# 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 T0444 numbered 1 through 326 Created new target T0444 from T0444.a2m # command:CPU_time= 6.334 sec, elapsed time= 6.435 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w68A/T0444-1w68A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w68A expands to /projects/compbio/data/pdb/1w68.pdb.gz 1w68A:# T0444 read from 1w68A/T0444-1w68A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w68A read from 1w68A/T0444-1w68A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w68A to template set # found chain 1w68A in template set Warning: unaligning (T0444)S33 because first residue in template chain is (1w68A)V68 Warning: unaligning (T0444)F313 because last residue in template chain is (1w68A)F348 T0444 34 :NEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENP 1w68A 69 :EDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENP # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 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 1w68A/T0444-1w68A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1w68A/T0444-1w68A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w68A read from 1w68A/T0444-1w68A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w68A in template set Warning: unaligning (T0444)S33 because first residue in template chain is (1w68A)V68 Warning: unaligning (T0444)F313 because last residue in template chain is (1w68A)F348 T0444 34 :NEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENP 1w68A 69 :EDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENP Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 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 1w68A/T0444-1w68A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1w68A/T0444-1w68A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w68A read from 1w68A/T0444-1w68A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w68A in template set Warning: unaligning (T0444)S33 because first residue in template chain is (1w68A)V68 Warning: unaligning (T0444)F313 because last residue in template chain is (1w68A)F348 T0444 34 :NEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENP 1w68A 69 :EDEPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENP Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 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 2rccA/T0444-2rccA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rccA expands to /projects/compbio/data/pdb/2rcc.pdb.gz 2rccA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 370, because occupancy 0.5 <= existing 0.500 in 2rccA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 564, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 568, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 991, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1550, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1554, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1556, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1755, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1757, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1759, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1761, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1763, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1765, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 1952, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2063, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2067, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2069, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2071, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2073, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2075, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2166, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2180, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2184, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2186, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2188, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2285, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2287, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2289, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2291, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2459, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2463, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2465, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2467, because occupancy 0.370 <= existing 0.380 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2469, because occupancy 0.500 <= existing 0.500 in 2rccA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2586, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2590, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2592, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2594, because occupancy 0.500 <= existing 0.500 in 2rccA Skipped atom 2596, because occupancy 0.500 <= existing 0.500 in 2rccA # T0444 read from 2rccA/T0444-2rccA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rccA read from 2rccA/T0444-2rccA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rccA to template set # found chain 2rccA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (2rccA)I312 T0444 22 :SMSDTNESEIKSNEEPLLRKSS 2rccA 5 :QKRKIYDTTASNASTGILNGKS T0444 44 :RRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENL 2rccA 28 :NVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2rccA 96 :MRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLV T0444 152 :DPKKREFLFNAIETMPYVKKKADWALRWIAD 2rccA 134 :PKATQDEIFEYWKHDDVLKERNEFIIDGYEK T0444 183 :RKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2rccA 170 :TPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFP T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQA 2rccA 246 :KTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPE T0444 310 :ENPFDF 2rccA 306 :HNPMKW Number of specific fragments extracted= 7 number of extra gaps= 0 total=10 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 2rccA/T0444-2rccA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2rccA/T0444-2rccA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rccA read from 2rccA/T0444-2rccA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rccA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (2rccA)I312 T0444 24 :SDTNESEIKSNEEPLLRKSSRRFVIFP 2rccA 7 :RKIYDTTASNASTGILNGKSSNVLNWD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENL 2rccA 35 :VRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 2rccA 96 :MRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSL T0444 151 :RDPKKREFLFNAIETMPYVKKKADWALRWIAD 2rccA 133 :VPKATQDEIFEYWKHDDVLKERNEFIIDGYEK T0444 183 :RKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2rccA 170 :TPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQA 2rccA 247 :TFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPE T0444 310 :ENPFDF 2rccA 306 :HNPMKW Number of specific fragments extracted= 7 number of extra gaps= 0 total=17 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 2rccA/T0444-2rccA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2rccA/T0444-2rccA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rccA read from 2rccA/T0444-2rccA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rccA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (2rccA)I312 T0444 20 :FQSMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENL 2rccA 4 :LQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 2rccA 96 :MRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLVPKATQ T0444 157 :EFLFNAIETMPYVKKKADWALRWIADRKS 2rccA 139 :DEIFEYWKHDDVLKERNEFIIDGYEKFVD T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2rccA 173 :TFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFP T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQA 2rccA 246 :KTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPE T0444 310 :ENPFDF 2rccA 306 :HNPMKW Number of specific fragments extracted= 6 number of extra gaps= 0 total=23 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 1syyA/T0444-1syyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1syyA expands to /projects/compbio/data/pdb/1syy.pdb.gz 1syyA:# T0444 read from 1syyA/T0444-1syyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1syyA read from 1syyA/T0444-1syyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1syyA to template set # found chain 1syyA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (1syyA)M318 T0444 21 :QSMSDTNESEIKSNEEPLLRKSS 1syyA 3 :ADILDGKQKRVNLNSKRLVNCNQ T0444 44 :RRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN 1syyA 27 :DVNQLVPIKYKWAWEHYLNGCANNWLPTEIPMGKDIELWK T0444 84 :KLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1syyA 69 :RLSEDERRVILLNLGFFSTAESLVGNNIVLAIFKHVTNPEARQYLLRQAFEEAVHTHTFLYICESLGLDEKE T0444 159 :LFNAIETMPYVKKKADWALRWIA 1syyA 141 :IFNAYNERAAIKAKDDFQMEITG T0444 182 :DRKSTFGERVVAF 1syyA 176 :EGLQEFVKNLVGY T0444 195 :AAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1syyA 190 :IIMEGIFFYSGFVMILSFHRQNKMIGIGEQYQYILRDETIHLNFGIDLINGIKEENP T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDF 1syyA 254 :QQEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERIGLKPIYHTKNPFPW Number of specific fragments extracted= 7 number of extra gaps= 0 total=30 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 1syyA/T0444-1syyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1syyA/T0444-1syyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1syyA read from 1syyA/T0444-1syyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1syyA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (1syyA)M318 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRF 1syyA 5 :ILDGKQKRVNLNSKRLVNCNQVDV T0444 47 :VIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN 1syyA 30 :QLVPIKYKWAWEHYLNGCANNWLPTEIPMGKDIELWK T0444 84 :KLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1syyA 69 :RLSEDERRVILLNLGFFSTAESLVGNNIVLAIFKHVTNPEARQYLLRQAFEEAVHTHTFLYICESLGLDEKE T0444 159 :LFNAIETMPYVKKKADWALRWI 1syyA 141 :IFNAYNERAAIKAKDDFQMEIT T0444 181 :ADRKSTFGERVVAFA 1syyA 175 :VEGLQEFVKNLVGYY T0444 196 :AVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1syyA 191 :IMEGIFFYSGFVMILSFHRQNKMIGIGEQYQYILRDETIHLNFGIDLINGIKEENPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDF 1syyA 255 :QEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERIGLKPIYHTKNPFPW Number of specific fragments extracted= 7 number of extra gaps= 0 total=37 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 1syyA/T0444-1syyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1syyA/T0444-1syyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1syyA read from 1syyA/T0444-1syyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1syyA in template set Warning: unaligning (T0444)M316 because last residue in template chain is (1syyA)M318 T0444 21 :QSMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNK 1syyA 4 :DILDGKQKRVNLNSKRLVNCNQVDVNQLVPIKYKWAWEHYLNGCANNWLPTEIPMGKDIELWKS T0444 85 :LKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1syyA 70 :LSEDERRVILLNLGFFSTAESLVGNNIVLAIFKHVTNPEARQYLLRQAFEEAVHTHTFLYICESLGLDEKE T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1syyA 141 :IFNAYNERAAIKAKDDFQMEITGKVLD T0444 186 :TFGERVVAFA 1syyA 180 :EFVKNLVGYY T0444 196 :AVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1syyA 191 :IMEGIFFYSGFVMILSFHRQNKMIGIGEQYQYILRDETIHLNFGIDLINGIKEENP T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDF 1syyA 254 :QQEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERIGLKPIYHTKNPFPW Number of specific fragments extracted= 6 number of extra gaps= 0 total=43 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 1mxrA/T0444-1mxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mxrA expands to /projects/compbio/data/pdb/1mxr.pdb.gz 1mxrA:# T0444 read from 1mxrA/T0444-1mxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxrA read from 1mxrA/T0444-1mxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mxrA to template set # found chain 1mxrA in template set Warning: unaligning (T0444)S22 because first residue in template chain is (1mxrA)A1 Warning: unaligning (T0444)S320 because last residue in template chain is (1mxrA)L339 T0444 23 :MSDTNESEIKSNEEPLLRKSS 1mxrA 2 :YTTFSQTKNDQLKEPMFFGQP T0444 44 :RRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1mxrA 24 :NVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIA 1mxrA 136 :VFDDIVTNEQIQKRAEGISSYYD T0444 182 :DRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mxrA 188 :ELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1mxrA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1mxrA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENI 1mxrA 329 :SNPIPWINTW Number of specific fragments extracted= 7 number of extra gaps= 0 total=50 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 1mxrA/T0444-1mxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mxrA/T0444-1mxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxrA read from 1mxrA/T0444-1mxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mxrA in template set Warning: unaligning (T0444)S320 because last residue in template chain is (1mxrA)L339 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1mxrA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1mxrA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWI 1mxrA 136 :VFDDIVTNEQIQKRAEGISSYY T0444 181 :ADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 1mxrA 187 :RELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRS T0444 249 :KPSE 1mxrA 257 :DDPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1mxrA 270 :QECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1mxrA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENI 1mxrA 329 :SNPIPWINTW Number of specific fragments extracted= 8 number of extra gaps= 0 total=58 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 1mxrA/T0444-1mxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mxrA/T0444-1mxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxrA read from 1mxrA/T0444-1mxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mxrA in template set Warning: unaligning (T0444)S320 because last residue in template chain is (1mxrA)L339 T0444 22 :SMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1mxrA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1mxrA 136 :VFDDIVTNEQIQKRAEGISSYYDELIE T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mxrA 192 :KLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1mxrA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1mxrA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENI 1mxrA 329 :SNPIPWINTW Number of specific fragments extracted= 6 number of extra gaps= 0 total=64 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 1kgnA/T0444-1kgnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kgnA expands to /projects/compbio/data/pdb/1kgn.pdb.gz 1kgnA:# T0444 read from 1kgnA/T0444-1kgnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgnA read from 1kgnA/T0444-1kgnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kgnA to template set # found chain 1kgnA in template set Warning: unaligning (T0444)G14 because first residue in template chain is (1kgnA)S2 Warning: unaligning (T0444)S320 because last residue in template chain is (1kgnA)S297 T0444 15 :TENLYFQSMSDTNESEIKSNE 1kgnA 3 :NEYDEYIANHTDPVKAINWNV T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 1kgnA 24 :IPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLAS T0444 153 :PKKREFLFNAIETMPYVKKKADWALRWIADRKS 1kgnA 125 :TPQINEAFRWSEENENLQRKAKIIMSYYNGDDP T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1kgnA 158 :LKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLS T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 1kgnA 229 :KAYTFDLMYDLYENEIEYTEDIYDD T0444 279 :IGMN 1kgnA 254 :LGWT T0444 284 :ILMKQYIEFVADRLLVELGFSKVFQAE 1kgnA 258 :EDVKRFLRYNANKALNNLGYEGLFPTD T0444 311 :NPFDFM 1kgnA 287 :KVSPAI T0444 317 :ENI 1kgnA 294 :SSL Number of specific fragments extracted= 9 number of extra gaps= 0 total=73 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 1kgnA/T0444-1kgnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1kgnA/T0444-1kgnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgnA read from 1kgnA/T0444-1kgnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kgnA in template set T0444 36 :EPLLRKSSRRFVIFP 1kgnA 8 :YIANHTDPVKAINWN T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 1kgnA 24 :IPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTL T0444 151 :RDPKKREFLFNAIETMPYVKKKADWALRWIADRKS 1kgnA 123 :ASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDP T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1kgnA 158 :LKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSE T0444 253 :ERVREIIVDAVKIEQEFLTEALPV 1kgnA 230 :AYTFDLMYDLYENEIEYTEDIYDD T0444 279 :IGMN 1kgnA 254 :LGWT T0444 284 :ILMKQYIEFVADRLLVELGFSKVFQAE 1kgnA 258 :EDVKRFLRYNANKALNNLGYEGLFPTD T0444 311 :NPF 1kgnA 286 :TKV T0444 314 :DFMEN 1kgnA 290 :PAILS Number of specific fragments extracted= 9 number of extra gaps= 0 total=82 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 1kgnA/T0444-1kgnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1kgnA/T0444-1kgnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgnA read from 1kgnA/T0444-1kgnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kgnA in template set Warning: unaligning (T0444)S29 because first residue in template chain is (1kgnA)S2 Warning: unaligning (T0444)L321 because last residue in template chain is (1kgnA)S297 T0444 30 :EIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 1kgnA 3 :NEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLAS T0444 153 :PKKREFLFNAIETMPYVKKKADWALRWIADRKS 1kgnA 125 :TPQINEAFRWSEENENLQRKAKIIMSYYNGDDP T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1kgnA 158 :LKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLS T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLI 1kgnA 229 :KAYTFDLMYDLYENEIEYTEDIYDDLGW T0444 283 :CILMKQYIEFVADRLLVELGFSKVFQA 1kgnA 257 :TEDVKRFLRYNANKALNNLGYEGLFPT T0444 310 :ENPFDFMENIS 1kgnA 286 :TKVSPAILSSL Number of specific fragments extracted= 6 number of extra gaps= 0 total=88 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 1jk0B/T0444-1jk0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jk0B expands to /projects/compbio/data/pdb/1jk0.pdb.gz 1jk0B:# T0444 read from 1jk0B/T0444-1jk0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0B read from 1jk0B/T0444-1jk0B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jk0B to template set # found chain 1jk0B in template set Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE in next template residue (1jk0B)P39 Warning: unaligning (T0444)P50 because of BadResidue code BAD_PEPTIDE at template residue (1jk0B)P39 Warning: unaligning (T0444)A101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)L100 Warning: unaligning (T0444)L111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jk0B)L100 Warning: unaligning (T0444)P275 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)H275 Warning: unaligning (T0444)F307 because last residue in template chain is (1jk0B)Y295 T0444 32 :KSNEEPLLRKSSRRFVI 1jk0B 21 :AEKDEILLMENSRRFVM T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFF 1jk0B 40 :IKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALS T0444 112 :VERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1jk0B 101 :IENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKN T0444 164 :ETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEAL 1jk0B 152 :ANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSL T0444 289 :YIEFVADRLLVELGFSKV 1jk0B 277 :YIEFVADGLLQGFGNEKY Number of specific fragments extracted= 5 number of extra gaps= 1 total=93 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 1jk0B/T0444-1jk0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1jk0B/T0444-1jk0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0B read from 1jk0B/T0444-1jk0B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jk0B in template set Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE in next template residue (1jk0B)P39 Warning: unaligning (T0444)P50 because of BadResidue code BAD_PEPTIDE at template residue (1jk0B)P39 Warning: unaligning (T0444)A101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)L100 Warning: unaligning (T0444)L111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jk0B)L100 Warning: unaligning (T0444)P275 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)H275 Warning: unaligning (T0444)K287 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jk0B)H275 Warning: unaligning (T0444)F307 because last residue in template chain is (1jk0B)Y295 T0444 31 :IKSNEEPLLRKSSRRFVI 1jk0B 20 :EAEKDEILLMENSRRFVM T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFF 1jk0B 40 :IKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALS T0444 112 :VERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1jk0B 101 :IENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKN T0444 160 :FNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEAL 1jk0B 148 :FKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSL T0444 288 :QYIEFVADRLLVELGFSKV 1jk0B 276 :TYIEFVADGLLQGFGNEKY Number of specific fragments extracted= 5 number of extra gaps= 1 total=98 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 1jk0B/T0444-1jk0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1jk0B/T0444-1jk0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0B read from 1jk0B/T0444-1jk0B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jk0B in template set Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE in next template residue (1jk0B)P39 Warning: unaligning (T0444)P50 because of BadResidue code BAD_PEPTIDE at template residue (1jk0B)P39 Warning: unaligning (T0444)A101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)L100 Warning: unaligning (T0444)L111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jk0B)L100 Warning: unaligning (T0444)P275 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jk0B)H275 Warning: unaligning (T0444)K287 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jk0B)H275 Warning: unaligning (T0444)F307 because last residue in template chain is (1jk0B)Y295 T0444 24 :SDTNESEIKSNEEPLLRKSSRRFVI 1jk0B 13 :KERHDMKEAEKDEILLMENSRRFVM T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFF 1jk0B 40 :IKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALS T0444 112 :VERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1jk0B 101 :IENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKN T0444 160 :FNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEAL 1jk0B 148 :FKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSL T0444 288 :QYIEFVADRLLVELGFSKV 1jk0B 276 :TYIEFVADGLLQGFGNEKY Number of specific fragments extracted= 5 number of extra gaps= 1 total=103 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 1xsm/T0444-1xsm-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xsm expands to /projects/compbio/data/pdb/1xsm.pdb.gz 1xsm:Warning: there is no chain 1xsm will retry with 1xsmA # T0444 read from 1xsm/T0444-1xsm-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xsm read from 1xsm/T0444-1xsm-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xsm to template set # found chain 1xsm in template set Warning: unaligning (T0444)E30 because first residue in template chain is (1xsm)N65 Warning: unaligning (T0444)S42 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)P78 Warning: unaligning (T0444)S43 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)P78 Warning: unaligning (T0444)F46 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)V82 Warning: unaligning (T0444)V47 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)V82 Warning: unaligning (T0444)I48 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F84 Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F84 Warning: unaligning (T0444)T222 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F258 Warning: unaligning (T0444)F223 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F258 Warning: unaligning (T0444)F315 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)M351 Warning: unaligning (T0444)M316 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)M351 Warning: unaligning (T0444)E317 because last residue in template chain is (1xsm)E352 T0444 31 :IKSNEEPLLRK 1xsm 66 :PSVEDEPLLRE T0444 44 :RR 1xsm 79 :RR T0444 50 :PIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGL 1xsm 85 :PIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGL T0444 224 :SNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFD 1xsm 259 :SNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENPFD Number of specific fragments extracted= 4 number of extra gaps= 4 total=107 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 1xsm/T0444-1xsm-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1xsm/T0444-1xsm-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xsm read from 1xsm/T0444-1xsm-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xsm in template set Warning: unaligning (T0444)E30 because first residue in template chain is (1xsm)N65 Warning: unaligning (T0444)S42 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)P78 Warning: unaligning (T0444)S43 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)P78 Warning: unaligning (T0444)F46 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)V82 Warning: unaligning (T0444)V47 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)V82 Warning: unaligning (T0444)I48 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F84 Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F84 Warning: unaligning (T0444)T222 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F258 Warning: unaligning (T0444)F223 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F258 Warning: unaligning (T0444)F315 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)M351 Warning: unaligning (T0444)M316 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)M351 Warning: unaligning (T0444)E317 because last residue in template chain is (1xsm)E352 T0444 31 :IKSNEEPLLRK 1xsm 66 :PSVEDEPLLRE T0444 44 :RR 1xsm 79 :RR T0444 50 :PIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGL 1xsm 85 :PIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGL T0444 224 :SNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFD 1xsm 259 :SNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENPFD Number of specific fragments extracted= 4 number of extra gaps= 4 total=111 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 1xsm/T0444-1xsm-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1xsm/T0444-1xsm-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xsm read from 1xsm/T0444-1xsm-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xsm in template set Warning: unaligning (T0444)E30 because first residue in template chain is (1xsm)N65 Warning: unaligning (T0444)S42 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)P78 Warning: unaligning (T0444)S43 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)P78 Warning: unaligning (T0444)F46 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)V82 Warning: unaligning (T0444)V47 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)V82 Warning: unaligning (T0444)I48 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F84 Warning: unaligning (T0444)F49 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F84 Warning: unaligning (T0444)T222 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)F258 Warning: unaligning (T0444)F223 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)F258 Warning: unaligning (T0444)F315 because of BadResidue code BAD_PEPTIDE in next template residue (1xsm)M351 Warning: unaligning (T0444)M316 because of BadResidue code BAD_PEPTIDE at template residue (1xsm)M351 Warning: unaligning (T0444)E317 because last residue in template chain is (1xsm)E352 T0444 31 :IKSNEEPLLRK 1xsm 66 :PSVEDEPLLRE T0444 44 :RR 1xsm 79 :RR T0444 50 :PIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGL 1xsm 85 :PIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDPKEREYLFNAIETMPCVKKKADWALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGL T0444 224 :SNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFD 1xsm 259 :SNELISRDEGLHCDFACLMFKHLVHKPAEQRVREIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFRVENPFD Number of specific fragments extracted= 4 number of extra gaps= 4 total=115 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 1jk0A/T0444-1jk0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jk0A expands to /projects/compbio/data/pdb/1jk0.pdb.gz 1jk0A:# T0444 read from 1jk0A/T0444-1jk0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0A read from 1jk0A/T0444-1jk0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jk0A to template set # found chain 1jk0A in template set Warning: unaligning (T0444)N318 because last residue in template chain is (1jk0A)N359 T0444 33 :SNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN 1jk0A 73 :EKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWN T0444 84 :KLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFME 1jk0A 125 :RMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFME Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 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 1jk0A/T0444-1jk0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1jk0A/T0444-1jk0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0A read from 1jk0A/T0444-1jk0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jk0A in template set Warning: unaligning (T0444)N318 because last residue in template chain is (1jk0A)N359 T0444 31 :IKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWN 1jk0A 71 :EMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWN T0444 84 :KLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFME 1jk0A 125 :RMNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFME Number of specific fragments extracted= 2 number of extra gaps= 0 total=119 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 1jk0A/T0444-1jk0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1jk0A/T0444-1jk0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jk0A read from 1jk0A/T0444-1jk0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jk0A in template set Warning: unaligning (T0444)N318 because last residue in template chain is (1jk0A)N359 T0444 17 :NLYFQSMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNK 1jk0A 57 :AYLKSHQVHRHKLKEMEKEEPLLNEDKERTVLFPIKYHEIWQAYKRAEASFWTAEEIDLSKDIHDWNN T0444 85 :LKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFME 1jk0A 126 :MNENERFFISRVLAFFAASDGIVNENLVENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIKDPKESEFLFNAIHTIPEIGEKAEWALRWIQDADALFGERLVAFASIEGVFFSGSFASIFWLKKRGMMPGLTFSNELICRDEGLHTDFACLLFAHLKNKPDPAIVEKIVTEAVEIEQRYFLDALPVALLGMNADLMNQYVEFVADRLLVAFGNKKYYKVENPFDFME Number of specific fragments extracted= 2 number of extra gaps= 0 total=121 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 1xikA/T0444-1xikA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xikA expands to /projects/compbio/data/pdb/1xik.pdb.gz 1xikA:Skipped atom 1771, because occupancy 0.500 <= existing 0.500 in 1xikA # T0444 read from 1xikA/T0444-1xikA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xikA