 0 total=803 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpwA/T0441-1vpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpwA expands to /projects/compbio/data/pdb/1vpw.pdb.gz 1vpwA:# T0441 read from 1vpwA/T0441-1vpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpwA read from 1vpwA/T0441-1vpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpwA to template set # found chain 1vpwA in template set Warning: unaligning (T0441)T14 because first residue in template chain is (1vpwA)T3 Warning: unaligning (T0441)Y293 because of BadResidue code BAD_PEPTIDE in next template residue (1vpwA)P285 Warning: unaligning (T0441)P294 because of BadResidue code BAD_PEPTIDE at template residue (1vpwA)P285 T0441 15 :LADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1vpwA 4 :IKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSMKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSKAS 1vpwA 139 :HIPMVVMDWGEAKAD T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHA 1vpwA 155 :TDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYF T0441 295 :SLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1vpwA 286 :ALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRAST 1vpwA 317 :QSIEVHPRLIERRSV Number of specific fragments extracted= 5 number of extra gaps= 1 total=808 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpwA/T0441-1vpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1vpwA/T0441-1vpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpwA read from 1vpwA/T0441-1vpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpwA in template set Warning: unaligning (T0441)T14 because first residue in template chain is (1vpwA)T3 Warning: unaligning (T0441)Y293 because of BadResidue code BAD_PEPTIDE in next template residue (1vpwA)P285 Warning: unaligning (T0441)P294 because of BadResidue code BAD_PEPTIDE at template residue (1vpwA)P285 T0441 15 :LADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1vpwA 4 :IKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSMKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSS 1vpwA 139 :HIPMVVMDWGEA T0441 161 :KASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHA 1vpwA 152 :ADFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYF T0441 295 :SLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1vpwA 286 :ALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRASTAI 1vpwA 317 :QSIEVHPRLIERRSVAD Number of specific fragments extracted= 5 number of extra gaps= 1 total=813 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpwA/T0441-1vpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1vpwA/T0441-1vpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpwA read from 1vpwA/T0441-1vpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpwA in template set Warning: unaligning (T0441)T14 because first residue in template chain is (1vpwA)T3 Warning: unaligning (T0441)Y293 because of BadResidue code BAD_PEPTIDE in next template residue (1vpwA)P285 Warning: unaligning (T0441)P294 because of BadResidue code BAD_PEPTIDE at template residue (1vpwA)P285 T0441 15 :LADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1vpwA 4 :IKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSMKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSK 1vpwA 139 :HIPMVVMDWGEAK T0441 162 :ASYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHA 1vpwA 153 :DFTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYF T0441 295 :SLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 1vpwA 286 :ALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVAD Number of specific fragments extracted= 4 number of extra gaps= 1 total=817 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qpzA/T0441-1qpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qpzA expands to /projects/compbio/data/pdb/1qpz.pdb.gz 1qpzA:# T0441 read from 1qpzA/T0441-1qpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpzA read from 1qpzA/T0441-1qpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qpzA to template set # found chain 1qpzA in template set T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1qpzA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSKAS 1qpzA 139 :HIPMVVMDWGEAKAD T0441 164 :YLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1qpzA 155 :TDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRAST 1qpzA 317 :QSIEVHPRLIERRSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=821 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qpzA/T0441-1qpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1qpzA/T0441-1qpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpzA read from 1qpzA/T0441-1qpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qpzA in template set Warning: unaligning (T0441)V13 because first residue in template chain is (1qpzA)A2 T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1qpzA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSKA 1qpzA 139 :HIPMVVMDWGEAKA T0441 163 :SYLNIGVDHFEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEE 1qpzA 154 :FTDAVIDNAFEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREE T0441 325 :RPTSMGFKLKRRASTAI 1qpzA 317 :QSIEVHPRLIERRSVAD Number of specific fragments extracted= 4 number of extra gaps= 0 total=825 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qpzA/T0441-1qpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0441 read from 1qpzA/T0441-1qpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpzA read from 1qpzA/T0441-1qpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qpzA in template set T0441 14 :TLADVAKQAGVGTMTVSRALRTPELVSDKLREKIQQVVDELGYIPNKAAGALASAESYSIALIIPSLFEKACAHFLPSFQQALNKAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEAS 1qpzA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLATSSEAAYFAEIIEAVEKNCFQKGYTLILGNAWNNLEKQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEY T0441 149 :NTPVLEIAELSSKASYLNIGVDH 1qpzA 139 :HIPMVVMDWGEAKADFTDAVIDN T0441 172 :FEVGKACTRHLIEQGFKNVGFIGARGNHSTLQRQLHGWQSAMIENYLTPDHFLTTHEAPSSQLGAEGLAKLLLRDSSLNALVCSHEEIAIGALFECHRRVLKVPTDIAIICLEGSSMGEHAYPSLTSAEFDYERMGTKAAEKLLHAIKGEPEERPTSMGFKLKRRASTAIN 1qpzA 163 :FEGGYMAGRYLIERGHREIGVIPGPLERNTGAGRLAGFMKAMEEAMIKVPESWIVQGDFEPESGYRAMQQILSQPHRPTAVFCGGDIMAMGALCAADEMGLRVPQDVSLIGYDNVRNARYFTPALTTIHQPKDSLGETAFNMLLDRIVNKREEPQSIEVHPRLIERRSVAD Number of specific fragments extracted= 3 number of extra gaps= 0 total=828 Will force an alignment to be made, even if fragment is small Number of alignments=102 # command:CPU_time= 41.834 sec, elapsed time= 49.680 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 102 Adding 2629 constraints to all_contacts Done adding distance constraints # command:CPU_time= 42.074 sec, elapsed time= 49.932 sec. # command:Reading probabilities from T0441.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 97.834 Optimizing... Probability sum: -560.554, CN propb: -560.554 weights: 0.480 constraints: 814 # command:CPU_time= 141.691 sec, elapsed time= 149.575 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 814 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 814 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1815 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1815 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 141.737 sec, elapsed time= 150.365 sec. # command: