# 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 T0291 numbered 1 through 310 Created new target T0291 from T0291.a2m # command:CPU_time= 6.363 sec, elapsed time= 6.705 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4oA/T0291-1p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p4oA expands to /projects/compbio/data/pdb/1p4o.pdb.gz 1p4oA:# T0291 read from 1p4oA/T0291-1p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4oA read from 1p4oA/T0291-1p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p4oA to template set # found chain 1p4oA in template set Warning: unaligning (T0291)H6 because first residue in template chain is (1p4oA)P948 T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK # choosing archetypes in rotamer library T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1p4oA 992 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLR T0291 119 :KHDA 1p4oA 1070 :NNPV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1p4oA 1076 :PPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1p4oA 1134 :DYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 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 1p4oA/T0291-1p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1p4oA/T0291-1p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4oA read from 1p4oA/T0291-1p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p4oA in template set T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1p4oA 992 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLRSL T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1p4oA 1077 :PSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1p4oA 1134 :DYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEM Number of specific fragments extracted= 4 number of extra gaps= 0 total=9 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 1p4oA/T0291-1p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1p4oA/T0291-1p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4oA read from 1p4oA/T0291-1p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p4oA in template set Warning: unaligning (T0291)H6 because first residue in template chain is (1p4oA)P948 T0291 7 :TYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1p4oA 949 :EYFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1p4oA 993 :KDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLR T0291 119 :KHD 1p4oA 1070 :NNP T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1p4oA 1075 :APPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYETDYY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1p4oA 1137 :RKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEP Number of specific fragments extracted= 5 number of extra gaps= 0 total=14 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 1fgkA/T0291-1fgkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fgkA expands to /projects/compbio/data/pdb/1fgk.pdb.gz 1fgkA:Skipped atom 908, because occupancy 0.5 <= existing 0.500 in 1fgkA # T0291 read from 1fgkA/T0291-1fgkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fgkA read from 1fgkA/T0291-1fgkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fgkA to template set # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 Warning: unaligning (T0291)G292 because last residue in template chain is (1fgkA)S762 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLK 1fgkA 492 :VVLAEAI T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMI T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fgkA 540 :KHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHH T0291 181 :PEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 651 :IDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=20 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 1fgkA/T0291-1fgkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fgkA/T0291-1fgkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fgkA read from 1fgkA/T0291-1fgkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLKL 1fgkA 492 :VVLAEAIG T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFD 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1fgkA 541 :HKNIINLLGACTQDGPLYVIVEYASKGNLREYLQAR T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHI T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 652 :DYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=26 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 1fgkA/T0291-1fgkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fgkA/T0291-1fgkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fgkA read from 1fgkA/T0291-1fgkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fgkA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1fgkA)E464 Warning: unaligning (T0291)G34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fgkA)Q491 Warning: unaligning (T0291)E40 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)Q491 Warning: unaligning (T0291)S50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)P505 Warning: unaligning (T0291)D121 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fgkA)E592 Warning: unaligning (T0291)G292 because last residue in template chain is (1fgkA)S762 T0291 14 :AVHEFAKELDATNISIDKVV 1fgkA 465 :LPEDPRWELPRDRLVLGKPL T0291 41 :VCSGRLKL 1fgkA 492 :VVLAEAIG T0291 51 :KKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1fgkA 506 :NRVTKVAVKMLKSDATEKDLSDLISEMEMMKMI T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fgkA 540 :KHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1fgkA 593 :EQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1fgkA 655 :KKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALT Number of specific fragments extracted= 6 number of extra gaps= 0 total=32 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 2evaA/T0291-2evaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2evaA expands to /projects/compbio/data/pdb/2eva.pdb.gz 2evaA:Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2evaA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2evaA # T0291 read from 2evaA/T0291-2evaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evaA read from 2evaA/T0291-2evaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2evaA to template set # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRL 2evaA 29 :HMIDYKEIEVEEVVGRGAFGVVCKAKW T0291 52 :KEISVAIKTLK 2evaA 56 :RAKDVAIKQIE T0291 66 :TEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 2evaA 67 :SESERKAFIVELRQLSRVNHPNIVKLYGACLNP T0291 101 :VMIVTEYMENGSLDSFLRKHDA 2evaA 100 :VCLVMEYAEGGSLYNVLHGAEP T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 2evaA 124 :YYTAAHAMSWCLQCSQGVAYLHS T0291 146 :MGYVHRDLAARNILINSNL 2evaA 150 :KALIHRDLKPPNLLLVAGG T0291 165 :VCKVSDFG 2evaA 170 :VLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVIT T0291 227 :GERPYW 2evaA 225 :RRKPFD T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEP T0291 298 :TSAAARPSNL 2evaA 302 :CQHSLPPGED Number of specific fragments extracted= 11 number of extra gaps= 0 total=43 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 2evaA/T0291-2evaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2evaA/T0291-2evaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evaA read from 2evaA/T0291-2evaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 2evaA 28 :LHMIDYKEIEVEEVVGRGAFGVVCKAKW T0291 52 :KEISVAIKTLKVG 2evaA 56 :RAKDVAIKQIESE T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 2evaA 69 :SERKAFIVELRQLSRVNHPNIVKLYGACLN T0291 100 :PVMIVTEYMENGSLDSFLRKHDA 2evaA 99 :PVCLVMEYAEGGSLYNVLHGAEP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMG 2evaA 124 :YYTAAHAMSWCLQCSQGVAYLHSMQ T0291 148 :YVHRDLAARNILI 2evaA 152 :LIHRDLKPPNLLL T0291 161 :NSNLVCKVSDFG 2evaA 166 :AGGTVLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVIT T0291 227 :GERPYWEMS 2evaA 225 :RRKPFDEIG T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2evaA 236 :AFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMR T0291 290 :NPGSLKIITSAAARPSN 2evaA 293 :GADEPLQYPCQHSLPPG Number of specific fragments extracted= 11 number of extra gaps= 0 total=54 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 2evaA/T0291-2evaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2evaA/T0291-2evaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evaA read from 2evaA/T0291-2evaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2evaA in template set Warning: unaligning (T0291)L173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2evaA)G191 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2evaA)G191 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 2evaA 29 :HMIDYKEIEVEEVVGRGAFGVVCKAKWRA T0291 51 :KKEISVAI 2evaA 58 :KDVAIKQI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 2evaA 66 :ESESERKAFIVELRQLSRVNHPNIVKLYGACLNP T0291 101 :VMIVTEYMENGSLDSFLRKHD 2evaA 100 :VCLVMEYAEGGSLYNVLHGAE T0291 122 :AQFTVIQLVGMLRGIASGMKYLSD 2evaA 123 :PYYTAAHAMSWCLQCSQGVAYLHS T0291 146 :MGYVHRDLAARNILI 2evaA 150 :KALIHRDLKPPNLLL T0291 161 :NSNLVCKVSDFG 2evaA 166 :AGGTVLKICDFG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYW 2evaA 192 :SAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDE T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 2evaA 233 :GGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRY T0291 291 :PGSLKIITSAAARPSNLLL 2evaA 294 :ADEPLQYPCQHSLPPGEDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=64 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 1jpaA/T0291-1jpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jpaA expands to /projects/compbio/data/pdb/1jpa.pdb.gz 1jpaA:# T0291 read from 1jpaA/T0291-1jpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jpaA read from 1jpaA/T0291-1jpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jpaA to template set # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 Warning: unaligning (T0291)I296 because last residue in template chain is (1jpaA)A900 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 603 :IFIDPFTFEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 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 1jpaA/T0291-1jpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jpaA/T0291-1jpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jpaA read from 1jpaA/T0291-1jpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 Warning: unaligning (T0291)I296 because last residue in template chain is (1jpaA)A900 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 603 :IFIDPFTFEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=70 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 1jpaA/T0291-1jpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jpaA/T0291-1jpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jpaA read from 1jpaA/T0291-1jpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jpaA in template set Warning: unaligning (T0291)L48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)R654 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)R654 Warning: unaligning (T0291)F171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jpaA)P797 Warning: unaligning (T0291)P193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jpaA)P797 T0291 8 :YEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jpaA 610 :FEDPNEAVREFAKEIDISCVKIEQVIGAGEFGEVCSGHLK T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSD 1jpaA 655 :EIFVAIKTLKSGYTEKQRRDFLSEASIMGQFDHPNVIHLEGVVTKSTPVMIITEFMENGSLDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLADMNYVHRDLAARNILVNSNLVCKVSD T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLK 1jpaA 798 :IRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMTNQDVINAIEQDYRLPPPMDCPSALHQLMLDCWQKDRNHRPKFGQIVNTLDKMIRNPNSLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=73 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 1ir3A/T0291-1ir3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ir3A expands to /projects/compbio/data/pdb/1ir3.pdb.gz 1ir3A:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1ir3A/T0291-1ir3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ir3A read from 1ir3A/T0291-1ir3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ir3A to template set # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ir3A 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQ 1ir3A 1098 :NPGRP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1104 :PTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHP Number of specific fragments extracted= 6 number of extra gaps= 0 total=79 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 1ir3A/T0291-1ir3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ir3A/T0291-1ir3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ir3A read from 1ir3A/T0291-1ir3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1ir3A 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSL T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1101 :RPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDK 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=84 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 1ir3A/T0291-1ir3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ir3A/T0291-1ir3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ir3A read from 1ir3A/T0291-1ir3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ir3A in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1ir3A)S981 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)E1159 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)E1159 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ir3A)R1164 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ir3A)R1164 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1ir3A 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARD T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ir3A 1020 :KGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1ir3A 1099 :PGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRD T0291 180 :D 1ir3A 1160 :T T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1ir3A 1165 :KGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=89 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 1opjA/T0291-1opjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1opjA expands to /projects/compbio/data/pdb/1opj.pdb.gz 1opjA:# T0291 read from 1opjA/T0291-1opjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opjA read from 1opjA/T0291-1opjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1opjA to template set # found chain 1opjA in template set T0291 3 :VDPHT 1opjA 244 :MDPSS T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1opjA 249 :PNYDKWEMERTDITMKHKLGGGQYGEVYEGVW T0291 50 :SKKEISVAIKTLKVGYTE 1opjA 281 :KKYSLTVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1opjA 353 :EVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDT T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1opjA 412 :YTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESS Number of specific fragments extracted= 6 number of extra gaps= 0 total=95 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 1opjA/T0291-1opjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1opjA/T0291-1opjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opjA read from 1opjA/T0291-1opjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1opjA in template set T0291 12 :TQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1opjA 246 :PSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVW T0291 50 :SKKEISVAIKTLKVGYTE 1opjA 281 :KKYSLTVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLREC T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1opjA 351 :RQEVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDT T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1opjA 412 :YTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES Number of specific fragments extracted= 5 number of extra gaps= 0 total=100 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 1opjA/T0291-1opjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1opjA/T0291-1opjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opjA read from 1opjA/T0291-1opjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1opjA in template set T0291 10 :DPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSK 1opjA 244 :MDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSL T0291 55 :SVAIKTLKVGYTE 1opjA 286 :TVAVKTLKEDTME T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1opjA 299 :VEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLR T0291 119 :KHD 1opjA 350 :NRQ T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1opjA 353 :EVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNP 1opjA 413 :TAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES Number of specific fragments extracted= 6 number of extra gaps= 0 total=106 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 1t46A/T0291-1t46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t46A expands to /projects/compbio/data/pdb/1t46.pdb.gz 1t46A:Skipped atom 685, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 687, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 689, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 691, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 705, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 707, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 709, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 870, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 872, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 874, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 876, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1079, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1081, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1193, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1195, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1819, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 1821, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 2311, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 2313, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 2315, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 2317, because occupancy 0.350 <= existing 0.650 in 1t46A Skipped atom 2319, because occupancy 0.350 <= existing 0.650 in 1t46A # T0291 read from 1t46A/T0291-1t46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t46A read from 1t46A/T0291-1t46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t46A to template set # found chain 1t46A in template set Warning: unaligning (T0291)V3 because first residue in template chain is (1t46A)G565 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAY T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1t46A 612 :IKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1t46A 649 :NHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKND T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 821 :SNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 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 1t46A/T0291-1t46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1t46A/T0291-1t46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t46A read from 1t46A/T0291-1t46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t46A in template set Warning: unaligning (T0291)V3 because first residue in template chain is (1t46A)G565 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAY T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFD 1t46A 612 :IKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1t46A 650 :HMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRK T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKND T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 821 :SNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 6 number of extra gaps= 0 total=118 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 1t46A/T0291-1t46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1t46A/T0291-1t46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t46A read from 1t46A/T0291-1t46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t46A in template set Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t46A)L762 Warning: unaligning (T0291)S293 because last residue in template chain is (1t46A)N933 T0291 4 :DPHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1t46A 566 :NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYG T0291 49 :PSK 1t46A 614 :SDA T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQF 1t46A 617 :AMTVAVKMLKPSAHLTEREALMSELKVLSYL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1t46A 649 :NHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1t46A 763 :ALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNY T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1t46A 824 :VVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMP T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1t46A 876 :DSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISEST Number of specific fragments extracted= 7 number of extra gaps= 0 total=125 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 1qpcA/T0291-1qpcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qpcA expands to /projects/compbio/data/pdb/1qpc.pdb.gz 1qpcA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1qpcA/T0291-1qpcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpcA read from 1qpcA/T0291-1qpcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qpcA to template set # found chain 1qpcA in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 1qpcA 234 :WEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGYTEK 1qpcA 265 :NGHTKVAVKSLKQGSMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 283 :DAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 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 1qpcA/T0291-1qpcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1qpcA/T0291-1qpcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpcA read from 1qpcA/T0291-1qpcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qpcA in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 Warning: unaligning (T0291)P291 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qpcA)E502 Warning: unaligning (T0291)G292 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qpcA)E502 T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1qpcA 233 :WWEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGY 1qpcA 265 :NGHTKVAVKSLKQGS T0291 66 :TEK 1qpcA 281 :SPD T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 284 :AFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 7 number of extra gaps= 1 total=138 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 1qpcA/T0291-1qpcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1qpcA/T0291-1qpcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qpcA read from 1qpcA/T0291-1qpcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qpcA in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qpcA)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qpcA)T395 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLP 1qpcA 235 :EDEWEVPRETLKLVERLGAGQFGEVWMGYYNGH T0291 51 :KKEISVAIKTLKV 1qpcA 268 :TKVAVKSLKQGSM T0291 66 :T 1qpcA 281 :S T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVT 1qpcA 282 :PDAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHD 1qpcA 309 :QEPIYIITEYMENGSLVDFLKTPS T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1qpcA 334 :IKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1qpcA 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTA Number of specific fragments extracted= 7 number of extra gaps= 0 total=145 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 1r0pA/T0291-1r0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r0pA expands to /projects/compbio/data/pdb/1r0p.pdb.gz 1r0pA:# T0291 read from 1r0pA/T0291-1r0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0pA read from 1r0pA/T0291-1r0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r0pA to template set # found chain 1r0pA in template set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 2 :YVDPHTYE 1r0pA 1052 :HIDLSALN T0291 12 :TQAVHEFAK 1r0pA 1060 :PELVQAVQH T0291 21 :ELDATNISI 1r0pA 1070 :VIGPSSLIV T0291 30 :DKVVGAGEFGEVCSGRL 1r0pA 1081 :NEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1r0pA 1151 :GSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKE T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1235 :DSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYV T0291 298 :TSAAA 1r0pA 1352 :VNATY Number of specific fragments extracted= 9 number of extra gaps= 1 total=154 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 1r0pA/T0291-1r0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1r0pA/T0291-1r0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0pA read from 1r0pA/T0291-1r0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r0pA in template set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 2 :YVDPHTYE 1r0pA 1052 :HIDLSALN T0291 12 :TQAVHEFA 1r0pA 1060 :PELVQAVQ T0291 20 :KELDATNISI 1r0pA 1069 :VVIGPSSLIV T0291 30 :DKVVGAGEFGEVCSGRL 1r0pA 1081 :NEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSK 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSE T0291 100 :PVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1r0pA 1152 :SPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKE T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1235 :DSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSA 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVN Number of specific fragments extracted= 8 number of extra gaps= 1 total=162 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 1r0pA/T0291-1r0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1r0pA/T0291-1r0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0pA read from 1r0pA/T0291-1r0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r0pA in template set Warning: unaligning (T0291)K47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r0pA)D1099 Warning: unaligning (T0291)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1r0pA)D1099 Warning: unaligning (T0291)E53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)K1104 Warning: unaligning (T0291)W232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0pA)I1292 Warning: unaligning (T0291)V239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0pA)I1292 T0291 19 :AKELDATNIS 1r0pA 1068 :HVVIGPSSLI T0291 29 :IDKVVGAGEFGEVCSGRL 1r0pA 1080 :FNEVIGRGHFGCVYHGTL T0291 54 :ISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1r0pA 1105 :IHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1r0pA 1151 :GSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKFLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEFD T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPY 1r0pA 1237 :VHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPY T0291 240 :IKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAA 1r0pA 1293 :TVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNAT Number of specific fragments extracted= 6 number of extra gaps= 1 total=168 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 1ywnA/T0291-1ywnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ywnA expands to /projects/compbio/data/pdb/1ywn.pdb.gz 1ywnA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1ywnA/T0291-1ywnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywnA read from 1ywnA/T0291-1ywnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ywnA to template set # found chain 1ywnA in template set Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1ywnA 819 :PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAF T0291 49 :PSKKEISVAIKT 1ywnA 856 :KTATCRTVAVKM T0291 67 :EKQRRDFLGEASIMGQF 1ywnA 874 :HSEHRALMSELKILIHI T0291 84 :DHPNIIRLEGVVTKS 1ywnA 892 :HHLNVVNLLGACTKP T0291 99 :KPVMIVTEYMENGSLDSFLR 1ywnA 908 :GPLMVIVEFCKFGNLSTYLR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANA Number of specific fragments extracted= 9 number of extra gaps= 0 total=177 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 1ywnA/T0291-1ywnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ywnA/T0291-1ywnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywnA read from 1ywnA/T0291-1ywnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ywnA in template set Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKK 1ywnA 821 :DASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKT T0291 53 :EISVAIKT 1ywnA 860 :CRTVAVKM T0291 67 :EKQRRDFLGEASIMGQFD 1ywnA 874 :HSEHRALMSELKILIHIG T0291 85 :HPNIIRLEGVVTK 1ywnA 893 :HLNVVNLLGACTK T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 1ywnA 907 :GGPLMVIVEFCKFGNLSTYLRSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=186 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 1ywnA/T0291-1ywnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ywnA/T0291-1ywnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywnA read from 1ywnA/T0291-1ywnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ywnA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1ywnA)L818 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)T873 Warning: unaligning (T0291)T66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)T873 Warning: unaligning (T0291)Q123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)F997 Warning: unaligning (T0291)D170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)I1051 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)I1051 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)K1053 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywnA)V1058 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ywnA)V1058 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1ywnA 819 :PYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFG T0291 49 :PSKKEISVAIKT 1ywnA 856 :KTATCRTVAVKM T0291 67 :EKQRRDFLGEASIMGQF 1ywnA 874 :HSEHRALMSELKILIHI T0291 84 :DHPNIIRLEGVVTKS 1ywnA 892 :HHLNVVNLLGACTKP T0291 99 :KPVMIVTEYMENGSLDSFLR 1ywnA 908 :GPLMVIVEFCKFGNLSTYLR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1ywnA 998 :LTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKIC T0291 180 :DP 1ywnA 1054 :DP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMS 1ywnA 1059 :RKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1ywnA 1110 :DEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=195 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 1gz8A/T0291-1gz8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gz8A expands to /projects/compbio/data/pdb/1gz8.pdb.gz 1gz8A:Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 1763, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1765, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1811, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1818, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1820, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1822, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1935, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1937, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1939, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1941, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1956, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1958, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1960, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1962, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1964, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 1966, because occupancy 0.400 <= existing 0.600 in 1gz8A Skipped atom 2086, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 2095, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 1gz8A Skipped atom 2099, because occupancy 0.500 <= existing 0.500 in 1gz8A # T0291 read from 1gz8A/T0291-1gz8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz8A read from 1gz8A/T0291-1gz8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gz8A to template set # found chain 1gz8A in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRL 1gz8A 21 :ARN T0291 50 :SKKEISVAIKTL 1gz8A 24 :KLTGEVVALKKI T0291 66 :TEK 1gz8A 45 :PST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDA 1gz8A 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1gz8A 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIA 1gz8A 158 :TYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMS 1gz8A 182 :TAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1gz8A 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQ T0291 292 :G 1gz8A 288 :D Number of specific fragments extracted= 13 number of extra gaps= 2 total=208 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 1gz8A/T0291-1gz8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1gz8A/T0291-1gz8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz8A read from 1gz8A/T0291-1gz8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gz8A in template set Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0291)M253 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRL 1gz8A 21 :ARN T0291 50 :SKKEISVAIKTL 1gz8A 24 :KLTGEVVALKKI T0291 66 :TEKQ 1gz8A 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1gz8A 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1gz8A 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIA 1gz8A 157 :RTYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMSY 1gz8A 182 :TAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1gz8A 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1gz8A 234 :PDYKPSFP T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAH T0291 292 :GSL 1gz8A 284 :PFF Number of specific fragments extracted= 14 number of extra gaps= 3 total=222 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 1gz8A/T0291-1gz8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1gz8A/T0291-1gz8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz8A read from 1gz8A/T0291-1gz8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gz8A in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1gz8A)M1 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gz8A)K20 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gz8A)K20 Warning: unaligning (T0291)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)V44 Warning: unaligning (T0291)Y204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gz8A)K178 Warning: unaligning (T0291)R205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gz8A)K178 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1gz8A)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)S181 Warning: unaligning (T0291)M253 because of BadResidue code BAD_PEPTIDE at template residue (1gz8A)P253 T0291 25 :TNISIDKVVGAGEFGEV 1gz8A 2 :ENFQKVEKIGEGTYGVV T0291 44 :GRLKLPSKKEISVAI 1gz8A 21 :ARNKLTGEVVALKKI T0291 66 :TEKQ 1gz8A 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1gz8A 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1gz8A 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1gz8A 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIA 1gz8A 158 :TYTHEVVTLWYRAPEILL T0291 206 :K 1gz8A 179 :Y T0291 209 :SASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1gz8A 182 :TAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1gz8A 236 :YKPSFPKWAR T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1gz8A 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPF T0291 291 :PGSLKIIT 1gz8A 286 :FQDVTKPV Number of specific fragments extracted= 12 number of extra gaps= 3 total=234 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 1mp8A/T0291-1mp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mp8A expands to /projects/compbio/data/pdb/1mp8.pdb.gz 1mp8A:# T0291 read from 1mp8A/T0291-1mp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp8A read from 1mp8A/T0291-1mp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mp8A to template set # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVIT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 492 :ENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=238 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 1mp8A/T0291-1mp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1mp8A/T0291-1mp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp8A read from 1mp8A/T0291-1mp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVV 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVI T0291 97 :KSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 491 :TENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=242 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 1mp8A/T0291-1mp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1mp8A/T0291-1mp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp8A read from 1mp8A/T0291-1mp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mp8A in template set Warning: unaligning (T0291)A19 because first residue in template chain is (1mp8A)D414 Warning: unaligning (T0291)P49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)P447 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)P447 Warning: unaligning (T0291)D170 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mp8A)L584 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mp8A)L584 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKL 1mp8A 415 :YEIQRERIELGRCIGEGQFGDVHQGIYMS T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1mp8A 448 :ALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVIT T0291 98 :SKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVS 1mp8A 492 :ENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLG T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1mp8A 585 :PIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILE Number of specific fragments extracted= 4 number of extra gaps= 0 total=246 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 1xbbA/T0291-1xbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xbbA expands to /projects/compbio/data/pdb/1xbb.pdb.gz 1xbbA:Skipped atom 172, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 174, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 176, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 956, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 958, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 960, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1159, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1161, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1479, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1481, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1519, because occupancy 0.350 <= existing 0.650 in 1xbbA Skipped atom 1521, because occupancy 0.350 <= existing 0.650 in 1xbbA # T0291 read from 1xbbA/T0291-1xbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbbA read from 1xbbA/T0291-1xbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xbbA to template set # found chain 1xbbA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKL 1xbbA 375 :KELGSGNFGTVKKGYYQM T0291 50 :SKKEISVAIKTL 1xbbA 393 :KKVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNRH T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 466 :VKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYY Number of specific fragments extracted= 7 number of extra gaps= 0 total=253 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 1xbbA/T0291-1xbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xbbA/T0291-1xbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbbA read from 1xbbA/T0291-1xbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xbbA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKLP 1xbbA 375 :KELGSGNFGTVKKGYYQMK T0291 51 :KKEISVAIKTL 1xbbA 394 :KVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNRH T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 466 :VKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYD Number of specific fragments extracted= 7 number of extra gaps= 0 total=260 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 1xbbA/T0291-1xbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xbbA/T0291-1xbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbbA read from 1xbbA/T0291-1xbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xbbA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1xbbA)V363 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)P411 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)P411 Warning: unaligning (T0291)T186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xbbA)K533 Warning: unaligning (T0291)K191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xbbA)K533 T0291 21 :ELDATNISID 1xbbA 364 :YLDRKLLTLE T0291 31 :KVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1xbbA 375 :KELGSGNFGTVKKGYYQMKKVVKTVAVKIL T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1xbbA 412 :ALKDELLAEANVMQQLDNPYIVRMIGICEA T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1xbbA 442 :ESWMLVMEMAELGPLNKYLQQNR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1xbbA 465 :HVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1xbbA 534 :WPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYY Number of specific fragments extracted= 6 number of extra gaps= 0 total=266 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 1fvrA/T0291-1fvrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fvrA expands to /projects/compbio/data/pdb/1fvr.pdb.gz 1fvrA:# T0291 read from 1fvrA/T0291-1fvrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fvrA read from 1fvrA/T0291-1fvrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fvrA to template set # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 Warning: unaligning (T0291)L308 because last residue in template chain is (1fvrA)E1121 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKK T0291 50 :SKKEISVAIKTLKV 1fvrA 846 :DGLRMDAAIKRMKE T0291 72 :DFLGEASIMGQF 1fvrA 868 :DFAGELEVLCKL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fvrA 881 :HHPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLR T0291 119 :KHDA 1fvrA 929 :ANST T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 935 :TLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKII 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNT T0291 298 :TSAAARPSNL 1fvrA 1111 :FTYAGIDCSA Number of specific fragments extracted= 9 number of extra gaps= 0 total=275 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 1fvrA/T0291-1fvrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fvrA/T0291-1fvrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fvrA read from 1fvrA/T0291-1fvrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKKDG T0291 52 :KEISVAIKTLKV 1fvrA 848 :LRMDAAIKRMKE T0291 72 :DFLGEASIMGQFD 1fvrA 868 :DFAGELEVLCKLG T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1fvrA 882 :HPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLRKS T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 935 :TLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSNL 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNTTLYEKFTYAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=282 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 1fvrA/T0291-1fvrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fvrA/T0291-1fvrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fvrA read from 1fvrA/T0291-1fvrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fvrA in template set Warning: unaligning (T0291)H16 because first residue in template chain is (1fvrA)P813 Warning: unaligning (T0291)G64 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)R867 Warning: unaligning (T0291)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)R867 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fvrA)L1000 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fvrA)L1000 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEI 1fvrA 814 :TIYPVLDWNDIKFQDVIGEGNFGQVLKARIKKDGLRMD T0291 56 :VAIKTLKV 1fvrA 852 :AAIKRMKE T0291 72 :DFLGEASIMGQF 1fvrA 868 :DFAGELEVLCKL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1fvrA 881 :HHPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1fvrA 931 :STASTLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSR T0291 180 :DPEAAYT 1fvrA 988 :GQEVYVK T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSN 1fvrA 1001 :PVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNTTLYEKFTYA Number of specific fragments extracted= 7 number of extra gaps= 0 total=289 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 1u59A/T0291-1u59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u59A expands to /projects/compbio/data/pdb/1u59.pdb.gz 1u59A:Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 1u59A Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 1u59A # T0291 read from 1u59A/T0291-1u59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u59A read from 1u59A/T0291-1u59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u59A to template set # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 363 :QIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYY Number of specific fragments extracted= 4 number of extra gaps= 0 total=293 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 1u59A/T0291-1u59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1u59A/T0291-1u59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u59A read from 1u59A/T0291-1u59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 53 :EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 363 :QIDVAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYYS Number of specific fragments extracted= 4 number of extra gaps= 0 total=297 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 1u59A/T0291-1u59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1u59A/T0291-1u59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u59A read from 1u59A/T0291-1u59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u59A in template set Warning: unaligning (T0291)K47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u59A)K362 Warning: unaligning (T0291)K51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u59A)K362 T0291 19 :AKELDATNISIDK 1u59A 329 :KLFLKRDNLLIAD T0291 32 :VVGAGEFGEVCSGRL 1u59A 343 :ELGCGNFGSVRQGVY T0291 52 :KEI 1u59A 363 :QID T0291 56 :VAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1u59A 366 :VAIKVLKQGTEKADTEEMMREAQIMHQLDNPYIVRLIGVCQA T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1u59A 408 :EALMLVMEMAGGGPLHKFLVGKREEIPVSNVAELLHQVSMGMKYLEEKNFVHRDLAARNVLLVNRHYAKISDFGLSKALGADDSYYTARSAGKWPLKWYAPECINFRKFSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPECPPELYALMSDCWIYKWEDRPDFLTVEQRMRACYY Number of specific fragments extracted= 5 number of extra gaps= 0 total=302 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 1ia8A/T0291-1ia8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ia8A expands to /projects/compbio/data/pdb/1ia8.pdb.gz 1ia8A:# T0291 read from 1ia8A/T0291-1ia8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ia8A read from 1ia8A/T0291-1ia8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ia8A to template set # found chain 1ia8A in template set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 Warning: unaligning (T0291)R303 because last residue in template chain is (1ia8A)P276 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGR 1ia8A 3 :VPFVEDWDLVQTLGEGAYGEVQLAV T0291 49 :PSKKEISVAIKTLKVG 1ia8A 28 :NRVTEEAVAVKIVDMK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFL 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRI T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1ia8A 97 :EPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRE T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 162 :RLLNKMCGTLPYVAPELLKRREFH T0291 209 :SASDVWSYGIVLWEVMS 1ia8A 187 :EPVDVWSCGIVLTAMLA T0291 227 :GERPYWEMSNQ 1ia8A 204 :GELPWDQPSDS T0291 238 :DVIKAVDEG 1ia8A 216 :QEYSDWKEK T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1ia8A 226 :TYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKD T0291 290 :NPGSLKIITSAAA 1ia8A 263 :RWYNKPLKKGAKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=312 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 1ia8A/T0291-1ia8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ia8A/T0291-1ia8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ia8A read from 1ia8A/T0291-1ia8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ia8A in template set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 Warning: unaligning (T0291)P304 because last residue in template chain is (1ia8A)P276 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1ia8A 5 :FVEDWDLVQTLGEGAYGEVQLAVN T0291 50 :SKKEISVAIKTLKVG 1ia8A 29 :RVTEEAVAVKIVDMK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIE T0291 121 :DAQ 1ia8A 98 :PDI T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1ia8A 102 :MPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYN T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 159 :NRERLLNKMCGTLPYVAPELLKRREFH T0291 210 :ASDVWSYGIVLWEVMS 1ia8A 188 :PVDVWSCGIVLTAMLA T0291 227 :GERPYWEMS 1ia8A 204 :GELPWDQPS T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1ia8A 215 :CQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIK T0291 289 :RNPGSLKIITSAAAR 1ia8A 261 :KDRWYNKPLKKGAKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=322 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 1ia8A/T0291-1ia8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1ia8A/T0291-1ia8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ia8A read from 1ia8A/T0291-1ia8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ia8A in template set Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ia8A)C48 Warning: unaligning (T0291)Q69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ia8A)C48 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1ia8A 4 :PFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDM T0291 64 :G 1ia8A 43 :K T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1ia8A 49 :PENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDI T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1ia8A 101 :GMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRE T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFT 1ia8A 162 :RLLNKMCGTLPYVAPELLKRREFH T0291 209 :SASDVWSYGIVLWEVMSYGERPYW 1ia8A 187 :EPVDVWSCGIVLTAMLAGELPWDQ T0291 233 :EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1ia8A 212 :SDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKD T0291 289 :RNPGSLKII 1ia8A 263 :RWYNKPLKK Number of specific fragments extracted= 8 number of extra gaps= 0 total=330 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 1t4hA/T0291-1t4hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t4hA expands to /projects/compbio/data/pdb/1t4h.pdb.gz 1t4hA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0291 read from 1t4hA/T0291-1t4hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4hA read from 1t4hA/T0291-1t4hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t4hA to template set # found chain 1t4hA in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1t4hA)A211 Warning: unaligning (T0291)T186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)T187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 19 :AKELDATNISIDK 1t4hA 212 :VGMSNDGRFLKFD T0291 32 :VVGAGEFGEVCSGRL 1t4hA 226 :EIGRGSFKTVYKGLD T0291 50 :SKKEISVAIKTLKV 1t4hA 241 :TETTVEVAWCELQD T0291 64 :GYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 1t4hA 256 :KLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWE T0291 97 :KSKP 1t4hA 291 :VKGK T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1t4hA 297 :IVLVTELMTSGTLKTYLKRFKV T0291 124 :FTVIQLVGMLRGIASGMKYLSD 1t4hA 319 :MKIKVLRSWCRQILKGLQFLHT T0291 146 :MGYVHRDLAARNILIN 1t4hA 343 :PPIIHRDLKCDNIFIT T0291 162 :SNLVCKVSDFGLGRVLEDD 1t4hA 360 :PTGSVKIGDLGLATLKRAS T0291 188 :RGGKIPIRWTSPEAIAY 1t4hA 381 :KAVIGTPEFMAPEMYEE T0291 206 :K 1t4hA 398 :K T0291 209 :SASDVWSYGIVLWEVMS 1t4hA 401 :ESVDVYAFGMCMLEMAT T0291 227 :GERPYWEM 1t4hA 418 :SEYPYSEC T0291 235 :SNQDVIKAVDEGYRLPPPMDC 1t4hA 427 :NAAQIYRRVTSGVKPASFDKV T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNH Number of specific fragments extracted= 15 number of extra gaps= 2 total=345 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 1t4hA/T0291-1t4hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1t4hA/T0291-1t4hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4hA read from 1t4hA/T0291-1t4hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t4hA in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1t4hA)A211 Warning: unaligning (T0291)P181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)A184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 19 :AKELDATNISIDK 1t4hA 212 :VGMSNDGRFLKFD T0291 32 :VVGAGEFGEVCSGRL 1t4hA 226 :EIGRGSFKTVYKGLD T0291 50 :SKKEISVAIKTLK 1t4hA 241 :TETTVEVAWCELQ T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGV 1t4hA 255 :RKLTKSERQRFKEEAEMLKGLQHPNIVRFYDS T0291 95 :VTKSKP 1t4hA 289 :STVKGK T0291 101 :VMIVTEYMENGSLDSFLRKHD 1t4hA 297 :IVLVTELMTSGTLKTYLKRFK T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMG 1t4hA 318 :VMKIKVLRSWCRQILKGLQFLHTRT T0291 148 :YVHRDLAARNILI 1t4hA 345 :IIHRDLKCDNIFI T0291 161 :NSNLVCKVSDFGLGRVLEDD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0291 185 :YTTR 1t4hA 381 :KAVI T0291 190 :GK 1t4hA 385 :GT T0291 194 :IRWTSPEAIA 1t4hA 387 :PEFMAPEMYE T0291 205 :RK 1t4hA 397 :EK T0291 209 :SASDVWSYGIVLWEVMS 1t4hA 401 :ESVDVYAFGMCMLEMAT T0291 227 :GERPYWEM 1t4hA 418 :SEYPYSEC T0291 235 :SNQDVIKAVDEGYRLPPPMDCP 1t4hA 427 :NAAQIYRRVTSGVKPASFDKVA T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVS 1t4hA 450 :PEVKEIIEGCIRQNKDERYSIKDLLN Number of specific fragments extracted= 17 number of extra gaps= 2 total=362 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 1t4hA/T0291-1t4hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1t4hA/T0291-1t4hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4hA read from 1t4hA/T0291-1t4hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t4hA in template set Warning: unaligning (T0291)T186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)A380 Warning: unaligning (T0291)T187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)A380 Warning: unaligning (T0291)F207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t4hA)D400 Warning: unaligning (T0291)T208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t4hA)D400 T0291 20 :KELDATNIS 1t4hA 213 :GMSNDGRFL T0291 29 :IDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1t4hA 223 :FDIEIGRGSFKTVYKGLDTETTVEVAWCELQ T0291 62 :KVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTK 1t4hA 254 :DRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWES T0291 98 :S 1t4hA 292 :K T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1t4hA 295 :KCIVLVTELMTSGTLKTYLKRFK T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1t4hA 318 :VMKIKVLRSWCRQILKGLQFLHT T0291 146 :MGYVHRDLAARNILI 1t4hA 343 :PPIIHRDLKCDNIFI T0291 161 :NSNLVCKVSDFGLGRVLEDD 1t4hA 359 :GPTGSVKIGDLGLATLKRAS T0291 188 :RGGKIPIRWTSPEAIAY 1t4hA 381 :KAVIGTPEFMAPEMYEE T0291 206 :K 1t4hA 398 :K T0291 209 :SASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDC 1t4hA 401 :ESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKV T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 1t4hA 449 :IPEVKEIIEGCIRQNKDERYSIKDLLNH Number of specific fragments extracted= 12 number of extra gaps= 2 total=374 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 1rdqE/T0291-1rdqE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rdqE expands to /projects/compbio/data/pdb/1rdq.pdb.gz 1rdqE:Skipped atom 105, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 107, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 173, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 175, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 177, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 199, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 201, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 975, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 977, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1079, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1081, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1083, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1085, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1087, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1089, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1263, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1265, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1267, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1269, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1384, because occupancy 0.320 <= existing 0.680 in 1rdqE Skipped atom 1386, because occupancy 0.320 <= existing 0.680 in 1rdqE Skipped atom 1388, because occupancy 0.320 <= existing 0.680 in 1rdqE Skipped atom 1390, because occupancy 0.320 <= existing 0.680 in 1rdqE Skipped atom 1392, because occupancy 0.320 <= existing 0.680 in 1rdqE Skipped atom 1424, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1426, because occupancy 0.350 <= existing 0.650 in 1rdqE Skipped atom 1428, because occupancy 0.350 <= existing 0.650 in 1rdqE Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 2039, because occupancy 0.390 <= existing 0.610 in 1rdqE Skipped atom 2041, because occupancy 0.390 <= existing 0.610 in 1rdqE Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1rdqE/T0291-1rdqE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdqE read from 1rdqE/T0291-1rdqE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rdqE to template set # found chain 1rdqE in template set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1rdqE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1rdqE 63 :KESGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHDA 1rdqE 125 :GGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TT 1rdqE 194 :RT T0291 191 :KIPIRWTSPEAIAY 1rdqE 199 :CGTPEALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1rdqE 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1rdqE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1rdqE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKR T0291 275 :PKFEQIV 1rdqE 300 :TDWIAIY T0291 288 :IRNPGSLKII 1rdqE 307 :QRKVEAPFIP Number of specific fragments extracted= 12 number of extra gaps= 2 total=386 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 1rdqE/T0291-1rdqE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1rdqE/T0291-1rdqE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdqE read from 1rdqE/T0291-1rdqE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdqE in template set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1rdqE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1rdqE 63 :KESGNHYAMKILD T0291 63 :VG 1rdqE 82 :LK T0291 66 :T 1rdqE 84 :Q T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHDA 1rdqE 125 :GGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1rdqE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0291 186 :T 1rdqE 195 :T T0291 190 :GKIP 1rdqE 199 :CGTP T0291 195 :RWTSPEAIAY 1rdqE 203 :EALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1rdqE 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDE 1rdqE 234 :GYPPFFADQPIQIYEKIVS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRP 1rdqE 253 :GKVRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 13 number of extra gaps= 2 total=399 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 1rdqE/T0291-1rdqE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1rdqE/T0291-1rdqE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdqE read from 1rdqE/T0291-1rdqE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdqE in template set Warning: unaligning (T0291)M108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)A124 Warning: unaligning (T0291)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)A124 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rdqE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rdqE)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rdqE)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rdqE)G214 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1rdqE 36 :NTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1rdqE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEY T0291 110 :NGSLDSFLRKHD 1rdqE 125 :GGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1rdqE 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TT 1rdqE 194 :RT T0291 191 :KIPIRWTSPEAIAY 1rdqE 199 :CGTPEALAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1rdqE 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGK T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRP 1rdqE 255 :VRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 8 number of extra gaps= 2 total=407 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 2b7aA/T0291-2b7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b7aA expands to /projects/compbio/data/pdb/2b7a.pdb.gz 2b7aA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 2b7aA/T0291-2b7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b7aA read from 2b7aA/T0291-2b7aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b7aA to template set # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLK 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYD T0291 48 :LPSKKEISVAIKTL 2b7aA 871 :LQDNTGEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTY T0291 230 :PYWEM 2b7aA 1051 :IEKSK T0291 236 :NQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1075 :VFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 8 number of extra gaps= 1 total=415 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 2b7aA/T0291-2b7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2b7aA/T0291-2b7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b7aA read from 2b7aA/T0291-2b7aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)P100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKK 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYDPLQDN T0291 53 :EISVAIKTL 2b7aA 876 :GEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTY T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1066 :GNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 7 number of extra gaps= 1 total=422 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 2b7aA/T0291-2b7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2b7aA/T0291-2b7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b7aA read from 2b7aA/T0291-2b7aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b7aA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (2b7aA)Q843 Warning: unaligning (T0291)K97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)N924 Warning: unaligning (T0291)P100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)N924 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (2b7aA)P933 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (2b7aA)P933 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7aA)K1009 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7aA)K1009 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKL 2b7aA 844 :FEERHLKFLQQLGKGNFGSVEMCRYDP T0291 49 :PSKKEISVAI 2b7aA 875 :TGEVVAVKKL T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVT 2b7aA 885 :QHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCY T0291 101 :VMIVTEY 2b7aA 925 :LKLIMEY T0291 110 :NGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2b7aA 934 :YGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDK T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGE 2b7aA 1010 :VKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIE T0291 231 :YWEMSNQDVIKA 2b7aA 1053 :KSKSPPAEFMRM T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 2b7aA 1082 :LKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRD Number of specific fragments extracted= 8 number of extra gaps= 1 total=430 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 1u46A/T0291-1u46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u46A expands to /projects/compbio/data/pdb/1u46.pdb.gz 1u46A:# T0291 read from 1u46A/T0291-1u46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u46A read from 1u46A/T0291-1u46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u46A to template set # found chain 1u46A in template set Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTKSKP 1u46A 185 :DHRNLIRLYGVVLTPPM T0291 102 :MIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 202 :KMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKE T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 348 :ERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 9 number of extra gaps= 3 total=439 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 1u46A/T0291-1u46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1u46A/T0291-1u46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u46A read from 1u46A/T0291-1u46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u46A in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1u46A)L117 Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 19 :A 1u46A 118 :T T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTK 1u46A 185 :DHRNLIRLYGVVLT T0291 99 :KPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 199 :PPMKMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKE T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 348 :ERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 10 number of extra gaps= 3 total=449 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 1u46A/T0291-1u46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1u46A/T0291-1u46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u46A read from 1u46A/T0291-1u46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u46A in template set Warning: unaligning (T0291)K20 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u46A)L120 Warning: unaligning (T0291)E21 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u46A)L120 Warning: unaligning (T0291)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)G138 Warning: unaligning (T0291)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)G138 Warning: unaligning (T0291)T60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)P168 Warning: unaligning (T0291)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)P168 Warning: unaligning (T0291)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)L184 Warning: unaligning (T0291)F83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)L184 Warning: unaligning (T0291)R175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u46A)A276 Warning: unaligning (T0291)V176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)A276 Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)D281 Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)D281 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1u46A)D282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u46A)V292 Warning: unaligning (T0291)I192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u46A)V292 Warning: unaligning (T0291)P193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u46A)P293 Warning: unaligning (T0291)I288 because last residue in template chain is (1u46A)Q389 T0291 22 :LDATNISIDKVV 1u46A 121 :IGEKDLRLLEKL T0291 40 :EVCSGRLKLPSKKEISVAIK 1u46A 139 :VVRRGEWDAPSGKTVSVAVK T0291 68 :KQRRDFLGEASIMG 1u46A 169 :EAMDDFIREVNAMH T0291 84 :DHPNIIRLEGVVTKSK 1u46A 185 :DHRNLIRLYGVVLTPP T0291 101 :VMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1u46A 201 :MKMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLM T0291 177 :LE 1u46A 277 :LP T0291 183 :AAY 1u46A 283 :HYV T0291 194 :IRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1u46A 294 :FAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHK T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1u46A 344 :DKEGERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEA Number of specific fragments extracted= 9 number of extra gaps= 3 total=458 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 2bikB/T0291-2bikB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bikB expands to /projects/compbio/data/pdb/2bik.pdb.gz 2bikB:Skipped atom 66, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 68, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 70, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 530, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 532, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 534, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 958, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 960, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 962, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 982, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 984, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 986, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1222, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1224, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1226, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1228, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1537, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1539, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1541, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1543, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1545, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1652, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1654, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1717, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1719, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1721, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1723, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1725, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1727, because occupancy 0.350 <= existing 0.650 in 2bikB Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1876, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1878, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1880, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 1882, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2038, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2040, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2042, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2044, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2046, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2048, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2050, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2155, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2157, because occupancy 0.350 <= existing 0.650 in 2bikB Skipped atom 2159, because occupancy 0.350 <= existing 0.650 in 2bikB # T0291 read from 2bikB/T0291-2bikB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bikB read from 2bikB/T0291-2bikB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bikB to template set # found chain 2bikB in template set Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLK 2bikB 34 :LESQYQVGPLLGSGGFGSVYSGIRV T0291 51 :KKEISVAIKTLKVGYT 2bikB 59 :SDNLPVAIKHVEKDRI T0291 67 :EK 2bikB 81 :PN T0291 75 :GEASIMGQFDHP 2bikB 88 :MEVVLLKKVSSG T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 2bikB 102 :GVIRLLDWFERPDSFVLILERPEP T0291 111 :GSLDSFLRKHDA 2bikB 127 :QDLFDFITERGA T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILIN 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILID T0291 162 :SNLVCKVSDFGLGRVLEDD 2bikB 178 :NRGELKLIDFGSGALLKDT T0291 186 :TTRGGKIPIRWTSPEAIAYRKFT 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0291 209 :SASDVWSYGIVLWEVMS 2bikB 221 :RSAAVWSLGILLYDMVC T0291 227 :GERPY 2bikB 238 :GDIPF T0291 234 :MSNQDVIK 2bikB 243 :EHDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVSILD 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHPW Number of specific fragments extracted= 14 number of extra gaps= 0 total=472 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 2bikB/T0291-2bikB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bikB/T0291-2bikB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bikB read from 2bikB/T0291-2bikB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bikB in template set Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 26 :NISIDKVVGAGEFGEVCSGRL 2bikB 37 :QYQVGPLLGSGGFGSVYSGIR T0291 50 :SKKEISVAIKTLKVGY 2bikB 58 :VSDNLPVAIKHVEKDR T0291 75 :GEASIMGQFDHP 2bikB 88 :MEVVLLKKVSSG T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 2bikB 102 :GVIRLLDWFERPDSFVLILERPEP T0291 112 :SLDSFLRKHDA 2bikB 128 :DLFDFITERGA T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bikB 139 :LQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILI T0291 161 :NSNLVCKVSDFGLGRVLEDDP 2bikB 177 :LNRGELKLIDFGSGALLKDTV T0291 184 :AYTTRGGK 2bikB 198 :YTDFDGTR T0291 195 :RWTSPEAIAYRKFT 2bikB 206 :VYSPPEWIRYHRYH T0291 210 :ASDVWSYGIVLWEVMS 2bikB 222 :SAAVWSLGILLYDMVC T0291 227 :GERPYW 2bikB 238 :GDIPFE T0291 235 :SNQDVIK 2bikB 244 :HDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVS 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQN Number of specific fragments extracted= 14 number of extra gaps= 0 total=486 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 2bikB/T0291-2bikB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bikB/T0291-2bikB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bikB read from 2bikB/T0291-2bikB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bikB in template set Warning: unaligning (T0291)L22 because first residue in template chain is (2bikB)P33 Warning: unaligning (T0291)P256 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bikB)E262 Warning: unaligning (T0291)A258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bikB)E262 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 2bikB 34 :LESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVE T0291 60 :TLKVGYTE 2bikB 77 :WGELPNGT T0291 75 :GEASIMGQF 2bikB 88 :MEVVLLKKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 2bikB 99 :GFSGVIRLLDWFERPDSFVLILERPEP T0291 111 :GSLDSFLRKHD 2bikB 127 :QDLFDFITERG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bikB 138 :ALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILI T0291 161 :NSNLVCKVSDFGLGRVLEDD 2bikB 177 :LNRGELKLIDFGSGALLKDT T0291 186 :TTRGGKIPIRWTSPEAIAYRKFT 2bikB 197 :VYTDFDGTRVYSPPEWIRYHRYH T0291 210 :ASDVWSYGIVLWEVMSYGERPY 2bikB 222 :SAAVWSLGILLYDMVCGDIPFE T0291 235 :SNQDVIK 2bikB 244 :HDEEIIG T0291 247 :YRLPPPMDC 2bikB 251 :GQVFFRQRV T0291 259 :LYQLMLDCWQKDRNNRPKFEQIVSIL 2bikB 263 :CQHLIRWCLALRPSDRPTFEEIQNHP Number of specific fragments extracted= 12 number of extra gaps= 0 total=498 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 1j1bA/T0291-1j1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j1bA expands to /projects/compbio/data/pdb/1j1b.pdb.gz 1j1bA:# T0291 read from 1j1bA/T0291-1j1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1bA read from 1j1bA/T0291-1j1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j1bA to template set # found chain 1j1bA in template set T0291 22 :LDATN 1j1bA 46 :QGPDR T0291 27 :ISIDKVVGAGEFGEVCSGRL 1j1bA 56 :YTDTKVIGNGSFGVVYQAKL T0291 50 :SKKEISVAIKTLKVGYTEK 1j1bA 76 :CDSGELVAIKKVLQDKRFK T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 98 :SKP 1j1bA 123 :KDE T0291 101 :VMIVTEYMEN 1j1bA 128 :LNLVLDYVPE T0291 112 :SLDSFLR 1j1bA 138 :TVYRVAR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 148 :RAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1j1bA 232 :TDYTSSIDVWSAGCVLAELLL T0291 227 :GERPYWEMS 1j1bA 253 :GQPIFPGDS T0291 236 :NQDVIKAVDEG 1j1bA 277 :TREQIREMNPN T0291 247 :YRLPPPM 1j1bA 289 :TEFKFPQ T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1j1bA 308 :RTPPEAIALCSRLLEYTPTARLTPLEACAH T0291 284 :LDKLIRNPGSLKIITSAAAR 1j1bA 340 :FDELRDPNVKLPNGRDTPAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=514 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 1j1bA/T0291-1j1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1j1bA/T0291-1j1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1bA read from 1j1bA/T0291-1j1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1bA in template set T0291 23 :DATNISI 1j1bA 50 :RPQEVSY T0291 30 :DKVVGAGEFGEVCSGRL 1j1bA 59 :TKVIGNGSFGVVYQAKL T0291 50 :SKKEISVAIK 1j1bA 76 :CDSGELVAIK T0291 60 :TLKVGYT 1j1bA 88 :LQDKRFK T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 98 :SKP 1j1bA 123 :KDE T0291 101 :VMIVTEYMEN 1j1bA 128 :LNLVLDYVPE T0291 112 :SLDSFLRKH 1j1bA 138 :TVYRVARHY T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 150 :KQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1j1bA 232 :TDYTSSIDVWSAGCVLAELLL T0291 227 :GERPYWEMSNQDVIKAVDE 1j1bA 253 :GQPIFPGDSGVDQLVEIIK T0291 247 :YRLPPP 1j1bA 289 :TEFKFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1j1bA 307 :PRTPPEAIALCSRLLEYTPTARLTPLEAC T0291 283 :ILDKLIRNPGSLKI 1j1bA 339 :FFDELRDPNVKLPN T0291 299 :SAAA 1j1bA 353 :GRDT Number of specific fragments extracted= 17 number of extra gaps= 0 total=531 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 1j1bA/T0291-1j1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1j1bA/T0291-1j1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1bA read from 1j1bA/T0291-1j1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1bA in template set T0291 3 :VDPHTYEDPTQAVH 1j1bA 42 :ATPGQGPDRPQEVS T0291 27 :ISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYT 1j1bA 56 :YTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKN T0291 75 :GEASIMGQFDHPNIIRLEGVVTK 1j1bA 96 :RELQIMRKLDHCNIVRLRYFFYS T0291 99 :K 1j1bA 124 :D T0291 100 :PVMIVTEYMEN 1j1bA 127 :YLNLVLDYVPE T0291 112 :SLDSFLR 1j1bA 138 :TVYRVAR T0291 119 :KHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1j1bA 148 :RAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD T0291 164 :LVCKVSDFGLGRVLEDDP 1j1bA 194 :AVLKLCDFGSAKQLVRGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1j1bA 212 :PNVSYICSRYYRAPELIFG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1j1bA 232 :TDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEI T0291 243 :VDEGYRLP 1j1bA 293 :FPQIKAHP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1j1bA 305 :FRPRTPPEAIALCSRLLEYTPTARLTPLEACAH T0291 284 :LDKLIRNPGSL 1j1bA 340 :FDELRDPNVKL Number of specific fragments extracted= 13 number of extra gaps= 0 total=544 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 1z57A/T0291-1z57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z57A expands to /projects/compbio/data/pdb/1z57.pdb.gz 1z57A:Skipped atom 406, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 408, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1026, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1028, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1181, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1184, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1255, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1257, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1259, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1261, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1263, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1499, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 1501, because occupancy 0.350 <= existing 0.650 in 1z57A Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1z57A Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1z57A # T0291 read from 1z57A/T0291-1z57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z57A read from 1z57A/T0291-1z57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z57A to template set # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 18 :FAKEL 1z57A 153 :SGDVL T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1z57A 158 :SARYEIVDTLGEGAFGKVVECID T0291 49 :PSKKEISVAIKTLKV 1z57A 181 :HKAGGRHVAVKIVKN T0291 66 :TEKQRRDFLGEASIMGQF 1z57A 196 :VDRYCEAARSEIQVLEHL T0291 84 :DHPN 1z57A 219 :NSTF T0291 88 :IIRLEGVVTKSKPVMIV 1z57A 224 :CVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHDA 1z57A 247 :STYDFIKENGF T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 259 :PFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLED 1z57A 316 :LINPDIKVVDFGSATYDDE T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1z57A 335 :HHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYL T0291 227 :GERPYWEMS 1z57A 375 :GFTVFPTHD T0291 236 :NQDVIKAV 1z57A 399 :PKHMIQKT T0291 244 :DEGYRLPPPM 1z57A 412 :FHHDRLDWDE T0291 255 :CPAALYQLMLDCWQKDRNNRPKFEQIVSI 1z57A 446 :EHERLFDLIQKMLEYDPAKRITLREALKH Number of specific fragments extracted= 15 number of extra gaps= 1 total=559 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 1z57A/T0291-1z57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1z57A/T0291-1z57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z57A read from 1z57A/T0291-1z57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 12 :TQAVHEFAKEL 1z57A -1 :MHLICQSGDVL T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1z57A 158 :SARYEIVDTLGEGAFGKVVECID T0291 49 :PSKKEISVAIKTLKVG 1z57A 181 :HKAGGRHVAVKIVKNV T0291 67 :EKQRRDFLGEASIMGQF 1z57A 197 :DRYCEAARSEIQVLEHL T0291 85 :HPNIIRLEGVVTKSKPVMIV 1z57A 221 :TFRCVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHDAQ 1z57A 247 :STYDFIKENGFL T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 260 :FRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLEDD 1z57A 316 :LINPDIKVVDFGSATYDDEH T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1z57A 336 :HSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYL T0291 227 :GERPYWEMSNQDVIKAVD 1z57A 375 :GFTVFPTHDSKEHLAMME T0291 246 :GYRLPPPMDC 1z57A 414 :HDRLDWDEHS T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVS 1z57A 448 :ERLFDLIQKMLEYDPAKRITLREALK Number of specific fragments extracted= 13 number of extra gaps= 1 total=572 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 1z57A/T0291-1z57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1z57A/T0291-1z57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z57A read from 1z57A/T0291-1z57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z57A in template set Warning: unaligning (T0291)T105 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1z57A)E242 Warning: unaligning (T0291)E106 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1z57A)E242 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKL 1z57A 158 :SARYEIVDTLGEGAFGKVVECIDHK T0291 49 :PSKKEISVAIK 1z57A 184 :GGRHVAVKIVK T0291 65 :YTEKQRRDFLGEASIMGQF 1z57A 195 :NVDRYCEAARSEIQVLEHL T0291 84 :DHPNIIRLEGVVTKSKPVMIV 1z57A 220 :STFRCVQMLEWFEHHGHICIV T0291 107 :YMEN 1z57A 243 :LLGL T0291 112 :SLDSFLRKHD 1z57A 247 :STYDFIKENG T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1z57A 258 :LPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILF T0291 161 :NSNLVCKVSDFGLGRVLEDD 1z57A 316 :LINPDIKVVDFGSATYDDEH T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1z57A 336 :HSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMM T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1z57A 440 :MLSQDVEHERLFDLIQKMLEYDPAKRITLREALKH Number of specific fragments extracted= 10 number of extra gaps= 1 total=582 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 1mq4A/T0291-1mq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mq4A expands to /projects/compbio/data/pdb/1mq4.pdb.gz 1mq4A:# T0291 read from 1mq4A/T0291-1mq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mq4A read from 1mq4A/T0291-1mq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mq4A to template set # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLKVGYTEK 1mq4A 153 :KQSKFILALKVLFKAQLEK T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1mq4A 174 :VEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 228 :FDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDEG 1mq4A 325 :GKPPFEANTYQETYKRISRV T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1mq4A 345 :EFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPW Number of specific fragments extracted= 8 number of extra gaps= 1 total=590 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 1mq4A/T0291-1mq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1mq4A/T0291-1mq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mq4A read from 1mq4A/T0291-1mq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 Warning: unaligning (T0291)R289 because last residue in template chain is (1mq4A)S388 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLK 1mq4A 153 :KQSKFILALKVLF T0291 67 :EKQRRD 1mq4A 166 :KAQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1mq4A 178 :LRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 228 :FDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 188 :RGGKI 1mq4A 289 :LCGTL T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1mq4A 294 :DYLPPEMIEGRMHDEKVDLWSLGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDE 1mq4A 325 :GKPPFEANTYQETYKRISR T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1mq4A 344 :VEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVL T0291 282 :SILDKLI 1mq4A 381 :PWITANS Number of specific fragments extracted= 11 number of extra gaps= 1 total=601 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 1mq4A/T0291-1mq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1mq4A/T0291-1mq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mq4A read from 1mq4A/T0291-1mq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mq4A in template set Warning: unaligning (T0291)K20 because first residue in template chain is (1mq4A)R126 Warning: unaligning (T0291)L177 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mq4A)P282 Warning: unaligning (T0291)E178 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mq4A)P282 Warning: unaligning (T0291)T186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mq4A)T288 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mq4A)T288 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1mq4A 127 :QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFK T0291 67 :EKQRR 1mq4A 167 :AQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1mq4A 178 :LRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLS T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1mq4A 227 :KFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVH T0291 179 :DD 1mq4A 283 :SS T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1mq4A 289 :LCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVE T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1mq4A 346 :FTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEH Number of specific fragments extracted= 7 number of extra gaps= 1 total=608 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 2bfxA/T0291-2bfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bfxA expands to /projects/compbio/data/pdb/2bfx.pdb.gz 2bfxA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 2bfxA/T0291-2bfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bfxA read from 2bfxA/T0291-2bfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bfxA to template set # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 Warning: unaligning (T0291)I296 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bfxA)Q356 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLKVGYT 2bfxA 113 :KQNKFIMALKVLFKSQL T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bfxA 132 :EGVEHQLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 188 :FDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bfxA 285 :GMPPFDSPSHTETHRRIVNV T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 305 :DLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPGSLK 2bfxA 342 :WVKANSRRVLPPV Number of specific fragments extracted= 9 number of extra gaps= 1 total=617 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 2bfxA/T0291-2bfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bfxA/T0291-2bfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bfxA read from 2bfxA/T0291-2bfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRL 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLARE T0291 50 :SKKEISVAIKTLK 2bfxA 113 :KQNKFIMALKVLF T0291 67 :EKQRRD 2bfxA 126 :KSQLEK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bfxA 138 :LRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 188 :FDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLV T0291 227 :GERPYWEMSNQDVIKAVDE 2bfxA 285 :GMPPFDSPSHTETHRRIVN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 304 :VDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPG 2bfxA 342 :WVKANSRRVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=627 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 2bfxA/T0291-2bfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bfxA/T0291-2bfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bfxA read from 2bfxA/T0291-2bfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bfxA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bfxA)R86 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bfxA)M249 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bfxA)M249 Warning: unaligning (T0291)I296 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bfxA)Q356 Warning: unaligning (T0291)I297 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bfxA)Q356 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 2bfxA 87 :KFTIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFK T0291 67 :EKQRR 2bfxA 127 :SQLEK T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bfxA 137 :QLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2bfxA 187 :RFDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSL T0291 186 :TT 2bfxA 245 :RR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAV 2bfxA 250 :CGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIV T0291 246 :GYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2bfxA 303 :NVDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVME T0291 283 :ILDKLIRNPGSLK 2bfxA 342 :WVKANSRRVLPPV Number of specific fragments extracted= 8 number of extra gaps= 1 total=635 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 1yhvA/T0291-1yhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yhvA expands to /projects/compbio/data/pdb/1yhv.pdb.gz 1yhvA:# T0291 read from 1yhvA/T0291-1yhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yhvA read from 1yhvA/T0291-1yhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yhvA to template set # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLK 1yhvA 260 :IVSVGDPKKKYTRFEKIGQGASGTVYTAMDV T0291 51 :KKEISVAIKTLKVGYTEK 1yhvA 291 :ATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1yhvA 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1yhvA 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=642 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 1yhvA/T0291-1yhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1yhvA/T0291-1yhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yhvA read from 1yhvA/T0291-1yhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLK 1yhvA 265 :DPKKKYTRFEKIGQGASGTVYTAMDV T0291 51 :KKEISVAIKTLK 1yhvA 291 :ATGQEVAIRQMN T0291 64 :GYT 1yhvA 306 :QPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1yhvA 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1yhvA 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELL T0291 290 :NPGSLKIITS 1yhvA 517 :QHQFLKIAKP Number of specific fragments extracted= 9 number of extra gaps= 1 total=651 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 1yhvA/T0291-1yhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1yhvA/T0291-1yhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yhvA read from 1yhvA/T0291-1yhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yhvA in template set Warning: unaligning (T0291)D180 because of BadResidue code BAD_PEPTIDE in next template residue (1yhvA)Q418 Warning: unaligning (T0291)P181 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)Q418 Warning: unaligning (T0291)E182 because of BadResidue code BAD_PEPTIDE at template residue (1yhvA)S419 T0291 22 :LDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVG 1yhvA 265 :DPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIRQMNLQQQP T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1yhvA 308 :KKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1yhvA 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITP T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1yhvA 420 :KRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLI T0291 243 :VDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1yhvA 478 :TNGTPELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ T0291 297 :ITSAAARPSNLL 1yhvA 518 :HQFLKIAKPLSS Number of specific fragments extracted= 6 number of extra gaps= 1 total=657 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 2f57A/T0291-2f57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f57A expands to /projects/compbio/data/pdb/2f57.pdb.gz 2f57A:Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2f57A Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 2f57A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2f57A # T0291 read from 2f57A/T0291-2f57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f57A read from 2f57A/T0291-2f57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f57A to template set # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 Warning: unaligning (T0291)L309 because last residue in template chain is (2f57A)Q715 T0291 1 :TYVDPHTYEDPTQAVHEFAKELDATN 2f57A -5 :LYFQSMSRVSHEQFRAALQLVVSPGD T0291 27 :ISIDKVVGA 2f57A 449 :LANFIKIGE T0291 38 :FGEVCSGRL 2f57A 460 :TGIVCIATE T0291 50 :SKKEISVAIKTLKVGYTEK 2f57A 469 :KHTGKQVAVKKMDLRKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2f57A 488 :RELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTHT T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2f57A 539 :RMNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVP T0291 186 :TT 2f57A 599 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMID T0291 227 :GERPYWEMSNQDVIKAVDEG 2f57A 639 :GEPPYFNEPPLQAMRRIRDS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELLG T0291 291 :PGSLKIITSAAARPSNLL 2f57A 697 :HPFLKLAGPPSCIVPLMR Number of specific fragments extracted= 11 number of extra gaps= 1 total=668 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 2f57A/T0291-2f57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2f57A/T0291-2f57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f57A read from 2f57A/T0291-2f57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0291 1 :TYVDPHTYEDPTQAVHEFAKELD 2f57A -5 :LYFQSMSRVSHEQFRAALQLVVS T0291 24 :ATNISIDKVVGA 2f57A 446 :REYLANFIKIGE T0291 38 :FGEVCSGRL 2f57A 460 :TGIVCIATE T0291 50 :SKKEISVAIKTLK 2f57A 469 :KHTGKQVAVKKMD T0291 63 :VGY 2f57A 485 :QQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRK 2f57A 488 :RELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTH T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2f57A 538 :TRMNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEV T0291 185 :YTT 2f57A 598 :PKR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMID T0291 227 :GERPYWEMSNQDVIKAVDEG 2f57A 639 :GEPPYFNEPPLQAMRRIRDS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELL T0291 290 :NP 2f57A 696 :GH T0291 293 :SLKIITSAAARPSNLLLD 2f57A 698 :PFLKLAGPPSCIVPLMRQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=681 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 2f57A/T0291-2f57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2f57A/T0291-2f57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f57A read from 2f57A/T0291-2f57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f57A in template set Warning: unaligning (T0291)G36 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2f57A)S459 Warning: unaligning (T0291)E37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2f57A)S459 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f57A)L603 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f57A)L603 T0291 22 :LDATNISIDKVVGA 2f57A 444 :DPREYLANFIKIGE T0291 38 :FGEVCSGRLKLPSKKEISVAIKTLKVG 2f57A 460 :TGIVCIATEKHTGKQVAVKKMDLRKQQ T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2f57A 487 :RRELLFNEVVIMRDYHHDNVVDMYSSYLVGDELWVVMEFLEGGALTDIVTHTR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2f57A 540 :MNEEQIATVCLSVLRALSYLHNQGVIHRDIKSDSILLTSDGRIKLSDFGFCAQVSKEVP T0291 186 :TT 2f57A 599 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 2f57A 604 :VGTPYWMAPEVISRLPYGTEVDIWSLGIMVIEMIDGEPPYFNEPPLQAMRRIRDSL T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 2f57A 661 :PRVKDLHKVSSVLRGFLDLMLVREPSQRATAQELLGH T0291 298 :TSAAARPSNLL 2f57A 698 :PFLKLAGPPSC Number of specific fragments extracted= 8 number of extra gaps= 1 total=689 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 1xjdA/T0291-1xjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xjdA expands to /projects/compbio/data/pdb/1xjd.pdb.gz 1xjdA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1xjdA/T0291-1xjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjdA read from 1xjdA/T0291-1xjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xjdA to template set # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEF T0291 50 :SKKEISVAIKTLKVGYT 1xjdA 400 :KKTNQFFAIKALKKDVV T0291 67 :EKQRRDFLGEASIMGQF 1xjdA 419 :DDDVECTMVEKRVLSLA T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xjdA 437 :EHPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCHK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDA T0291 186 :TT 1xjdA 535 :KT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLI T0291 227 :GERPYWEMSNQDVIKAVDEG 1xjdA 575 :GQSPFHGQDEEELFHSIRMD T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1xjdA 595 :NPFYPRWLEKEAKDLLVKLFVREPEKR T0291 275 :PKFEQIVS 1xjdA 637 :INWEELER Number of specific fragments extracted= 10 number of extra gaps= 0 total=699 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 1xjdA/T0291-1xjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xjdA/T0291-1xjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjdA read from 1xjdA/T0291-1xjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEF T0291 50 :SKKEISVAIKTLK 1xjdA 400 :KKTNQFFAIKALK T0291 63 :VGYTEKQRRDFLGEASIMGQ 1xjdA 418 :MDDDVECTMVEKRVLSLAWE T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xjdA 438 :HPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCHK T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1xjdA 476 :FDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLG T0291 182 :EAAY 1xjdA 533 :DAKT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLI T0291 227 :GERPYWEMSNQDVIKAVDE 1xjdA 575 :GQSPFHGQDEEELFHSIRM T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRP 1xjdA 594 :DNPFYPRWLEKEAKDLLVKLFVREPEKRL T0291 276 :KFEQIV 1xjdA 638 :NWEELE Number of specific fragments extracted= 10 number of extra gaps= 0 total=709 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 1xjdA/T0291-1xjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xjdA/T0291-1xjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjdA read from 1xjdA/T0291-1xjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjdA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1xjdA)I377 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjdA)F539 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjdA)F539 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1xjdA 378 :EDFILHKMLGKGSFGKVFLAEFKKTNQFFAIKALKK T0291 66 :TE 1xjdA 414 :DV T0291 68 :KQRRDFLGEASIMGQF 1xjdA 420 :DDVECTMVEKRVLSLA T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1xjdA 437 :EHPFLTHMFCTFQTKENLFFVMEYLNGGDLMYHIQSCH T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1xjdA 475 :KFDLSRATFYAAEIILGLQFLHSKGIVYRDLKLDNILLDKDGHIKIADFGMCKENMLGDA T0291 186 :TT 1xjdA 535 :KT T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1xjdA 540 :CGTPDYIAPEILLGQKYNHSVDWWSFGVLLYEMLIGQSPFHGQDEEELFHSIRMDN T0291 249 :LPPPMDCPAALYQLMLDCWQKDRNNRP 1xjdA 596 :PFYPRWLEKEAKDLLVKLFVREPEKRL T0291 276 :KFEQIV 1xjdA 638 :NWEELE Number of specific fragments extracted= 9 number of extra gaps= 0 total=718 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 1irk/T0291-1irk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1irk expands to /projects/compbio/data/pdb/1irk.pdb.gz 1irk:Warning: there is no chain 1irk will retry with 1irkA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 1irk Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1irk # T0291 read from 1irk/T0291-1irk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1irk read from 1irk/T0291-1irk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1irk to template set # found chain 1irk in template set Warning: unaligning (T0291)D4 because first residue in template chain is (1irk)S981 T0291 5 :PHTYEDPT 1irk 982 :SVFVPDEW T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLK 1irk 990 :EVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1irk 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 119 :KHDAQ 1irk 1098 :NPGRP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGR 1irk 1104 :PTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTR T0291 177 :LEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1irk 1156 :DIYETDYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLH Number of specific fragments extracted= 6 number of extra gaps= 0 total=724 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 1irk/T0291-1irk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1irk/T0291-1irk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1irk read from 1irk/T0291-1irk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1irk in template set Warning: unaligning (T0291)D4 because first residue in template chain is (1irk)S981 T0291 5 :PHTYED 1irk 982 :SVFVPD T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1irk 988 :EWEVSREKITLLRELGQGSFGMVYEGNAR T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1irk 1019 :IKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSL T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1irk 1101 :RPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYET T0291 182 :EAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1irk 1161 :DYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=729 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 1irk/T0291-1irk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1irk/T0291-1irk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1irk read from 1irk/T0291-1irk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1irk in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1irk)S981 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1irk 982 :SVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARD T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1irk 1020 :KGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLR T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1irk 1100 :GRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDY T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKL 1irk 1163 :YRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDD Number of specific fragments extracted= 4 number of extra gaps= 0 total=733 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 1lufA/T0291-1lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lufA expands to /projects/compbio/data/pdb/1luf.pdb.gz 1lufA:# T0291 read from 1lufA/T0291-1lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lufA read from 1lufA/T0291-1lufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lufA to template set # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAP T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1lufA 597 :LPYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSA T0291 182 :EAA 1lufA 753 :DYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 5 number of extra gaps= 0 total=738 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 1lufA/T0291-1lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1lufA/T0291-1lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lufA read from 1lufA/T0291-1lufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAP T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 1lufA 597 :LPYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLRSM T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSA T0291 182 :EAA 1lufA 753 :DYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 5 number of extra gaps= 0 total=743 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 1lufA/T0291-1lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1lufA/T0291-1lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lufA read from 1lufA/T0291-1lufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lufA in template set Warning: unaligning (T0291)Q13 because first residue in template chain is (1lufA)L560 Warning: unaligning (T0291)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)P694 Warning: unaligning (T0291)Y185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lufA)D761 Warning: unaligning (T0291)G190 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lufA)D761 Warning: unaligning (T0291)R289 because last residue in template chain is (1lufA)E860 T0291 14 :AVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1lufA 561 :NPKLLSLEYPRNNIEYVRDIGEGAFGRVFQARAPG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLR 1lufA 598 :PYEPFTMVAVKMLKEEASADMQADFQREAALMAEFDNPNIVKLLGVCAVGKPMCLLFEYMAYGDLNEFLR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1lufA 695 :PLSCAEQLCIARQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYSADYY T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 1lufA 762 :AIPIRWMPPESIFYNRYTTESDVWAYGVVLWEIFSYGLQPYYGMAHEEVIYYVRDGNILACPENCPLELYNLMRLCWSKLPADRPSFCSIHRILQRMC Number of specific fragments extracted= 4 number of extra gaps= 0 total=747 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmk/T0291-1fmk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fmk expands to /projects/compbio/data/pdb/1fmk.pdb.gz 1fmk:Warning: there is no chain 1fmk will retry with 1fmkA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1fmk/T0291-1fmk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmk read from 1fmk/T0291-1fmk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fmk to template set # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 3 :VDPHTYEDP 1fmk 247 :TSKPQTQGL T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 1fmk 256 :AKDAWEIPRESLRLEVKLGQGCFGEVWMGTW T0291 51 :KKEISVAIKTLKVGYTEK 1fmk 287 :NGTTRVAIKTLKPGTMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEG 1fmk 305 :EAFLQEAQVMKKLRHEKLVQLYA T0291 96 :T 1fmk 330 :S T0291 98 :S 1fmk 331 :E T0291 101 :VMIVTEYMENGSLDSFLRKH 1fmk 334 :IYIVTEYMSKGSLLDFLKGE T0291 121 :D 1fmk 356 :K T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 357 :YLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :ITS 1fmk 529 :PGE Number of specific fragments extracted= 12 number of extra gaps= 3 total=759 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmk/T0291-1fmk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fmk/T0291-1fmk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmk read from 1fmk/T0291-1fmk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 3 :VDPHT 1fmk 247 :TSKPQ T0291 12 :TQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRL 1fmk 252 :TQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTW T0291 51 :KKEISVAIKTLKVGY 1fmk 287 :NGTTRVAIKTLKPGT T0291 66 :TEKQ 1fmk 303 :SPEA T0291 73 :FLGEASIMGQFDHPNIIRLEG 1fmk 307 :FLQEAQVMKKLRHEKLVQLYA T0291 97 :KS 1fmk 330 :SE T0291 101 :VMIVTEYMENGSLDSFLRKH 1fmk 334 :IYIVTEYMSKGSLLDFLKGE T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 356 :KYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :IT 1fmk 529 :PG Number of specific fragments extracted= 11 number of extra gaps= 3 total=770 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmk/T0291-1fmk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1fmk/T0291-1fmk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmk read from 1fmk/T0291-1fmk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmk in template set Warning: unaligning (T0291)V94 because of BadResidue code BAD_PEPTIDE in next template residue (1fmk)V329 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)V329 Warning: unaligning (T0291)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)P333 Warning: unaligning (T0291)P100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)P333 Warning: unaligning (T0291)R175 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)F424 Warning: unaligning (T0291)I192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)F424 Warning: unaligning (T0291)N290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fmk)T523 Warning: unaligning (T0291)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fmk)T523 Warning: unaligning (T0291)G292 because of BadResidue code BAD_PEPTIDE at template residue (1fmk)E524 Warning: unaligning (T0291)L294 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmk)Q528 Warning: unaligning (T0291)I296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmk)Q528 T0291 5 :PHTYEDPTQAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 1fmk 245 :CPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTT T0291 55 :SVAIKTLKVG 1fmk 291 :RVAIKTLKPG T0291 65 :YTEK 1fmk 302 :MSPE T0291 72 :DFLGEASIMGQFDHPNIIRLEG 1fmk 306 :AFLQEAQVMKKLRHEKLVQLYA T0291 96 :T 1fmk 330 :S T0291 98 :S 1fmk 331 :E T0291 101 :VMIVTEYMENGSLDSFLRK 1fmk 334 :IYIVTEYMSKGSLLDFLKG T0291 120 :H 1fmk 355 :G T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLG 1fmk 356 :KYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLA T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1fmk 425 :PIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFT T0291 293 :S 1fmk 525 :P T0291 297 :IT 1fmk 529 :PG Number of specific fragments extracted= 12 number of extra gaps= 3 total=782 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6lA/T0291-1o6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o6lA expands to /projects/compbio/data/pdb/1o6l.pdb.gz 1o6lA:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1o6lA/T0291-1o6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6lA read from 1o6lA/T0291-1o6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o6lA to template set # found chain 1o6lA in template set Warning: unaligning (T0291)E21 because first residue in template chain is (1o6lA)K146 Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRL 1o6lA 154 :YLKLLGKGTFGKVILVRE T0291 50 :SKKEISVAIKTLKVGYT 1o6lA 172 :KATGRYYAMKILRKEVI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1o6lA 191 :KDEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERV T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1o6lA 247 :FTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGIS T0291 181 :PEA 1o6lA 303 :DGA T0291 186 :TT 1o6lA 306 :TM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMC T0291 227 :GERPYWEMSNQDVIKAVDEG 1o6lA 346 :GRLPFYNQDHERLFELILME T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 366 :EIRFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVS 1o6lA 412 :INWQDVVQ T0291 290 :NPGSLKII 1o6lA 420 :KKLLPPFK Number of specific fragments extracted= 12 number of extra gaps= 1 total=794 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6lA/T0291-1o6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1o6lA/T0291-1o6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6lA read from 1o6lA/T0291-1o6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o6lA in template set Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRL 1o6lA 154 :YLKLLGKGTFGKVILVRE T0291 50 :SKKEISVAIKTLK 1o6lA 172 :KATGRYYAMKILR T0291 63 :VGY 1o6lA 191 :KDE T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1o6lA 194 :VAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRER T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1o6lA 246 :VFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISD T0291 184 :AYTT 1o6lA 304 :GATM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMC T0291 227 :GERPYWEMSNQDVIKAVDE 1o6lA 346 :GRLPFYNQDHERLFELILM T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 365 :EEIRFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVSI 1o6lA 412 :INWQDVVQK Number of specific fragments extracted= 11 number of extra gaps= 1 total=805 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6lA/T0291-1o6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1o6lA/T0291-1o6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6lA read from 1o6lA/T0291-1o6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o6lA in template set Warning: unaligning (T0291)I27 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6lA)D153 Warning: unaligning (T0291)S28 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6lA)D153 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6lA)F310 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6lA)F310 T0291 22 :LDATN 1o6lA 147 :VTMND T0291 29 :IDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1o6lA 154 :YLKLLGKGTFGKVILVREKATGRYYAMKILRK T0291 67 :E 1o6lA 186 :E T0291 68 :KQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1o6lA 192 :DEVAHTVTESRVLQNTRHPFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRER T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1o6lA 246 :VFTEERARFYGAEIVSALEYLHSRDVVYRDIKLENLMLDKDGHIKITDFGLCKEGISDGA T0291 186 :TT 1o6lA 306 :TM T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1o6lA 311 :CGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHERLFELILMEEI T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNR 1o6lA 368 :RFPRTLSPEAKSLLAGLLKKDPKQR T0291 275 :PKFEQIVSI 1o6lA 412 :INWQDVVQK T0291 289 :RNPGSLKIITSAA 1o6lA 421 :KLLPPFKPQVTSE Number of specific fragments extracted= 10 number of extra gaps= 1 total=815 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdwA/T0291-2bdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bdwA expands to /projects/compbio/data/pdb/2bdw.pdb.gz 2bdwA:# T0291 read from 2bdwA/T0291-2bdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdwA read from 2bdwA/T0291-2bdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bdwA to template set # found chain 2bdwA in template set Warning: unaligning (T0291)T12 because first residue in template chain is (2bdwA)S5 T0291 13 :QAVH 2bdwA 6 :TKFS T0291 25 :TNISIDKVVGAGEFGEVCSGRL 2bdwA 11 :DNYDVKEELGKGAFSVVRRCVH T0291 50 :SKKEISVAIKTLKV 2bdwA 33 :KTTGLEFAAKIINT T0291 64 :GYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 2bdwA 48 :KLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVAREF T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 107 :YSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDP 2bdwA 147 :AKGAAVKLADFGLAIEVNDSE T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bdwA 169 :AWHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bdwA 209 :GYPPFWDEDQHRLYAQIKAG T0291 249 :LPPPM 2bdwA 230 :YDYPS T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 2bdwA 239 :TVTPEAKSLIDSMLTVNPKKRITADQALKVPW Number of specific fragments extracted= 10 number of extra gaps= 0 total=825 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdwA/T0291-2bdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bdwA/T0291-2bdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdwA read from 2bdwA/T0291-2bdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdwA in template set T0291 26 :NISIDKVVGAGEFGEVCSGRL 2bdwA 12 :NYDVKEELGKGAFSVVRRCVH T0291 50 :SKKEISVAIKTLK 2bdwA 33 :KTTGLEFAAKIIN T0291 63 :VGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bdwA 47 :KKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVARE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 106 :FYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDPEAA 2bdwA 147 :AKGAAVKLADFGLAIEVNDSEAWH T0291 189 :GGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2bdwA 172 :GFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLV T0291 227 :GERPYWEMSNQDVIKAVDEG 2bdwA 209 :GYPPFWDEDQHRLYAQIKAG T0291 247 :YRLPPP 2bdwA 230 :YDYPSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKF 2bdwA 238 :DTVTPEAKSLIDSMLTVNPKKRITA T0291 278 :EQIVSILDKLI 2bdwA 284 :QDTVDCLKKFN Number of specific fragments extracted= 10 number of extra gaps= 0 total=835 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdwA/T0291-2bdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2bdwA/T0291-2bdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdwA read from 2bdwA/T0291-2bdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdwA in template set Warning: unaligning (T0291)K20 because first residue in template chain is (2bdwA)S5 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 2bdwA 6 :TKFSDNYDVKEELGKGAFSVVRRCVHKTTGLEFAAKIIN T0291 62 :KVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 2bdwA 46 :TKKLSARDFQKLEREARICRKLQHPNIVRLHDSIQEESFHYLVFDLVTGGELFEDIVARE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 2bdwA 106 :FYSEADASHCIQQILESIAYCHSNGIVHRNLKPENLLL T0291 161 :NSNLVCKVSDFGLGRVLEDDPE 2bdwA 147 :AKGAAVKLADFGLAIEVNDSEA T0291 187 :TRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLP 2bdwA 170 :WHGFAGTPGYLSPEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYAQIKAGAYDYP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 2bdwA 236 :EWDTVTPEAKSLIDSMLTVNPKKRITADQALKVP Number of specific fragments extracted= 6 number of extra gaps= 0 total=841 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lck/T0291-3lck-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lck expands to /projects/compbio/data/pdb/3lck.pdb.gz 3lck:Warning: there is no chain 3lck will retry with 3lckA Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 155, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 157, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 159, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 163, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 250, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 252, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 254, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 256, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 258, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 260, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 262, because occupancy 0.230 <= existing 0.770 in 3lck Skipped atom 390, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 392, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 394, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 396, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 398, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 400, because occupancy 0.350 <= existing 0.650 in 3lck Skipped atom 419, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 421, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 423, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 425, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 427, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 429, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 431, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 433, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 435, because occupancy 0.360 <= existing 0.640 in 3lck Skipped atom 461, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 463, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 465, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 467, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 469, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 471, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 473, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 666, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 668, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 670, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 672, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 674, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 676, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 678, because occupancy 0.250 <= existing 0.750 in 3lck Skipped atom 739, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 741, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 743, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 745, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 747, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 749, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 751, because occupancy 0.180 <= existing 0.820 in 3lck Skipped atom 753, because occupancy 0.180 <= existing 0.820 in 3lck Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1618, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1620, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1622, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1624, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1626, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1628, because occupancy 0.160 <= existing 0.840 in 3lck Skipped atom 1659, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1661, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1663, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1665, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1667, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1669, because occupancy 0.260 <= existing 0.740 in 3lck Skipped atom 1762, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1764, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1766, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1768, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1770, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1772, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1774, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1776, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1778, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1780, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1782, because occupancy 0.420 <= existing 0.580 in 3lck Skipped atom 1875, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1877, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1879, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1881, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1883, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1885, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1887, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 1889, because occupancy 0.400 <= existing 0.600 in 3lck Skipped atom 2034, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2036, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2038, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2040, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2042, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2044, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2046, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2048, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2050, because occupancy 0.490 <= existing 0.510 in 3lck Skipped atom 2264, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2266, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2268, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2270, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2272, because occupancy 0.290 <= existing 0.710 in 3lck Skipped atom 2274, because occupancy 0.290 <= existing 0.710 in 3lck # T0291 read from 3lck/T0291-3lck-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lck read from 3lck/T0291-3lck-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lck to template set # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRL 3lck 234 :WEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGYTEK 3lck 265 :NGHTKVAVKSLKQGSMSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVT 3lck 283 :DAFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 3lck 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 6 number of extra gaps= 0 total=847 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lck/T0291-3lck-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 3lck/T0291-3lck-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lck read from 3lck/T0291-3lck-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 15 :VHEFAKELDATNISIDKVVGAGEFGEVCSGRL 3lck 233 :WWEDEWEVPRETLKLVERLGAGQFGEVWMGYY T0291 51 :KKEISVAIKTLKVGY 3lck 265 :NGHTKVAVKSLKQGS T0291 66 :TEK 3lck 281 :SPD T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVT 3lck 284 :AFLAEANLMKQLQHQRLVRLYAVVT T0291 98 :SKPVMIVTEYMENGSLDSFLRKH 3lck 309 :QEPIYIITEYMENGSLVDFLKTP T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 335 :KLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 7 number of extra gaps= 0 total=854 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lck/T0291-3lck-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 3lck/T0291-3lck-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lck read from 3lck/T0291-3lck-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lck in template set Warning: unaligning (T0291)P181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3lck)T395 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lck)T395 T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRLKLPS 3lck 235 :EDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHT T0291 52 :KEISV 3lck 269 :KVAVK T0291 60 :TLKVG 3lck 274 :SLKQG T0291 65 :YTE 3lck 280 :MSP T0291 71 :RDFLGEASIMGQFDHPNIIRLEGVVTK 3lck 283 :DAFLAEANLMKQLQHQRLVRLYAVVTQ T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 3lck 310 :EPIYIITEYMENGSLVDFLKTPS T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 3lck 334 :IKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 3lck 396 :AREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFT Number of specific fragments extracted= 8 number of extra gaps= 0 total=862 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c30A/T0291-2c30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c30A expands to /projects/compbio/data/pdb/2c30.pdb.gz 2c30A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 699, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 701, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 904, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 906, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 908, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1238, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1240, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1242, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1244, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1246, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1248, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1278, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1280, because occupancy 0.350 <= existing 0.650 in 2c30A Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1523, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1525, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1533, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1535, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1537, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1539, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1541, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1762, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1764, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1826, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 1955, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1957, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 1959, because occupancy 0.350 <= existing 0.650 in 2c30A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 2c30A Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 2c30A # T0291 read from 2c30A/T0291-2c30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c30A read from 2c30A/T0291-2c30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c30A to template set # found chain 2c30A in template set Warning: unaligning (T0291)E9 because first residue in template chain is (2c30A)V385 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)G246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 10 :DPTQAVHEFAKELDATN 2c30A 386 :THEQFKAALRMVVDQGD T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRL 2c30A 424 :ARE T0291 50 :SKKEISVAIKTLKVGYTEK 2c30A 427 :KHSGRQVAVKMMDLRKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2c30A 446 :RELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2c30A 497 :RLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVP T0291 186 :TT 2c30A 557 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVD T0291 227 :GERPYWEMSNQDVIKAVD 2c30A 597 :GEPPYFSDSPVQAMKRLR T0291 247 :YRLPP 2c30A 617 :PPPKL T0291 252 :PM 2c30A 624 :SH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGS 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDHPFLLQTGLPE Number of specific fragments extracted= 12 number of extra gaps= 3 total=874 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c30A/T0291-2c30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2c30A/T0291-2c30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c30A read from 2c30A/T0291-2c30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c30A in template set Warning: unaligning (T0291)E9 because first residue in template chain is (2c30A)V385 Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)G246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 10 :DPTQAVHEFAKELDATN 2c30A 386 :THEQFKAALRMVVDQGD T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRL 2c30A 424 :ARE T0291 50 :SKKEISVAIKTLK 2c30A 427 :KHSGRQVAVKMMD T0291 63 :VGYTE 2c30A 441 :RKQQR T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRK 2c30A 446 :RELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQ T0291 122 :AQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 2c30A 496 :VRLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKD T0291 184 :AYTT 2c30A 555 :VPKR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVD T0291 227 :GERPYWEMSNQDVIKAVD 2c30A 597 :GEPPYFSDSPVQAMKRLR T0291 247 :YRLPP 2c30A 617 :PPPKL T0291 252 :PM 2c30A 624 :SH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVS 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLD T0291 291 :PGSLKIITS 2c30A 655 :HPFLLQTGL Number of specific fragments extracted= 14 number of extra gaps= 3 total=888 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c30A/T0291-2c30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2c30A/T0291-2c30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c30A read from 2c30A/T0291-2c30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c30A in template set Warning: unaligning (T0291)C42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)L423 Warning: unaligning (T0291)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)L423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c30A)L561 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c30A)L561 Warning: unaligning (T0291)D244 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c30A)S616 Warning: unaligning (T0291)E245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c30A)S616 Warning: unaligning (T0291)D254 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2c30A)V627 Warning: unaligning (T0291)C255 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2c30A)V627 T0291 27 :ISIDKVVGAGEFGEV 2c30A 407 :LDSYVKIGEGSTGIV T0291 44 :GRLKLPSKKEISVAIKTLKVG 2c30A 424 :AREKHSGRQVAVKMMDLRKQQ T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKH 2c30A 445 :RRELLFNEVVIMRDYQHFNVVEMYKSYLVGEELWVLMEFLQGGALTDIVSQV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2c30A 497 :RLNEEQIATVCEAVLQALAYLHAQGVIHRDIKSDSILLTLDGRVKLSDFGFCAQISKDVP T0291 186 :TT 2c30A 557 :KR T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAV 2c30A 562 :VGTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEPPYFSDSPVQAMKRLR T0291 246 :GY 2c30A 617 :PP T0291 249 :LP 2c30A 619 :PK T0291 251 :PPM 2c30A 623 :NSH T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSI 2c30A 628 :SPVLRDFLERMLVRDPQERATAQELLDH T0291 298 :TSAAARPSNLL 2c30A 656 :PFLLQTGLPEC Number of specific fragments extracted= 11 number of extra gaps= 3 total=899 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jksA/T0291-1jksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jksA expands to /projects/compbio/data/pdb/1jks.pdb.gz 1jksA:Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 1jksA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 1jksA # T0291 read from 1jksA/T0291-1jksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jksA read from 1jksA/T0291-1jksA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jksA to template set # found chain 1jksA in template set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 8 :YEDPT 1jksA 5 :RQENV T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1jksA 10 :DDYYDTGEELGSGQFAVVKKCRE T0291 50 :SKKEISVAIKTLKVGYTEK 1jksA 33 :KSTGLQYAAKFIKKRRTKS T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1jksA 57 :SREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKES T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLS T0291 227 :GERPYWEMSNQDVIKAVDEG 1jksA 213 :GASPFLGDTKQETLANVSAV T0291 248 :RLPPPM 1jksA 233 :NYEFED T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1jksA 243 :NTSALAKDFIRRLLVKDPKKRMTIQDSLQH Number of specific fragments extracted= 10 number of extra gaps= 1 total=909 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jksA/T0291-1jksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jksA/T0291-1jksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jksA read from 1jksA/T0291-1jksA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jksA in template set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 7 :TYEDP 1jksA 5 :RQENV T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1jksA 10 :DDYYDTGEELGSGQFAVVKKCRE T0291 50 :SKKEISVAIKTLK 1jksA 33 :KSTGLQYAAKFIK T0291 63 :VGYTEK 1jksA 54 :RGVSRE T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1jksA 60 :DIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKES T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 111 :LTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLS T0291 227 :GERPYWEMSNQDVIKAVDEG 1jksA 213 :GASPFLGDTKQETLANVSAV T0291 247 :YRLP 1jksA 234 :YEFE T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQ Number of specific fragments extracted= 11 number of extra gaps= 1 total=920 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jksA/T0291-1jksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jksA/T0291-1jksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jksA read from 1jksA/T0291-1jksA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jksA in template set Warning: unaligning (T0291)N161 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jksA)V152 T0291 21 :ELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEK 1jksA 7 :ENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRR T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1jksA 57 :SREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKE T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1jksA 110 :SLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIML T0291 162 :SNLVCKVSDFGLGRVLEDDP 1jksA 153 :PKPRIKIIDFGLAHKIDFGN T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLP 1jksA 173 :EFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFE T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1jksA 242 :SNTSALAKDFIRRLLVKDPKKRMTIQDSLQH Number of specific fragments extracted= 6 number of extra gaps= 1 total=926 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu3A/T0291-1uu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uu3A expands to /projects/compbio/data/pdb/1uu3.pdb.gz 1uu3A:Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 1uu3A Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1uu3A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1uu3A # T0291 read from 1uu3A/T0291-1uu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu3A read from 1uu3A/T0291-1uu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uu3A to template set # found chain 1uu3A in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLKVGYT 1uu3A 103 :ATSREYAIKILEKRHI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1uu3A 121 :ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1uu3A 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVSILDKLIRNPGSLKIIT 1uu3A 333 :YGPLKAHPFFESVTWENLHQQT Number of specific fragments extracted= 8 number of extra gaps= 1 total=934 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu3A/T0291-1uu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1uu3A/T0291-1uu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu3A read from 1uu3A/T0291-1uu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uu3A in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLK 1uu3A 103 :ATSREYAIKILE T0291 68 :KQRRD 1uu3A 116 :RHIIK T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1uu3A 127 :VTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1uu3A 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVS 1uu3A 333 :YGPLKA Number of specific fragments extracted= 9 number of extra gaps= 1 total=943 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uu3A/T0291-1uu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1uu3A/T0291-1uu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uu3A read from 1uu3A/T0291-1uu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uu3A in template set Warning: unaligning (T0291)F18 because first residue in template chain is (1uu3A)Q73 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uu3A)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uu3A)F242 Warning: unaligning (T0291)K276 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uu3A)G332 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1uu3A 74 :PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1uu3A 119 :IKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1uu3A 176 :SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKV T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1uu3A 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1uu3A 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 277 :FEQIVSIL 1uu3A 333 :YGPLKAHP T0291 290 :NPGSLKIITSAAA 1uu3A 341 :FFESVTWENLHQQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=950 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/T0291-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1csn expands to /projects/compbio/data/pdb/1csn.pdb.gz 1csn:Warning: there is no chain 1csn will retry with 1csnA # T0291 read from 1csn/T0291-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0291-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1csn to template set # found chain 1csn in template set T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1csn 9 :GVHYKVGRRIGEGSFGVIFEGTNL T0291 51 :KKEISVAIKTLKV 1csn 33 :LNNQQVAIKFEPR T0291 66 :TEK 1csn 46 :RSD T0291 73 :FLGEASIMGQF 1csn 52 :LRDEYRTYKLL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 1csn 64 :GCTGIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILIN 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIG T0291 162 :SNLVCKVSDFGLGRVLEDDPEA 1csn 146 :NANMIYVVDFGMVKFYRDPVTK T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1csn 172 :YREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLR T0291 227 :GERPYWEMS 1csn 214 :GSLPWQGLK T0291 236 :NQDVIKAVDEG 1csn 230 :YERIGEKKQST T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKI 1csn 248 :GFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTED T0291 302 :ARPS 1csn 291 :ENFD Number of specific fragments extracted= 12 number of extra gaps= 0 total=962 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/T0291-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1csn/T0291-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0291-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1csn in template set T0291 25 :TNISIDKVVGAGEFGEVCSGRLK 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNL T0291 49 :PS 1csn 33 :LN T0291 53 :EISVAIKTLK 1csn 35 :NQQVAIKFEP T0291 63 :VGYTE 1csn 47 :SDAPQ T0291 70 :RRDFLGEASIMGQFD 1csn 52 :LRDEYRTYKLLAGCT T0291 87 :NIIRLEGVVTKSKPVMIVTEYMEN 1csn 67 :GIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLI T0291 161 :NSNLVCKVSDFGLGRVLEDDPEAAYTTRGGK 1csn 145 :KNANMIYVVDFGMVKFYRDPVTKQHIPYREK T0291 192 :IPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1csn 180 :GTARYMSINTHLGREQSRRDDLEALGHVFMYFLR T0291 227 :GERPYWEMS 1csn 214 :GSLPWQGLK T0291 236 :NQDVIKAVDEG 1csn 230 :YERIGEKKQST T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSL 1csn 247 :AGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTT T0291 300 :AAARP 1csn 289 :EDENF Number of specific fragments extracted= 13 number of extra gaps= 0 total=975 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1csn/T0291-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1csn/T0291-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0291-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1csn in template set T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKT 1csn 10 :VHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPR T0291 62 :KVGYTE 1csn 46 :RSDAPQ T0291 73 :FLGEASIMGQF 1csn 52 :LRDEYRTYKLL T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMEN 1csn 64 :GCTGIPNVYYFGQEGLHNVLVIDLLGP T0291 112 :SLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILI 1csn 91 :SLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLI T0291 161 :NSNLVCKVSDFGLGRVLEDDPEA 1csn 145 :KNANMIYVVDFGMVKFYRDPVTK T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYW 1csn 172 :YREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQG T0291 233 :EMSNQDVIKA 1csn 223 :AATNKQKYER T0291 243 :VDEG 1csn 245 :LCAG T0291 255 :CPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAAR 1csn 249 :FPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNL Number of specific fragments extracted= 10 number of extra gaps= 0 total=985 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xh9A/T0291-1xh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xh9A expands to /projects/compbio/data/pdb/1xh9.pdb.gz 1xh9A:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1xh9A/T0291-1xh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xh9A read from 1xh9A/T0291-1xh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xh9A to template set # found chain 1xh9A in template set Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1xh9A 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1xh9A 63 :METGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xh9A 82 :LKEIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKG T0291 186 :TT 1xh9A 194 :RT T0291 191 :KIPIRWTSPEAIAY 1xh9A 199 :CGTPEYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1xh9A 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1xh9A 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1xh9A 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF T0291 276 :KFEQIVSI 1xh9A 287 :GVNDIKNH T0291 284 :LDKLIRNPGSLKII 1xh9A 302 :WIAIYQRKVEAPFI Number of specific fragments extracted= 11 number of extra gaps= 1 total=996 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xh9A/T0291-1xh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xh9A/T0291-1xh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xh9A read from 1xh9A/T0291-1xh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xh9A in template set Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1xh9A 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1xh9A 63 :METGNHYAMKILD T0291 63 :VG 1xh9A 82 :LK T0291 66 :T 1xh9A 84 :E T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1xh9A 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1xh9A 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKGR T0291 186 :T 1xh9A 195 :T T0291 190 :GKIP 1xh9A 199 :CGTP T0291 195 :RWTSPEAIAY 1xh9A 203 :EYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMS 1xh9A 215 :YNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDE 1xh9A 234 :GYPPFFADQPIQIYEKIVS T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNR 1xh9A 253 :GKVRFPSHFSSDLKDLLRNLLQVDLTKR Number of specific fragments extracted= 12 number of extra gaps= 1 total=1008 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xh9A/T0291-1xh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1xh9A/T0291-1xh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xh9A read from 1xh9A/T0291-1xh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xh9A in template set Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xh9A)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xh9A)L198 Warning: unaligning (T0291)R205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xh9A)G214 Warning: unaligning (T0291)K206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xh9A)G214 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1xh9A 36 :NTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1xh9A 80 :VKLKEIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1xh9A 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGLAKRVKG T0291 186 :TT 1xh9A 194 :RT T0291 191 :KIPIRWTSPEAIAY 1xh9A 199 :CGTPEYLAPEIILS T0291 207 :FTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1xh9A 215 :YNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1xh9A 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF Number of specific fragments extracted= 7 number of extra gaps= 1 total=1015 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1wA/T0291-1h1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h1wA expands to /projects/compbio/data/pdb/1h1w.pdb.gz 1h1wA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1h1wA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2282, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2284, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2286, because occupancy 0.500 <= existing 0.500 in 1h1wA Skipped atom 2288, because occupancy 0.500 <= existing 0.500 in 1h1wA # T0291 read from 1h1wA/T0291-1h1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1wA read from 1h1wA/T0291-1h1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h1wA to template set # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1h1wA 73 :QPRKKRPEDFKFGKILGEGSFSTVVLARE T0291 50 :SKKEISVAIKTLKVGYT 1h1wA 102 :LATSREYAIKILEKRHI T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1h1wA 121 :ENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1h1wA 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVSILDK 1h1wA 332 :GYGPLKAHPFF T0291 299 :SAAARPSNLLLD 1h1wA 343 :ESVTWENLHQQT Number of specific fragments extracted= 10 number of extra gaps= 0 total=1025 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1wA/T0291-1h1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1h1wA/T0291-1h1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1wA read from 1h1wA/T0291-1h1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLK 1h1wA 74 :PRKKRPEDFKFGKILGEGSFSTVVLAREL T0291 51 :KKEISVAIKTLK 1h1wA 103 :ATSREYAIKILE T0291 63 :VGYTEKQR 1h1wA 120 :KENKVPYV T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1h1wA 128 :TRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGS T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 177 :FDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVA T0291 227 :GERPYWEMSNQDVIKAVDEG 1h1wA 278 :GLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVS 1h1wA 332 :GYGPLKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1035 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1wA/T0291-1h1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1h1wA/T0291-1h1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1wA read from 1h1wA/T0291-1h1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1wA in template set Warning: unaligning (T0291)D179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)A237 Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)A237 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h1wA)F242 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h1wA)F242 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1h1wA 74 :PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHI T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1h1wA 119 :IKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLE 1h1wA 176 :SFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLS T0291 186 :TT 1h1wA 238 :RA T0291 191 :KIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDE 1h1wA 243 :VGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKL T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1h1wA 298 :EYDFPEKFFPKARDLVEKLLVLDATKRL T0291 276 :KFEQIVSI 1h1wA 332 :GYGPLKAH T0291 289 :RNPGSLKIITSAAARPS 1h1wA 340 :PFFESVTWENLHQQTPP Number of specific fragments extracted= 8 number of extra gaps= 0 total=1043 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jqhA/T0291-1jqhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jqhA expands to /projects/compbio/data/pdb/1jqh.pdb.gz 1jqhA:# T0291 read from 1jqhA/T0291-1jqhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jqhA read from 1jqhA/T0291-1jqhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jqhA to template set # found chain 1jqhA in template set Warning: unaligning (T0291)T12 because first residue in template chain is (1jqhA)A984 Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jqhA 985 :DVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1022 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1jqhA 1075 :TLVIMELMTRGDLKSYLRSLRP T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1jqhA 1166 :YRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEP Number of specific fragments extracted= 5 number of extra gaps= 2 total=1048 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jqhA/T0291-1jqhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jqhA/T0291-1jqhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jqhA read from 1jqhA/T0291-1jqhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jqhA in template set Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 16 :HEFAKELDATNISIDKVVGAGEFGEVCSGRLK 1jqhA 988 :VPDEWEVAREKITMSRELGQGSFGMVYEGVAK T0291 48 :LPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1022 :VKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLRKH 1jqhA 1075 :TLVIMELMTRGDLKSYLRSL T0291 121 :DA 1jqhA 1104 :LA T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 184 :AYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1jqhA 1166 :YRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSI Number of specific fragments extracted= 6 number of extra gaps= 2 total=1054 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jqhA/T0291-1jqhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jqhA/T0291-1jqhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jqhA read from 1jqhA/T0291-1jqhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jqhA in template set Warning: unaligning (T0291)K99 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1074 Warning: unaligning (T0291)P100 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1074 Warning: unaligning (T0291)H120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)V1103 Warning: unaligning (T0291)Q123 because of BadResidue code BAD_PEPTIDE in next template residue (1jqhA)P1107 Warning: unaligning (T0291)F124 because of BadResidue code BAD_PEPTIDE at template residue (1jqhA)P1107 Warning: unaligning (T0291)G174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jqhA)Y1165 Warning: unaligning (T0291)E182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jqhA)Y1165 T0291 13 :QAVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKL 1jqhA 985 :DVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKG T0291 49 :PSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1jqhA 1023 :KDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQG T0291 101 :VMIVTEYMENGSLDSFLR 1jqhA 1075 :TLVIMELMTRGDLKSYLR T0291 121 :DA 1jqhA 1104 :LA T0291 125 :TVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGL 1jqhA 1108 :SLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGM T0291 183 :A 1jqhA 1166 :Y T0291 185 :YTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1jqhA 1167 :RKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEME Number of specific fragments extracted= 7 number of extra gaps= 2 total=1061 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1apmE/T0291-1apmE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1apmE expands to /projects/compbio/data/pdb/1apm.pdb.gz 1apmE:Skipped atom 336, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 338, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 340, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 342, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 344, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 346, because occupancy 0.460 <= existing 0.540 in 1apmE Skipped atom 348, because occupancy 0.460 <= existing 0.540 in 1apmE # T0291 read from 1apmE/T0291-1apmE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1apmE read from 1apmE/T0291-1apmE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1apmE to template set # found chain 1apmE in template set T0291 17 :EFAKELDATNISIDKVVGAGEFGEVCSGRL 1apmE 33 :PSQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1apmE 63 :KESGNHYAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1apmE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1apmE 194 :RTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1apmE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNRP 1apmE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKRF T0291 276 :KFEQIVSI 1apmE 287 :GVNDIKNH T0291 284 :LDKLIRNPGSLKII 1apmE 302 :WIAIYQRKVEAPFI T0291 298 :T 1apmE 337 :V Number of specific fragments extracted= 10 number of extra gaps= 0 total=1071 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1apmE/T0291-1apmE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1apmE/T0291-1apmE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1apmE read from 1apmE/T0291-1apmE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1apmE in template set T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1apmE 34 :SQNTAQLDQFDRIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1apmE 63 :KESGNHYAMKILD T0291 63 :VG 1apmE 82 :LK T0291 66 :T 1apmE 84 :Q T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1apmE 85 :IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDD 1apmE 138 :FAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGR T0291 186 :TTRGGKIP 1apmE 195 :TWTLCGTP T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1apmE 203 :EYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1apmE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDCWQKDRNNR 1apmE 254 :KVRFPSHFSSDLKDLLRNLLQVDLTKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=1081 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1apmE/T0291-1apmE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1apmE/T0291-1apmE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1apmE read from 1apmE/T0291-1apmE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1apmE in template set T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1apmE 35 :QNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1apmE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLED 1apmE 137 :RFAEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKG T0291 186 :TTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1apmE 194 :RTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNR 1apmE 256 :RFPSHFSSDLKDLLRNLLQVDLTKR T0291 275 :PKFEQIVS 1apmE 300 :TDWIAIYQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=1087 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1phk/T0291-1phk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1phk expands to /projects/compbio/data/pdb/1phk.pdb.gz 1phk:Warning: there is no chain 1phk will retry with 1phkA # T0291 read from 1phk/T0291-1phk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1phk read from 1phk/T0291-1phk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1phk to template set # found chain 1phk in template set Warning: unaligning (T0291)D23 because first residue in template chain is (1phk)F15 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1phk 16 :YENYEPKEILGRGVSSVVRRCIH T0291 50 :SKKEISVAIKTLKV 1phk 39 :KPTCKEYAVKIIDV T0291 64 :GYTEK 1phk 57 :SFSAE T0291 69 :QRRDFLGEASIMGQF 1phk 66 :LREATLKEVDILRKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1phk 82 :GHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 121 :LSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIA 1phk 179 :KLREVCGTPSYLAPEIIE T0291 204 :YRKFTSASDVWSYGIVLWEVMS 1phk 203 :HPGYGKEVDMWSTGVIMYTLLA T0291 227 :GERPYWEMSNQDVIKAVDEG 1phk 225 :GSPPFWHRKQMLMLRMIMSG T0291 248 :RLPPPM 1phk 245 :NYQFGS T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDK 1phk 255 :DYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1098 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1phk/T0291-1phk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1phk/T0291-1phk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1phk read from 1phk/T0291-1phk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1phk in template set T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1phk 16 :YENYEPKEILGRGVSSVVRRCIH T0291 50 :SKKEISVAIKTLK 1phk 39 :KPTCKEYAVKIID T0291 63 :VGYTEKQRRDFLG 1phk 56 :GSFSAEEVQELRE T0291 76 :EASIMGQFD 1phk 73 :EVDILRKVS T0291 85 :HPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDA 1phk 83 :HPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 121 :LSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1phk 179 :KLREVCGTPSYLAPEIIEC T0291 205 :RKFTSASDVWSYGIVLWEVMS 1phk 204 :PGYGKEVDMWSTGVIMYTLLA T0291 227 :GERPYWEMSNQDVIKAVDEG 1phk 225 :GSPPFWHRKQMLMLRMIMSG T0291 247 :YRLPPP 1phk 246 :YQFGSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1phk 254 :DDYSDTVKDLVSRFLVVQPQKRYTAEEALA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1109 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1phk/T0291-1phk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1phk/T0291-1phk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1phk read from 1phk/T0291-1phk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1phk in template set Warning: unaligning (T0291)D23 because first residue in template chain is (1phk)F15 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1phk 16 :YENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIID T0291 60 :TLKVGYTEKQRRDFLG 1phk 53 :TGGGSFSAEEVQELRE T0291 76 :EASIMGQF 1phk 73 :EVDILRKV T0291 84 :DHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1phk 82 :GHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKV T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1phk 120 :TLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGE T0291 186 :TTRGGKIPIRWTSPEAIAY 1phk 179 :KLREVCGTPSYLAPEIIEC T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPP 1phk 204 :PGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1phk 254 :DDYSDTVKDLVSRFLVVQPQKRYTAEEALAH Number of specific fragments extracted= 8 number of extra gaps= 0 total=1117 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6yA/T0291-1o6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o6yA expands to /projects/compbio/data/pdb/1o6y.pdb.gz 1o6yA:# T0291 read from 1o6yA/T0291-1o6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6yA read from 1o6yA/T0291-1o6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o6yA to template set # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)A242 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDL T0291 51 :KKEISVAIKTLKVG 1o6yA 32 :RLHRDVAVKVLRAD T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1o6yA 48 :RDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAE T0291 99 :K 1o6yA 85 :G T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1o6yA 88 :PYIVMEYVDGVTLRDIVHTEGP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLT T0291 227 :GERPYWEMSNQDVI 1o6yA 212 :GEPPFTGDSPVSVA T0291 243 :VDEG 1o6yA 228 :HVRE T0291 248 :RLPPPM 1o6yA 232 :DPIPPS T0291 254 :DCPAALYQLMLDCWQKDRNNRP 1o6yA 242 :GLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 12 number of extra gaps= 3 total=1129 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6yA/T0291-1o6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1o6yA/T0291-1o6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6yA read from 1o6yA/T0291-1o6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)A242 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDL T0291 51 :KKEISVAIKTLKVGY 1o6yA 32 :RLHRDVAVKVLRADL T0291 66 :TEKQRRDFLGEASIMGQFDHPNIIRLE 1o6yA 49 :DPSFYLRFRREAQNAAALNHPAIVAVY T0291 93 :GVVTKSKP 1o6yA 78 :GEAETPAG T0291 101 :VMIVTEYMENGSLDSFLRKHDA 1o6yA 88 :PYIVMEYVDGVTLRDIVHTEGP T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 110 :MTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLT T0291 227 :GERPYWEMSNQDVI 1o6yA 212 :GEPPFTGDSPVSVA T0291 243 :VDEG 1o6yA 228 :HVRE T0291 248 :RLPPP 1o6yA 232 :DPIPP T0291 253 :MDCPAALYQLMLDCWQKDRNNRP 1o6yA 241 :EGLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 12 number of extra gaps= 3 total=1141 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6yA/T0291-1o6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1o6yA/T0291-1o6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o6yA read from 1o6yA/T0291-1o6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o6yA in template set Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)A180 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o6yA)A180 Warning: unaligning (T0291)I240 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1o6yA)Q227 Warning: unaligning (T0291)K241 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1o6yA)Q227 Warning: unaligning (T0291)R289 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o6yA)G279 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIK 1o6yA 8 :SDRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLR T0291 61 :LKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKS 1o6yA 44 :ADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAE T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1o6yA 86 :PLPYIVMEYVDGVTLRDIVHTEG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1o6yA 109 :PMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARA T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDV 1o6yA 181 :QYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVA T0291 242 :AVDEGYRLP 1o6yA 228 :HVREDPIPP T0291 251 :PPMDCPAALYQLMLDCWQKDRNNRP 1o6yA 239 :RHEGLSADLDAVVLKALAKNPENRY T0291 276 :KFEQIVSILDKLI 1o6yA 265 :TAAEMRADLVRVH Number of specific fragments extracted= 8 number of extra gaps= 3 total=1149 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a19B/T0291-2a19B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a19B expands to /projects/compbio/data/pdb/2a19.pdb.gz 2a19B:# T0291 read from 2a19B/T0291-2a19B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a19B read from 2a19B/T0291-2a19B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a19B to template set # found chain 2a19B in template set Warning: unaligning (T0291)Y65 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)T66 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 27 :ISIDKVVGAGEFGEVCSGRL 2a19B 267 :FKEIELIGSGGFGQVFKAKH T0291 50 :SKKEISVAIKTLKVG 2a19B 287 :RIDGKTYVIKRVKYN T0291 67 :E 2a19B 304 :K T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTK 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWDG T0291 101 :VMIVTEYMENGSLDSFLRKH 2a19B 362 :LFIQMEFCDKGTLEQWIEKR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDG T0291 186 :T 2a19B 444 :K T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSY 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHV T0291 233 :EMSNQDV 2a19B 485 :CDTAFET T0291 240 :IKAVDEG 2a19B 495 :FTDLRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 11 number of extra gaps= 2 total=1160 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a19B/T0291-2a19B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2a19B/T0291-2a19B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a19B read from 2a19B/T0291-2a19B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a19B in template set Warning: unaligning (T0291)Y65 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)E67 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)A183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 27 :ISIDKVVGAGEFGEVCSGRL 2a19B 267 :FKEIELIGSGGFGQVFKAKH T0291 50 :SKKEISVAIKTLKVG 2a19B 287 :RIDGKTYVIKRVKYN T0291 68 :KQ 2a19B 304 :KA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTK 2a19B 306 :EREVKALAKLDHVNIVHYNGCWDG T0291 99 :K 2a19B 357 :S T0291 101 :VMIVTEYMENGSLDSFLRKH 2a19B 362 :LFIQMEFCDKGTLEQWIEKR T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDGK T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGER 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVCDT T0291 235 :SNQDVIKAVDEG 2a19B 490 :ETSKFFTDLRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 10 number of extra gaps= 2 total=1170 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a19B/T0291-2a19B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 2a19B/T0291-2a19B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a19B read from 2a19B/T0291-2a19B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a19B in template set Warning: unaligning (T0291)K62 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E303 Warning: unaligning (T0291)V63 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E303 Warning: unaligning (T0291)D121 because of BadResidue code BAD_PEPTIDE in next template residue (2a19B)E384 Warning: unaligning (T0291)A122 because of BadResidue code BAD_PEPTIDE at template residue (2a19B)E384 Warning: unaligning (T0291)T187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a19B)R447 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2a19B)R447 Warning: unaligning (T0291)R289 because last residue in template chain is (2a19B)K541 T0291 26 :NISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTL 2a19B 266 :DFKEIELIGSGGFGQVFKAKHRIDGKTYVIKRVKYN T0291 64 :G 2a19B 304 :K T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKS 2a19B 305 :AEREVKALAKLDHVNIVHYNGCWDGF T0291 99 :KPVMIVTEYMENGSLDSFLRK 2a19B 360 :KCLFIQMEFCDKGTLEQWIEK T0291 120 :H 2a19B 382 :R T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 2a19B 385 :KLDKVLALELFEQITKGVDYIHSKKLINRDLKPSNIFLVDTKQVKIGDFGLVTSLKNDG T0291 186 :T 2a19B 444 :K T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYG 2a19B 448 :SKGTLRYMSPEQISSQDYGKEVDLYALGLILAELLHVC T0291 234 :MSNQDVIKA 2a19B 486 :DTAFETSKF T0291 243 :VDEG 2a19B 498 :LRDG T0291 250 :PPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLI 2a19B 502 :IISDIFDKKEKTLLQKLLSKKPEDRPNTSEILRTLTVWK Number of specific fragments extracted= 11 number of extra gaps= 2 total=1181 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3mC/T0291-1f3mC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f3mC expands to /projects/compbio/data/pdb/1f3m.pdb.gz 1f3mC:# T0291 read from 1f3mC/T0291-1f3mC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3mC read from 1f3mC/T0291-1f3mC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f3mC to template set # found chain 1f3mC in template set Warning: unaligning (T0291)D10 because first residue in template chain is (1f3mC)S249 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 11 :PTQAVHEFAKELDATN 1f3mC 250 :DEEILEKLRSIVSVGD T0291 27 :ISIDKVVGAGEFGEVCSGRL 1f3mC 270 :YTRFEKIGQGASGTVYTAMD T0291 50 :SKKEISVAIKTLKVGYTEK 1f3mC 290 :VATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1f3mC 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=1189 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3mC/T0291-1f3mC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1f3mC/T0291-1f3mC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3mC read from 1f3mC/T0291-1f3mC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f3mC in template set Warning: unaligning (T0291)D10 because first residue in template chain is (1f3mC)S249 Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 11 :PTQAVHEFAKELDATN 1f3mC 250 :DEEILEKLRSIVSVGD T0291 27 :ISIDKVVGAGEFGEVCSGRL 1f3mC 270 :YTRFEKIGQGASGTVYTAMD T0291 50 :SKKEISVAIKTLKVGYTEK 1f3mC 290 :VATGQEVAIRQMNLQQQPK T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 309 :KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 189 :GGKIP 1f3mC 424 :MVGTP T0291 195 :RWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1f3mC 429 :YWMAPEVVTRKAYGPKVDIWSLGIMAIEMIE T0291 227 :GERPYWEMSNQDVIKAVDEG 1f3mC 460 :GEPPYLNENPLRALYLIATN T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIV 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELL T0291 290 :NPGSLKIITSA 1f3mC 517 :QHQFLKIAKPL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1199 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3mC/T0291-1f3mC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1f3mC/T0291-1f3mC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3mC read from 1f3mC/T0291-1f3mC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f3mC in template set Warning: unaligning (T0291)E178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f3mC)T423 Warning: unaligning (T0291)G189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f3mC)T423 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISV 1f3mC 268 :KKYTRFEKIGQGASGTVYTAMDVATGQEVAIR T0291 60 :TLKVGYTE 1f3mC 300 :QMNLQQQP T0291 69 :QRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHD 1f3mC 308 :KKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETC T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVL 1f3mC 361 :MDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQI T0291 190 :GKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEG 1f3mC 424 :MVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNG T0291 247 :YRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVS 1f3mC 482 :PELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQ T0291 297 :ITSAAARPSNLL 1f3mC 518 :HQFLKIAKPLSS Number of specific fragments extracted= 7 number of extra gaps= 0 total=1206 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1py5A/T0291-1py5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1py5A expands to /projects/compbio/data/pdb/1py5.pdb.gz 1py5A:# T0291 read from 1py5A/T0291-1py5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1py5A read from 1py5A/T0291-1py5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1py5A to template set # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKV 1py5A 225 :RGEEVAVKIFSS T0291 68 :KQRRDFLGEASIMGQF 1py5A 237 :REERSWFREAEIYQTV T0291 84 :DHPNIIRLEGVVTK 1py5A 255 :RHENILGFIAADNK T0291 98 :SK 1py5A 271 :GT T0291 101 :VMIVTEYMENGSLDSFLRKH 1py5A 276 :LWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1py5A 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1py5A 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :AYTTRGGKIPIRWTSPEAIA 1py5A 366 :DIAPNHRVGTKRYMAPEVLD T0291 205 :RKFTSA 1py5A 386 :DSINMK T0291 211 :SDVWSYGIVLWEVMSY 1py5A 399 :ADIYAMGLVFWEIARR T0291 228 :ERPYW 1py5A 425 :QLPYY T0291 233 :EMSNQDVIKAVDEG 1py5A 435 :DPSVEEMRKVVCEQ T0291 247 :YRLPPPM 1py5A 450 :LRPNIPN T0291 255 :C 1py5A 461 :C T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1222 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1py5A/T0291-1py5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1py5A/T0291-1py5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1py5A read from 1py5A/T0291-1py5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRL 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKVGY 1py5A 225 :RGEEVAVKIFSSRE T0291 70 :RRDFLGEASIMGQ 1py5A 239 :ERSWFREAEIYQT T0291 83 :FDHPNIIRLEGVVTK 1py5A 254 :LRHENILGFIAADNK T0291 98 :SKPVMIVTEYMENGSLDSFLRK 1py5A 273 :WTQLWLVSDYHEHGSLFDYLNR T0291 122 :AQFTVIQLVGMLRGIASGMKYLS 1py5A 295 :YTVTVEGMIKLALSTASGLAHLH T0291 146 :MG 1py5A 323 :TQ T0291 148 :YVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAYTTR 1py5A 329 :IAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAP T0291 189 :GGKIPIRWTSPEAI 1py5A 371 :HRVGTKRYMAPEVL T0291 204 :YRKFTSA 1py5A 385 :DDSINMK T0291 211 :SDVWSYGIVLWEVMSYG 1py5A 399 :ADIYAMGLVFWEIARRC T0291 228 :ERPYWE 1py5A 425 :QLPYYD T0291 234 :MSNQDVIKAVDEG 1py5A 436 :PSVEEMRKVVCEQ T0291 247 :YRLPPPMD 1py5A 450 :LRPNIPNR T0291 255 :CP 1py5A 461 :CE T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1238 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1py5A/T0291-1py5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1py5A/T0291-1py5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1py5A read from 1py5A/T0291-1py5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1py5A in template set Warning: unaligning (T0291)L22 because first residue in template chain is (1py5A)T200 T0291 23 :DATNISIDKVVGAGEFGEVCSGRLK 1py5A 201 :IARTIVLQESIGKGRFGEVWRGKWR T0291 50 :SKKEISVAI 1py5A 226 :GEEVAVKIF T0291 66 :TEKQRRDFLGEASIMGQF 1py5A 235 :SSREERSWFREAEIYQTV T0291 84 :DHPNIIRLEGVVTKS 1py5A 255 :RHENILGFIAADNKD T0291 99 :KPVMIVTEYMENGSLDSFLRKH 1py5A 274 :TQLWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1py5A 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1py5A 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :AYTTRGGKIPIRWTSPEAIAY 1py5A 366 :DIAPNHRVGTKRYMAPEVLDD T0291 206 :KFTSA 1py5A 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYGER 1py5A 399 :ADIYAMGLVFWEIARRCSI T0291 230 :PYWEMSNQDVIKA 1py5A 432 :VPSDPSVEEMRKV T0291 243 :VDEGYRLPPPMD 1py5A 446 :CEQKLRPNIPNR T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIR 1py5A 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=1251 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjyA/T0291-1vjyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjyA expands to /projects/compbio/data/pdb/1vjy.pdb.gz 1vjyA:# T0291 read from 1vjyA/T0291-1vjyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjyA read from 1vjyA/T0291-1vjyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjyA to template set # found chain 1vjyA in template set Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjyA)R372 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTL 1vjyA 225 :RGEEVAVKIF T0291 66 :TEKQRRDFLGEASIMG 1vjyA 235 :SSREERSWFREAEIYQ T0291 82 :QFDHPNIIRLEGVVT 1vjyA 253 :MLRHENILGFIAADN T0291 97 :KSKP 1vjyA 270 :NGTW T0291 101 :VMIVTEYMENGSLDSFLRKH 1vjyA 276 :LWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1vjyA 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1vjyA 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :A 1vjyA 366 :D T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSY 1vjyA 399 :ADIYAMGLVFWEIARR T0291 228 :ERPYW 1vjyA 425 :QLPYY T0291 233 :EMSNQDVIKAVDEG 1vjyA 435 :DPSVEEMRKVVCEQ T0291 247 :YRLPPPM 1vjyA 450 :LRPNIPN T0291 254 :DC 1vjyA 460 :SC T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1vjyA 464 :LRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEG Number of specific fragments extracted= 17 number of extra gaps= 0 total=1268 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjyA/T0291-1vjyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1vjyA/T0291-1vjyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjyA read from 1vjyA/T0291-1vjyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjyA in template set Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRL 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKW T0291 52 :KEISVAIKTLKVG 1vjyA 225 :RGEEVAVKIFSSR T0291 69 :QRRDFLGEASIM 1vjyA 238 :EERSWFREAEIY T0291 81 :GQFDHPNIIRLEGVVTKSKP 1vjyA 252 :VMLRHENILGFIAADNKDNG T0291 101 :VMIVTEYMENGSLDSFLRK 1vjyA 276 :LWLVSDYHEHGSLFDYLNR T0291 122 :AQFTVIQLVGMLRGIASGMKYLS 1vjyA 295 :YTVTVEGMIKLALSTASGLAHLH T0291 147 :G 1vjyA 324 :Q T0291 148 :YVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEAAY 1vjyA 329 :IAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTID T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYG 1vjyA 399 :ADIYAMGLVFWEIARRC T0291 228 :ERPYWE 1vjyA 425 :QLPYYD T0291 234 :MSNQDVIKAVDEG 1vjyA 436 :PSVEEMRKVVCEQ T0291 247 :YRLPPPM 1vjyA 450 :LRPNIPN T0291 254 :DCP 1vjyA 460 :SCE T0291 257 :AALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1vjyA 465 :RVMAKIMRECWYANGAARLTALRIKKTLSQLSQQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1284 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjyA/T0291-1vjyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1vjyA/T0291-1vjyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjyA read from 