read from 1xikA/T0444-1xikA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xikA to template set # found chain 1xikA in template set Warning: unaligning (T0444)T148 because of BadResidue code BAD_PEPTIDE in next template residue (1xikA)I129 Warning: unaligning (T0444)Y149 because of BadResidue code BAD_PEPTIDE at template residue (1xikA)I129 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1xikA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLID 1xikA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIR T0444 150 :IRDPKK 1xikA 130 :VNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIA 1xikA 136 :VFDDIVTNEQIQKRAEGISSYYD T0444 182 :DRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1xikA 188 :ELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1xikA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1xikA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMEN 1xikA 329 :SNPIPWINT Number of specific fragments extracted= 8 number of extra gaps= 1 total=129 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 1xikA/T0444-1xikA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1xikA/T0444-1xikA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xikA read from 1xikA/T0444-1xikA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xikA in template set Warning: unaligning (T0444)T148 because of BadResidue code BAD_PEPTIDE in next template residue (1xikA)I129 Warning: unaligning (T0444)Y149 because of BadResidue code BAD_PEPTIDE at template residue (1xikA)I129 Warning: unaligning (T0444)L321 because last residue in template chain is (1xikA)V340 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1xikA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLID 1xikA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIR T0444 150 :IRDPKK 1xikA 130 :VNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWI 1xikA 136 :VFDDIVTNEQIQKRAEGISSYY T0444 181 :ADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 1xikA 187 :RELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRS T0444 249 :KPSE 1xikA 257 :DDPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1xikA 270 :QECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1xikA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENIS 1xikA 329 :SNPIPWINTWL Number of specific fragments extracted= 9 number of extra gaps= 1 total=138 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 1xikA/T0444-1xikA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1xikA/T0444-1xikA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xikA read from 1xikA/T0444-1xikA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xikA in template set Warning: unaligning (T0444)T148 because of BadResidue code BAD_PEPTIDE in next template residue (1xikA)I129 Warning: unaligning (T0444)Y149 because of BadResidue code BAD_PEPTIDE at template residue (1xikA)I129 Warning: unaligning (T0444)L321 because last residue in template chain is (1xikA)V340 T0444 22 :SMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLID 1xikA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIR T0444 150 :IRDPKK 1xikA 130 :VNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1xikA 136 :VFDDIVTNEQIQKRAEGISSYYDELIE T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1xikA 192 :KLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1xikA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1xikA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENIS 1xikA 329 :SNPIPWINTWL Number of specific fragments extracted= 7 number of extra gaps= 1 total=145 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 1r2fA/T0444-1r2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r2fA expands to /projects/compbio/data/pdb/1r2f.pdb.gz 1r2fA:# T0444 read from 1r2fA/T0444-1r2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2fA read from 1r2fA/T0444-1r2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r2fA to template set # found chain 1r2fA in template set Warning: unaligning (T0444)E28 because first residue in template chain is (1r2fA)I6 Warning: unaligning (T0444)L321 because last residue in template chain is (1r2fA)P288 T0444 29 :SEIKSNE 1r2fA 7 :SAINWNK T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1r2fA 14 :IQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLC T0444 152 :DPKKREFLFNAIETMPYVKKKADWALRWIADRKS 1r2fA 114 :QTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEP T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1r2fA 148 :LKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLS T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 1r2fA 219 :KLFALDLLMELYDNEIRYTEALYAE T0444 279 :IGM 1r2fA 244 :TGW T0444 283 :CILMKQYIEFVADRLLVELGFSKVFQAE 1r2fA 247 :VNDVKAFLCYNANKALMNLGYEALFPPE T0444 311 :NP 1r2fA 279 :NP T0444 314 :DFMENIS 1r2fA 281 :AILAALS Number of specific fragments extracted= 9 number of extra gaps= 0 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 1r2fA/T0444-1r2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1r2fA/T0444-1r2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2fA read from 1r2fA/T0444-1r2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r2fA in template set T0444 49 :FPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 1r2fA 12 :NKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTL T0444 151 :RDPKKREFLFNAIETMPYVKKKADWALRWIADR 1r2fA 113 :CQTKEVDAAYAWSEENPPLQRKAQIILAHYVSD T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1r2fA 146 :EPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSA T0444 253 :ERVREIIVDAVKIEQEFLTEALPV 1r2fA 220 :LFALDLLMELYDNEIRYTEALYAE T0444 279 :IGM 1r2fA 244 :TGW T0444 283 :CILMKQYIEFVADRLLVELGFSKVFQAE 1r2fA 247 :VNDVKAFLCYNANKALMNLGYEALFPPE T0444 311 :NPFDFMEN 1r2fA 277 :DVNPAILA Number of specific fragments extracted= 7 number of extra gaps= 0 total=161 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 1r2fA/T0444-1r2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1r2fA/T0444-1r2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r2fA read from 1r2fA/T0444-1r2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r2fA in template set Warning: unaligning (T0444)S43 because first residue in template chain is (1r2fA)I6 T0444 44 :RRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1r2fA 7 :SAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEV T0444 157 :EFLFNAIETMPYVKKKADWALRWIADRKS 1r2fA 119 :DAAYAWSEENPPLQRKAQIILAHYVSDEP T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1r2fA 148 :LKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLS T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1r2fA 219 :KLFALDLLMELYDNEIRYTEALYAET T0444 281 :MNCILMKQYIEFVADRLLVELGFSKVFQA 1r2fA 245 :GWVNDVKAFLCYNANKALMNLGYEALFPP T0444 310 :ENPFDFMENIS 1r2fA 276 :ADVNPAILAAL Number of specific fragments extracted= 6 number of extra gaps= 0 total=167 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 3chhA/T0444-3chhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3chhA expands to /projects/compbio/data/pdb/3chh.pdb.gz 3chhA:# T0444 read from 3chhA/T0444-3chhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chhA read from 3chhA/T0444-3chhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3chhA to template set # found chain 3chhA in template set Warning: unaligning (T0444)Q52 because first residue in template chain is (3chhA)G24 T0444 53 :YPDIWKMYKQAQA 3chhA 25 :SATLGRLVRAWPR T0444 66 :SFWTAEEVDLSKDLPHWNKLKADEKYFISHILAF 3chhA 58 :VPDYPLEIVPFAEHPLFLAAEPHQRQRVLTGMWI T0444 100 :FAASDGIVNENLVERFS 3chhA 97 :VIATEQLIAEPAFDLVM T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 3chhA 118 :PGSDDPLIRKSVQQAIVDESFHTYMHMLAIDRTRE T0444 163 :IETMP 3chhA 153 :LRKIS T0444 171 :KKADWALRWIAD 3chhA 166 :VTYRRLRRVLAD T0444 183 :RKSTFGERVVAFAAVEGVFFS 3chhA 181 :QWERDIAVLVWGAVAETCINA T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 3chhA 202 :LLALLARDATIQPMHSLITTLHLRDETAHGSIVVEVVRELYARMN T0444 252 :EERVREIIVDAVKIEQ 3chhA 250 :RRALVRCLPIALEAFA T0444 268 :EFLTEALPV 3chhA 270 :SALLLELNA T0444 279 :IGM 3chhA 279 :AGI T0444 283 :CILMKQ 3chhA 284 :AEEIVG T0444 309 :AE 3chhA 300 :LV T0444 311 :NPFDFMENISLEG 3chhA 306 :GARKMVEQLGLDD Number of specific fragments extracted= 14 number of extra gaps= 0 total=181 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 3chhA/T0444-3chhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 3chhA/T0444-3chhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chhA read from 3chhA/T0444-3chhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3chhA in template set Warning: unaligning (T0444)Q52 because first residue in template chain is (3chhA)G24 T0444 53 :YPDIWKMYKQAQA 3chhA 25 :SATLGRLVRAWPR T0444 66 :SFWTAEEVDLSKDLPHWNKLKADEKYFISHI 3chhA 58 :VPDYPLEIVPFAEHPLFLAAEPHQRQRVLTG T0444 97 :LAFFAASDGIVNENLVERFS 3chhA 94 :NERVIATEQLIAEPAFDLVM T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 3chhA 118 :PGSDDPLIRKSVQQAIVDESFHTYMHMLAIDRT T0444 160 :FNAIETMP 3chhA 151 :RELRKISE T0444 168 :YVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFS 3chhA 166 :VTYRRLRRVLADMPEQWERDIAVLVWGAVAETCINA T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 3chhA 202 :LLALLARDATIQPMHSLITTLHLRDETAHGSIVVEVVRELYARMNE T0444 253 :ERVREIIVDAVKIEQ 3chhA 251 :RALVRCLPIALEAFA T0444 268 :EFLTEALPV 3chhA 270 :SALLLELNA T0444 278 :LIG 3chhA 281 :IRG T0444 283 :CILMKQ 3chhA 284 :AEEIVG T0444 293 :VADRLLVELGFSK 3chhA 306 :GARKMVEQLGLDD Number of specific fragments extracted= 12 number of extra gaps= 0 total=193 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 3chhA/T0444-3chhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 3chhA/T0444-3chhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chhA read from 3chhA/T0444-3chhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3chhA in template set T0444 66 :SFWTAEEVDLSK 3chhA 59 :PDYPLEIVPFAE T0444 79 :LPHWNKLKADEKYFISH 3chhA 71 :HPLFLAAEPHQRQRVLT T0444 96 :ILAFFAASDGIVNENLVERFS 3chhA 93 :YNERVIATEQLIAEPAFDLVM T0444 117 :QEVQVPEARCFYGFQILIENVHSEMY 3chhA 118 :PGSDDPLIRKSVQQAIVDESFHTYMH T0444 157 :EFLFNAIETM 3chhA 144 :MLAIDRTREL T0444 168 :YVKKKADWALRWIAD 3chhA 166 :VTYRRLRRVLADMPE T0444 186 :TFGERVVAFAAVEGVFFSGS 3chhA 182 :WERDIAVLVWGAVAETCINA T0444 208 :AIFWLKKRGLM 3chhA 202 :LLALLARDATI T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEER 3chhA 214 :PMHSLITTLHLRDETAHGSIVVEVVRELYARMNEQQ T0444 256 :REIIVDAVKIEQEFLT 3chhA 250 :RRALVRCLPIALEAFA T0444 280 :GMNCILMK 3chhA 266 :EQDLSALL T0444 296 :RLLVELGFS 3chhA 274 :LELNAAGIR Number of specific fragments extracted= 12 number of extra gaps= 0 total=205 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 2jcdA/T0444-2jcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2jcdA expands to /projects/compbio/data/pdb/2jcd.pdb.gz 2jcdA:Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1150, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 1603, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1604, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1605, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1606, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1607, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1608, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1609, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1610, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1721, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1722, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1723, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1724, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1725, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1726, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1727, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 1728, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2257, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2258, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2259, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2260, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2261, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2262, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2263, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2264, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2265, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2266, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2267, because occupancy 0.400 <= existing 0.600 in 2jcdA Skipped atom 2341, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2343, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2344, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2345, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2347, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2348, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2349, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2351, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2476, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2477, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2478, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2479, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2480, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2481, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2482, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2483, because occupancy 0.500 <= existing 0.500 in 2jcdA Skipped atom 2484, because occupancy 0.500 <= existing 0.500 in 2jcdA # T0444 read from 2jcdA/T0444-2jcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jcdA read from 2jcdA/T0444-2jcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2jcdA to template set # found chain 2jcdA in template set Warning: unaligning (T0444)T15 because first residue in template chain is (2jcdA)H7 Warning: unaligning (T0444)Q308 because last residue in template chain is (2jcdA)D321 T0444 16 :ENLYFQSMSDTNES 2jcdA 8 :LATTWAARGWVEEE T0444 50 :PIQYPDIWKMYKQAQA 2jcdA 22 :GIGSATLGRLVRAWPR T0444 66 :SFWTAEEVDLSKDLPHWNKLKADEKYFISH 2jcdA 58 :VPDYPLEIVPFAEHPLFLAAEPHQRQRVLT T0444 96 :ILAFFAASDGIVNENLVERFSQEV 2jcdA 93 :YNERVIATEQLIAEPAFDLVMHGV T0444 120 :Q 2jcdA 118 :P T0444 121 :VPEARCFYGFQILIENVHSEMYSLLIDTYIRD 2jcdA 122 :DPLIRKSVQQAIVDESFHTYMHMLAIDRTREL T0444 168 :YVKKKADWALRWIADRKSTFGERVVAFAAVEGVFF 2jcdA 166 :VTYRRLRRVLADMPEQWERDIAVLVWGAVAETCIN T0444 207 :AAIFWLKKRGLM 2jcdA 201 :ALLALLARDATI T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2jcdA 214 :PMHSLITTLHLRDETAHGSIVVEVVRELYARMN T0444 252 :EERVREIIVDAVKIE 2jcdA 250 :RRALVRCLPIALEAF T0444 267 :QEFLTEALPV 2jcdA 269 :LSALLLELNA T0444 279 :IGMN 2jcdA 279 :AGIR T0444 283 :CILMKQYIE 2jcdA 284 :AEEIVGDLR T0444 293 :VADRLLVELGFSKVF 2jcdA 306 :GARKMVEQLGLDDAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=219 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 2jcdA/T0444-2jcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2jcdA/T0444-2jcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jcdA read from 2jcdA/T0444-2jcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jcdA in template set Warning: unaligning (T0444)M23 because first residue in template chain is (2jcdA)H7 Warning: unaligning (T0444)Q308 because last residue in template chain is (2jcdA)D321 T0444 24 :SDTNESEIKSNEEP 2jcdA 8 :LATTWAARGWVEEE T0444 50 :PIQYPDIWKMYKQAQA 2jcdA 22 :GIGSATLGRLVRAWPR T0444 69 :TAEEVDLSKDLPHWNKLKADEKYFISHI 2jcdA 61 :YPLEIVPFAEHPLFLAAEPHQRQRVLTG T0444 97 :LAFFAASDGIVNENLVERFS 2jcdA 94 :NERVIATEQLIAEPAFDLVM T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 2jcdA 118 :PGSDDPLIRKSVQQAIVDESFHTYMHMLAIDRT T0444 160 :FNAIETMP 2jcdA 151 :RELRKISE T0444 168 :YVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFS 2jcdA 166 :VTYRRLRRVLADMPEQWERDIAVLVWGAVAETCINA T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2jcdA 202 :LLALLARDATIQPMHSLITTLHLRDETAHGSIVVEVVRELYARMNE T0444 253 :ERVREIIVDAVKIEQ 2jcdA 251 :RALVRCLPIALEAFA T0444 268 :EFLTEALPV 2jcdA 270 :SALLLELNA T0444 279 :IGMN 2jcdA 279 :AGIR T0444 283 :CILMKQYIE 2jcdA 284 :AEEIVGDLR T0444 293 :VADRLLVELGFSKVF 2jcdA 306 :GARKMVEQLGLDDAV Number of specific fragments extracted= 13 number of extra gaps= 0 total=232 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 2jcdA/T0444-2jcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2jcdA/T0444-2jcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jcdA read from 2jcdA/T0444-2jcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jcdA in template set Warning: unaligning (T0444)Q308 because last residue in template chain is (2jcdA)D321 T0444 23 :MSDTNESEIKSNE 2jcdA 9 :ATTWAARGWVEEE T0444 50 :PIQYPDIWKMYKQAQASF 2jcdA 22 :GIGSATLGRLVRAWPRRA T0444 68 :WTAEEVDLSK 2jcdA 61 :YPLEIVPFAE T0444 79 :LPHWNKLKADEKY 2jcdA 71 :HPLFLAAEPHQRQ T0444 92 :FISHILAFFAASDGIVNENLVERFS 2jcdA 89 :MWIGYNERVIATEQLIAEPAFDLVM T0444 117 :QEVQVPEARCFYGFQILIENVHSEMY 2jcdA 118 :PGSDDPLIRKSVQQAIVDESFHTYMH T0444 157 :EFLFNAIETM 2jcdA 144 :MLAIDRTREL T0444 175 :WALRWIADRKS 2jcdA 166 :VTYRRLRRVLA T0444 186 :TFGERVVAFAAVEGVF 2jcdA 185 :DIAVLVWGAVAETCIN T0444 206 :FAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2jcdA 201 :ALLALLARDATIQPMHSLITTLHLRDETAHGSIVVEVVRELYARMN T0444 252 :EERVREIIVDAVKIEQ 2jcdA 250 :RRALVRCLPIALEAFA T0444 268 :EFLTEALPVG 2jcdA 270 :SALLLELNAA T0444 278 :LIG 2jcdA 281 :IRG T0444 283 :CILMKQYIE 2jcdA 284 :AEEIVGDLR T0444 293 :VADRLLVELGFSKVF 2jcdA 306 :GARKMVEQLGLDDAV Number of specific fragments extracted= 15 number of extra gaps= 0 total=247 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 1ribA/T0444-1ribA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ribA expands to /projects/compbio/data/pdb/1rib.pdb.gz 1ribA:# T0444 read from 1ribA/T0444-1ribA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ribA read from 1ribA/T0444-1ribA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ribA to template set # found chain 1ribA in template set Warning: unaligning (T0444)S22 because first residue in template chain is (1ribA)A1 Warning: unaligning (T0444)M23 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)Y2 Warning: unaligning (T0444)E36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ribA)P16 Warning: unaligning (T0444)P37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ribA)P16 Warning: unaligning (T0444)L39 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)F19 Warning: unaligning (T0444)R40 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)F19 Warning: unaligning (T0444)R44 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)Q24 Warning: unaligning (T0444)R45 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)Q24 Warning: unaligning (T0444)N318 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)L339 Warning: unaligning (T0444)I319 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)L339 Warning: unaligning (T0444)S320 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)V340 T0444 24 :SDTNESEIKSNE 1ribA 3 :TTFSATKNDQLK T0444 38 :L 1ribA 17 :M T0444 41 :KSS 1ribA 20 :GQP T0444 46 :FVIFP 1ribA 25 :VARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1ribA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIA 1ribA 136 :VFDDIVTNEQIQKRAEGISSYYD T0444 182 :DRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1ribA 188 :ELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1ribA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1ribA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFNT T0444 310 :ENPFDFME 1ribA 329 :SNPIPWIN Number of specific fragments extracted= 10 number of extra gaps= 4 total=257 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 1ribA/T0444-1ribA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1ribA/T0444-1ribA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ribA read from 1ribA/T0444-1ribA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ribA in template set Warning: unaligning (T0444)M23 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)Y2 Warning: unaligning (T0444)E36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ribA)P16 Warning: unaligning (T0444)P37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ribA)P16 Warning: unaligning (T0444)L39 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)F19 Warning: unaligning (T0444)R40 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)F19 Warning: unaligning (T0444)R44 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)Q24 Warning: unaligning (T0444)R45 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)Q24 Warning: unaligning (T0444)I319 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)L339 Warning: unaligning (T0444)S320 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)L339 Warning: unaligning (T0444)L321 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)V340 T0444 24 :SDTNESEIKSNE 1ribA 3 :TTFSATKNDQLK T0444 38 :L 1ribA 17 :M T0444 41 :KSS 1ribA 20 :GQP T0444 46 :FVIFP 1ribA 25 :VARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1ribA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWI 1ribA 136 :VFDDIVTNEQIQKRAEGISSYY T0444 181 :ADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNK 1ribA 187 :RELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSG T0444 250 :PSE 1ribA 258 :DPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1ribA 270 :QECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1ribA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFNT T0444 310 :ENPFDFMEN 1ribA 329 :SNPIPWINT Number of specific fragments extracted= 11 number of extra gaps= 5 total=268 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 1ribA/T0444-1ribA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1ribA/T0444-1ribA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ribA read from 1ribA/T0444-1ribA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ribA in template set Warning: unaligning (T0444)E35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ribA)P16 Warning: unaligning (T0444)E36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ribA)P16 Warning: unaligning (T0444)L38 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)F19 Warning: unaligning (T0444)L39 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)F19 Warning: unaligning (T0444)S43 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)Q24 Warning: unaligning (T0444)R44 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)Q24 Warning: unaligning (T0444)I319 because of BadResidue code BAD_PEPTIDE in next template residue (1ribA)L339 Warning: unaligning (T0444)S320 because of BadResidue code BAD_PEPTIDE at template residue (1ribA)L339 T0444 23 :MSDTNESEIKSN 1ribA 3 :TTFSATKNDQLK T0444 37 :P 1ribA 17 :M T0444 40 :RKS 1ribA 20 :GQP T0444 45 :RFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1ribA 25 :VARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1ribA 136 :VFDDIVTNEQIQKRAEGISSYYDELIE T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1ribA 192 :KLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1ribA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1ribA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFNT T0444 310 :ENPFDFMEN 1ribA 329 :SNPIPWINT Number of specific fragments extracted= 9 number of extra gaps= 4 total=277 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 1av8A/T0444-1av8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1av8A expands to /projects/compbio/data/pdb/1av8.pdb.gz 1av8A:# T0444 read from 1av8A/T0444-1av8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1av8A read from 1av8A/T0444-1av8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1av8A to template set # found chain 1av8A in template set T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1av8A 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1av8A 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIA 1av8A 136 :VFDDIVTNEQIQKRAEGISSYYD T0444 182 :DRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1av8A 188 :ELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1av8A 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1av8A 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENI 1av8A 329 :SNPIPWINTW Number of specific fragments extracted= 7 number of extra gaps= 0 total=284 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 1av8A/T0444-1av8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1av8A/T0444-1av8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1av8A read from 1av8A/T0444-1av8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1av8A in template set T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1av8A 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1av8A 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWI 1av8A 136 :VFDDIVTNEQIQKRAEGISSYY T0444 181 :ADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNK 1av8A 187 :RELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSG T0444 250 :PSE 1av8A 257 :DDP T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1av8A 270 :QECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1av8A 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENIS 1av8A 329 :SNPIPWINTWL Number of specific fragments extracted= 8 number of extra gaps= 0 total=292 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 1av8A/T0444-1av8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1av8A/T0444-1av8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1av8A read from 1av8A/T0444-1av8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1av8A in template set T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1av8A 3 :TTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1av8A 136 :VFDDIVTNEQIQKRAEGISSYYDELIE T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1av8A 192 :KLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1av8A 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1av8A 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENI 1av8A 329 :SNPIPWINTW Number of specific fragments extracted= 6 number of extra gaps= 0 total=298 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 1biqA/T0444-1biqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1biqA expands to /projects/compbio/data/pdb/1biq.pdb.gz 1biqA:# T0444 read from 1biqA/T0444-1biqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1biqA read from 1biqA/T0444-1biqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1biqA to template set # found chain 1biqA in template set Warning: unaligning (T0444)F201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1biqA)Y209 Warning: unaligning (T0444)S203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1biqA)Y209 Warning: unaligning (T0444)S320 because last residue in template chain is (1biqA)V340 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1biqA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1biqA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSFTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIA 1biqA 136 :VFDDIVTNEQIQKRAEGISSYYD T0444 182 :DRKSTFGERVVAFAAVEGV 1biqA 188 :ELKKKLYLCLMSVNALEAI T0444 204 :GSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1biqA 210 :VSFACSFAFAERELMEGNAKIIRLIARDAALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1biqA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1biqA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFME 1biqA 329 :SNPIPWIN T0444 318 :NI 1biqA 338 :WL Number of specific fragments extracted= 9 number of extra gaps= 0 total=307 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 1biqA/T0444-1biqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1biqA/T0444-1biqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1biqA read from 1biqA/T0444-1biqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1biqA in template set Warning: unaligning (T0444)F201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1biqA)Y209 Warning: unaligning (T0444)S203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1biqA)Y209 Warning: unaligning (T0444)L321 because last residue in template chain is (1biqA)V340 T0444 23 :MSDTNESEIKSNEEPLLRKSSRRFVIFP 1biqA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYD T0444 51 :IQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1biqA 31 :QKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSFTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWI 1biqA 136 :VFDDIVTNEQIQKRAEGISSYY T0444 181 :ADRKSTFGERVVAFAAVEGV 1biqA 187 :RELKKKLYLCLMSVNALEAI T0444 204 :GSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNK 1biqA 210 :VSFACSFAFAERELMEGNAKIIRLIARDAALHLTGTQHMLNLLRSG T0444 250 :PSE 1biqA 258 :DPE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1biqA 270 :QECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1biqA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENIS 1biqA 329 :SNPIPWINTWL Number of specific fragments extracted= 9 number of extra gaps= 0 total=316 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 1biqA/T0444-1biqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1biqA/T0444-1biqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1biqA read from 1biqA/T0444-1biqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1biqA in template set Warning: unaligning (T0444)F201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1biqA)Y209 Warning: unaligning (T0444)S203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1biqA)Y209 Warning: unaligning (T0444)L321 because last residue in template chain is (1biqA)V340 T0444 22 :SMSDTNESEIKSNEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKK 1biqA 2 :YTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSFTHIIRNIVNDPSV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1biqA 136 :VFDDIVTNEQIQKRAEGISSYYDELIE T0444 186 :TFGERVVAFAAVEGV 1biqA 192 :KLYLCLMSVNALEAI T0444 204 :GSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1biqA 210 :VSFACSFAFAERELMEGNAKIIRLIARDAALHLTGTQHMLNLLRSGAD T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1biqA 269 :KQECYDLFVQAAQQEKDWADYLFRDG T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKVFQA 1biqA 296 :MIGLNKDILCQYVEYITNIRMQAVGLDLPFQT T0444 310 :ENPFDFMENIS 1biqA 329 :SNPIPWINTWL Number of specific fragments extracted= 7 number of extra gaps= 0 total=323 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 1mhyB/T0444-1mhyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mhyB expands to /projects/compbio/data/pdb/1mhy.pdb.gz 1mhyB:# T0444 read from 1mhyB/T0444-1mhyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mhyB read from 1mhyB/T0444-1mhyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mhyB to template set # found chain 1mhyB in template set T0444 7 :HSSGV 1mhyB 67 :AGGLD T0444 25 :DTNESEIKSNEEPLLRKSS 1mhyB 72 :WGDWTQKFHGGRPSWGNES T0444 44 :RRFVIFPIQYP 1mhyB 94 :RTTDWYRHRDP T0444 55 :DIWKMYKQAQA 1mhyB 122 :YTQRFLAAYSS T0444 79 :LPHWNKLKADEKY 1mhyB 133 :EGSIRTIDPYWRD T0444 92 :FISHILAFFAASDGIV 1mhyB 148 :LNKYFGALLYSEYGLF T0444 110 :NLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1mhyB 164 :NAHSSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIA T0444 152 :DPK 1mhyB 207 :VPG T0444 155 :KREFLFNAIETMPYVKKKADWALRWIADRK 1mhyB 213 :STDVPKKIWTTDPIYSGARATVQEIWQGVQ T0444 186 :TFGERVVAF 1mhyB 243 :DWNEILWAG T0444 195 :AAVEGVFFSGSF 1mhyB 253 :AVYDATFGQFAR T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mhyB 266 :EFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDS T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 1mhyB 317 :RTFLNAWTEHYLASSVAALKDFVGL T0444 278 :LIGMN 1mhyB 342 :YAKVE T0444 283 :CILMKQYIEFVADRL 1mhyB 354 :SAGVSEALQRVFGDW T0444 298 :LVELGFS 1mhyB 373 :ADKIGFR Number of specific fragments extracted= 16 number of extra gaps= 0 total=339 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 1mhyB/T0444-1mhyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mhyB/T0444-1mhyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mhyB read from 1mhyB/T0444-1mhyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mhyB in template set T0444 21 :QSMSDTNESEIKSNEEPLLRKSSRR 1mhyB 68 :GGLDWGDWTQKFHGGRPSWGNESTE T0444 46 :FVIFPIQY 1mhyB 100 :RHRDPARR T0444 54 :PDIWKMYKQAQAS 1mhyB 110 :HPYVKDKSEEARY T0444 73 :VDLSKDLPHWNKLKADEKY 1mhyB 127 :LAAYSSEGSIRTIDPYWRD T0444 92 :FISHILAFFAASDGIVNENL 1mhyB 147 :ILNKYFGALLYSEYGLFNAH T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1mhyB 167 :SSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIA T0444 151 :RDPKK 1mhyB 212 :ASTDV T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 1mhyB 217 :PKKIWTTDPIYSGARATVQEIWQGVQD T0444 187 :FGERVVAFAAV 1mhyB 244 :WNEILWAGHAV T0444 198 :EGVFFSGSF 1mhyB 256 :DATFGQFAR T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1mhyB 266 :EFFQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDSE T0444 253 :ERVREIIVDAVKIEQEFLTEALPV 1mhyB 318 :TFLNAWTEHYLASSVAALKDFVGL T0444 279 :IGMN 1mhyB 350 :GATD T0444 283 :CILMKQYIEFVADRLLVELGFS 1mhyB 358 :SEALQRVFGDWKIDYADKIGFR Number of specific fragments extracted= 14 number of extra gaps= 0 total=353 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 1mhyB/T0444-1mhyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mhyB/T0444-1mhyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mhyB read from 1mhyB/T0444-1mhyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mhyB in template set T0444 54 :PDIWKMYKQAQAS 1mhyB 121 :RYTQRFLAAYSSE T0444 80 :PHWNKLKADEKY 1mhyB 134 :GSIRTIDPYWRD T0444 92 :FISHILAFFAASDGIVNENL 1mhyB 147 :ILNKYFGALLYSEYGLFNAH T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 1mhyB 167 :SSVGRDCLSDTIRQTAVFAALDKVDNAQMIQMERLFIAK T0444 152 :DPKK 1mhyB 207 :VPGF T0444 156 :REFLFNAIETMPYVKKK 1mhyB 214 :TDVPKKIWTTDPIYSGA T0444 177 :LRWIADRKS 1mhyB 231 :RATVQEIWQ T0444 186 :TFGERVVAFAAVEGVFFSGSF 1mhyB 244 :WNEILWAGHAVYDATFGQFAR T0444 209 :IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mhyB 268 :FQRLATVYGDTLTPFFTAQSQTYFQTTRGAIDDLFVYCLANDS T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1mhyB 317 :RTFLNAWTEHYLASSVAALKDFVGLY T0444 278 :L 1mhyB 348 :V T0444 282 :NCILMKQYIEFVADRL 1mhyB 353 :DSAGVSEALQRVFGDW T0444 298 :LVELGFS 1mhyB 373 :ADKIGFR Number of specific fragments extracted= 13 number of extra gaps= 0 total=366 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 2inpC/T0444-2inpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2inpC expands to /projects/compbio/data/pdb/2inp.pdb.gz 2inpC:# T0444 read from 2inpC/T0444-2inpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpC read from 2inpC/T0444-2inpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2inpC to template set # found chain 2inpC in template set Warning: unaligning (T0444)I51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2inpC)Y80 Warning: unaligning (T0444)Q52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2inpC)Y80 Warning: unaligning (T0444)E164 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)D191 Warning: unaligning (T0444)T165 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)D191 Warning: unaligning (T0444)S205 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)Y231 Warning: unaligning (T0444)F206 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)Y231 T0444 7 :HSSGVDLGTENLYFQSMSDTNESEIKSNEEPLLRKSSR 2inpC 39 :IEAKTNFHYRPQWDSEHTLNDPTRTAIRMEDWCAVSDP T0444 49 :FP 2inpC 77 :RQ T0444 53 :YPDIWKMYKQAQAS 2inpC 81 :YGAYVGNRAKMQES T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2inpC 106 :NLLTRLSEETQKQLLRLLVPLRHVELGANMNN T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2inpC 138 :AKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIALMID T0444 151 :RDPKKREFLFNAI 2inpC 177 :STGAALDESKAYW T0444 166 :MPYVKKKADWALRWIADRKS 2inpC 192 :DEMWQPMRKLVEDTLVVDDW T0444 188 :GERVVAF 2inpC 212 :FELTLVQ T0444 195 :AAVEGVFFSG 2inpC 220 :ILIDGMMYPL T0444 207 :AAIF 2inpC 232 :DKMD T0444 211 :WLKKRGL 2inpC 237 :WFESQGA T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2inpC 244 :EDVSMLTEFMRDWYKESLRWTNAMMKAVAGESE T0444 252 :EERVREIIVDAVKIEQEFLTEALP 2inpC 279 :RELLQKWIDHWEPQAYEALKPLAE T0444 279 :IGMNCILMKQYIEF 2inpC 303 :ASVGIDGLNEARAE T0444 294 :ADRLLVELGFS 2inpC 317 :LSARLKKFELQ Number of specific fragments extracted= 15 number of extra gaps= 3 total=381 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 2inpC/T0444-2inpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2inpC/T0444-2inpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpC read from 2inpC/T0444-2inpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2inpC in template set Warning: unaligning (T0444)E164 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)D191 Warning: unaligning (T0444)T165 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)D191 Warning: unaligning (T0444)S205 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)Y231 Warning: unaligning (T0444)F206 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)Y231 T0444 54 :PDIWKMYKQAQA 2inpC 93 :ESAETSFGFCEK T0444 79 :LPHWNKLKADEKYFISHILAFFAASDGIVNENL 2inpC 105 :RNLLTRLSEETQKQLLRLLVPLRHVELGANMNN T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2inpC 138 :AKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIALMID T0444 151 :RDPKKREFLFNAI 2inpC 177 :STGAALDESKAYW T0444 166 :MPYVKKKADWALRWIADR 2inpC 192 :DEMWQPMRKLVEDTLVVD T0444 186 :TFGERVVAFA 2inpC 210 :DWFELTLVQN T0444 196 :AVEGVFFSG 2inpC 221 :LIDGMMYPL T0444 207 :AAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2inpC 232 :DKMDQWFESQGAEDVSMLTEFMRDWYKESLRWTNAMMKAVAGESET T0444 253 :ERVREIIVDAVKIEQEFLTEALPV 2inpC 284 :KWIDHWEPQAYEALKPLAEASVGI T0444 284 :ILMKQYIEFV 2inpC 308 :DGLNEARAEL T0444 295 :DRLLVELGFS 2inpC 318 :SARLKKFELQ Number of specific fragments extracted= 11 number of extra gaps= 2 total=392 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 2inpC/T0444-2inpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2inpC/T0444-2inpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpC read from 2inpC/T0444-2inpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2inpC in template set Warning: unaligning (T0444)E164 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)D191 Warning: unaligning (T0444)T165 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)D191 Warning: unaligning (T0444)S205 because of BadResidue code BAD_PEPTIDE in next template residue (2inpC)Y231 Warning: unaligning (T0444)F206 because of BadResidue code BAD_PEPTIDE at template residue (2inpC)Y231 T0444 54 :PDIWKMYKQAQAS 2inpC 93 :ESAETSFGFCEKR T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2inpC 106 :NLLTRLSEETQKQLLRLLVPLRHVELGANMNN T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2inpC 138 :AKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIALMID T0444 151 :RDPKKREFLFNAI 2inpC 177 :STGAALDESKAYW T0444 166 :MPYVKK 2inpC 192 :DEMWQP T0444 176 :ALRWIADRKS 2inpC 198 :MRKLVEDTLV T0444 186 :TFGERVVAFAAVEGVFFSG 2inpC 211 :WFELTLVQNILIDGMMYPL T0444 207 :AAIF 2inpC 232 :DKMD T0444 211 :WLKKRG 2inpC 237 :WFESQG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2inpC 243 :AEDVSMLTEFMRDWYKESLRWTNAMMKAVAGESE T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 2inpC 279 :RELLQKWIDHWEPQAYEALKPLAEAS T0444 279 :I 2inpC 306 :G T0444 283 :CILMKQYIEFV 2inpC 307 :IDGLNEARAEL T0444 295 :DRLLVELGF 2inpC 318 :SARLKKFEL Number of specific fragments extracted= 14 number of extra gaps= 2 total=406 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 2incA/T0444-2incA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2incA expands to /projects/compbio/data/pdb/2inc.pdb.gz 2incA:# T0444 read from 2incA/T0444-2incA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incA read from 2incA/T0444-2incA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2incA to template set # found chain 2incA in template set Warning: unaligning (T0444)K249 because of BadResidue code BAD_PEPTIDE in next template residue (2incA)G249 Warning: unaligning (T0444)P250 because of BadResidue code BAD_PEPTIDE at template residue (2incA)G249 Warning: unaligning (T0444)S251 because of BadResidue code BAD_PEPTIDE at template residue (2incA)K250 T0444 54 :PDIWKMYKQAQA 2incA 67 :SGAYSIKAALER T0444 79 :LPHWNKLKADEKYFISHILAFFAASDGIVNENL 2incA 79 :DGFVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2incA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANV T0444 155 :K 2incA 156 :D T0444 159 :LFNAIET 2incA 157 :WAHKAIH T0444 172 :KADWALRWIA 2incA 167 :WAAIAARSFF T0444 182 :DRKS 2incA 182 :TRDS T0444 188 :GERVVAF 2incA 186 :VAVSIML T0444 195 :AAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 2incA 194 :FAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVE T0444 252 :EERVREIIVDAVKIEQEFLT 2incA 251 :KDEAQQMVDVAIWRSWKLFS T0444 272 :EALPVGLIGMN 2incA 279 :YYTPLESRNQS T0444 283 :CILMKQYIEFVADRLLVELGFS 2incA 291 :KEFMLEWIVAQFERQLLDLGLD Number of specific fragments extracted= 12 number of extra gaps= 1 total=418 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 2incA/T0444-2incA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2incA/T0444-2incA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incA read from 2incA/T0444-2incA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2incA in template set Warning: unaligning (T0444)K249 because of BadResidue code BAD_PEPTIDE in next template residue (2incA)G249 Warning: unaligning (T0444)P250 because of BadResidue code BAD_PEPTIDE at template residue (2incA)G249 Warning: unaligning (T0444)S251 because of BadResidue code BAD_PEPTIDE at template residue (2incA)K250 T0444 55 :DIWKMYKQAQAS 2incA 68 :GAYSIKAALERD T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2incA 80 :GFVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWI 2incA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDM T0444 186 :TFGERVVAFAAV 2incA 184 :DSVAVSIMLTFA T0444 198 :EGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 2incA 197 :ETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVE T0444 252 :EERVREIIVDAVKIEQ 2incA 251 :KDEAQQMVDVAIWRSW T0444 268 :EFLTEALPVG 2incA 275 :PIMDYYTPLE T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKV 2incA 286 :RNQSFKEFMLEWIVAQFERQLLDLGLDKP Number of specific fragments extracted= 8 number of extra gaps= 1 total=426 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 2incA/T0444-2incA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2incA/T0444-2incA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incA read from 2incA/T0444-2incA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2incA in template set Warning: unaligning (T0444)K249 because of BadResidue code BAD_PEPTIDE in next template residue (2incA)G249 Warning: unaligning (T0444)P250 because of BadResidue code BAD_PEPTIDE at template residue (2incA)G249 Warning: unaligning (T0444)S251 because of BadResidue code BAD_PEPTIDE at template residue (2incA)K250 T0444 54 :PDIWKMYKQAQASF 2incA 67 :SGAYSIKAALERDG T0444 81 :HWNKLKADEKYFISHILAFFAASDGIVNENL 2incA 81 :FVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIA 2incA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMM T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 2incA 185 :SVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVE T0444 252 :EERVREIIVDAVKIEQEFLTEA 2incA 251 :KDEAQQMVDVAIWRSWKLFSVL T0444 275 :PVG 2incA 282 :PLE T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSKV 2incA 286 :RNQSFKEFMLEWIVAQFERQLLDLGLDKP Number of specific fragments extracted= 7 number of extra gaps= 1 total=433 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 2incB/T0444-2incB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2incB expands to /projects/compbio/data/pdb/2inc.pdb.gz 2incB:# T0444 read from 2incB/T0444-2incB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incB read from 2incB/T0444-2incB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2incB to template set # found chain 2incB in template set Warning: unaligning (T0444)L278 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2incB)P308 Warning: unaligning (T0444)I279 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2incB)P308 Warning: unaligning (T0444)G302 because last residue in template chain is (2incB)G329 T0444 9 :SGVDLGTENL 2incB 47 :ELDSNLPMQT T0444 21 :QSMSDTNESEIKSNEEPLLRKS 2incB 57 :WYKKYCFDSPLKHDDWNAFRDP T0444 49 :FPIQYPDIWKMYKQAQAS 2incB 79 :DQLVYRTYNLLQDGQESY T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2incB 108 :GHDQMLTREWVETLARFYTPARYLFHALQMGS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRD 2incB 140 :VYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANC T0444 159 :LFNAIETMPYVKKKADWALRWIADRKS 2incB 189 :ERDVWENDPAWQGFRELIEKALIAWDW T0444 188 :GERVVAF 2incB 216 :GEAFTAI T0444 195 :AAVEGVFFSGSFAAIF 2incB 224 :LVTKPAVEEALLQQLG T0444 211 :WLKKRG 2incB 241 :LAQSEG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2incB 247 :DTLLGLLAQAQKRDAERHRRWSSALVKMALEKEG T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 2incB 282 :REVLQKWVAKWEPLADKAIEAYCSA T0444 280 :G 2incB 309 :D T0444 283 :CILMKQYIEFVADRLLVEL 2incB 310 :GENAIVEAKSASRYVRQMM Number of specific fragments extracted= 13 number of extra gaps= 1 total=446 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 2incB/T0444-2incB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2incB/T0444-2incB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incB read from 2incB/T0444-2incB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2incB in template set Warning: unaligning (T0444)D78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2incB)R107 Warning: unaligning (T0444)L79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2incB)R107 Warning: unaligning (T0444)L278 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2incB)P308 Warning: unaligning (T0444)I279 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2incB)P308 Warning: unaligning (T0444)G302 because last residue in template chain is (2incB)G329 T0444 56 :IWKMYKQAQASF 2incB 93 :QESYVQGLFDQL T0444 77 :K 2incB 105 :N T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2incB 108 :GHDQMLTREWVETLARFYTPARYLFHALQMGS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2incB 140 :VYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELA T0444 151 :RDPK 2incB 179 :CYPD T0444 159 :LFNAIETMPYVKKKADWALRWIAD 2incB 189 :ERDVWENDPAWQGFRELIEKALIA T0444 185 :STFGERVVAFAAV 2incB 213 :WDWGEAFTAINLV T0444 198 :EGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2incB 227 :KPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGN T0444 253 :ERVREIIVDAVKIEQEFLTEALPV 2incB 283 :EVLQKWVAKWEPLADKAIEAYCSA T0444 283 :CILMKQYIEFVADRLLVEL 2incB 310 :GENAIVEAKSASRYVRQMM Number of specific fragments extracted= 10 number of extra gaps= 2 total=456 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 2incB/T0444-2incB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2incB/T0444-2incB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2incB read from 2incB/T0444-2incB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2incB in template set Warning: unaligning (T0444)L79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2incB)R107 Warning: unaligning (T0444)G277 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2incB)P308 Warning: unaligning (T0444)L278 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2incB)P308 T0444 55 :DIWKMYKQAQASF 