1vjyA/T0291-1vjyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjyA in template set Warning: unaligning (T0291)Y185 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjyA)R372 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjyA)R372 T0291 24 :ATNISIDKVVGAGEFGEVCSGRLK 1vjyA 202 :ARTIVLQESIGKGRFGEVWRGKWR T0291 50 :SKKEISVAI 1vjyA 226 :GEEVAVKIF T0291 66 :TEKQRRDFLGEASIMG 1vjyA 235 :SSREERSWFREAEIYQ T0291 82 :QFDHPNIIRLEGVVTKS 1vjyA 253 :MLRHENILGFIAADNKD T0291 99 :KPVMIVTEYMENGSLDSFLRKH 1vjyA 274 :TQLWLVSDYHEHGSLFDYLNRY T0291 123 :QFTVIQLVGMLRGIASGMKYLSD 1vjyA 296 :TVTVEGMIKLALSTASGLAHLHM T0291 146 :MGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPEA 1vjyA 327 :PAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDT T0291 184 :A 1vjyA 366 :D T0291 191 :KIPIRWTSPEAIAY 1vjyA 373 :VGTKRYMAPEVLDD T0291 206 :KFTSA 1vjyA 387 :SINMK T0291 211 :SDVWSYGIVLWEVMSYGER 1vjyA 399 :ADIYAMGLVFWEIARRCSI T0291 230 :PYWEMSNQDVIKA 1vjyA 432 :VPSDPSVEEMRKV T0291 243 :VDEGYRLPPPMD 1vjyA 446 :CEQKLRPNIPNR T0291 256 :PAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRN 1vjyA 464 :LRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1298 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hcl/T0291-1hcl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hcl expands to /projects/compbio/data/pdb/1hcl.pdb.gz 1hcl:Warning: there is no chain 1hcl will retry with 1hclA Skipped atom 1022, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1024, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1026, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1028, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 1030, because occupancy 0.200 <= existing 0.800 in 1hcl Skipped atom 2093, because occupancy 0.370 <= existing 0.660 in 1hcl # T0291 read from 1hcl/T0291-1hcl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hcl read from 1hcl/T0291-1hcl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hcl to template set # found chain 1hcl in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1hcl 24 :KLTGEVVALKKI T0291 64 :GYTEK 1hcl 43 :GVPST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDAQ 1hcl 86 :DLKKFMDASALT T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1hcl 99 :IPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1hcl 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1hcl 178 :KYYSTAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1hcl 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1hcl 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPF Number of specific fragments extracted= 10 number of extra gaps= 0 total=1308 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hcl/T0291-1hcl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1hcl/T0291-1hcl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hcl read from 1hcl/T0291-1hcl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hcl in template set Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1hcl 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1hcl 24 :KLTGEVVALKKI T0291 63 :VGYTEKQ 1hcl 42 :EGVPSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1hcl 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1hcl 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIAY 1hcl 157 :RTYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSY 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1hcl 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1hcl 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1hcl 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSL 1hcl 282 :AHPFF Number of specific fragments extracted= 12 number of extra gaps= 0 total=1320 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hcl/T0291-1hcl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1hcl/T0291-1hcl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hcl read from 1hcl/T0291-1hcl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hcl in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1hcl)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hcl)T41 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAI 1hcl 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0291 63 :VGYTEKQR 1hcl 42 :EGVPSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1hcl 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1hcl 86 :DLKKFMD T0291 119 :KHD 1hcl 95 :ALT T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1hcl 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1hcl 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1hcl 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1hcl 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1hcl 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHP T0291 287 :LIRNPGS 1hcl 285 :FFQDVTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=1331 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvpP/T0291-1jvpP-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jvpP expands to /projects/compbio/data/pdb/1jvp.pdb.gz 1jvpP:Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1jvpP Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 1jvpP # T0291 read from 1jvpP/T0291-1jvpP-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvpP read from 1jvpP/T0291-1jvpP-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jvpP to template set # found chain 1jvpP in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1jvpP 24 :KLTGEVVALKKI T0291 66 :TEK 1jvpP 45 :PST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKHDA 1jvpP 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMS 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVT T0291 227 :GERPYWEMSNQDVIKAVDEGYRLPPPM 1jvpP 199 :RRALFPGDSEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG 1jvpP 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKP Number of specific fragments extracted= 10 number of extra gaps= 0 total=1341 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvpP/T0291-1jvpP-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jvpP/T0291-1jvpP-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvpP read from 1jvpP/T0291-1jvpP-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvpP in template set Warning: unaligning (T0291)K62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKTL 1jvpP 24 :KLTGEVVALKKI T0291 66 :TEKQ 1jvpP 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLRKH 1jvpP 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSY 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTR T0291 228 :ERPYWEMSNQDVIKAVD 1jvpP 200 :RALFPGDSEIDQLFRIF T0291 245 :EGYRLPPP 1jvpP 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1jvpP 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSLKIITSAAARPS 1jvpP 282 :AHPFFQDVTKPVPHLR Number of specific fragments extracted= 12 number of extra gaps= 0 total=1353 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvpP/T0291-1jvpP-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1jvpP/T0291-1jvpP-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvpP read from 1jvpP/T0291-1jvpP-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvpP in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1jvpP)M1 Warning: unaligning (T0291)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V44 Warning: unaligning (T0291)L177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvpP)V163 Warning: unaligning (T0291)K191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvpP)V163 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAI 1jvpP 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKI T0291 66 :TEKQR 1jvpP 45 :PSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMEN 1jvpP 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQ T0291 112 :SLDSFLR 1jvpP 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRV 1jvpP 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARA T0291 192 :IPIRWTSPEAIAY 1jvpP 164 :VTLWYRAPEILLG T0291 205 :RKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKA 1jvpP 178 :KYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRI T0291 243 :VDEGYRLPPP 1jvpP 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSILD 1jvpP 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAHPF T0291 288 :IRNPG 1jvpP 286 :FQDVT Number of specific fragments extracted= 10 number of extra gaps= 0 total=1363 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cdkA/T0291-1cdkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cdkA expands to /projects/compbio/data/pdb/1cdk.pdb.gz 1cdkA:# T0291 read from 1cdkA/T0291-1cdkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cdkA read from 1cdkA/T0291-1cdkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cdkA to template set # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)I194 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)Q237 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 Warning: unaligning (T0291)K276 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)V288 Warning: unaligning (T0291)F277 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)V288 Warning: unaligning (T0291)I283 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K295 T0291 18 :FAKELDATNISIDKVVGAGEFGEVCSGRL 1cdkA 34 :AQNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1cdkA 63 :KETGNHFAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 82 :LKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHDA 1cdkA 132 :LRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :D 1cdkA 193 :G T0291 186 :TTRGGKIP 1cdkA 194 :RTWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMS 1cdkA 234 :GYPPFFADQ T0291 238 :DVIKAVDEG 1cdkA 245 :QIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDC 1cdkA 254 :KVRFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NRP 1cdkA 279 :KRF T0291 278 :EQIVS 1cdkA 289 :NDIKN T0291 284 :LDKLIRNPGSLKII 1cdkA 302 :WIAIYQRKVEAPFI T0291 298 :TSAAARPSNL 1cdkA 337 :VSINEKCGKE Number of specific fragments extracted= 17 number of extra gaps= 9 total=1380 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cdkA/T0291-1cdkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1cdkA/T0291-1cdkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cdkA read from 1cdkA/T0291-1cdkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)P193 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)Q237 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 T0291 19 :AKELDATNISIDKVVGAGEFGEVCSGRL 1cdkA 35 :QNTAHLDQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1cdkA 63 :KETGNHFAMKILD T0291 63 :V 1cdkA 82 :L T0291 65 :YTEK 1cdkA 83 :KQIE T0291 72 :DFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 87 :HTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHDA 1cdkA 132 :LRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 138 :FSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :DD 1cdkA 193 :GR T0291 186 :TTRGGKI 1cdkA 195 :TWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMS 1cdkA 234 :GYPPFFADQ T0291 238 :DVIKAVDEG 1cdkA 245 :QIYEKIVSG T0291 248 :RLPPPMDCPAALYQLMLDC 1cdkA 254 :KVRFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NR 1cdkA 279 :KR Number of specific fragments extracted= 16 number of extra gaps= 7 total=1396 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cdkA/T0291-1cdkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1cdkA/T0291-1cdkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cdkA read from 1cdkA/T0291-1cdkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cdkA in template set Warning: unaligning (T0291)D114 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)S130 Warning: unaligning (T0291)S115 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)S130 Warning: unaligning (T0291)F116 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)H131 Warning: unaligning (T0291)R151 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)D166 Warning: unaligning (T0291)D152 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)D166 Warning: unaligning (T0291)L177 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)K192 Warning: unaligning (T0291)E178 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)K192 Warning: unaligning (T0291)I194 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)E203 Warning: unaligning (T0291)R195 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)E203 Warning: unaligning (T0291)S235 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)I244 Warning: unaligning (T0291)N236 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)I244 Warning: unaligning (T0291)W267 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)Q274 Warning: unaligning (T0291)Q268 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)Q274 Warning: unaligning (T0291)R271 because of BadResidue code BAD_PEPTIDE in next template residue (1cdkA)T278 Warning: unaligning (T0291)N272 because of BadResidue code BAD_PEPTIDE at template residue (1cdkA)T278 T0291 20 :KELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1cdkA 36 :NTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSL 1cdkA 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEM T0291 117 :LRKHD 1cdkA 132 :LRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVH 1cdkA 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIY T0291 153 :LAARNILINSNLVCKVSDFGLGRV 1cdkA 167 :LKPENLLIDQQGYIQVTDFGFAKR T0291 179 :D 1cdkA 193 :G T0291 186 :TTRGGKIP 1cdkA 194 :RTWTLCGT T0291 196 :WTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEM 1cdkA 204 :YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQ T0291 237 :QDVIKAVDEGY 1cdkA 245 :QIYEKIVSGKV T0291 250 :PPPMDCPAALYQLMLDC 1cdkA 256 :RFPSHFSSDLKDLLRNL T0291 269 :KD 1cdkA 275 :VD T0291 273 :NRP 1cdkA 279 :KRF Number of specific fragments extracted= 12 number of extra gaps= 7 total=1408 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmkE/T0291-1cmkE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cmkE expands to /projects/compbio/data/pdb/1cmk.pdb.gz 1cmkE:Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0291 read from 1cmkE/T0291-1cmkE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cmkE read from 1cmkE/T0291-1cmkE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cmkE to template set # found chain 1cmkE in template set Warning: unaligning (T0291)F18 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)Q35 Warning: unaligning (T0291)A19 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)Q35 Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 Warning: unaligning (T0291)V281 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)N293 Warning: unaligning (T0291)S282 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)N293 Warning: unaligning (T0291)K295 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)F314 Warning: unaligning (T0291)I296 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)F314 Warning: unaligning (T0291)T298 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)I339 Warning: unaligning (T0291)A300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)I339 Warning: unaligning (T0291)A301 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)E341 Warning: unaligning (T0291)A302 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)E341 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLKVGYT 1cmkE 63 :KETGNHFAMKILDKQKV T0291 67 :EKQRRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 82 :LKQIEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLED 1cmkE 180 :IQVTDFGFAKRVKG T0291 186 :TT 1cmkE 194 :RT T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1cmkE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCP 1cmkE 254 :KVRFPSHFS T0291 259 :LYQLMLDCWQKDRNNRP 1cmkE 265 :LKDLLRNLLQVDLTKRF T0291 276 :KFEQI 1cmkE 287 :GVNDI T0291 284 :LDKLIRNPGSL 1cmkE 302 :WIAIYQRKVEA T0291 297 :I 1cmkE 315 :I T0291 303 :RPSN 1cmkE 342 :KCGK Number of specific fragments extracted= 16 number of extra gaps= 7 total=1424 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmkE/T0291-1cmkE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1cmkE/T0291-1cmkE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cmkE read from 1cmkE/T0291-1cmkE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cmkE in template set Warning: unaligning (T0291)A19 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)Q35 Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKH T0291 50 :SKKEISVAIKTLK 1cmkE 63 :KETGNHFAMKILD T0291 70 :RRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 85 :IEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHDA 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIGR T0291 124 :FTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 138 :FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLEDD 1cmkE 180 :IQVTDFGFAKRVKGR T0291 187 :T 1cmkE 195 :T T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMS 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAA T0291 227 :GERPYWEMSNQDVIKAVDEG 1cmkE 234 :GYPPFFADQPIQIYEKIVSG T0291 248 :RLPPPMDCP 1cmkE 254 :KVRFPSHFS T0291 259 :LYQLMLDCWQKDRNNR 1cmkE 265 :LKDLLRNLLQVDLTKR Number of specific fragments extracted= 12 number of extra gaps= 5 total=1436 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmkE/T0291-1cmkE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1cmkE/T0291-1cmkE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cmkE read from 1cmkE/T0291-1cmkE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cmkE in template set Warning: unaligning (T0291)D23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L40 Warning: unaligning (T0291)A24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L40 Warning: unaligning (T0291)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)K111 Warning: unaligning (T0291)T96 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)K111 Warning: unaligning (T0291)K97 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)N113 Warning: unaligning (T0291)S98 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)N113 Warning: unaligning (T0291)L164 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cmkE)Y179 Warning: unaligning (T0291)V165 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cmkE)Y179 Warning: unaligning (T0291)R188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cmkE)L198 Warning: unaligning (T0291)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cmkE)L198 Warning: unaligning (T0291)K191 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)G200 Warning: unaligning (T0291)I192 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)G200 Warning: unaligning (T0291)A257 because of BadResidue code BAD_PEPTIDE in next template residue (1cmkE)D264 Warning: unaligning (T0291)A258 because of BadResidue code BAD_PEPTIDE at template residue (1cmkE)D264 T0291 20 :KEL 1cmkE 36 :NTA T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKV 1cmkE 41 :DQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKV T0291 65 :YTEKQRRDFLGEASIMGQFDHPNIIRLEGV 1cmkE 80 :VKLKQIEHTLNEKRILQAVNFPFLVKLEYS T0291 99 :KPVMIVTEYMENGSLDSFLRKHD 1cmkE 114 :SNLYMVMEYVPGGEMFSHLRRIG T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSN 1cmkE 137 :RFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQ T0291 166 :CKVSDFGLGRVLED 1cmkE 180 :IQVTDFGFAKRVKG T0291 186 :TT 1cmkE 194 :RT T0291 193 :PIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGY 1cmkE 201 :TPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKV T0291 250 :PPPMDCP 1cmkE 256 :RFPSHFS T0291 259 :LYQLMLDCWQKDRNNRP 1cmkE 265 :LKDLLRNLLQVDLTKRF Number of specific fragments extracted= 10 number of extra gaps= 4 total=1446 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1xA/T0291-1e1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e1xA expands to /projects/compbio/data/pdb/1e1x.pdb.gz 1e1xA:# T0291 read from 1e1xA/T0291-1e1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1xA read from 1e1xA/T0291-1e1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e1xA to template set # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)M234 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKT 1e1xA 24 :KLTGEVVALKK T0291 67 :EK 1e1xA 46 :ST T0291 73 :FLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 48 :AIREISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLRKHDA 1e1xA 86 :DLKKFMDASAL T0291 123 :QFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1e1xA 98 :GIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1e1xA 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMS 1e1xA 182 :TAVDIWSLGCIFAEMVT T0291 227 :GERPYW 1e1xA 199 :RRALFP T0291 235 :SNQDVIKAVDEGYRLPPPM 1e1xA 207 :SEIDQLFRIFRTLGTPDEV T0291 254 :DCPAALYQLMLDCWQKDRNNRPKFEQIVSIL 1e1xA 254 :PLDEDGRSLLSQMLHYDPNKRISAKAALAHP T0291 293 :SLKI 1e1xA 285 :FFQD Number of specific fragments extracted= 14 number of extra gaps= 3 total=1460 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1xA/T0291-1e1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1e1xA/T0291-1e1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1xA read from 1e1xA/T0291-1e1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)L61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)M234 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRL 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARN T0291 50 :SKKEISVAIKT 1e1xA 24 :KLTGEVVALKK T0291 66 :TEKQ 1e1xA 45 :PSTA T0291 74 :LGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 49 :IREISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLRKH 1e1xA 86 :DLKKFMDAS T0291 121 :DAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDP 1e1xA 96 :LTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPV T0291 185 :YTTRGGKIPIRWTSPEAIAY 1e1xA 157 :RTYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMSY 1e1xA 182 :TAVDIWSLGCIFAEMVTR T0291 228 :ERPYW 1e1xA 200 :RALFP T0291 235 :SNQDVIKAVD 1e1xA 207 :SEIDQLFRIF T0291 245 :EGYRLPPP 1e1xA 234 :PDYKPSFP T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIV 1e1xA 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAAL T0291 290 :NPGSLKIITSAAARPS 1e1xA 282 :AHPFFQDVTKPVPHLR Number of specific fragments extracted= 15 number of extra gaps= 3 total=1475 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1xA/T0291-1e1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0291 read from 1e1xA/T0291-1e1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1xA read from 1e1xA/T0291-1e1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e1xA in template set Warning: unaligning (T0291)A24 because first residue in template chain is (1e1xA)M1 Warning: unaligning (T0291)I58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1e1xA)V44 Warning: unaligning (T0291)Y65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1e1xA)V44 Warning: unaligning (T0291)M108 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)H84 Warning: unaligning (T0291)E109 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)H84 Warning: unaligning (T0291)F207 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)S181 Warning: unaligning (T0291)T208 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)S181 Warning: unaligning (T0291)W232 because of BadResidue code BAD_PEPTIDE in next template residue (1e1xA)D206 Warning: unaligning (T0291)E233 because of BadResidue code BAD_PEPTIDE at template residue (1e1xA)D206 T0291 25 :TNISIDKVVGAGEFGEVCSGRLKLPSKKEISVA 1e1xA 2 :ENFQKVEKIGEGTYGVVYKARNKLTGEVVALKK T0291 66 :TEKQR 1e1xA 45 :PSTAI T0291 75 :GEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEY 1e1xA 50 :REISLLKELNHPNIVKLLDVIHTENKLYLVFEF T0291 110 :N 1e1xA 85 :Q T0291 112 :SLDSFLR 1e1xA 86 :DLKKFMD T0291 120 :HDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLGRVLEDDPE 1e1xA 95 :ALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVR T0291 186 :TTRGGKIPIRWTSPEAIAY 1e1xA 158 :TYTHEVVTLWYRAPEILLG T0291 205 :RK 1e1xA 178 :KY T0291 209 :SASDVWSYGIVLWEVMSYGERPY 1e1xA 182 :TAVDIWSLGCIFAEMVTRRALFP T0291 234 :MSNQDVIKA 1e1xA 207 :SEIDQLFRI T0291 243 :VDEGYRLPPP 1e1xA 236 :YKPSFPKWAR T0291 253 :MDCPAALYQLMLDCWQKDRNNRPKFEQIVSI 1e1xA 253 :PPLDEDGRSLLSQMLHYDPNKRISAKAALAH T0291 298 :TSAAARP 1e1xA 284 :PFFQDVT Number of specific fragments extracted= 13 number of extra gaps= 3 total=1488 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mqbA/T0291-1mqbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mqbA/T0291-1mqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mqbA/T0291-1mqbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y57A/T0291-1y57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y57A/T0291-1y57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y57A/T0291-1y57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ptk/T0291-2ptk-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ptk/T0291-2ptk-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ptk/T0291-2ptk-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qcfA/T0291-1qcfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qcfA/T0291-1qcfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qcfA/T0291-1qcfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # command:CPU_time= 51.859 sec, elapsed time= 57.165 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 159 undertaker: Constraint.h:101: Constraint::Constraint(int, int, const ChainsResiduesAndAtoms*, float, float, float, float, bool): Assertion `mind <= d && d <= maxd' failed.