2incB 92 :GQESYVQGLFDQL T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 2incB 108 :GHDQMLTREWVETLARFYTPARYLFHALQMGS T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 2incB 140 :VYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELAN T0444 157 :EFLFNAIETMPYV 2incB 187 :KRERDVWENDPAW T0444 174 :DWALRWIADRKS 2incB 200 :QGFRELIEKALI T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2incB 215 :WGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEG T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 2incB 282 :REVLQKWVAKWEPLADKAIEAYCSA T0444 279 :I 2incB 309 :D T0444 283 :CILMKQYIEFVADRLLVEL 2incB 310 :GENAIVEAKSASRYVRQMM Number of specific fragments extracted= 9 number of extra gaps= 2 total=465 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 1t0qA/T0444-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0qA expands to /projects/compbio/data/pdb/1t0q.pdb.gz 1t0qA:# T0444 read from 1t0qA/T0444-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0444-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0qA to template set # found chain 1t0qA in template set T0444 55 :DIWKMYKQAQAS 1t0qA 61 :IQREKDSGAYSI T0444 70 :AE 1t0qA 77 :ER T0444 79 :LPHWNKLKADEKYFISHILAFFAASDGIVNENL 1t0qA 79 :DGFVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1t0qA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANV T0444 151 :RD 1t0qA 151 :RS T0444 157 :E 1t0qA 156 :D T0444 159 :LFNAIE 1t0qA 157 :WAHKAI T0444 165 :TMPYVKKKADWALRWI 1t0qA 164 :TNEWAAIAARSFFDDM T0444 182 :DRKS 1t0qA 182 :TRDS T0444 188 :GERVVAF 1t0qA 186 :VAVSIML T0444 195 :AAVEGVFFSGSFAAIF 1t0qA 194 :FAFETGFTNMQFLGLA T0444 211 :WLKKRG 1t0qA 211 :DAAEAG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEA 1t0qA 217 :DHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVL T0444 274 :LPVG 1t0qA 281 :TPLE T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFS 1t0qA 286 :RNQSFKEFMLEWIVAQFERQLLDLGLD Number of specific fragments extracted= 15 number of extra gaps= 0 total=480 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 1t0qA/T0444-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1t0qA/T0444-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0444-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qA in template set Warning: unaligning (T0444)K305 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0444)V306 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qA)P314 T0444 58 :KMYKQAQASF 1t0qA 64 :EKDSGAYSIK T0444 74 :DLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENL 1t0qA 74 :AALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWI 1t0qA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDM T0444 186 :TFGERVVAFAAV 1t0qA 184 :DSVAVSIMLTFA T0444 198 :EGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFL 1t0qA 197 :ETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLF T0444 271 :TEALPVG 1t0qA 278 :DYYTPLE T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFS 1t0qA 286 :RNQSFKEFMLEWIVAQFERQLLDLGLD Number of specific fragments extracted= 7 number of extra gaps= 1 total=487 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 1t0qA/T0444-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1t0qA/T0444-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0444-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qA in template set Warning: unaligning (T0444)K305 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0444)V306 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qA)P314 T0444 55 :DIWKMYKQAQASF 1t0qA 61 :IQREKDSGAYSIK T0444 79 :LP 1t0qA 77 :ER T0444 81 :HWNKLKADEKYFISHILAFFAASDGIVNENL 1t0qA 81 :FVDRADPGWVSTMQLHFGAIALEEYAASTAE T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMP 1t0qA 112 :ARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNE T0444 175 :WALRWIADRKS 1t0qA 167 :WAAIAARSFFD T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIF 1t0qA 185 :SVAVSIMLTFAFETGFTNMQFLGLA T0444 211 :WLKKRG 1t0qA 211 :DAAEAG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQE 1t0qA 217 :DHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWK T0444 269 :FLTEALPVG 1t0qA 276 :IMDYYTPLE T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFS 1t0qA 286 :RNQSFKEFMLEWIVAQFERQLLDLGLD Number of specific fragments extracted= 10 number of extra gaps= 1 total=497 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 2j2fA/T0444-2j2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2j2fA expands to /projects/compbio/data/pdb/2j2f.pdb.gz 2j2fA:# T0444 read from 2j2fA/T0444-2j2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j2fA read from 2j2fA/T0444-2j2fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2j2fA to template set # found chain 2j2fA in template set T0444 3 :HHHHHSSGVDLGTENLYFQ 2j2fA 21 :PREVHVQVTHSMPPQKIEI T0444 23 :MS 2j2fA 40 :FK T0444 25 :DTNESEIKSNEEPLLRKSS 2j2fA 55 :LKPVEKCWQPQDFLPDPAS T0444 52 :QYPDIWKMYKQAQAS 2j2fA 75 :GFDEQVRELRERAKE T0444 85 :LKA 2j2fA 90 :IPD T0444 91 :YFISHILAFFAASD 2j2fA 93 :DYFVVLVGDMITEE T0444 107 :VNENLVERFSQEV 2j2fA 107 :ALPTYQTMLNTLD T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYI 2j2fA 128 :SPTSWAIWTRAWTAEENRHGDLLNKYLYLSG T0444 151 :RDPKKREFLFNAI 2j2fA 160 :VDMRQIEKTIQYL T0444 170 :KKK 2j2fA 173 :IGS T0444 182 :DRK 2j2fA 182 :ENS T0444 187 :FGERVVAFAAVE 2j2fA 185 :PYLGFIYTSFQE T0444 200 :VFFSGSFAAIF 2j2fA 197 :RADFISHGNTA T0444 211 :WLKKRGL 2j2fA 209 :QAKEHGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2j2fA 216 :IKLAQICGTIAADEKRHETAYTKIVEKLFEIDP T0444 252 :EERVREIIVDA 2j2fA 279 :FDHFSAVAQRL T0444 263 :VKIEQEFLTEA 2j2fA 298 :ADILEFLVGRW T0444 275 :P 2j2fA 309 :K T0444 276 :VGLIGMN 2j2fA 311 :DKLTGLS T0444 284 :ILMKQYIEFVADRL 2j2fA 318 :AEGQKAQDYVCRLP Number of specific fragments extracted= 20 number of extra gaps= 0 total=517 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 2j2fA/T0444-2j2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2j2fA/T0444-2j2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j2fA read from 2j2fA/T0444-2j2fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j2fA in template set Warning: unaligning (T0444)M23 because first residue in template chain is (2j2fA)K16 Warning: unaligning (T0444)S24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2j2fA)F18 Warning: unaligning (T0444)D25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2j2fA)F18 T0444 26 :TNESEIKSNEEPLL 2j2fA 19 :MPPREVHVQVTHSM T0444 52 :Q 2j2fA 33 :P T0444 54 :PDIWKMYKQ 2j2fA 34 :PQKIEIFKS T0444 63 :AQAS 2j2fA 47 :AEEN T0444 67 :FWTAEEVDLSKDLPHW 2j2fA 61 :CWQPQDFLPDPASDGF T0444 83 :NKLKADEKYFISHILAFFAASDGIVNE 2j2fA 88 :KEIPDDYFVVLVGDMITEEALPTYQTM T0444 115 :FS 2j2fA 115 :LN T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 2j2fA 125 :TGASPTSWAIWTRAWTAEENRHGDLLNKYLYLSG T0444 151 :RDPKK 2j2fA 160 :VDMRQ T0444 169 :VKKKADWALRWIAD 2j2fA 165 :IEKTIQYLIGSGMD T0444 183 :RKSTFGERVVAFAAVEGVFFSGSFAAIF 2j2fA 180 :RTENSPYLGFIYTSFQERADFISHGNTA T0444 211 :WLKKRGL 2j2fA 209 :QAKEHGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2j2fA 216 :IKLAQICGTIAADEKRHETAYTKIVEKLFEIDPD T0444 253 :ERVREIIVDA 2j2fA 280 :DHFSAVAQRL T0444 263 :VKIEQEFLT 2j2fA 298 :ADILEFLVG T0444 273 :ALPVG 2j2fA 307 :RWKVD T0444 278 :LIGMN 2j2fA 313 :LTGLS T0444 284 :ILMKQYIEFVADRL 2j2fA 318 :AEGQKAQDYVCRLP Number of specific fragments extracted= 18 number of extra gaps= 0 total=535 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 2j2fA/T0444-2j2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2j2fA/T0444-2j2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j2fA read from 2j2fA/T0444-2j2fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j2fA in template set T0444 54 :PDIWKMYKQAQAS 2j2fA 34 :PQKIEIFKSLDNW T0444 67 :FWTAEEVDLSKDLPHW 2j2fA 61 :CWQPQDFLPDPASDGF T0444 83 :NKLKADEK 2j2fA 81 :RELRERAK T0444 91 :YFISHILAFFAASDGIVNENLVERFSQEV 2j2fA 93 :DYFVVLVGDMITEEALPTYQTMLNTLDGV T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYIR 2j2fA 128 :SPTSWAIWTRAWTAEENRHGDLLNKYLYLSGR T0444 165 :TMPYVKKKADWALRW 2j2fA 161 :DMRQIEKTIQYLIGS T0444 180 :IAD 2j2fA 181 :TEN T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGL 2j2fA 184 :SPYLGFIYTSFQERADFISHGNTARQAKEHGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2j2fA 216 :IKLAQICGTIAADEKRHETAYTKIVEKLFEIDP T0444 262 :AVKIEQEFLTEA 2j2fA 278 :LFDHFSAVAQRL T0444 277 :GLI 2j2fA 290 :GVY T0444 282 :NCILMKQY 2j2fA 293 :TAKDYADI T0444 294 :ADRLLVELGFSKVFQA 2j2fA 301 :LEFLVGRWKVDKLTGL Number of specific fragments extracted= 13 number of extra gaps= 0 total=548 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 2oc5A/T0444-2oc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2oc5A expands to /projects/compbio/data/pdb/2oc5.pdb.gz 2oc5A:Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2oc5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 448, because occupancy 0.300 <= existing 0.700 in 2oc5A Skipped atom 450, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 451, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 453, because occupancy 0.300 <= existing 0.700 in 2oc5A Skipped atom 455, because occupancy 0.300 <= existing 0.700 in 2oc5A Skipped atom 457, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 458, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 460, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 461, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 463, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 464, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 466, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 467, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 469, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 470, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 472, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 473, because occupancy 0.300 <= existing 0.350 in 2oc5A Skipped atom 475, because occupancy 0.350 <= existing 0.350 in 2oc5A Skipped atom 476, because occupancy 0.300 <= existing 0.350 in 2oc5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 864, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 2oc5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1675, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 2oc5A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 2oc5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0444 read from 2oc5A/T0444-2oc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oc5A read from 2oc5A/T0444-2oc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oc5A to template set # found chain 2oc5A in template set Warning: unaligning (T0444)A70 because first residue in template chain is (2oc5A)E20 T0444 71 :EEVDLSK 2oc5A 21 :ALPDFTS T0444 87 :ADEKYFISHILAFFAASDGIVNENL 2oc5A 28 :DRYKDAYSRINAIVIEGEQEAHDNY T0444 113 :ERFSQEV 2oc5A 53 :IAIGTLL T0444 122 :PEARCFYGFQILIENVHSEMYSLLIDTYI 2oc5A 60 :PDHVEELKRLAKMEMRHKKGFTACGKNLG T0444 151 :RDP 2oc5A 91 :ADM T0444 167 :PYVKKKADWALRWIA 2oc5A 94 :DFAREFFAPLRDNFQ T0444 182 :DRKS 2oc5A 113 :QGKT T0444 187 :FGERVVAFAAVEGVFF 2oc5A 117 :PTCLLIQALLIEAFAI T0444 204 :GSFAAIF 2oc5A 133 :SAYHTYI T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKP 2oc5A 144 :PFARKITEGVVKDEYTHLNYGEAWLKANLESC T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 2oc5A 176 :REELLEANRENLPLIRRMLDQVAGDA T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSK 2oc5A 203 :VLQMDKEDLIEDFLIAYQESLTEIGFNT Number of specific fragments extracted= 12 number of extra gaps= 0 total=560 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 2oc5A/T0444-2oc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2oc5A/T0444-2oc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oc5A read from 2oc5A/T0444-2oc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oc5A in template set Warning: unaligning (T0444)A70 because first residue in template chain is (2oc5A)E20 T0444 71 :EEVDLS 2oc5A 21 :ALPDFT T0444 86 :KADEKYFISHILAFFAASDGIVNENL 2oc5A 27 :SDRYKDAYSRINAIVIEGEQEAHDNY T0444 113 :ERFSQEV 2oc5A 53 :IAIGTLL T0444 122 :PEARCFYGFQILIENVHSEMYSLLIDTYI 2oc5A 60 :PDHVEELKRLAKMEMRHKKGFTACGKNLG T0444 151 :RDPKKREFLFNA 2oc5A 91 :ADMDFAREFFAP T0444 169 :VKKKADWALR 2oc5A 103 :LRDNFQTALG T0444 182 :DR 2oc5A 113 :QG T0444 185 :STFGERVVAFAAVEGVFFSGSFAA 2oc5A 115 :KTPTCLLIQALLIEAFAISAYHTY T0444 217 :LMPGLTFSNELISRDEGLHCDFACLMFQYLVN 2oc5A 142 :SDPFARKITEGVVKDEYTHLNYGEAWLKANLE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 2oc5A 177 :EELLEANRENLPLIRRMLDQVAGDA T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFS 2oc5A 203 :VLQMDKEDLIEDFLIAYQESLTEIGFN Number of specific fragments extracted= 11 number of extra gaps= 0 total=571 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 2oc5A/T0444-2oc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2oc5A/T0444-2oc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oc5A read from 2oc5A/T0444-2oc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oc5A in template set Warning: unaligning (T0444)A70 because first residue in template chain is (2oc5A)E20 T0444 71 :EEVDLSK 2oc5A 21 :ALPDFTS T0444 87 :ADEKYFISHILAFFAASDGIVNENL 2oc5A 28 :DRYKDAYSRINAIVIEGEQEAHDNY T0444 113 :ERFSQEVQVP 2oc5A 53 :IAIGTLLPDH T0444 125 :RCFYGFQILIENVHSEMYSLLIDTYIRDPKK 2oc5A 63 :VEELKRLAKMEMRHKKGFTACGKNLGVEADM T0444 167 :PYVKKKADWALRWIADRKS 2oc5A 94 :DFAREFFAPLRDNFQTALG T0444 186 :TFGERVVAFAAVEGVFFSGSFAA 2oc5A 116 :TPTCLLIQALLIEAFAISAYHTY T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNK 2oc5A 144 :PFARKITEGVVKDEYTHLNYGEAWLKANLES T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 2oc5A 176 :REELLEANRENLPLIRRMLDQVAGDA T0444 278 :LIGMNCILMKQYIEFVADRLLVELGFSK 2oc5A 203 :VLQMDKEDLIEDFLIAYQESLTEIGFNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=580 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 1za0A/T0444-1za0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1za0A expands to /projects/compbio/data/pdb/1za0.pdb.gz 1za0A:Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1za0A Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1za0A # T0444 read from 1za0A/T0444-1za0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1za0A read from 1za0A/T0444-1za0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1za0A to template set # found chain 1za0A in template set Warning: unaligning (T0444)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1za0A)I31 Warning: unaligning (T0444)I106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)D94 Warning: unaligning (T0444)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0444)K155 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0444)D182 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0444 54 :PDIWKMYKQAQAS 1za0A 16 :PVVEANMTRHLDT T0444 68 :WTAEEVDLSKDLPHWNK 1za0A 32 :WFAHDYVPFDQGENFAF T0444 85 :LKADEKYFI 1za0A 61 :LPRTITDAC T0444 98 :AFFAASDG 1za0A 70 :EILLILKD T0444 123 :EARCFYGFQILIENVHSEMYSLLIDTYI 1za0A 95 :WWGRWLGRWTAEEHLHAIALREYLVVTR T0444 151 :RDPK 1za0A 130 :EDVR T0444 183 :RKS 1za0A 146 :YTQ T0444 188 :GERVVAFAAVEG 1za0A 149 :VETLVYMAFYER T0444 204 :GSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 1za0A 161 :CGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLVTHCLD T0444 251 :SEERVREIIVDAVKI 1za0A 207 :TRDETIAAIAARAAD T0444 268 :EFLTEALPVGLIG 1za0A 234 :DKLQNVADAGIFG T0444 283 :CILMKQYI 1za0A 247 :KPQLRQLI T0444 295 :DRLLVELGFSKV 1za0A 255 :SDRITAWGLAGE T0444 314 :DFME 1za0A 267 :PSLK Number of specific fragments extracted= 14 number of extra gaps= 1 total=594 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 1za0A/T0444-1za0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1za0A/T0444-1za0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1za0A read from 1za0A/T0444-1za0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1za0A in template set Warning: unaligning (T0444)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1za0A)I31 Warning: unaligning (T0444)I106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)D94 Warning: unaligning (T0444)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0444)Y168 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0444)D182 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0444 54 :PDIWKMYKQAQAS 1za0A 16 :PVVEANMTRHLDT T0444 68 :WTAEEVDLSKDLPHW 1za0A 32 :WFAHDYVPFDQGENF T0444 83 :N 1za0A 57 :S T0444 84 :KLKADEKY 1za0A 60 :TLPRTITD T0444 96 :ILAFFAASDG 1za0A 68 :ACEILLILKD T0444 123 :EARCFYGFQILIENVHSEMYSLLIDTYI 1za0A 95 :WWGRWLGRWTAEEHLHAIALREYLVVTR T0444 151 :RDPKK 1za0A 124 :VDPVA T0444 163 :IETMP 1za0A 129 :NEDVR T0444 183 :RKS 1za0A 146 :YTQ T0444 188 :GERVVAFAAVE 1za0A 149 :VETLVYMAFYE T0444 203 :SGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVN 1za0A 160 :RCGAVFCRNLAAQIEEPILAGLIDRIARDEVRHEEFFANLVTHCLD T0444 252 :EERVREIIVDAVKI 1za0A 208 :RDETIAAIAARAAD T0444 268 :EFLTEALPVGLIG 1za0A 234 :DKLQNVADAGIFG T0444 284 :IL 1za0A 248 :PQ T0444 290 :IEFVADRLLVELGFSK 1za0A 250 :LRQLISDRITAWGLAG Number of specific fragments extracted= 15 number of extra gaps= 1 total=609 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 1za0A/T0444-1za0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1za0A/T0444-1za0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1za0A read from 1za0A/T0444-1za0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1za0A in template set Warning: unaligning (T0444)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1za0A)I31 Warning: unaligning (T0444)I106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)D94 Warning: unaligning (T0444)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)D94 Warning: unaligning (T0444)K155 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1za0A)K145 Warning: unaligning (T0444)D182 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1za0A)K145 T0444 56 :IWKMYKQAQAS 1za0A 18 :VEANMTRHLDT T0444 68 :WTAEEVDLSKDLPHWN 1za0A 32 :WFAHDYVPFDQGENFA T0444 84 :KLKAD 1za0A 60 :TLPRT T0444 93 :ISHILAFFAASDG 1za0A 65 :ITDACEILLILKD T0444 123 :EARCFYGFQILIENVHSEMYSLLIDTYIR 1za0A 95 :WWGRWLGRWTAEEHLHAIALREYLVVTRE T0444 152 :DPK 1za0A 131 :DVR T0444 183 :RKS 1za0A 146 :YTQ T0444 188 :GERVVAFAAVEGVFFSG 1za0A 149 :VETLVYMAFYERCGAVF T0444 209 :IFWLKKR 1za0A 166 :CRNLAAQ T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKP 1za0A 175 :EPILAGLIDRIARDEVRHEEFFANLVTHCLDYT T0444 252 :EERVREIIVDAVKI 1za0A 208 :RDETIAAIAARAAD T0444 269 :FLTEALPVGLI 1za0A 235 :KLQNVADAGIF T0444 282 :NCILMKQYIEFVADR 1za0A 246 :GKPQLRQLISDRITA T0444 301 :LGFSKVFQA 1za0A 264 :AGEPSLKQF Number of specific fragments extracted= 14 number of extra gaps= 1 total=623 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 1mtyD/T0444-1mtyD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mtyD expands to /projects/compbio/data/pdb/1mty.pdb.gz 1mtyD:# T0444 read from 1mtyD/T0444-1mtyD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyD read from 1mtyD/T0444-1mtyD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mtyD to template set # found chain 1mtyD in template set T0444 10 :GVDLGTENLYFQSMSDTNESEIKSNEEP 1mtyD 16 :ANRAPTSVNAQEVHRWLQSFNWDFKNNR T0444 38 :LLRKSSRRFVIFPIQYPDIWKMYKQAQAS 1mtyD 49 :KYKMANETKEQFKLIAKEYARMEAVKDER T0444 80 :PHWNKLKADEKYFISHILAFFAASDGIVNENL 1mtyD 90 :NAGVRVHPKWNETMKVVSNFLEVGEYNAIAAT T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1mtyD 122 :GMLWDSAQAAEQKNGYLAQVLDEIRHTHQCAYVNYYFA T0444 178 :RWIA 1mtyD 160 :KNGQ T0444 182 :DRKS 1mtyD 194 :SGDA T0444 188 :GERVVAF 1mtyD 198 :VECSLNL T0444 195 :AAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mtyD 206 :LVGEACFTNPLIVAVTEWAAANGDEITPTVFLSIETDELRHMANGYQTVVSIANDPA T0444 252 :EERVREIIVDA 1mtyD 264 :AKYLNTDLNNA T0444 263 :VKIEQEFLT 1mtyD 302 :VKTWDRWVY T0444 272 :EALPV 1mtyD 316 :IWIGR T0444 277 :GLIGMN 1mtyD 322 :GKYGVE T0444 283 :CILMKQYIEFVADRLLVEL 1mtyD 332 :LKDAKQDAYWAHHDLYLLA Number of specific fragments extracted= 13 number of extra gaps= 0 total=636 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 1mtyD/T0444-1mtyD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mtyD/T0444-1mtyD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyD read from 1mtyD/T0444-1mtyD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mtyD in template set T0444 42 :SSRRFVIFP 1mtyD 46 :YATKYKMAN T0444 51 :IQYP 1mtyD 56 :TKEQ T0444 55 :DIWKMYKQAQAS 1mtyD 66 :EYARMEAVKDER T0444 78 :DLPHWNKLKADEKYFISHILAFFAASDGIVNENL 1mtyD 88 :RLNAGVRVHPKWNETMKVVSNFLEVGEYNAIAAT T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 1mtyD 122 :GMLWDSAQAAEQKNGYLAQVLDEIRHTHQCAYVNYYF T0444 177 :LRWI 1mtyD 159 :AKNG T0444 186 :TFGERVVAF 1mtyD 196 :DAVECSLNL T0444 195 :AAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNK 1mtyD 206 :LVGEACFTNPLIVAVTEWAAANGDEITPTVFLSIETDELRHMANGYQTVVSIAND T0444 253 :ERVR 1mtyD 261 :PASA T0444 284 :ILMKQYIEFVADRLLVEL 1mtyD 265 :KYLNTDLNNAFWTQQKYF Number of specific fragments extracted= 10 number of extra gaps= 0 total=646 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 1mtyD/T0444-1mtyD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mtyD/T0444-1mtyD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyD read from 1mtyD/T0444-1mtyD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mtyD in template set T0444 7 :HSSGVDLGTE 1mtyD 44 :TKYATKYKMA T0444 49 :FPIQY 1mtyD 54 :NETKE T0444 54 :PDIWKMYKQAQASF 1mtyD 65 :KEYARMEAVKDERQ T0444 79 :LPHWNKLKADEKYFISHILAFFAASDGIVNENL 1mtyD 89 :LNAGVRVHPKWNETMKVVSNFLEVGEYNAIAAT T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 1mtyD 122 :GMLWDSAQAAEQKNGYLAQVLDEIRHTHQCAYVNYYFAK T0444 180 :IADRKS 1mtyD 168 :HNDARR T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNK 1mtyD 197 :AVECSLNLQLVGEACFTNPLIVAVTEWAAANGDEITPTVFLSIETDELRHMANGYQTVVSIAND T0444 253 :ERVREIIVDAVKIEQEFLTEAL 1mtyD 261 :PASAKYLNTDLNNAFWTQQKYF T0444 276 :VGLIGMNCILMKQYI 1mtyD 295 :KFKVEPWVKTWDRWV Number of specific fragments extracted= 9 number of extra gaps= 0 total=655 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 2inpA/T0444-2inpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2inpA expands to /projects/compbio/data/pdb/2inp.pdb.gz 2inpA:# T0444 read from 2inpA/T0444-2inpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpA read from 2inpA/T0444-2inpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2inpA to template set # found chain 2inpA in template set Warning: unaligning (T0444)R178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2inpA)R168 Warning: unaligning (T0444)W179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2inpA)R168 T0444 11 :VDLGTENLYFQSMSDTNESEIKSNEEPLLR 2inpA 22 :AWEPTYQDKKDIFPEEDFEGIKITDWSQWE T0444 47 :VIFPIQYPD 2inpA 52 :DPFRLTMDA T0444 56 :IWKMYKQAQAS 2inpA 72 :LYAIFDAFAQN T0444 80 :PHWNKL 2inpA 83 :NGHQNI T0444 86 :KADEKYFISHILAFFAASDGIVNENL 2inpA 90 :DARYVNALKLFISGISPLEHAAFQGY T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRD 2inpA 116 :SKVGRQFSGAGARVACQMQAIDELRHSQTQQHAMSHYNKH T0444 171 :KKADWAL 2inpA 160 :HDGPHMH T0444 180 :IA 2inpA 169 :VW T0444 182 :DRKS 2inpA 184 :SAGP T0444 188 :GERVVAF 2inpA 188 :FEFLTAI T0444 195 :AAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2inpA 196 :FSFEYVLTNLLFVPFMSGAAYNGDMATVTFGFSAQSDEARHMTLGLEVIKFILEQHE T0444 252 :EERVREIIVDAVKIEQEFLT 2inpA 255 :VPIVQRWIDKWFWRGFRLLS T0444 272 :EA 2inpA 279 :MM T0444 274 :LPVG 2inpA 282 :YMLP T0444 278 :LIGM 2inpA 287 :KVMS T0444 283 :CILMKQYIEFVADRLLVEL 2inpA 292 :SEAWEVYYEQNGGALFKDL T0444 302 :GFS 2inpA 314 :GIR Number of specific fragments extracted= 17 number of extra gaps= 1 total=672 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 2inpA/T0444-2inpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2inpA/T0444-2inpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpA read from 2inpA/T0444-2inpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2inpA in template set Warning: unaligning (T0444)D174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2inpA)R168 T0444 55 :DIWKMYKQAQASF 2inpA 71 :KLYAIFDAFAQNN T0444 81 :HWNKL 2inpA 84 :GHQNI T0444 86 :KADEKYFISHILAFFAASDGIVNENL 2inpA 90 :DARYVNALKLFISGISPLEHAAFQGY T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 2inpA 116 :SKVGRQFSGAGARVACQMQAIDELRHSQTQQHAMSHY T0444 160 :FNAIETMPYVKKKA 2inpA 153 :NKHFNGLHDGPHMH T0444 175 :WALRWI 2inpA 173 :SVPKSF T0444 186 :T 2inpA 184 :S T0444 187 :FGERVVAFA 2inpA 187 :PFEFLTAIS T0444 196 :AVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2inpA 197 :SFEYVLTNLLFVPFMSGAAYNGDMATVTFGFSAQSDEARHMTLGLEVIKFILEQHED T0444 253 :ERVREIIVDAVKIEQ 2inpA 256 :PIVQRWIDKWFWRGF T0444 268 :EFLTEALPVGLIGM 2inpA 278 :MMMDYMLPNKVMSW T0444 283 :CILMKQYIEFVADRLLVEL 2inpA 292 :SEAWEVYYEQNGGALFKDL T0444 302 :GFSK 2inpA 314 :GIRP Number of specific fragments extracted= 13 number of extra gaps= 1 total=685 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 2inpA/T0444-2inpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2inpA/T0444-2inpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2inpA read from 2inpA/T0444-2inpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2inpA in template set Warning: unaligning (T0444)E164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2inpA)R168 Warning: unaligning (T0444)T165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2inpA)R168 T0444 36 :EPLLRKSSRRFVIFPIQY 2inpA 35 :PEEDFEGIKITDWSQWED T0444 54 :PDIWKMYKQAQAS 2inpA 70 :KKLYAIFDAFAQN T0444 80 :PHWNK 2inpA 83 :NGHQN T0444 85 :LKADEKYFISHILAFFAASDGIVNENL 2inpA 89 :SDARYVNALKLFISGISPLEHAAFQGY T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 2inpA 116 :SKVGRQFSGAGARVACQMQAIDELRHSQTQQHAMSHYNK T0444 157 :EFLFNAI 2inpA 160 :HDGPHMH T0444 166 :MPYVK 2inpA 169 :VWYLS T0444 172 :KADWALRWIADRKS 2inpA 174 :VPKSFFDDARSAGP T0444 187 :FGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2inpA 188 :FEFLTAISFSFEYVLTNLLFVPFMSGAAYNGDMATVTFGFSAQSDEARHMTLGLEVIKFILEQHE T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 2inpA 255 :VPIVQRWIDKWFWRGFRLLSLVSMMM T0444 278 :LIGMNCILMKQYIEFVADRLLVEL 2inpA 287 :KVMSWSEAWEVYYEQNGGALFKDL T0444 305 :KVFQAENP 2inpA 311 :ERYGIRPP Number of specific fragments extracted= 12 number of extra gaps= 1 total=697 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 2uw1A/T0444-2uw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2uw1A expands to /projects/compbio/data/pdb/2uw1.pdb.gz 2uw1A:Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2366, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2368, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2370, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2372, because occupancy 0.500 <= existing 0.500 in 2uw1A Skipped atom 2374, because occupancy 0.500 <= existing 0.500 in 2uw1A # T0444 read from 2uw1A/T0444-2uw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uw1A read from 2uw1A/T0444-2uw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2uw1A to template set # found chain 2uw1A in template set Warning: unaligning (T0444)E291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2uw1A)E324 Warning: unaligning (T0444)F292 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2uw1A)E324 T0444 25 :DTNESEIKSNEEPLLRKSSR 2uw1A 50 :LKSVEKSWQPQDYLPDPVSD T0444 52 :QYPDIWKMYKQAQAS 2uw1A 70 :GFEEQVRELRERAKE T0444 85 :LK 2uw1A 85 :IP T0444 90 :KYFISHILAFFAASDGI 2uw1A 87 :DDYFVVLVGDMITEEAL T0444 109 :ENLVERFS 2uw1A 104 :PTYMSMLN T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 2uw1A 120 :TGAEPSAWAMWTRAWTAEENRHGDLLNKYLYLSGR T0444 164 :ETMPYVKKKADWALRWIA 2uw1A 155 :VDMRKIEKTIQYLIGSGM T0444 184 :KSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGL 2uw1A 177 :ENSPYLGFIYTSFQERATFISHANTAKLAQHYGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2uw1A 211 :KKLAHICGSIASDEKRHATAYTKIVEKLAEIDP T0444 252 :EERVREIIVDA 2uw1A 274 :FKHFTAVAQRL T0444 263 :VKIEQEFLTEALP 2uw1A 289 :ALDYCDILEFLVD T0444 276 :VGLIGMN 2uw1A 306 :ERLTGLS T0444 283 :CILMKQYI 2uw1A 315 :GRKAQEYV T0444 293 :VADRLLVE 2uw1A 325 :LGPKIRRL Number of specific fragments extracted= 14 number of extra gaps= 1 total=711 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 2uw1A/T0444-2uw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2uw1A/T0444-2uw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uw1A read from 2uw1A/T0444-2uw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uw1A in template set T0444 65 :AS 2uw1A 48 :IH T0444 67 :FWTAEEVDLSKDLPHW 2uw1A 56 :SWQPQDYLPDPVSDGF T0444 83 :NKLK 2uw1A 83 :KEIP T0444 90 :KYFISHILAFFAASDGIVNENLVERFSQEV 2uw1A 87 :DDYFVVLVGDMITEEALPTYMSMLNRCDGI T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYI 2uw1A 123 :EPSAWAMWTRAWTAEENRHGDLLNKYLYLSG T0444 151 :RDPKKREFLF 2uw1A 155 :VDMRKIEKTI T0444 174 :DWALRWIAD 2uw1A 165 :QYLIGSGMD T0444 183 :RKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGL 2uw1A 176 :SENSPYLGFIYTSFQERATFISHANTAKLAQHYGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 2uw1A 211 :KKLAHICGSIASDEKRHATAYTKIVEKLAEIDPD T0444 253 :ERVREIIVDA 2uw1A 275 :KHFTAVAQRL T0444 263 :VK 2uw1A 293 :CD T0444 293 :VADRLLVELGFSKV 2uw1A 295 :ILEFLVDKWNVERL Number of specific fragments extracted= 12 number of extra gaps= 0 total=723 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 2uw1A/T0444-2uw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2uw1A/T0444-2uw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uw1A read from 2uw1A/T0444-2uw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uw1A in template set T0444 22 :S 2uw1A 49 :H T0444 25 :DTNESEIKSNEEPLLRKSS 2uw1A 50 :LKSVEKSWQPQDYLPDPVS T0444 54 :PDIWKMYKQAQASF 2uw1A 69 :DGFEEQVRELRERA T0444 83 :NKLK 2uw1A 83 :KEIP T0444 90 :KYFISHILAFFAASDGIVNENLVERFSQEV 2uw1A 87 :DDYFVVLVGDMITEEALPTYMSMLNRCDGI T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYIR 2uw1A 123 :EPSAWAMWTRAWTAEENRHGDLLNKYLYLSGR T0444 152 :D 2uw1A 156 :D T0444 166 :MPYVKKKADWALRW 2uw1A 157 :MRKIEKTIQYLIGS T0444 182 :DRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGL 2uw1A 175 :KSENSPYLGFIYTSFQERATFISHANTAKLAQHYGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 2uw1A 211 :KKLAHICGSIASDEKRHATAYTKIVEKLAEIDP T0444 252 :EERVREIIVDA 2uw1A 274 :FKHFTAVAQRL T0444 282 :NCILMKQ 2uw1A 288 :SALDYCD T0444 293 :VADRLLVELGFSKVFQA 2uw1A 295 :ILEFLVDKWNVERLTGL Number of specific fragments extracted= 13 number of extra gaps= 0 total=736 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 1mtyB/T0444-1mtyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mtyB expands to /projects/compbio/data/pdb/1mty.pdb.gz 1mtyB:# T0444 read from 1mtyB/T0444-1mtyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyB read from 1mtyB/T0444-1mtyB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mtyB to template set # found chain 1mtyB in template set T0444 26 :TNESEIKSNEEPLLRKSS 1mtyB 70 :GDWTQKFHGGRPSWGNET T0444 44 :RRFVIFPIQYP 1mtyB 91 :RTVDWFKHRDP T0444 55 :DIWKMYKQAQAS 1mtyB 119 :YTDRFLQGYSAD T0444 80 :PHWNKLKADEKY 1mtyB 131 :GQIRAMNPTWRD T0444 96 :ILAFFAASDGIVNENL 1mtyB 148 :YWGAFLFNEYGLFNAH T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYI 1mtyB 164 :SQGAREALSDVTRVSLAFWGFDKIDIAQMIQLERGFLA T0444 151 :RDPK 1mtyB 203 :IVPG T0444 155 :KREFLFNAIETMPYVKKKADWALRWIADRK 1mtyB 210 :STAVPKAEWTNGEVYKSARLAVEGLWQEVF T0444 186 :TFGERVVAF 1mtyB 240 :DWNESAFSV T0444 195 :AAVEGVFFSGSFAA 1mtyB 250 :AVYDALFGQFVRRE T0444 209 :IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mtyB 265 :FQRLAPRFGDNLTPFFINQAQTYFQIAKQGVQDLYYNCLGDDP T0444 252 :EERVREIIVDAVKIEQEFLTEA 1mtyB 314 :RTVMRNWTGKWLEPTIAALRDF T0444 274 :LP 1mtyB 342 :LP T0444 279 :IGMN 1mtyB 344 :AGTT T0444 283 :CILMKQYIEFVADRLLVEL 1mtyB 349 :KEEITASLYRVVDDWIEDY T0444 302 :GFS 1mtyB 372 :DFK Number of specific fragments extracted= 16 number of extra gaps= 0 total=752 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 1mtyB/T0444-1mtyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mtyB/T0444-1mtyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyB read from 1mtyB/T0444-1mtyB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mtyB in template set T0444 54 :PDIWKMYKQAQA 1mtyB 118 :RYTDRFLQGYSA T0444 79 :LPHWNKLKADEKY 1mtyB 130 :DGQIRAMNPTWRD T0444 96 :ILAFFAASDGIVNENL 1mtyB 148 :YWGAFLFNEYGLFNAH T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 1mtyB 164 :SQGAREALSDVTRVSLAFWGFDKIDIAQMIQLERGFL T0444 151 :RDPKK 1mtyB 209 :ESTAV T0444 159 :LFNAIETMPYVKKKADWALRWIADR 1mtyB 214 :PKAEWTNGEVYKSARLAVEGLWQEV T0444 185 :STFGERVVAFAAV 1mtyB 239 :FDWNESAFSVHAV T0444 198 :EGVFFSGSFA 1mtyB 253 :DALFGQFVRR T0444 208 :AIFWLKKRG 1mtyB 265 :FQRLAPRFG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1mtyB 274 :DNLTPFFINQAQTYFQIAKQGVQDLYYNCLGDDPE T0444 253 :ERVREIIVDAVKIEQEFLTEA 1mtyB 315 :TVMRNWTGKWLEPTIAALRDF T0444 274 :LPVGLI 1mtyB 342 :LPAGTT T0444 283 :CILMKQYIEFVADRLLVEL 1mtyB 349 :KEEITASLYRVVDDWIEDY T0444 302 :GFS 1mtyB 372 :DFK T0444 311 :NPF 1mtyB 375 :ADR Number of specific fragments extracted= 15 number of extra gaps= 0 total=767 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 1mtyB/T0444-1mtyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1mtyB/T0444-1mtyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mtyB read from 1mtyB/T0444-1mtyB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mtyB in template set T0444 21 :QSMSDTNESEIKSNEEP 1mtyB 101 :PLRRWHAPYVKDKAEEW T0444 54 :PDIWKMYKQAQAS 1mtyB 118 :RYTDRFLQGYSAD T0444 80 :PHWNKLKADEKY 1mtyB 131 :GQIRAMNPTWRD T0444 96 :ILAFFAASDGIVNENL 1mtyB 148 :YWGAFLFNEYGLFNAH T0444 113 :ERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIR 1mtyB 164 :SQGAREALSDVTRVSLAFWGFDKIDIAQMIQLERGFLAK T0444 153 :PKK 1mtyB 205 :PGF T0444 156 :REFLFNAIETMPYVKKKADWALRWIADRKS 1mtyB 211 :TAVPKAEWTNGEVYKSARLAVEGLWQEVFD T0444 187 :FGERVVAFAAVEGVFFSGSFAA 1mtyB 241 :WNESAFSVHAVYDALFGQFVRR T0444 209 :IFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1mtyB 265 :FQRLAPRFGDNLTPFFINQAQTYFQIAKQGVQDLYYNCLGDDP T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 1mtyB 314 :RTVMRNWTGKWLEPTIAALRDFMGLF T0444 279 :I 1mtyB 343 :P T0444 281 :MNCILMKQYIEFVADRLLVEL 1mtyB 347 :TDKEEITASLYRVVDDWIEDY T0444 305 :KVFQAENPFDFMENISL 1mtyB 369 :SRIDFKADRDQIVKAVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=780 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 1t0qB/T0444-1t0qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0qB expands to /projects/compbio/data/pdb/1t0q.pdb.gz 1t0qB:# T0444 read from 1t0qB/T0444-1t0qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qB read from 1t0qB/T0444-1t0qB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0qB to template set # found chain 1t0qB in template set Warning: unaligning (T0444)E30 because of BadResidue code BAD_PEPTIDE in next template residue (1t0qB)L67 Warning: unaligning (T0444)I31 because of BadResidue code BAD_PEPTIDE at template residue (1t0qB)L67 Warning: unaligning (T0444)A98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qB)P127 Warning: unaligning (T0444)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qB)P127 Warning: unaligning (T0444)V119 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qB)P147 Warning: unaligning (T0444)Q120 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qB)P147 Warning: unaligning (T0444)G302 because last residue in template chain is (1t0qB)G329 T0444 5 :HHHSSGVDLG 1t0qB 43 :ERPWELDSNL T0444 17 :NLYFQSMSDTNES 1t0qB 53 :PMQTWYKKYCFDS T0444 32 :KSNEEPLLRKS 1t0qB 68 :KHDDWNAFRDP T0444 49 :FPIQYPDIWKMYKQAQAS 1t0qB 79 :DQLVYRTYNLLQDGQESY T0444 80 :PHWNKLKADEKYFISHIL 1t0qB 108 :GHDQMLTREWVETLARFY T0444 100 :FAASDGIVNENL 1t0qB 128 :ARYLFHALQMGS T0444 113 :ERFSQE 1t0qB 140 :VYIHQI T0444 121 :VPEARCFYGFQILIENVHSEMYSLLIDTYIRD 1t0qB 148 :ASTITNCATYETADHLRWLTHTAYRTRELANC T0444 159 :LFNAIETMPYVKKKADWALRWIADRK 1t0qB 189 :ERDVWENDPAWQGFRELIEKALIAWD T0444 187 :FGERVVAF 1t0qB 215 :WGEAFTAI T0444 195 :AAVEGVFFSGSFAAIF 1t0qB 224 :LVTKPAVEEALLQQLG T0444 211 :WLKKRG 1t0qB 241 :LAQSEG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1t0qB 247 :DTLLGLLAQAQKRDAERHRRWSSALVKMALEKEG T0444 252 :EERVREIIVDAVKIEQEFLTEALPV 1t0qB 282 :REVLQKWVAKWEPLADKAIEAYCSA T0444 279 :IG 1t0qB 307 :LP T0444 282 :NCILMKQYIEFVADRLLVEL 1t0qB 309 :DGENAIVEAKSASRYVRQMM Number of specific fragments extracted= 16 number of extra gaps= 3 total=796 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 1t0qB/T0444-1t0qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1t0qB/T0444-1t0qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qB read from 1t0qB/T0444-1t0qB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qB in template set Warning: unaligning (T0444)A98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qB)P127 Warning: unaligning (T0444)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qB)P127 Warning: unaligning (T0444)V119 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qB)P147 Warning: unaligning (T0444)Q120 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qB)P147 Warning: unaligning (T0444)G302 because last residue in template chain is (1t0qB)G329 T0444 55 :DIWKMYKQAQA 1t0qB 96 :YVQGLFDQLND T0444 79 :LPHWNKLKADEKYFISHIL 1t0qB 107 :RGHDQMLTREWVETLARFY T0444 100 :FAASDGIVNENL 1t0qB 128 :ARYLFHALQMGS T0444 113 :ERFSQE 1t0qB 140 :VYIHQI T0444 121 :VPEARCFYGFQILIENVHSEMYSLLIDTYI 1t0qB 148 :ASTITNCATYETADHLRWLTHTAYRTRELA T0444 151 :RDPK 1t0qB 179 :CYPD T0444 157 :EFLFNAIETMPYVKKKADWALRWIAD 1t0qB 187 :KRERDVWENDPAWQGFRELIEKALIA T0444 185 :STFGERVVAFAAV 1t0qB 213 :WDWGEAFTAINLV T0444 198 :EGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1t0qB 227 :KPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGN T0444 253 :ERVREIIVDAVKIEQEFLTEALPVG 1t0qB 283 :EVLQKWVAKWEPLADKAIEAYCSAL T0444 280 :G 1t0qB 308 :P T0444 282 :NCILMKQYIEFVADRLLVEL 1t0qB 309 :DGENAIVEAKSASRYVRQMM Number of specific fragments extracted= 12 number of extra gaps= 2 total=808 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 1t0qB/T0444-1t0qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1t0qB/T0444-1t0qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qB read from 1t0qB/T0444-1t0qB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qB in template set Warning: unaligning (T0444)A98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qB)P127 Warning: unaligning (T0444)F99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qB)P127 Warning: unaligning (T0444)V119 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qB)P147 Warning: unaligning (T0444)Q120 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qB)P147 Warning: unaligning (T0444)G302 because last residue in template chain is (1t0qB)G329 T0444 54 :PDIWKMYKQAQASF 1t0qB 91 :DGQESYVQGLFDQL T0444 79 :LPHWNKLKADEKYFISHIL 1t0qB 107 :RGHDQMLTREWVETLARFY T0444 100 :FAASDGIVNENL 1t0qB 128 :ARYLFHALQMGS T0444 113 :ERFSQE 1t0qB 140 :VYIHQI T0444 121 :VPEARCFYGFQILIENVHSEMYSLLIDTYIR 1t0qB 148 :ASTITNCATYETADHLRWLTHTAYRTRELAN T0444 157 :EFLFNAIETMPYVK 1t0qB 187 :KRERDVWENDPAWQ T0444 175 :WALRWIADRKS 1t0qB 201 :GFRELIEKALI T0444 186 :TFGERVVAFAA 1t0qB 214 :DWGEAFTAINL T0444 197 :VEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1t0qB 226 :TKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEG T0444 252 :EERVREIIVDAVKIEQEFLTEALPVGLI 1t0qB 282 :REVLQKWVAKWEPLADKAIEAYCSALPD T0444 283 :CILMKQYIEFVADRLLVEL 1t0qB 310 :GENAIVEAKSASRYVRQMM Number of specific fragments extracted= 11 number of extra gaps= 2 total=819 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 1oq9A/T0444-1oq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oq9A expands to /projects/compbio/data/pdb/1oq9.pdb.gz 1oq9A:# T0444 read from 1oq9A/T0444-1oq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oq9A read from 1oq9A/T0444-1oq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oq9A to template set # found chain 1oq9A in template set Warning: unaligning (T0444)F303 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1oq9A)K346 T0444 3 :HHHHHSSGVDLGTENLYFQSMS 1oq9A 24 :VHVQVTHSMPPQKIEIFKSLDN T0444 25 :DTNESEIKSNEEPLLRKSS 1oq9A 55 :LKPVEKCWQPQDFLPDPAS T0444 52 :QYPDIWKMYKQAQAS 1oq9A 75 :GFDEQVRELRERAKE T0444 85 :LKA 1oq9A 90 :IPD T0444 91 :YFISHILAFFAASD 1oq9A 93 :DYFVVLVGDMITEE T0444 107 :VNENLVERFSQEV 1oq9A 107 :ALPTYQTMLNTLD T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYI 1oq9A 128 :SPTSWAIWTRAWTAEENRHGDLLNKYLYLSG T0444 151 :RDPKK 1oq9A 160 :VDMRQ T0444 169 :VKKKADWALRWIA 1oq9A 165 :IEKTIQYLIGSGM T0444 182 :DRK 1oq9A 182 :ENS T0444 188 :GERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1oq9A 185 :PYLGFIYTSFQERATFISHGNTARQAKEHGDIKLAQICGTIAADEKRHETAYTKIVEKLFEIDP T0444 252 :EERVREIIVD 1oq9A 279 :FDHFSAVAQR T0444 263 :VKIEQEFLT 1oq9A 298 :ADILEFLVG T0444 273 :ALPVG 1oq9A 307 :RWKVD T0444 278 :LIGMN 1oq9A 313 :LTGLS T0444 284 :ILMKQYIEFVADRLLVELG 1oq9A 318 :AEGQKAQDYVCRLPPRIRR Number of specific fragments extracted= 16 number of extra gaps= 0 total=835 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 1oq9A/T0444-1oq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1oq9A/T0444-1oq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oq9A read from 1oq9A/T0444-1oq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oq9A in template set T0444 24 :SDTNESEIKSNEEPLLRKS 1oq9A 25 :HVQVTHSMPPQKIEIFKSL T0444 54 :PDIWK 1oq9A 45 :NWAEE T0444 62 :QAQAS 1oq9A 50 :NILVH T0444 67 :FWTAEEVDLSKDLPHW 1oq9A 61 :CWQPQDFLPDPASDGF T0444 87 :ADEKYFISHIL 1oq9A 77 :DEQVRELRERA T0444 98 :AFFAASDGIVNENLVERFSQEV 1oq9A 94 :YFVVLVGDMITEEALPTYQTML T0444 120 :QVPEARCFYGFQILIENVHSEMYSLLIDTYI 1oq9A 128 :SPTSWAIWTRAWTAEENRHGDLLNKYLYLSG T0444 151 :RDP 1oq9A 160 :VDM T0444 167 :PYVKKKADWALRWIAD 1oq9A 163 :RQIEKTIQYLIGSGMD T0444 183 :RKST 1oq9A 180 :RTEN T0444 187 :FGERVVAFAAVEGVFFSGSFAAIFWLKKRGL 1oq9A 185 :PYLGFIYTSFQERATFISHGNTARQAKEHGD T0444 219 :PGLTFSNELISRDEGLHCDFACLMFQYLVNKPSE 1oq9A 216 :IKLAQICGTIAADEKRHETAYTKIVEKLFEIDPD T0444 284 :ILMKQYIEF 1oq9A 280 :DHFSAVAQR T0444 293 :VADRLLVELGFSKV 1oq9A 300 :ILEFLVGRWKVDKL Number of specific fragments extracted= 14 number of extra gaps= 0 total=849 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 1oq9A/T0444-1oq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 1oq9A/T0444-1oq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oq9A read from 1oq9A/T0444-1oq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oq9A in template set T0444 23 :MSDTNESEIKSNEEPLLRKSSR 1oq9A 52 :LVHLKPVEKCWQPQDFLPDPAS T0444 54 :PDIWKMYKQAQA 1oq9A 74 :DGFDEQVRELRE T0444 81 :HWNKLK 1oq9A 86 :RAKEIP T0444 90 :KYFISHILAFFAASDGIVNENLVER 1oq9A 92 :DDYFVVLVGDMITEEALPTYQTMLN T0444 117 :QEVQVPEARCFYGFQILIENVHSEMYSLLIDTY 1oq9A 125 :TGASPTSWAIWTRAWTAEENRHGDLLNKYLYLS T0444 151 :R 1oq9A 159 :R T0444 152 :D 1oq9A 161 :D T0444 166 :MPYVKKKADWALRW 1oq9A 162 :MRQIEKTIQYLIGS T0444 186 :TFGERVVAFAAVEGVFFSGSFAAIFWLKKRG 1oq9A 184 :SPYLGFIYTSFQERATFISHGNTARQAKEHG T0444 218 :MPGLTFSNELISRDEGLHCDFACLMFQYLVNKPS 1oq9A 215 :DIKLAQICGTIAADEKRHETAYTKIVEKLFEIDP T0444 262 :AVKIEQEFLTEA 1oq9A 278 :LFDHFSAVAQRL T0444 277 :GLI 1oq9A 290 :GVY T0444 282 :NCILMKQYIEFVADR 1oq9A 293 :TAKDYADILEFLVGR Number of specific fragments extracted= 13 number of extra gaps= 0 total=862 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 2qcxA/T0444-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qcxA expands to /projects/compbio/data/pdb/2qcx.pdb.gz 2qcxA:Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2qcxA # T0444 read from 2qcxA/T0444-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0444-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qcxA to template set # found chain 2qcxA in template set Warning: unaligning (T0444)M281 because last residue in template chain is (2qcxA)D220 T0444 59 :MYKQAQAS 2qcxA 23 :FVQGIGDG T0444 84 :KLKAD 2qcxA 31 :TLPID T0444 92 :FISHILAFFAASDGIVNENL 2qcxA 36 :RFKYYVLQDSYYLTHFAKVQ T0444 113 :ERFSQEVQVPEARCFYGFQILIEN 2qcxA 56 :SFGAAYAKDLYTTGRMASHAQGTY T0444 137 :VHSEMYSLLIDTYIRDPKKRE 2qcxA 81 :AEMALHREFAELLEISEEERK T0444 165 :TMPYVKKKADWALRWIADRKS 2qcxA 105 :PSPTAYSFTSHMYRSVLSGNF T0444 188 :GERVVAFAAVEGVFF 2qcxA 126 :AEILAALLPCYWLYY T0444 207 :AAIFWL 2qcxA 141 :EVGEKL T0444 215 :RGLMPGLTFSNELISR 2qcxA 147 :LHCDPGHPIYQKWIGT T0444 231 :DEGLHCDFACLMFQYLVNKPSEE 2qcxA 167 :WFRQQVEEQINRFDELAENSTEE T0444 254 :RVREIIVDAVKIEQEFLTEALPVGLIG 2qcxA 193 :KMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 11 number of extra gaps= 0 total=873 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 2qcxA/T0444-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2qcxA/T0444-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0444-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qcxA in template set Warning: unaligning (T0444)M281 because last residue in template chain is (2qcxA)D220 T0444 58 :KMYKQAQA 2qcxA 13 :EWWEGSFV T0444 79 :LPHW 2qcxA 21 :HPFV T0444 83 :N 2qcxA 29 :D T0444 84 :KLKADE 2qcxA 31 :TLPIDR T0444 93 :ISHILAFFAASDGI 2qcxA 37 :FKYYVLQDSYYLTH T0444 108 :NENLVERFSQEVQVPEARCFYGFQILIENVHS 2qcxA 51 :FAKVQSFGAAYAKDLYTTGRMASHAQGTYEAE T0444 140 :EMYSLLIDTYIRDPKK 2qcxA 84 :ALHREFAELLEISEEE T0444 160 :FNAIETMPYVKKKADWALRWIADR 2qcxA 100 :RKAFKPSPTAYSFTSHMYRSVLSG T0444 186 :TFGERVVAFAAVEGVFFSG 2qcxA 124 :NFAEILAALLPCYWLYYEV T0444 211 :WLKKRGL 2qcxA 143 :GEKLLHC T0444 218 :MPG 2qcxA 151 :PGH T0444 221 :LTFSNELISR 2qcxA 156 :YQKWIGTYGG T0444 231 :DEGLHCDFACLMFQYLVNKPSE 2qcxA 167 :WFRQQVEEQINRFDELAENSTE T0444 253 :ERVREIIVDAVKIEQEFLTEALPVGLIG 2qcxA 192 :AKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 14 number of extra gaps= 0 total=887 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 2qcxA/T0444-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0444 read from 2qcxA/T0444-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0444-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qcxA in template set T0444 59 :MYKQAQAS 2qcxA 23 :FVQGIGDG T0444 84 :KLKAD 2qcxA 31 :TLPID T0444 92 :FISHILAFFAASDGIVNENL 2qcxA 36 :RFKYYVLQDSYYLTHFAKVQ T0444 113 :ERFSQEVQVPEARCFYGFQIL 2qcxA 56 :SFGAAYAKDLYTTGRMASHAQ T0444 134 :IEN 2qcxA 80 :EAE T0444 139 :SEMYSLLIDTYIRDPKK 2qcxA 83 :MALHREFAELLEISEEE T0444 160 :FNAIETMPYVKKKADWALRWIADRK 2qcxA 100 :RKAFKPSPTAYSFTSHMYRSVLSGN T0444 187 :FGERVVAFAAVEGVFFSGSF 2qcxA 125 :FAEILAALLPCYWLYYEVGE T0444 213 :KKRGLM 2qcxA 145 :KLLHCD T0444 219 :PGLTFSNELISR 2qcxA 154 :PIYQKWIGTYGG T0444 236 :CDFACLMFQYLVNKPS 2qcxA 172 :VEEQINRFDELAENST T0444 252 :EERVREIIVDAVKIEQEFLTEALPVG 2qcxA 191 :RAKMKENFVISSYYEYQFWGMAYRKE Number of specific fragments extracted= 12 number of extra gaps= 0 total=899 Will force an alignment to be made, even if fragment is small Number of alignments=90 # command:CPU_time= 37.504 sec, elapsed time= 56.624 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 90 Adding 3572 constraints to all_contacts Done adding distance constraints # command:CPU_time= 37.692 sec, elapsed time= 56.822 sec. # command:Reading probabilities from T0444.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 87.038 Optimizing... Probability sum: -567.115, CN propb: -567.115 weights: 0.341 constraints: 564 # command:CPU_time= 331.330 sec, elapsed time= 350.433 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 564 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 564 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 3008 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 3008 # 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= 331.390 sec, elapsed time= 351.224 sec. # command: