# 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 T0318 numbered 1 through 491 Created new target T0318 from T0318.a2m # command:CPU_time= 5.165 sec, elapsed time= 5.330 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lam/T0318-1lam-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lam expands to /projects/compbio/data/pdb/1lam.pdb.gz 1lam:Warning: there is no chain 1lam will retry with 1lamA Skipped atom 2205, because occupancy 0.5 <= existing 0.500 in 1lam Skipped atom 2207, because occupancy 0.500 <= existing 0.500 in 1lam Skipped atom 2209, because occupancy 0.500 <= existing 0.500 in 1lam Skipped atom 2211, because occupancy 0.500 <= existing 0.500 in 1lam Skipped atom 2596, because occupancy 0.500 <= existing 0.500 in 1lam Skipped atom 2598, because occupancy 0.500 <= existing 0.500 in 1lam # T0318 read from 1lam/T0318-1lam-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lam read from 1lam/T0318-1lam-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lam to template set # found chain 1lam in template set T0318 10 :IQAVG 1lam 8 :IYSKE # choosing archetypes in rotamer library T0318 15 :DGLTSLIIVGKKSVLKNVTFEGKFKEVAQKFVTDGDSWNSMISR 1lam 16 :DEPQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHE T0318 60 :PASGRHPLHYELAHL 1lam 60 :DFPSVVVVGLGKKTA T0318 76 :TVPDASSRGNTPTNAHSIYKELKPINYPEDTKNVHFVLFAEYPDVLSHVAAIARTFCKFS 1lam 75 :GIDEQENWHEGKENIRAAVAAGCRQIQDLEIPSVEVDPCGDAQAAAEGAVLGLYEYDDLK T0318 138 :TSGIRELNVNI 1lam 135 :QKRKVVVSAKL T0318 152 :CDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lam 146 :HGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEV 1lam 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKG T0318 241 :PGSTEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lam 239 :NASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKSSIADMKNSN 1lam 347 :HTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIG T0318 428 :KMDGPPSAVAGLLIGAHIGFG 1lam 423 :KYRSAGACTAAAFLKEFVTHP T0318 452 :RWLHLDIAAPAEVGD 1lam 444 :KWAHLDIAGVMTNKD T0318 467 :RGTGYGPALFSTLLGKYT 1lam 466 :GMAGRPTRTLIEFLFRFS Number of specific fragments extracted= 12 number of extra gaps= 0 total=12 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 1lam/T0318-1lam-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lam/T0318-1lam-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lam read from 1lam/T0318-1lam-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lam in template set T0318 16 :GLTSLIIVGKKSVLKNVT 1lam 2 :KGLVLGIYSKEKEEDEPQ T0318 34 :FEGKFKEVAQKFVTDGDSWNSMISRIPASGRH 1lam 27 :FNKLVSGKLREILNISGPPLKAGKTRTFYGLH T0318 66 :PLHYELAHLITVPDAS 1lam 60 :DFPSVVVVGLGKKTAG T0318 82 :SRGN 1lam 78 :EQEN T0318 86 :TPTNAHSIYKELKPINYP 1lam 89 :IRAAVAAGCRQIQDLEIP T0318 111 :FVLFAEYPDVLSHVAAIARTFCKFSMKTSGIR 1lam 107 :SVEVDPCGDAQAAAEGAVLGLYEYDDLKQKRK T0318 144 :LNVNID 1lam 139 :VVVSAK T0318 151 :VCDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lam 145 :LHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEV 1lam 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKG T0318 241 :PGSTEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lam 239 :NASEPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKSSIADMKNSNLGKMDG 1lam 347 :HTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGKYRSAG T0318 434 :SAVAGLLIGAHIGFG 1lam 429 :ACTAAAFLKEFVTHP T0318 452 :RWLHLDIAAPA 1lam 444 :KWAHLDIAGVM T0318 463 :EVGDRGTGYGPALFSTLLGKY 1lam 462 :YLRKGMAGRPTRTLIEFLFRF Number of specific fragments extracted= 14 number of extra gaps= 0 total=26 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 1lam/T0318-1lam-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lam/T0318-1lam-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lam read from 1lam/T0318-1lam-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lam in template set T0318 15 :DGLTSLIIVGKKSVLKNVTFEGKFKEVAQ 1lam 16 :DEPQFTSAGENFNKLVSGKLREILNISGP T0318 45 :FVTDGDSWNSMISRIPASGRHPLHYELAHLIT 1lam 45 :PLKAGKTRTFYGLHEDFPSVVVVGLGKKTAGI T0318 77 :VPDASSRGNTPTNAHSIYKELKPI 1lam 83 :HEGKENIRAAVAAGCRQIQDLEIP T0318 108 :NVHFVLFAEYPDVLSHVAAIARTFCKFSM 1lam 107 :SVEVDPCGDAQAAAEGAVLGLYEYDDLKQ T0318 139 :SG 1lam 136 :KR T0318 143 :ELNVN 1lam 138 :KVVVS T0318 149 :DVVCDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lam 143 :AKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1lam 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lam 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKSSIADMKNSNL 1lam 347 :HTFNPKVIINAATLTGAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDCQLADVNNIGK T0318 429 :MDGPPSAVAGLLIGAHIG 1lam 424 :YRSAGACTAAAFLKEFVT T0318 450 :GLRWLHLDIAAPAEVGDRGTGYGPALFSTLLGKYTSVP 1lam 442 :HPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFL Number of specific fragments extracted= 12 number of extra gaps= 0 total=38 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 1bllE/T0318-1bllE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bllE expands to /projects/compbio/data/pdb/1bll.pdb.gz 1bllE:# T0318 read from 1bllE/T0318-1bllE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bllE read from 1bllE/T0318-1bllE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bllE to template set # found chain 1bllE in template set Warning: unaligning (T0318)D15 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D16 Warning: unaligning (T0318)G16 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)E17 Warning: unaligning (T0318)F131 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)D131 Warning: unaligning (T0318)C132 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D131 Warning: unaligning (T0318)S371 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)G369 Warning: unaligning (T0318)G372 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)G369 Warning: unaligning (T0318)R373 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)S370 Warning: unaligning (T0318)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)R396 Warning: unaligning (T0318)L399 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)R396 T0318 17 :LTSLIIVGKKSVLKNVTFEGKFKEVAQKFVTDGDSWNSMISR 1bllE 18 :PQFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHE T0318 60 :PASGRHPLHYELA 1bllE 60 :DFPSVVVVGLGKK T0318 73 :HLITVPDASSRGNTPTNAHSIYKE 1bllE 80 :ENWHEGKENIRAAVAAGCRQIQDL T0318 105 :DTKNVHFVLFAEYPDVLSHVAAIART 1bllE 104 :EIPSVEVDPCGDAQAAAEGAVLGLYE T0318 133 :KFS 1bllE 132 :DLK T0318 138 :TSGIRELNVNI 1bllE 135 :QKRKVVVSAKL T0318 152 :CDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1bllE 146 :HGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1bllE 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1bllE 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWL 1bllE 347 :HTFNPKVIINAATLTGAMDIA T0318 374 :LHGAAMTNDEQLENEIIKAGKASG 1bllE 371 :GATGVFTNSSWLWNKLFEASIETG T0318 400 :VAPMLFAPDLFFGDLKSSIADMKNSN 1bllE 397 :VWRMPLFEHYTRQVIDCQLADVNNIG T0318 428 :KMDGPPSAVAGLLIGAHIGFG 1bllE 423 :KYRSAGACTAAAFLKEFVTHP T0318 452 :RWLHLDIAAPAEVGD 1bllE 444 :KWAHLDIAGVMTNKD T0318 467 :RGTGYGPALFSTLLGKYT 1bllE 466 :GMAGRPTRTLIEFLFRFS Number of specific fragments extracted= 15 number of extra gaps= 3 total=53 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 1bllE/T0318-1bllE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1bllE/T0318-1bllE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bllE read from 1bllE/T0318-1bllE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bllE in template set Warning: unaligning (T0318)D15 because first residue in template chain is (1bllE)T1 Warning: unaligning (T0318)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)L6 Warning: unaligning (T0318)L20 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)L6 Warning: unaligning (T0318)K25 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)E15 Warning: unaligning (T0318)K26 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)E15 Warning: unaligning (T0318)K30 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D16 Warning: unaligning (T0318)N31 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)E17 Warning: unaligning (T0318)F134 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)D131 Warning: unaligning (T0318)S135 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D131 Warning: unaligning (T0318)S371 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)G369 Warning: unaligning (T0318)G372 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)G369 Warning: unaligning (T0318)R373 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)S370 Warning: unaligning (T0318)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)R396 Warning: unaligning (T0318)L399 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)R396 T0318 16 :GLT 1bllE 2 :KGL T0318 21 :IIVG 1bllE 7 :GIYS T0318 32 :VT 1bllE 18 :PQ T0318 34 :FEGKFKEVAQKFVTDGDSWNSMISRIPASGRH 1bllE 27 :FNKLVSGKLREILNISGPPLKAGKTRTFYGLH T0318 66 :PLHYELAHLITVPDAS 1bllE 60 :DFPSVVVVGLGKKTAG T0318 82 :SRGN 1bllE 78 :EQEN T0318 86 :TPTNAHSIYKELKPINY 1bllE 89 :IRAAVAAGCRQIQDLEI T0318 110 :HFVLFAEYPDVLSHVAAIARTFCK 1bllE 106 :PSVEVDPCGDAQAAAEGAVLGLYE T0318 136 :MKTSGIR 1bllE 132 :DLKQKRK T0318 144 :LNVNI 1bllE 139 :VVVSA T0318 150 :VVCDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1bllE 144 :KLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1bllE 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1bllE 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWL 1bllE 347 :HTFNPKVIINAATLTGAMDIA T0318 374 :LHGAAMTNDEQLENEIIKAGKASG 1bllE 371 :GATGVFTNSSWLWNKLFEASIETG T0318 400 :VAPMLFAPDLFFGDLKSSIADMKNSNLGKMDG 1bllE 397 :VWRMPLFEHYTRQVIDCQLADVNNIGKYRSAG T0318 434 :SAVAGLLIGAHIGFG 1bllE 429 :ACTAAAFLKEFVTHP T0318 452 :RWLHLDIAAPA 1bllE 444 :KWAHLDIAGVM T0318 463 :EVGDRGTGYGPALFSTLLGKYT 1bllE 462 :YLRKGMAGRPTRTLIEFLFRFS Number of specific fragments extracted= 19 number of extra gaps= 5 total=72 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 1bllE/T0318-1bllE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1bllE/T0318-1bllE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bllE read from 1bllE/T0318-1bllE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bllE in template set Warning: unaligning (T0318)D15 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D16 Warning: unaligning (T0318)G16 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)E17 Warning: unaligning (T0318)F131 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)D131 Warning: unaligning (T0318)C132 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)D131 Warning: unaligning (T0318)S371 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)G369 Warning: unaligning (T0318)G372 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)G369 Warning: unaligning (T0318)R373 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)S370 Warning: unaligning (T0318)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1bllE)R396 Warning: unaligning (T0318)L399 because of BadResidue code BAD_PEPTIDE at template residue (1bllE)R396 T0318 17 :LTSLIIVGKKSVLKNVTFEGKFKEVAQKFV 1bllE 18 :PQFTSAGENFNKLVSGKLREILNISGPPLK T0318 48 :DGDSWNSMISRIPASGRHPLHYELAHLITVP 1bllE 48 :AGKTRTFYGLHEDFPSVVVVGLGKKTAGIDE T0318 79 :DASSRGNTPTNAHSIYKELKPIN 1bllE 85 :GKENIRAAVAAGCRQIQDLEIPS T0318 110 :HFVLFAEYPDVLSHVAAIART 1bllE 109 :EVDPCGDAQAAAEGAVLGLYE T0318 133 :KF 1bllE 132 :DL T0318 137 :KTSGIRELN 1bllE 134 :KQKRKVVVS T0318 149 :DVVCDKLTNEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1bllE 143 :AKLHGSEDQEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1bllE 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1bllE 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMATLTGAQAWL 1bllE 347 :HTFNPKVIINAATLTGAMDIA T0318 374 :LHGAAMTNDEQLENEIIKAGKASG 1bllE 371 :GATGVFTNSSWLWNKLFEASIETG T0318 400 :VAPMLFAPDLFFGDLKSSIADMKNSNL 1bllE 397 :VWRMPLFEHYTRQVIDCQLADVNNIGK T0318 429 :MDGPPSAVAGLLIGAHIG 1bllE 424 :YRSAGACTAAAFLKEFVT T0318 450 :GLRWLHLDIAAPAEVGDRGTGYGPALFSTLLGKYTSVP 1bllE 442 :HPKWAHLDIAGVMTNKDEVPYLRKGMAGRPTRTLIEFL Number of specific fragments extracted= 14 number of extra gaps= 3 total=86 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 1lap/T0318-1lap-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lap expands to /projects/compbio/data/pdb/1lap.pdb.gz 1lap:Warning: there is no chain 1lap will retry with 1lapA # T0318 read from 1lap/T0318-1lap-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lap read from 1lap/T0318-1lap-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lap to template set # found chain 1lap in template set Warning: unaligning (T0318)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)P18 Warning: unaligning (T0318)L17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)P18 Warning: unaligning (T0318)R129 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)E129 Warning: unaligning (T0318)T130 because of BadResidue code BAD_PEPTIDE at template residue (1lap)E129 Warning: unaligning (T0318)L155 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)D150 Warning: unaligning (T0318)T156 because of BadResidue code BAD_PEPTIDE at template residue (1lap)D150 Warning: unaligning (T0318)L363 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)T361 Warning: unaligning (T0318)T364 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)T361 Warning: unaligning (T0318)S417 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)L415 Warning: unaligning (T0318)I418 because of BadResidue code BAD_PEPTIDE at template residue (1lap)L415 Warning: unaligning (T0318)D457 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)I450 Warning: unaligning (T0318)I458 because of BadResidue code BAD_PEPTIDE at template residue (1lap)I450 Warning: unaligning (T0318)S485 because last residue in template chain is (1lap)Q484 T0318 15 :D 1lap 16 :D T0318 18 :TSLIIVGKKSVLKNVTFEGKFKEVAQKFVTDGDSWNSMISR 1lap 19 :QFTSAGENFNKLVSGKLREILNISGPPLKAGKTRTFYGLHE T0318 60 :PASGRHPLHYE 1lap 60 :DFPSVVVVGLG T0318 71 :LAHLITVPDASSRGNTPTNAHSIYKE 1lap 78 :EQENWHEGKENIRAAVAAGCRQIQDL T0318 105 :DTKNVHFVLFAEYPDVLSHVAAIA 1lap 104 :EIPSVEVDPCGDAQAAAEGAVLGL T0318 131 :FCKF 1lap 130 :YDDL T0318 137 :KTSGIRELNVNI 1lap 134 :KQKRKVVVSAKL T0318 152 :CDK 1lap 146 :HGS T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lap 151 :QEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1lap 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lap 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMAT 1lap 347 :HTFNPKVIINAAT T0318 365 :GAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKS 1lap 362 :GAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDC T0318 419 :ADMKNSN 1lap 416 :ADVNNIG T0318 428 :KMDGPPSAVAGLLIGAHIGFG 1lap 423 :KYRSAGACTAAAFLKEFVTHP T0318 452 :RWLHL 1lap 444 :KWAHL T0318 459 :AAPAEVGD 1lap 451 :AGVMTNKD T0318 467 :RGTGYGPALFSTLLGKYT 1lap 466 :GMAGRPTRTLIEFLFRFS Number of specific fragments extracted= 18 number of extra gaps= 6 total=104 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 1lap/T0318-1lap-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lap/T0318-1lap-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lap read from 1lap/T0318-1lap-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lap in template set Warning: unaligning (T0318)D15 because first residue in template chain is (1lap)T1 Warning: unaligning (T0318)K25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lap)E15 Warning: unaligning (T0318)K26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lap)E15 Warning: unaligning (T0318)N31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)P18 Warning: unaligning (T0318)V32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)P18 Warning: unaligning (T0318)C132 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)E129 Warning: unaligning (T0318)K133 because of BadResidue code BAD_PEPTIDE at template residue (1lap)E129 Warning: unaligning (T0318)L155 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)D150 Warning: unaligning (T0318)T156 because of BadResidue code BAD_PEPTIDE at template residue (1lap)D150 Warning: unaligning (T0318)L363 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)T361 Warning: unaligning (T0318)T364 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)T361 Warning: unaligning (T0318)S417 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)L415 Warning: unaligning (T0318)I418 because of BadResidue code BAD_PEPTIDE at template residue (1lap)L415 Warning: unaligning (T0318)D457 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)I450 Warning: unaligning (T0318)I458 because of BadResidue code BAD_PEPTIDE at template residue (1lap)I450 Warning: unaligning (T0318)S485 because last residue in template chain is (1lap)Q484 T0318 16 :GLTSLIIVG 1lap 2 :KGLVLGIYS T0318 30 :K 1lap 16 :D T0318 33 :T 1lap 19 :Q T0318 34 :FEGKFKEVAQKFVTDGDSWNSMISRIPASGRH 1lap 27 :FNKLVSGKLREILNISGPPLKAGKTRTFYGLH T0318 66 :PLHYELAHLITVPDAS 1lap 60 :DFPSVVVVGLGKKTAG T0318 82 :SRGN 1lap 78 :EQEN T0318 86 :TPTNAHSIYKELKPINY 1lap 89 :IRAAVAAGCRQIQDLEI T0318 110 :HFVLFAEYPDVLSHVAAIARTF 1lap 106 :PSVEVDPCGDAQAAAEGAVLGL T0318 134 :FSMKTSGI 1lap 130 :YDDLKQKR T0318 143 :ELNVNID 1lap 138 :KVVVSAK T0318 151 :VCDK 1lap 145 :LHGS T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lap 151 :QEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1lap 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lap 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMAT 1lap 347 :HTFNPKVIINAAT T0318 365 :GAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKS 1lap 362 :GAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDC T0318 419 :ADMKNSNLGKMDG 1lap 416 :ADVNNIGKYRSAG T0318 434 :SAVAGLLIGAHIGFG 1lap 429 :ACTAAAFLKEFVTHP T0318 452 :RWLHL 1lap 444 :KWAHL T0318 459 :AAPAEVGD 1lap 451 :AGVMTNKD T0318 467 :RGTGYGPALFSTLLGKYT 1lap 466 :GMAGRPTRTLIEFLFRFS Number of specific fragments extracted= 21 number of extra gaps= 7 total=125 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 1lap/T0318-1lap-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lap/T0318-1lap-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lap read from 1lap/T0318-1lap-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lap in template set Warning: unaligning (T0318)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)P18 Warning: unaligning (T0318)L17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)P18 Warning: unaligning (T0318)C132 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)E129 Warning: unaligning (T0318)K133 because of BadResidue code BAD_PEPTIDE at template residue (1lap)E129 Warning: unaligning (T0318)L155 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)D150 Warning: unaligning (T0318)T156 because of BadResidue code BAD_PEPTIDE at template residue (1lap)D150 Warning: unaligning (T0318)L363 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lap)T361 Warning: unaligning (T0318)T364 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lap)T361 Warning: unaligning (T0318)S417 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)L415 Warning: unaligning (T0318)I418 because of BadResidue code BAD_PEPTIDE at template residue (1lap)L415 Warning: unaligning (T0318)D457 because of BadResidue code BAD_PEPTIDE in next template residue (1lap)I450 Warning: unaligning (T0318)I458 because of BadResidue code BAD_PEPTIDE at template residue (1lap)I450 T0318 18 :TSLIIVGKKSVLKNVTFEGKFKEVAQKFV 1lap 19 :QFTSAGENFNKLVSGKLREILNISGPPLK T0318 48 :DGDSWNSMISRIPASGRHPLHYELAHLITVP 1lap 48 :AGKTRTFYGLHEDFPSVVVVGLGKKTAGIDE T0318 79 :DASSRGNTPTNAHSIYKELKPIN 1lap 85 :GKENIRAAVAAGCRQIQDLEIPS T0318 109 :VHFVLFAEYPDVLSHVAAIA 1lap 108 :VEVDPCGDAQAAAEGAVLGL T0318 134 :FSM 1lap 130 :YDD T0318 137 :KTSGIRELN 1lap 134 :KQKRKVVVS T0318 149 :DVVCDK 1lap 143 :AKLHGS T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1lap 151 :QEAWQRGVLFASGQNLARRLMETPANEMTPTKFAEIVEENLKSA T0318 201 :GSKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1lap 197 :KTDVFIRPKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYKGSPN T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1lap 242 :EPPLVFVGKGITFDSGGISIKAAANMDLMRADMGGAATICSAIVSAAKLDLPINIVGLAPLCENMPSGKANKPGDVVRARNGKTIQVDNTDAEGRLILADALCYA T0318 350 :ETLKATTIFDMAT 1lap 347 :HTFNPKVIINAAT T0318 365 :GAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDLFFGDLKS 1lap 362 :GAMDIALGSGATGVFTNSSWLWNKLFEASIETGDRVWRMPLFEHYTRQVIDC T0318 419 :ADMKNSNL 1lap 416 :ADVNNIGK T0318 429 :MDGPPSAVAGLLIGAHIG 1lap 424 :YRSAGACTAAAFLKEFVT T0318 450 :GLRWLHL 1lap 442 :HPKWAHL T0318 459 :AAPAEVGDRGTGYGPALFSTLLGKYTSVP 1lap 451 :AGVMTNKDEVPYLRKGMAGRPTRTLIEFL Number of specific fragments extracted= 16 number of extra gaps= 6 total=141 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 1gytA/T0318-1gytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gytA expands to /projects/compbio/data/pdb/1gyt.pdb.gz 1gytA:# T0318 read from 1gytA/T0318-1gytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gytA read from 1gytA/T0318-1gytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gytA to template set # found chain 1gytA in template set T0318 4 :VLVRNGIQAVGDGLTSLIIVGKKSVLKNVTFEGKFKEVAQKFVTDGDSWNSMISRIPASGRHPLHYELAHLITVPDASSRGNTPTNAHSIYKELKPINYPEDTKNVHFVLFAEYPDVLSHVAAIARTFCKFSMKTSGIRELNVNIDVVCDKLT 1gytA 13 :QRSACIVVGVFEPRRLSPIAEQLDKISDGYISALLRRGELEGKPGQTLLLHHVPNVLSERILLIGCGKERELDERQYKQVIQKTINTLNDTGSMEAVCFLTELHVKGRNNYWKVRQAVETAKETLYSFDQLKTNKSEPRRPLRKMVFNVPTRR T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1gytA 171 :ERAIQHGLAIAAGIKAAKDLGNMPPNICNAAYLASQARQLADSY T0318 202 :SKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEV 1gytA 218 :VITRVIGEQQMKELGMHSYLAVGQGSQNESLMSVIEYKG T0318 241 :PGSTEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1gytA 259 :SEDARPIVLVGKGLTFDSGGISIKPSEGMDEMKYDMCGAAAVYGVMRMVAELQLPINVIGVLAGCENMPGGRAYRPGDVLTTMSGQTVEVLNTDAEGRLVLCDVLTYV T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPD 1gytA 367 :ERFEPEAVIDVATLTGACVIALGHHITGLMANHNPLAHELIAASEQSGDRAWRLPLGDE T0318 410 :FFGDLKSSIADMKNS 1gytA 426 :YQEQLESNFADMANI T0318 428 :KMDGPPSAVAGLLIGAHI 1gytA 441 :GGRPGGAITAGCFLSRFT T0318 449 :EGLRWLHLDIAAPAEVGD 1gytA 459 :RKYNWAHLDIAGTAWRSG T0318 467 :RGTGYGPALFSTLLGKYTSVP 1gytA 480 :GATGRPVALLAQFLLNRAGFN Number of specific fragments extracted= 9 number of extra gaps= 0 total=150 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 1gytA/T0318-1gytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1gytA/T0318-1gytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gytA read from 1gytA/T0318-1gytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gytA in template set T0318 1 :MTQVLVRNGIQAVGDGLTSLIIVGKKSVLKNVT 1gytA 1 :MEFSVKSGSPEKQRSACIVVGVFEPRRLSPIAE T0318 34 :FEGKFKEVAQKFVTDGDSWNSMISRIPASGRHPLH 1gytA 35 :LDKISDGYISALLRRGELEGKPGQTLLLHHVPNVL T0318 69 :YELAHLITVPDASSRGNTPTNAHSIYKELKPINYPEDTKNVHFVLFAE 1gytA 72 :RILLIGCGKERELDERQYKQVIQKTINTLNDTGSMEAVCFLTELHVKG T0318 117 :YPDVLSHVAAIARTFCKFSMKTSGIRELNVNIDVVC 1gytA 123 :YWKVRQAVETAKETLYSFDQLKTNKSEPRRPLRKMV T0318 154 :KLT 1gytA 163 :TRR T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1gytA 171 :ERAIQHGLAIAAGIKAAKDLGNMPPNICNAAYLASQARQLADSY T0318 202 :SKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEV 1gytA 218 :VITRVIGEQQMKELGMHSYLAVGQGSQNESLMSVIEYKG T0318 241 :PGSTEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1gytA 259 :SEDARPIVLVGKGLTFDSGGISIKPSEGMDEMKYDMCGAAAVYGVMRMVAELQLPINVIGVLAGCENMPGGRAYRPGDVLTTMSGQTVEVLNTDAEGRLVLCDVLTYV T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPD 1gytA 367 :ERFEPEAVIDVATLTGACVIALGHHITGLMANHNPLAHELIAASEQSGDRAWRLPLGDE T0318 410 :FFGDLKSSIADMKNSN 1gytA 426 :YQEQLESNFADMANIG T0318 427 :GKMDG 1gytA 442 :GRPGG T0318 434 :SAVAGLLIGAHI 1gytA 447 :AITAGCFLSRFT T0318 449 :EGLRWLHLDIAAPAEVGD 1gytA 459 :RKYNWAHLDIAGTAWRSG T0318 467 :RGTGYGPALFSTLLGKYTSVP 1gytA 480 :GATGRPVALLAQFLLNRAGFN Number of specific fragments extracted= 14 number of extra gaps= 0 total=164 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 1gytA/T0318-1gytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1gytA/T0318-1gytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gytA read from 1gytA/T0318-1gytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gytA in template set T0318 3 :QVLVRNGIQAVGDGLTSLIIVGKKSVLKNVTFEGKFKEVAQKFVTDGDSWNSMISRIPASGRHPLHYELAHLITVPDASSRGNTPTNAHSIYKELKPINYPEDTKNVHFVLFAEYPDVLSHVAAIARTFCKFSMKTSGIRELNVNIDVVC 1gytA 12 :KQRSACIVVGVFEPRRLSPIAEQLDKISDGYISALLRRGELEGKPGQTLLLHHVPNVLSERILLIGCGKERELDERQYKQVIQKTINTLNDTGSMEAVCFLTELHVKGRNNYWKVRQAVETAKETLYSFDQLKTNKSEPRRPLRKMVFNV T0318 155 :LT 1gytA 164 :RR T0318 157 :NEDAVFLTDLSESVRETARLIDTPANILTTDALVDEAVKVGNAT 1gytA 171 :ERAIQHGLAIAAGIKAAKDLGNMPPNICNAAYLASQARQLADSY T0318 202 :SKITVIRGEELLKAGFGGIYHVGKAGPTPPAFVVLSHEVPGS 1gytA 218 :VITRVIGEQQMKELGMHSYLAVGQGSQNESLMSVIEYKGNAS T0318 244 :TEHIALVGKGVVYDTGGLQIKTKTGMPNMKRDMGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTVEINNTDAEGRLILADGVFYA 1gytA 262 :ARPIVLVGKGLTFDSGGISIKPSEGMDEMKYDMCGAAAVYGVMRMVAELQLPINVIGVLAGCENMPGGRAYRPGDVLTTMSGQTVEVLNTDAEGRLVLCDVLTYV T0318 350 :ETLKATTIFDMATLTGAQAWLSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDL 1gytA 367 :ERFEPEAVIDVATLTGACVIALGHHITGLMANHNPLAHELIAASEQSGDRAWRLPLGDEY T0318 411 :FGDLKSSIADMKNSNL 1gytA 427 :QEQLESNFADMANIGG T0318 430 :DGPPSAVAGLLIGAHIG 1gytA 443 :RPGGAITAGCFLSRFTR T0318 450 :GLRWLHLDIAAPAEVGDRGTGYGPALFSTLLGKYTSV 1gytA 460 :KYNWAHLDIAGTAWRSGKAKGATGRPVALLAQFLLNR Number of specific fragments extracted= 9 number of extra gaps= 0 total=173 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 2ewbA/T0318-2ewbA-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 2ewbA/T0318-2ewbA-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 2ewbA/T0318-2ewbA-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 1tkjA/T0318-1tkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1tkjA/T0318-1tkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tkjA read from 1tkjA/T0318-1tkjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tkjA in training set Warning: unaligning (T0318)A232 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1tkjA)N66 Warning: unaligning (T0318)F233 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1tkjA)N66 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tkjA)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)G168 Warning: unaligning (T0318)M429 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)G201 Warning: unaligning (T0318)D430 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)G201 T0318 153 :DKLTNEDAVF 1tkjA 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1tkjA 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1tkjA 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPP 1tkjA 58 :TSGGATG T0318 234 :VVLSHEV 1tkjA 67 :LIANWPG T0318 242 :G 1tkjA 74 :G T0318 244 :TEHIALVGKGV 1tkjA 76 :PNKVLMAGAHL T0318 264 :KTKTGMPNMK 1tkjA 87 :DSVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tkjA 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tkjA 121 :KHLRFAWWGAEEL T0318 317 :DD 1tkjA 134 :GL T0318 343 :DGVFYAKETL 1tkjA 136 :IGSKFYVNNL T0318 353 :KATTIFDMATL 1tkjA 152 :KLAGYLNFDMI T0318 370 :LSG 1tkjA 163 :GSP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLF 1tkjA 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETE T0318 428 :K 1tkjA 199 :G T0318 431 :GPPSA 1tkjA 202 :RSDHA T0318 443 :AHIG 1tkjA 207 :PFKN T0318 449 :EGLRWLHL 1tkjA 211 :VGVPVGGL Number of specific fragments extracted= 19 number of extra gaps= 4 total=192 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 1tkjA/T0318-1tkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1tkjA/T0318-1tkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tkjA read from 1tkjA/T0318-1tkjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tkjA in training set Warning: unaligning (T0318)A232 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1tkjA)N66 Warning: unaligning (T0318)F233 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1tkjA)N66 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tkjA)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)G168 Warning: unaligning (T0318)P407 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)G201 Warning: unaligning (T0318)D408 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)G201 T0318 153 :DKLTNEDAVF 1tkjA 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1tkjA 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1tkjA 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPP 1tkjA 58 :TSGGATG T0318 234 :VVLSH 1tkjA 67 :LIANW T0318 240 :VPG 1tkjA 72 :PGG T0318 244 :TEHIALVGKGVV 1tkjA 76 :PNKVLMAGAHLD T0318 265 :TKTGMPNMK 1tkjA 88 :SVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tkjA 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tkjA 121 :KHLRFAWWGAEEL T0318 317 :DD 1tkjA 134 :GL T0318 343 :DGVFYAKETLK 1tkjA 136 :IGSKFYVNNLP T0318 354 :ATTIFDMATL 1tkjA 153 :LAGYLNFDMI T0318 370 :LSG 1tkjA 163 :GSP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLFA 1tkjA 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETEG T0318 415 :KSSIADMKN 1tkjA 202 :RSDHAPFKN T0318 449 :EGLRWLHLDIAAP 1tkjA 211 :VGVPVGGLFTGAG Number of specific fragments extracted= 17 number of extra gaps= 4 total=209 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 1tkjA/T0318-1tkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1tkjA/T0318-1tkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tkjA read from 1tkjA/T0318-1tkjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tkjA in training set Warning: unaligning (T0318)A232 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1tkjA)N66 Warning: unaligning (T0318)F233 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1tkjA)N66 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tkjA)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tkjA)G168 Warning: unaligning (T0318)P407 because of BadResidue code BAD_PEPTIDE in next template residue (1tkjA)G201 Warning: unaligning (T0318)D408 because of BadResidue code BAD_PEPTIDE at template residue (1tkjA)G201 T0318 153 :DKLTNEDAVFL 1tkjA 2 :PDIPLANVKAH T0318 166 :LSESVRETARLIDT 1tkjA 13 :LTQLSTIAANNGGN T0318 180 :PANILTTDALVDEAVKVGNATGSKITVIR 1tkjA 28 :AHGRPGYKASVDYVKAKLDAAGYTTTLQQ T0318 226 :AGPTPP 1tkjA 59 :SGGATG T0318 234 :VVLSH 1tkjA 67 :LIANW T0318 242 :GS 1tkjA 72 :PG T0318 244 :TEHIALVGKG 1tkjA 76 :PNKVLMAGAH T0318 263 :IKTKTGMPNMK 1tkjA 86 :LDSVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tkjA 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tkjA 121 :KHLRFAWWGAEEL T0318 344 :GVFYAKET 1tkjA 137 :GSKFYVNN T0318 352 :LKATTIFDMATLT 1tkjA 151 :SKLAGYLNFDMIG T0318 371 :SG 1tkjA 164 :SP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLFA 1tkjA 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETEG T0318 409 :LF 1tkjA 202 :RS T0318 426 :L 1tkjA 204 :D T0318 441 :IGAHIG 1tkjA 205 :HAPFKN T0318 449 :EGLRWLHL 1tkjA 211 :VGVPVGGL Number of specific fragments extracted= 18 number of extra gaps= 4 total=227 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 1qq9A/T0318-1qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq9A expands to /projects/compbio/data/pdb/1qq9.pdb.gz 1qq9A:# T0318 read from 1qq9A/T0318-1qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq9A read from 1qq9A/T0318-1qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq9A to template set # found chain 1qq9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1qq9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1qq9A)N98 T0318 153 :DKLTNEDAVF 1qq9A 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1qq9A 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1qq9A 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHEV 1qq9A 58 :TSGGATGYNLIANWPG T0318 242 :G 1qq9A 74 :G T0318 244 :TEHIALVGKGVV 1qq9A 76 :PNKVLMAGAHLD T0318 265 :TKTGMPNMK 1qq9A 88 :SVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1qq9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1qq9A 121 :KHLRFAWWGAEEL T0318 317 :DD 1qq9A 134 :GL T0318 343 :DGVFYAKETL 1qq9A 136 :IGSKFYVNNL T0318 353 :KATTIFDMATL 1qq9A 152 :KLAGYLNFDMI T0318 370 :LSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPD 1qq9A 163 :GSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDG T0318 431 :GPPSA 1qq9A 202 :RSDHA T0318 443 :AHIG 1qq9A 207 :PFKN T0318 449 :EGLR 1qq9A 211 :VGVP Number of specific fragments extracted= 16 number of extra gaps= 1 total=243 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 1qq9A/T0318-1qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1qq9A/T0318-1qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq9A read from 1qq9A/T0318-1qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1qq9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1qq9A)N98 T0318 153 :DKLTNEDAVF 1qq9A 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1qq9A 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1qq9A 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHE 1qq9A 58 :TSGGATGYNLIANWP T0318 241 :PG 1qq9A 73 :GG T0318 244 :TEHIALVGKGVV 1qq9A 76 :PNKVLMAGAHLD T0318 265 :TKTGMPNMK 1qq9A 88 :SVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1qq9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1qq9A 121 :KHLRFAWWGAEEL T0318 317 :DD 1qq9A 134 :GL T0318 343 :DGVFYAKETLK 1qq9A 136 :IGSKFYVNNLP T0318 354 :ATTIFDMATL 1qq9A 153 :LAGYLNFDMI T0318 370 :LSGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPD 1qq9A 163 :GSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDG T0318 415 :KSSIADMKNSN 1qq9A 202 :RSDHAPFKNVG T0318 451 :LRWLHLDIAA 1qq9A 213 :VPVGGLFTGA Number of specific fragments extracted= 15 number of extra gaps= 1 total=258 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 1qq9A/T0318-1qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1qq9A/T0318-1qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq9A read from 1qq9A/T0318-1qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1qq9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1qq9A)N98 T0318 153 :DKLTNEDAVFL 1qq9A 2 :PDIPLANVKAH T0318 166 :LSESVRETARLIDT 1qq9A 13 :LTQLSTIAANNGGN T0318 180 :PANILTTDALVDEAVKVGNATGSKITVIR 1qq9A 28 :AHGRPGYKASVDYVKAKLDAAGYTTTLQQ T0318 226 :AGPTPPAFVVLSH 1qq9A 59 :SGGATGYNLIANW T0318 242 :GS 1qq9A 72 :PG T0318 244 :TEHIALVGK 1qq9A 76 :PNKVLMAGA T0318 262 :QIKTKTGMPNMK 1qq9A 85 :HLDSVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1qq9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1qq9A 121 :KHLRFAWWGAEEL T0318 344 :GVFYAKET 1qq9A 137 :GSKFYVNN T0318 352 :LKATTIFDMATLT 1qq9A 151 :SKLAGYLNFDMIG T0318 371 :SGRLHGAAMTNDEQLENEIIKAGKASGDLVAPMLFAPDL 1qq9A 164 :SPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDGR T0318 424 :SNL 1qq9A 203 :SDH T0318 442 :GAHIG 1qq9A 206 :APFKN T0318 449 :EGLRWLHL 1qq9A 211 :VGVPVGGL Number of specific fragments extracted= 15 number of extra gaps= 1 total=273 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 1tf9A/T0318-1tf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tf9A expands to /projects/compbio/data/pdb/1tf9.pdb.gz 1tf9A:Skipped atom 14, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 16, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 18, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 20, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 22, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 24, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 26, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 28, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 77, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 79, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 81, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 83, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 85, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 340, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 342, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 344, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 346, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 348, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 444, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 1tf9A Skipped atom 625, because occupancy 0.220 <= existing 0.780 in 1tf9A Skipped atom 627, because occupancy 0.220 <= existing 0.780 in 1tf9A Skipped atom 629, because occupancy 0.220 <= existing 0.780 in 1tf9A Skipped atom 631, because occupancy 0.220 <= existing 0.780 in 1tf9A Skipped atom 696, because occupancy 0.230 <= existing 0.770 in 1tf9A Skipped atom 698, because occupancy 0.230 <= existing 0.770 in 1tf9A Skipped atom 841, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 843, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 845, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 847, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 849, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 851, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 853, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1051, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1053, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1055, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1057, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1059, because occupancy 0.320 <= existing 0.680 in 1tf9A Skipped atom 1126, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1128, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1147, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1149, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1151, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1153, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1155, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1157, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1159, because occupancy 0.380 <= existing 0.620 in 1tf9A Skipped atom 1165, because occupancy 0.370 <= existing 0.630 in 1tf9A Skipped atom 1167, because occupancy 0.370 <= existing 0.630 in 1tf9A Skipped atom 1400, because occupancy 0.460 <= existing 0.540 in 1tf9A Skipped atom 1402, because occupancy 0.460 <= existing 0.540 in 1tf9A Skipped atom 1404, because occupancy 0.460 <= existing 0.540 in 1tf9A Skipped atom 1406, because occupancy 0.460 <= existing 0.540 in 1tf9A Skipped atom 1408, because occupancy 0.460 <= existing 0.540 in 1tf9A Skipped atom 1432, because occupancy 0.430 <= existing 0.570 in 1tf9A Skipped atom 1434, because occupancy 0.430 <= existing 0.570 in 1tf9A Skipped atom 1436, because occupancy 0.430 <= existing 0.570 in 1tf9A Skipped atom 1438, because occupancy 0.430 <= existing 0.570 in 1tf9A Skipped atom 1440, because occupancy 0.430 <= existing 0.570 in 1tf9A Skipped atom 1494, because occupancy 0.340 <= existing 0.660 in 1tf9A Skipped atom 1496, because occupancy 0.340 <= existing 0.660 in 1tf9A Skipped atom 1498, because occupancy 0.340 <= existing 0.660 in 1tf9A Skipped atom 1500, because occupancy 0.340 <= existing 0.660 in 1tf9A Skipped atom 1924, because occupancy 0.280 <= existing 0.720 in 1tf9A Skipped atom 1926, because occupancy 0.280 <= existing 0.720 in 1tf9A Skipped atom 1960, because occupancy 0.310 <= existing 0.690 in 1tf9A Skipped atom 1962, because occupancy 0.310 <= existing 0.690 in 1tf9A # T0318 read from 1tf9A/T0318-1tf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf9A read from 1tf9A/T0318-1tf9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tf9A to template set # found chain 1tf9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tf9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tf9A)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tf9A)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)G168 Warning: unaligning (T0318)K428 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tf9A)R202 Warning: unaligning (T0318)G431 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tf9A)R202 T0318 153 :DKLTNEDAVF 1tf9A 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1tf9A 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1tf9A 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHEV 1tf9A 58 :TSGGATGYNLIANWPG T0318 244 :TEHIALVGKGV 1tf9A 76 :PNKVLMAGAHL T0318 264 :KTKTGMPNMK 1tf9A 87 :DSVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tf9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tf9A 121 :KHLRFAWWGAEEL T0318 317 :DD 1tf9A 134 :GL T0318 343 :DGVFYAKETLK 1tf9A 136 :IGSKFYVNNLP T0318 354 :ATTIFDMATL 1tf9A 153 :LAGYLNFDMI T0318 370 :LSG 1tf9A 163 :GSP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLF 1tf9A 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETE T0318 432 :PPS 1tf9A 203 :SDH T0318 442 :GAHIG 1tf9A 206 :APFKN T0318 449 :EGLRWL 1tf9A 211 :VGVPVG Number of specific fragments extracted= 16 number of extra gaps= 2 total=289 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 1tf9A/T0318-1tf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1tf9A/T0318-1tf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf9A read from 1tf9A/T0318-1tf9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tf9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tf9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tf9A)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tf9A)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)G168 Warning: unaligning (T0318)A406 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tf9A)R202 Warning: unaligning (T0318)K428 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tf9A)R202 T0318 153 :DKLTNEDAVF 1tf9A 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1tf9A 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1tf9A 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHEV 1tf9A 58 :TSGGATGYNLIANWPG T0318 243 :S 1tf9A 74 :G T0318 244 :TEHIALVGKGVV 1tf9A 76 :PNKVLMAGAHLD T0318 265 :TKTGMPNMK 1tf9A 88 :SVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tf9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tf9A 121 :KHLRFAWWGAEEL T0318 317 :DD 1tf9A 134 :GL T0318 343 :DGVFYAKETLK 1tf9A 136 :IGSKFYVNNLP T0318 354 :ATTIFDMATL 1tf9A 153 :LAGYLNFDMI T0318 370 :LSG 1tf9A 163 :GSP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLF 1tf9A 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETE T0318 429 :MDG 1tf9A 203 :SDH T0318 442 :GAHI 1tf9A 206 :APFK T0318 448 :GEGLRWLHLDIAAP 1tf9A 210 :NVGVPVGGLFTGAG T0318 464 :VGD 1tf9A 247 :HSS T0318 467 :RGTG 1tf9A 255 :NIND T0318 471 :YGPALFSTLLGKYT 1tf9A 263 :RNSDAAAHAIWTLS Number of specific fragments extracted= 20 number of extra gaps= 2 total=309 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 1tf9A/T0318-1tf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1tf9A/T0318-1tf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf9A read from 1tf9A/T0318-1tf9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tf9A in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1tf9A)N98 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1tf9A)N98 Warning: unaligning (T0318)R373 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tf9A)P167 Warning: unaligning (T0318)L374 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)P167 Warning: unaligning (T0318)H375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tf9A)G168 T0318 153 :DKLTNEDAVFL 1tf9A 2 :PDIPLANVKAH T0318 166 :LSESVRETARLIDT 1tf9A 13 :LTQLSTIAANNGGN T0318 180 :PANILTTDALVDEAVKVGNATGSKITVIR 1tf9A 28 :AHGRPGYKASVDYVKAKLDAAGYTTTLQQ T0318 226 :AGPTPPAFVVLSH 1tf9A 59 :SGGATGYNLIANW T0318 242 :GS 1tf9A 72 :PG T0318 244 :TEHIALVGKG 1tf9A 76 :PNKVLMAGAH T0318 263 :IKTKTGMPNMK 1tf9A 86 :LDSVSSGAGIN T0318 276 :MGGAAGMLEAYSALVKHGFS 1tf9A 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1tf9A 121 :KHLRFAWWGAEEL T0318 343 :DGVFYAKET 1tf9A 136 :IGSKFYVNN T0318 352 :LKATTIFDMATLT 1tf9A 151 :SKLAGYLNFDMIG T0318 371 :SG 1tf9A 164 :SP T0318 376 :GAAMTNDEQLENEIIKAGKASGDLVAPMLF 1tf9A 169 :YFVYDDDPVIEKTFKNYFAGLNVPTEIETE Number of specific fragments extracted= 13 number of extra gaps= 2 total=322 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 1rtqA/T0318-1rtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1rtqA/T0318-1rtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtqA read from 1rtqA/T0318-1rtqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtqA in training set Warning: unaligning (T0318)L261 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)H105 Warning: unaligning (T0318)Q262 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)H105 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)D118 Warning: unaligning (T0318)I304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rtqA)A150 Warning: unaligning (T0318)V305 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rtqA)A150 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)N182 T0318 168 :ESVRETARLIDTPANIL 1rtqA 21 :QITGTISSLESFTNRFY T0318 186 :TDALVDEAVKVGNATG 1rtqA 46 :SDWIASEWQALSASLP T0318 202 :SKITVI 1rtqA 63 :ASVKQV T0318 225 :KAGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1rtqA 69 :SHSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGG 1rtqA 100 :STIG T0318 263 :IKTKTGMPNMK 1rtqA 106 :TNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGFS 1rtqA 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLC 1rtqA 141 :RSIAFMAY T0318 306 :EN 1rtqA 151 :EE T0318 336 :EGR 1rtqA 156 :RGS T0318 343 :DGVFYAKET 1rtqA 160 :DLANQYKSE T0318 353 :KAT 1rtqA 169 :GKN T0318 356 :TIFDMAT 1rtqA 174 :SALQLDM T0318 370 :LSGRLHGAAM 1rtqA 183 :YKGSAQDVVF T0318 380 :TNDEQLENEIIKAGKA 1rtqA 196 :YTDSNFTQYLTQLMDE T0318 410 :FFGDLK 1rtqA 212 :YLPSLT T0318 425 :NLGKMDGPPSAVAGLL 1rtqA 219 :GFDTCGYACSDHASWH T0318 449 :EGLRW 1rtqA 236 :AGYPA T0318 459 :AAPAEVGD 1rtqA 241 :AMPFESKF T0318 467 :RGTGYGPALFSTLLGK 1rtqA 266 :DPTGSHAKKFTQLGLA Number of specific fragments extracted= 20 number of extra gaps= 4 total=342 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 1rtqA/T0318-1rtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1rtqA/T0318-1rtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtqA read from 1rtqA/T0318-1rtqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtqA in training set Warning: unaligning (T0318)L261 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)H105 Warning: unaligning (T0318)Q262 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)H105 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)D118 Warning: unaligning (T0318)I304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rtqA)A150 Warning: unaligning (T0318)V305 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rtqA)A150 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)N182 T0318 92 :SIYKELKPI 1rtqA 9 :TVTAWLPQV T0318 116 :EYPDVLSHVAAIARTFCKFSMK 1rtqA 18 :DASQITGTISSLESFTNRFYTT T0318 171 :RETARL 1rtqA 40 :TSGAQA T0318 186 :TDALVDEAVKVGNATG 1rtqA 46 :SDWIASEWQALSASLP T0318 202 :SKITVI 1rtqA 63 :ASVKQV T0318 225 :KAGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1rtqA 69 :SHSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGG 1rtqA 100 :STIG T0318 263 :IKTKTGMPNMK 1rtqA 106 :TNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGF 1rtqA 119 :ASGIAAVTEVIRVLSENNF T0318 295 :SQTLHACLC 1rtqA 140 :KRSIAFMAY T0318 306 :EN 1rtqA 151 :EE T0318 336 :EGR 1rtqA 156 :RGS T0318 343 :DGVFYAKET 1rtqA 160 :DLANQYKSE T0318 353 :KAT 1rtqA 169 :GKN T0318 356 :TIFDMAT 1rtqA 174 :SALQLDM T0318 365 :G 1rtqA 183 :Y T0318 371 :SGRLHGAAM 1rtqA 184 :KGSAQDVVF T0318 380 :TNDEQLENEIIKAGKA 1rtqA 196 :YTDSNFTQYLTQLMDE T0318 410 :FFGDLK 1rtqA 212 :YLPSLT T0318 424 :SNLGKMDGPPSAVAGLL 1rtqA 218 :YGFDTCGYACSDHASWH T0318 448 :GEGLRWL 1rtqA 235 :NAGYPAA T0318 460 :APA 1rtqA 242 :MPF T0318 467 :RGTGYGPALFSTLLGK 1rtqA 266 :DPTGSHAKKFTQLGLA Number of specific fragments extracted= 23 number of extra gaps= 4 total=365 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 1rtqA/T0318-1rtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1rtqA/T0318-1rtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtqA read from 1rtqA/T0318-1rtqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtqA in training set Warning: unaligning (T0318)T267 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)H105 Warning: unaligning (T0318)G268 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)H105 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)D118 Warning: unaligning (T0318)I304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rtqA)A150 Warning: unaligning (T0318)V305 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rtqA)A150 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1rtqA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1rtqA)N182 T0318 157 :N 1rtqA 19 :A T0318 167 :SESVRETARLIDTPANILTTDALVD 1rtqA 20 :SQITGTISSLESFTNRFYTTTSGAQ T0318 192 :EAVKVGNAT 1rtqA 48 :WIASEWQAL T0318 201 :GSKITVIR 1rtqA 62 :NASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 1rtqA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTK 1rtqA 98 :LDSTIG T0318 269 :MPN 1rtqA 106 :TNE T0318 272 :MK 1rtqA 115 :AD T0318 276 :MGGAAGMLEAYSALVKHGFS 1rtqA 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLC 1rtqA 141 :RSIAFMAY T0318 306 :ENN 1rtqA 151 :EEV T0318 310 :SP 1rtqA 154 :GL T0318 343 :DGVFYAKET 1rtqA 160 :DLANQYKSE T0318 352 :LKATTIFDMAT 1rtqA 170 :KNVVSALQLDM T0318 371 :SGRLHGAAMTND 1rtqA 184 :KGSAQDVVFITD T0318 383 :EQLENEIIKAGKAS 1rtqA 199 :SNFTQYLTQLMDEY T0318 414 :LKSSIADMKNSNL 1rtqA 213 :LPSLTYGFDTCGY T0318 430 :DGPPS 1rtqA 226 :ACSDH T0318 438 :GLLIG 1rtqA 231 :ASWHN T0318 449 :EGLRWLHLDIAAPAE 1rtqA 236 :AGYPAAMPFESKFND T0318 464 :VGDRGTGYGPALFSTLLGKYTSV 1rtqA 256 :HTTQDTLANSDPTGSHAKKFTQL Number of specific fragments extracted= 21 number of extra gaps= 4 total=386 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 1xjo/T0318-1xjo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xjo expands to /projects/compbio/data/pdb/1xjo.pdb.gz 1xjo:Warning: there is no chain 1xjo will retry with 1xjoA # T0318 read from 1xjo/T0318-1xjo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjo read from 1xjo/T0318-1xjo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xjo to template set # found chain 1xjo in template set Warning: unaligning (T0318)K273 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xjo)D97 Warning: unaligning (T0318)R274 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)D97 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1xjo)N98 Warning: unaligning (T0318)A361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)I162 Warning: unaligning (T0318)L363 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)I162 Warning: unaligning (T0318)P402 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)R202 Warning: unaligning (T0318)G431 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)R202 Warning: unaligning (T0318)P432 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)S203 T0318 153 :DKLTNEDAVF 1xjo 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1xjo 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1xjo 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHEV 1xjo 58 :TSGGATGYNLIANWPG T0318 244 :TEHIALVGKGVVYDTGGL 1xjo 76 :PNKVLMAGAHLDSVSSGA T0318 271 :NM 1xjo 94 :GI T0318 276 :MGGAAGMLEAYSALVKHGFS 1xjo 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1xjo 121 :KHLRFAWWGAEEL T0318 317 :DD 1xjo 134 :GL T0318 343 :DGVFYAKETLK 1xjo 136 :IGSKFYVNNLP T0318 354 :ATTIFDM 1xjo 153 :LAGYLNF T0318 370 :LSGRLHGAAMTNDEQLENEIIKAGKASGDLVA 1xjo 163 :GSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTE T0318 433 :PS 1xjo 204 :DH T0318 442 :GAHIGFG 1xjo 206 :APFKNVG Number of specific fragments extracted= 14 number of extra gaps= 1 total=400 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 1xjo/T0318-1xjo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1xjo/T0318-1xjo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjo read from 1xjo/T0318-1xjo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjo in template set Warning: unaligning (T0318)K273 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xjo)D97 Warning: unaligning (T0318)R274 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)D97 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1xjo)N98 Warning: unaligning (T0318)A361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)I162 Warning: unaligning (T0318)L363 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)I162 Warning: unaligning (T0318)P402 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)R202 Warning: unaligning (T0318)K415 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)R202 Warning: unaligning (T0318)S416 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)S203 T0318 153 :DKLTNEDAVF 1xjo 2 :PDIPLANVKA T0318 165 :DLSESVRETARLIDTPANIL 1xjo 12 :HLTQLSTIAANNGGNRAHGR T0318 185 :TTDALVDEAVKVGNATGSKITVIR 1xjo 33 :GYKASVDYVKAKLDAAGYTTTLQQ T0318 225 :KAGPTPPAFVVLSHEV 1xjo 58 :TSGGATGYNLIANWPG T0318 242 :G 1xjo 74 :G T0318 244 :TEHIALVGKGVVYDTGGLQ 1xjo 76 :PNKVLMAGAHLDSVSSGAG T0318 272 :M 1xjo 95 :I T0318 276 :MGGAAGMLEAYSALVKHGFS 1xjo 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1xjo 121 :KHLRFAWWGAEEL T0318 317 :DD 1xjo 134 :GL T0318 343 :DGVFYAKETLK 1xjo 136 :IGSKFYVNNLP T0318 354 :ATTIFDM 1xjo 153 :LAGYLNF T0318 370 :LSGRLHGAAMTNDEQLENEIIKAGKASGDLVA 1xjo 163 :GSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTE T0318 417 :SIADMKNSNL 1xjo 204 :DHAPFKNVGV Number of specific fragments extracted= 14 number of extra gaps= 1 total=414 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 1xjo/T0318-1xjo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1xjo/T0318-1xjo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjo read from 1xjo/T0318-1xjo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjo in template set Warning: unaligning (T0318)K273 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xjo)D97 Warning: unaligning (T0318)R274 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)D97 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1xjo)N98 Warning: unaligning (T0318)A361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)I162 Warning: unaligning (T0318)L363 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)I162 Warning: unaligning (T0318)P402 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xjo)R202 Warning: unaligning (T0318)G431 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xjo)R202 Warning: unaligning (T0318)P432 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xjo)S203 T0318 153 :DKLTNEDAVFL 1xjo 2 :PDIPLANVKAH T0318 166 :LSESVRETARLIDTPA 1xjo 13 :LTQLSTIAANNGGNRA T0318 182 :NILTTDALVDEAVKVGNATGSKITVIR 1xjo 30 :GRPGYKASVDYVKAKLDAAGYTTTLQQ T0318 226 :AGPTPPAFVVLSH 1xjo 59 :SGGATGYNLIANW T0318 242 :GS 1xjo 72 :PG T0318 244 :TEHIALVGKG 1xjo 76 :PNKVLMAGAH T0318 263 :IKTKTGMPNM 1xjo 86 :LDSVSSGAGI T0318 276 :MGGAAGMLEAYSALVKHGFS 1xjo 99 :GSGSAAVLETALAVSRAGYQ T0318 296 :QTLHACLCIVENN 1xjo 121 :KHLRFAWWGAEEL T0318 343 :DGVFYAKET 1xjo 136 :IGSKFYVNN T0318 352 :LKATTIFDM 1xjo 151 :SKLAGYLNF T0318 364 :T 1xjo 163 :G T0318 371 :SGRLHGAAMTNDEQLENEIIKAGKASGDLVA 1xjo 164 :SPNPGYFVYDDDPVIEKTFKNYFAGLNVPTE T0318 433 :P 1xjo 204 :D T0318 441 :IGAHIG 1xjo 205 :HAPFKN T0318 449 :EGLRWLHL 1xjo 211 :VGVPVGGL Number of specific fragments extracted= 16 number of extra gaps= 1 total=430 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 1x13A/T0318-1x13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x13A expands to /projects/compbio/data/pdb/1x13.pdb.gz 1x13A:# T0318 read from 1x13A/T0318-1x13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x13A read from 1x13A/T0318-1x13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x13A to template set # found chain 1x13A in template set Warning: unaligning (T0318)V240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x13A)G1223 T0318 36 :GKFKEVAQKFVTDGDSWNSMI 1x13A 1048 :KAFVQAGAEIVEGNSVWQSEI T0318 57 :SRIPASGRHPLHYELAHL 1x13A 1081 :ALLNPGTTLVSFIWPAQN T0318 87 :PTNAHSIYKELKP 1x13A 1099 :PELMQKLAERNVT T0318 100 :INYPEDTKNVHFVLF 1x13A 1118 :VPRISRAQSLDALSS T0318 116 :EYPDVLSHVAAIARTF 1x13A 1133 :MANIAGYRAIVEAAHE T0318 132 :CKFSMK 1x13A 1150 :GRFFTG T0318 138 :TSGIRELNVNIDVVCDKL 1x13A 1158 :TAAGKVPPAKVMVIGAGV T0318 165 :DLSE 1x13A 1176 :AGLA T0318 193 :AVKVGNATGSKITVIR 1x13A 1180 :AIGAANSLGAIVRAFD T0318 209 :GEELLKAGFGGI 1x13A 1201 :KEQVQSMGAEFL T0318 241 :P 1x13A 1224 :D T0318 246 :HIALV 1x13A 1250 :DIIVT T0318 261 :LQIKTKTGMPNMKR 1x13A 1255 :TALIPGKPAPKLIT T0318 275 :D 1x13A 1270 :E T0318 290 :VKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTV 1x13A 1271 :MVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKV T0318 330 :INNTDAEGR 1x13A 1310 :IGYTDLPGR Number of specific fragments extracted= 16 number of extra gaps= 0 total=446 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 1x13A/T0318-1x13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1x13A/T0318-1x13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x13A read from 1x13A/T0318-1x13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x13A in template set T0318 13 :VGDGLTSLIIVGKKSV 1x13A 1083 :LNPGTTLVSFIWPAQN T0318 39 :KEVAQKFVTD 1x13A 1099 :PELMQKLAER T0318 66 :PLHYELAHLITVPDASSRGNTPTNAHSIY 1x13A 1109 :NVTVMAMDSVPRISRAQSLDALSSMANIA T0318 120 :VLSHVAAIARTFCKFSMKTSGIRELNVNIDVVC 1x13A 1138 :GYRAIVEAAHEFGRFFTGQITAAGKVPPAKVMV T0318 153 :DK 1x13A 1173 :AG T0318 164 :TDLSE 1x13A 1175 :VAGLA T0318 193 :AVKVGNATGSKITVIR 1x13A 1180 :AIGAANSLGAIVRAFD T0318 209 :GEELLKAGFGGI 1x13A 1201 :KEQVQSMGAEFL T0318 246 :HIALV 1x13A 1250 :DIIVT T0318 261 :LQIKTKTGMPNMKRDM 1x13A 1255 :TALIPGKPAPKLITRE T0318 290 :VKHGFSQTLHACLCIVENNVSPIANKPDDIIKMLSGKTV 1x13A 1271 :MVDSMKAGSVIVDLAAQNGGNCEYTVPGEIFTTENGVKV T0318 330 :INNTDAEGRL 1x13A 1310 :IGYTDLPGRL T0318 340 :ILADGVFYAKE 1x13A 1326 :LYGTNLVNLLK Number of specific fragments extracted= 13 number of extra gaps= 0 total=459 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 1x13A/T0318-1x13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1x13A/T0318-1x13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x13A read from 1x13A/T0318-1x13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x13A in template set T0318 59 :IPASGRHPLHYELAHL 1x13A 1083 :LNPGTTLVSFIWPAQN T0318 88 :TNAHSIYKELKPI 1x13A 1099 :PELMQKLAERNVT T0318 101 :NYPEDTKNVHFVLFAEYPDVLSHVAAIARTFCKFSM 1x13A 1119 :PRISRAQSLDALSSMANIAGYRAIVEAAHEFGRFFT T0318 137 :KTSGIRELNVNIDVVCD 1x13A 1158 :TAAGKVPPAKVMVIGAG T0318 155 :L 1x13A 1175 :V T0318 165 :DLS 1x13A 1176 :AGL T0318 192 :EAVKVGNATGSKITVIR 1x13A 1179 :AAIGAANSLGAIVRAFD T0318 209 :GEELLKAGFGGI 1x13A 1201 :KEQVQSMGAEFL T0318 229 :TPPAFVVLSHEVPGS 1x13A 1248 :EVDIIVTTALIPGKP T0318 244 :TEHI 1x13A 1264 :PKLI T0318 265 :TKTGMPNMKRD 1x13A 1268 :TREMVDSMKAG T0318 299 :HACLCIVENNVSPIANKPDDIIKMLSGKTV 1x13A 1280 :VIVDLAAQNGGNCEYTVPGEIFTTENGVKV T0318 330 :INNTDAEGRL 1x13A 1310 :IGYTDLPGRL Number of specific fragments extracted= 13 number of extra gaps= 0 total=472 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 1v71A/T0318-1v71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v71A expands to /projects/compbio/data/pdb/1v71.pdb.gz 1v71A:# T0318 read from 1v71A/T0318-1v71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v71A read from 1v71A/T0318-1v71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v71A to template set # found chain 1v71A in template set T0318 74 :LITVPDA 1v71A 7 :LPTYDDV T0318 88 :TNAHSIYKELKPINYPEDTKNVHFVLFA 1v71A 14 :ASASERIKKFANKTPVLTSSTVNKEFVA T0318 120 :VLSHVAAIARTFCKFSMKT 1v71A 57 :KFRGALNALSQLNEAQRKA T0318 147 :NIDVVCDK 1v71A 76 :GVLTFSSG T0318 165 :DLSESVRETARLIDTPA 1v71A 84 :NHAQAIALSAKILGIPA T0318 183 :ILTTDALVDEA 1v71A 106 :LDAPEAKVAAT T0318 198 :NATGSKITVIR 1v71A 117 :KGYGGQVIMYD T0318 209 :GEELLKAGFGGI 1v71A 138 :KEISEREGLTII T0318 230 :PPA 1v71A 150 :PPY T0318 243 :STEHIALVGKG 1v71A 173 :GPLDALFVCLG T0318 259 :G 1v71A 184 :G T0318 279 :A 1v71A 185 :G T0318 281 :GMLEAYSALVKHGFS 1v71A 186 :GLLSGSALAARHFAP T0318 296 :QTLHACLC 1v71A 202 :CEVYGVEP T0318 343 :DGVFYAKET 1v71A 214 :DGQQSFRKG T0318 353 :KAT 1v71A 229 :TPK T0318 373 :RLHGAAMTND 1v71A 232 :TIADGAQTQH T0318 383 :EQLENEIIKA 1v71A 244 :NYTFSIIKEK T0318 397 :GDLVAPM 1v71A 254 :VDDILTV T0318 406 :APDLFFGDLKSSIADMKNS 1v71A 261 :SDEELIDCLKFYAARMKIV T0318 428 :KMDGPPSAVAGLL 1v71A 280 :VEPTGCLSFAAAR T0318 445 :I 1v71A 298 :L T0318 449 :EGLRWLHLDIAAPA 1v71A 299 :KNKRIGIIISGGNV Number of specific fragments extracted= 23 number of extra gaps= 0 total=495 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 1v71A/T0318-1v71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1v71A/T0318-1v71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v71A read from 1v71A/T0318-1v71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v71A in template set T0318 39 :KEVAQKFVTDGDSWNSMISRIPA 1v71A 10 :YDDVASASERIKKFANKTPVLTS T0318 66 :PLHYELAHLITV 1v71A 40 :VAEVFFKCENFQ T0318 82 :SRGNT 1v71A 52 :KMGAF T0318 89 :NAHSIYKELK 1v71A 57 :KFRGALNALS T0318 101 :NYPEDTKNVHFVLFAEYPDVLSHVAAIART 1v71A 67 :QLNEAQRKAGVLTFSSGNHAQAIALSAKIL T0318 145 :NVNIDVVC 1v71A 97 :GIPAKIIM T0318 153 :DKLTNED 1v71A 106 :LDAPEAK T0318 194 :VKVGNATGSKITVIRG 1v71A 113 :VAATKGYGGQVIMYDR T0318 210 :EELLKAGFGGI 1v71A 139 :EISEREGLTII T0318 230 :PPA 1v71A 150 :PPY T0318 243 :STEHIALVGKG 1v71A 173 :GPLDALFVCLG T0318 278 :GA 1v71A 184 :GG T0318 281 :GMLEAYSALVKHGFS 1v71A 186 :GLLSGSALAARHFAP T0318 296 :QTLHACLC 1v71A 202 :CEVYGVEP T0318 308 :NVSPIANKPDD 1v71A 232 :TIADGAQTQHL T0318 343 :DGVFYAKET 1v71A 245 :YTFSIIKEK T0318 354 :ATTIFDM 1v71A 254 :VDDILTV T0318 381 :NDEQLENEIIKAGKASGDLVAPM 1v71A 261 :SDEELIDCLKFYAARMKIVVEPT T0318 430 :DG 1v71A 284 :GC T0318 434 :SAVAGLL 1v71A 286 :LSFAAAR T0318 443 :AHIGFGEGLRWLHLDIAAPA 1v71A 293 :AMKEKLKNKRIGIIISGGNV Number of specific fragments extracted= 21 number of extra gaps= 0 total=516 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 1v71A/T0318-1v71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1v71A/T0318-1v71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v71A read from 1v71A/T0318-1v71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v71A in template set T0318 75 :ITVPDASSRGNTP 1v71A 8 :PTYDDVASASERI T0318 95 :KE 1v71A 21 :KK T0318 105 :DTKNVHFVLFAEYPDVL 1v71A 23 :FANKTPVLTSSTVNKEF T0318 145 :NVNIDVVC 1v71A 40 :VAEVFFKC T0318 153 :DKLTNEDAVF 1v71A 66 :SQLNEAQRKA T0318 165 :DLSESVRETARLIDTPA 1v71A 84 :NHAQAIALSAKILGIPA T0318 182 :NILTTDALVDEA 1v71A 105 :PLDAPEAKVAAT T0318 198 :NATGSKITVIRG 1v71A 117 :KGYGGQVIMYDR T0318 210 :EELLKAGFGGI 1v71A 139 :EISEREGLTII T0318 230 :PPA 1v71A 150 :PPY T0318 243 :STEHIALVGKG 1v71A 173 :GPLDALFVCLG T0318 278 :GAAGMLEAYSALVKHGFSQTLHACLC 1v71A 184 :GGGLLSGSALAARHFAPNCEVYGVEP T0318 304 :IVENNVSPIANKPDD 1v71A 215 :GQQSFRKGSIVHIDT T0318 333 :TDAEGR 1v71A 232 :TIADGA T0318 343 :DGVFYAKETL 1v71A 245 :YTFSIIKEKV T0318 355 :TTIFDM 1v71A 255 :DDILTV T0318 381 :NDEQLENEIIKAGKASGDLV 1v71A 261 :SDEELIDCLKFYAARMKIVV T0318 429 :MDGPPSAVAGL 1v71A 281 :EPTGCLSFAAA T0318 442 :GA 1v71A 292 :RA T0318 445 :IGFGEGLRWLHLDIAAP 1v71A 294 :MKEKLKNKRIGIIISGG Number of specific fragments extracted= 20 number of extra gaps= 0 total=536 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 1cg2A/T0318-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cg2A expands to /projects/compbio/data/pdb/1cg2.pdb.gz 1cg2A:# T0318 read from 1cg2A/T0318-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0318-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cg2A to template set # found chain 1cg2A in template set Warning: unaligning (T0318)D153 because first residue in template chain is (1cg2A)Q26 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1cg2A)D142 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1cg2A)D142 T0318 154 :KLTNEDAVFLTDL 1cg2A 27 :KRDNVLFQAATDE T0318 167 :SESVRETARLIDTPANILTTD 1cg2A 41 :PAVIKTLEKLVNIETGTGDAE T0318 188 :ALVDEAVKVGNATGSKITVIR 1cg2A 65 :AAGNFLEAELKNLGFTVTRSK T0318 225 :KAGPTPPAFVVLSHEVPGSTEHIALVGKGVVY 1cg2A 86 :SAGLVVGDNIVGKIKGRGGKNLLLMSHMDTVY T0318 261 :LQIKTKTG 1cg2A 125 :APFRVEGD T0318 269 :MPNMK 1cg2A 136 :GPGIA T0318 276 :MGGAAGMLEAYSALVKHGFS 1cg2A 143 :KGGNAVILHTLKLLKEYGVR T0318 325 :GKTVEINNTDAE 1cg2A 165 :GTITVLFNTDEE T0318 342 :ADGVFYAKET 1cg2A 183 :RDLIQEEAKL T0318 354 :ATTIFDMAT 1cg2A 193 :ADYVLSFEP Number of specific fragments extracted= 10 number of extra gaps= 1 total=546 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 1cg2A/T0318-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1cg2A/T0318-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0318-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cg2A in template set Warning: unaligning (T0318)D153 because first residue in template chain is (1cg2A)Q26 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1cg2A)D142 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1cg2A)D142 T0318 154 :KLTNEDAVFLTDL 1cg2A 27 :KRDNVLFQAATDE T0318 167 :SESVRETARLIDTPANILTTD 1cg2A 41 :PAVIKTLEKLVNIETGTGDAE T0318 188 :ALVDEAVKVGNATGSKITVIR 1cg2A 65 :AAGNFLEAELKNLGFTVTRSK T0318 225 :KAGPTPPAFVVLSHEVPGSTEHIALVGKGVVY 1cg2A 86 :SAGLVVGDNIVGKIKGRGGKNLLLMSHMDTVY T0318 261 :LQIKTKTG 1cg2A 125 :APFRVEGD T0318 269 :MPNMK 1cg2A 136 :GPGIA T0318 276 :MGGAAGMLEAYSALVKHGFS 1cg2A 143 :KGGNAVILHTLKLLKEYGVR T0318 325 :GKTVEINNTDAE 1cg2A 165 :GTITVLFNTDEE T0318 342 :ADGVFYAKET 1cg2A 183 :RDLIQEEAKL T0318 354 :ATTIFDMA 1cg2A 193 :ADYVLSFE Number of specific fragments extracted= 10 number of extra gaps= 1 total=556 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 1cg2A/T0318-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1cg2A/T0318-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0318-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cg2A in template set Warning: unaligning (T0318)D153 because first residue in template chain is (1cg2A)Q26 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1cg2A)D142 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1cg2A)D142 T0318 154 :KLTNEDAVFLTDL 1cg2A 27 :KRDNVLFQAATDE T0318 167 :SESVRETARLIDTPANILTTD 1cg2A 41 :PAVIKTLEKLVNIETGTGDAE T0318 188 :ALVDEAVKVGNATGSKITVIR 1cg2A 65 :AAGNFLEAELKNLGFTVTRSK T0318 225 :KAGPTPPAFVVLSHEVPGS 1cg2A 86 :SAGLVVGDNIVGKIKGRGG T0318 245 :EHIALVGK 1cg2A 105 :KNLLLMSH T0318 267 :TGM 1cg2A 119 :KGI T0318 270 :PNMK 1cg2A 137 :PGIA T0318 276 :MGGAAGMLEAYSALVKHGFS 1cg2A 143 :KGGNAVILHTLKLLKEYGVR T0318 325 :GKTVEINNTDAE 1cg2A 165 :GTITVLFNTDEE T0318 342 :ADGVFYAKE 1cg2A 183 :RDLIQEEAK T0318 353 :KATTIFDMA 1cg2A 192 :LADYVLSFE Number of specific fragments extracted= 11 number of extra gaps= 1 total=567 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 1a9xA/T0318-1a9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a9xA expands to /projects/compbio/data/pdb/1a9x.pdb.gz 1a9xA:Skipped atom 3749, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3751, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3753, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3755, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3757, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3759, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3761, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3984, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3986, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3988, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 3990, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 4283, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 4285, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 4287, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 4289, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 5865, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 5867, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 5869, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 5871, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 6242, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 6244, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 6246, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 6248, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 6250, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7199, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7201, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7203, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7205, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7680, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7682, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7684, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7686, because occupancy 0.500 <= existing 0.500 in 1a9xA Skipped atom 7688, because occupancy 0.500 <= existing 0.500 in 1a9xA # T0318 read from 1a9xA/T0318-1a9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xA read from 1a9xA/T0318-1a9xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a9xA to template set # found chain 1a9xA in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)D558 T0318 83 :RGNTPTNAHSIYKELKP 1a9xA 417 :DPEALTKIRRELKDAGA T0318 116 :EYPDVLSHVAA 1a9xA 434 :DRIWYIADAFR T0318 153 :DKLTNEDA 1a9xA 445 :AGLSVDGV T0318 161 :VFLTDLSESVRETARLIDTPANILTTDALVD 1a9xA 461 :WFLVQIEELVRLEEKVAEVGITGLNADFLRQ T0318 192 :EAVKVGNATGSKITVIR 1a9xA 512 :EIRKLRDQYDLHPVYKR T0318 217 :FGGIYHVGKAGPTPPA 1a9xA 538 :TDTAYMYSTYEEECEA T0318 239 :EVP 1a9xA 554 :NPS T0318 244 :TEHIALVGKGVVY 1a9xA 559 :REKIMVLGGGPNR T0318 272 :MKRDMGGAAGMLEAYSALVKHGF 1a9xA 572 :IGQGIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNVSPIA 1a9xA 595 :ETIMVNCNPETVSTDYD T0318 324 :SGKTVEINNTDAE 1a9xA 612 :TSDRLYFEPVTLE T0318 343 :DGVFYA 1a9xA 625 :DVLEIV T0318 350 :ETLKATTIF 1a9xA 631 :RIEKPKGVI T0318 361 :ATLTGAQAW 1a9xA 640 :VQYGGQTPL T0318 370 :LSGRLHGAAMTNDEQL 1a9xA 654 :LEAAGVPVIGTSPDAI T0318 386 :ENEIIKAGKASGDLVAPM 1a9xA 675 :RERFQHAVERLKLKQPAN T0318 404 :LFAPDLFFGDLKS 1a9xA 695 :VTAIEMAVEKAKE Number of specific fragments extracted= 17 number of extra gaps= 1 total=584 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 1a9xA/T0318-1a9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1a9xA/T0318-1a9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xA read from 1a9xA/T0318-1a9xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a9xA in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)D558 Warning: unaligning (T0318)G442 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)T740 Warning: unaligning (T0318)A443 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)T740 Warning: unaligning (T0318)H444 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a9xA)V750 Warning: unaligning (T0318)I445 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a9xA)V750 T0318 76 :TVPDASSRGN 1a9xA 408 :GFDPKVSLDD T0318 87 :PTNAHSIYKELKPINYP 1a9xA 418 :PEALTKIRRELKDAGAD T0318 120 :VLSHVAAIARTFCKFSMKTS 1a9xA 435 :RIWYIADAFRAGLSVDGVFN T0318 160 :AVFLTDLSESVRETARLIDTPANILTTDALVD 1a9xA 460 :RWFLVQIEELVRLEEKVAEVGITGLNADFLRQ T0318 192 :EAVKVGNATGSKITVIR 1a9xA 512 :EIRKLRDQYDLHPVYKR T0318 217 :FGGIYHVGKAGPTPPA 1a9xA 538 :TDTAYMYSTYEEECEA T0318 239 :EVP 1a9xA 554 :NPS T0318 244 :TEHIALVGKGVV 1a9xA 559 :REKIMVLGGGPN T0318 271 :NMKRDMGGAAGMLEAYSALVKHGF 1a9xA 571 :RIGQGIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNVSPIAN 1a9xA 595 :ETIMVNCNPETVSTDYDT T0318 325 :GKTVEINNTDAE 1a9xA 613 :SDRLYFEPVTLE T0318 343 :DGVFYA 1a9xA 625 :DVLEIV T0318 350 :ETLKATTIF 1a9xA 631 :RIEKPKGVI T0318 361 :ATLTGAQAW 1a9xA 640 :VQYGGQTPL T0318 370 :LSGRLHGAAMTNDEQL 1a9xA 654 :LEAAGVPVIGTSPDAI T0318 386 :ENEIIKAGKASGDLVAPM 1a9xA 675 :RERFQHAVERLKLKQPAN T0318 404 :LFAPDLFFGDLKSS 1a9xA 695 :VTAIEMAVEKAKEI T0318 425 :NLG 1a9xA 709 :GYP T0318 430 :DG 1a9xA 729 :YD T0318 434 :SAVAGLLI 1a9xA 731 :EADLRRYF T0318 446 :GFGEGLRWLHLDIAAPA 1a9xA 754 :HFLDDAVEVDVDAICDG T0318 467 :RGTGYGPALFSTLLGK 1a9xA 800 :TLSQEIQDVMRQQVQK Number of specific fragments extracted= 22 number of extra gaps= 2 total=606 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 1a9xA/T0318-1a9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1a9xA/T0318-1a9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a9xA read from 1a9xA/T0318-1a9xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a9xA in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1a9xA)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1a9xA)D558 T0318 74 :LITVPDASSRGNTPTNAHSI 1a9xA 446 :GLSVDGVFNLTNIDRWFLVQ T0318 117 :YPDVLSHVAAIART 1a9xA 466 :IEELVRLEEKVAEV T0318 151 :VCDKLTNEDAVFLTDLSESVRETARLIDTP 1a9xA 480 :GITGLNADFLRQLKRKGFADARLAKLAGVR T0318 190 :VDEAVKVGNATGSKITVIR 1a9xA 510 :EAEIRKLRDQYDLHPVYKR T0318 223 :VGKAG 1a9xA 529 :VDTCA T0318 228 :PTPPAFVVLSHEVP 1a9xA 537 :ATDTAYMYSTYEEE T0318 244 :TEHIALVGKG 1a9xA 559 :REKIMVLGGG T0318 262 :QIKTK 1a9xA 569 :PNRIG T0318 274 :RDMGGAAGMLEAYSALVKHGF 1a9xA 574 :QGIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNV 1a9xA 595 :ETIMVNCNPETVS T0318 333 :TDAEGR 1a9xA 608 :TDYDTS T0318 339 :LILADGVFYA 1a9xA 621 :VTLEDVLEIV T0318 350 :ETLKATTIF 1a9xA 631 :RIEKPKGVI T0318 363 :LTGAQAWLSGR 1a9xA 650 :LARALEAAGVP T0318 377 :AAMTNDEQL 1a9xA 661 :VIGTSPDAI T0318 386 :ENEIIKAGKASG 1a9xA 675 :RERFQHAVERLK Number of specific fragments extracted= 16 number of extra gaps= 1 total=622 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 1lokA/T0318-1lokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lokA expands to /projects/compbio/data/pdb/1lok.pdb.gz 1lokA:Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 1lokA Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 1lokA Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1lokA Skipped atom 161, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 163, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 165, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 235, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 316, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 318, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 395, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 402, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 404, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 406, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 408, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 496, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 510, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 512, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 514, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 516, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 828, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 830, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 832, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 834, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1083, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1187, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1189, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1191, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1193, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1195, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1342, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1344, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1613, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1615, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1724, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1726, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1728, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1730, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1732, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 1734, because occupancy 1.000 <= existing 1.000 in 1lokA Skipped atom 2097, because occupancy 1.000 <= existing 1.000 in 1lokA # T0318 read from 1lokA/T0318-1lokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lokA read from 1lokA/T0318-1lokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lokA to template set # found chain 1lokA in template set Warning: unaligning (T0318)A199 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)L60 Warning: unaligning (T0318)T200 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)L60 Warning: unaligning (T0318)G201 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N62 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)D118 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N182 T0318 168 :ESVRETARLIDTPANILT 1lokA 21 :QITGTISSLESFTNRFYT T0318 186 :TDALVDEAVKVGN 1lokA 46 :SDWIASEWQALSA T0318 202 :SKITVIR 1lokA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1lokA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGGLQIKTKTGMPNMK 1lokA 100 :STIGSHTNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGFS 1lokA 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLCIVEN 1lokA 141 :RSIAFMAYAAEE T0318 336 :EGR 1lokA 156 :RGS T0318 343 :DGVFYAKET 1lokA 160 :DLANQYKSE T0318 352 :LKATTIFDMAT 1lokA 170 :KNVVSALQLDM T0318 365 :G 1lokA 183 :Y T0318 371 :SGRLHGAAM 1lokA 184 :KGSAQDVVF T0318 380 :TNDEQLENEIIKAGKA 1lokA 196 :YTDSNFTQYLTQLMDE T0318 410 :FFGDLKS 1lokA 212 :YLPSLTY T0318 425 :NLGKMDGPPSAVAGLL 1lokA 219 :GFDTCGYACSDHASWH T0318 449 :EGLRWL 1lokA 236 :AGYPAA T0318 460 :APAE 1lokA 242 :MPFE T0318 465 :GD 1lokA 246 :SK T0318 467 :RGTGYGPALFSTLLG 1lokA 266 :DPTGSHAKKFTQLGL Number of specific fragments extracted= 19 number of extra gaps= 4 total=641 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 1lokA/T0318-1lokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lokA/T0318-1lokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lokA read from 1lokA/T0318-1lokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lokA in template set Warning: unaligning (T0318)A199 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)L60 Warning: unaligning (T0318)T200 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)L60 Warning: unaligning (T0318)G201 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N62 Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)D118 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N182 T0318 92 :SIYKELKPI 1lokA 9 :TVTAWLPQV T0318 116 :EYPDVLSHVAAIA 1lokA 18 :DASQITGTISSLE T0318 133 :KFSMKTS 1lokA 31 :SFTNRFY T0318 154 :KL 1lokA 38 :TT T0318 171 :RETARL 1lokA 40 :TSGAQA T0318 186 :TDALVDEAVKVGN 1lokA 46 :SDWIASEWQALSA T0318 202 :SKITVIR 1lokA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1lokA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGGLQIKTKTGMPNMK 1lokA 100 :STIGSHTNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGF 1lokA 119 :ASGIAAVTEVIRVLSENNF T0318 295 :SQTLHACLCIVEN 1lokA 140 :KRSIAFMAYAAEE T0318 336 :EGR 1lokA 156 :RGS T0318 342 :ADGVFYAKET 1lokA 159 :QDLANQYKSE T0318 352 :LKATTIFDMAT 1lokA 170 :KNVVSALQLDM T0318 365 :G 1lokA 183 :Y T0318 371 :SGRLHGAAM 1lokA 184 :KGSAQDVVF T0318 380 :TNDEQLENEIIKAGKA 1lokA 196 :YTDSNFTQYLTQLMDE T0318 410 :FFGDLK 1lokA 212 :YLPSLT T0318 424 :SNLGKMDGPPSAVAGLL 1lokA 218 :YGFDTCGYACSDHASWH T0318 448 :GEGLRWL 1lokA 235 :NAGYPAA T0318 456 :LDI 1lokA 242 :MPF T0318 467 :RGTGYGPALFSTLLG 1lokA 266 :DPTGSHAKKFTQLGL Number of specific fragments extracted= 22 number of extra gaps= 4 total=663 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 1lokA/T0318-1lokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1lokA/T0318-1lokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lokA read from 1lokA/T0318-1lokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lokA in template set Warning: unaligning (T0318)G201 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N62 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)D118 Warning: unaligning (T0318)L363 because of BadResidue code BAD_PEPTIDE in next template residue (1lokA)N182 Warning: unaligning (T0318)T364 because of BadResidue code BAD_PEPTIDE at template residue (1lokA)N182 T0318 166 :LSESVRETARLIDTPANILTTDALVD 1lokA 19 :ASQITGTISSLESFTNRFYTTTSGAQ T0318 192 :EAVKVGNAT 1lokA 48 :WIASEWQAL T0318 202 :SKITVIR 1lokA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 1lokA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTKTGMPNMKR 1lokA 98 :LDSTIGSHTNEQSV T0318 276 :MGGAAGMLEAYSALVKHGFS 1lokA 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLCIVEN 1lokA 141 :RSIAFMAYAAEE T0318 309 :VSP 1lokA 153 :VGL T0318 343 :DGVFYAKET 1lokA 160 :DLANQYKSE T0318 352 :LKATTIFDMAT 1lokA 170 :KNVVSALQLDM T0318 371 :SGRLHGAAMTND 1lokA 184 :KGSAQDVVFITD T0318 383 :EQLENEIIKAGKAS 1lokA 199 :SNFTQYLTQLMDEY T0318 406 :APDL 1lokA 213 :LPSL T0318 418 :IADMKNSNL 1lokA 217 :TYGFDTCGY T0318 430 :DGPPSA 1lokA 226 :ACSDHA T0318 439 :LLIG 1lokA 232 :SWHN T0318 449 :EGLRWLHLDIAAPAE 1lokA 236 :AGYPAAMPFESKFND T0318 464 :VGDRGTGYGPALFSTLLGKYTSV 1lokA 256 :HTTQDTLANSDPTGSHAKKFTQL Number of specific fragments extracted= 18 number of extra gaps= 3 total=681 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 1amp/T0318-1amp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1amp expands to /projects/compbio/data/pdb/1amp.pdb.gz 1amp:Warning: there is no chain 1amp will retry with 1ampA # T0318 read from 1amp/T0318-1amp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1amp read from 1amp/T0318-1amp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1amp to template set # found chain 1amp in template set Warning: unaligning (T0318)N198 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)S59 Warning: unaligning (T0318)A199 because of BadResidue code BAD_PEPTIDE at template residue (1amp)S59 Warning: unaligning (T0318)R274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1amp)D118 Warning: unaligning (T0318)D275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1amp)D118 Warning: unaligning (T0318)A361 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)M180 Warning: unaligning (T0318)T362 because of BadResidue code BAD_PEPTIDE at template residue (1amp)M180 T0318 167 :SESVRETARLIDTPANI 1amp 20 :SQITGTISSLESFTNRF T0318 186 :TDALVDEAVKVG 1amp 46 :SDWIASEWQALS T0318 200 :TG 1amp 60 :LP T0318 202 :SKITVIR 1amp 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1amp 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGGLQIKTKTGMPNMK 1amp 100 :STIGSHTNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGFS 1amp 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLCIVENN 1amp 141 :RSIAFMAYAAEEV T0318 335 :AEGRL 1amp 155 :LRGSQ T0318 343 :DGVFYAKET 1amp 160 :DLANQYKSE T0318 352 :LKATTIFDM 1amp 170 :KNVVSALQL T0318 363 :LTG 1amp 181 :TNY T0318 371 :SGRLHGAAM 1amp 184 :KGSAQDVVF T0318 380 :TNDEQLENEIIKAGK 1amp 196 :YTDSNFTQYLTQLMD T0318 412 :GDLKSSIADMK 1amp 211 :EYLPSLTYGFD T0318 428 :KMDGPPSAVAGLL 1amp 222 :TCGYACSDHASWH T0318 449 :EGLRW 1amp 236 :AGYPA T0318 459 :AAPAE 1amp 241 :AMPFE T0318 465 :GD 1amp 246 :SK T0318 467 :RGTGYGPALFSTLLGKY 1amp 266 :DPTGSHAKKFTQLGLAY Number of specific fragments extracted= 20 number of extra gaps= 3 total=701 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 1amp/T0318-1amp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1amp/T0318-1amp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1amp read from 1amp/T0318-1amp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1amp in template set Warning: unaligning (T0318)N198 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)S59 Warning: unaligning (T0318)A199 because of BadResidue code BAD_PEPTIDE at template residue (1amp)S59 Warning: unaligning (T0318)R274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1amp)D118 Warning: unaligning (T0318)D275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1amp)D118 Warning: unaligning (T0318)A361 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)M180 Warning: unaligning (T0318)T362 because of BadResidue code BAD_PEPTIDE at template residue (1amp)M180 T0318 92 :SIYKELKPI 1amp 9 :TVTAWLPQV T0318 116 :EYPDVLSHVAAIA 1amp 18 :DASQITGTISSLE T0318 133 :KFSMKT 1amp 31 :SFTNRF T0318 153 :DKL 1amp 37 :YTT T0318 158 :E 1amp 40 :T T0318 165 :DLSES 1amp 41 :SGAQA T0318 186 :TDALVDEAVKVG 1amp 46 :SDWIASEWQALS T0318 200 :TG 1amp 60 :LP T0318 202 :SKITVIR 1amp 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKGVV 1amp 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGHLD T0318 257 :DTGGLQIKTKTGMPNMK 1amp 100 :STIGSHTNEQSVAPGAD T0318 276 :MGGAAGMLEAYSALVKHGFS 1amp 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLCIVENN 1amp 141 :RSIAFMAYAAEEV T0318 335 :AEGRL 1amp 155 :LRGSQ T0318 343 :DGVFYAKET 1amp 160 :DLANQYKSE T0318 352 :LKATTIFDM 1amp 170 :KNVVSALQL T0318 363 :LTG 1amp 181 :TNY T0318 371 :SGRLHGAAM 1amp 184 :KGSAQDVVF T0318 380 :TNDEQLENEIIKAGK 1amp 196 :YTDSNFTQYLTQLMD T0318 412 :GDLKSSIAD 1amp 211 :EYLPSLTYG T0318 426 :LGKMDGPPSAVAGLL 1amp 220 :FDTCGYACSDHASWH T0318 448 :GEGLRW 1amp 235 :NAGYPA T0318 459 :AAPA 1amp 241 :AMPF T0318 467 :RGTGYGPALFSTLLGKY 1amp 266 :DPTGSHAKKFTQLGLAY Number of specific fragments extracted= 24 number of extra gaps= 3 total=725 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 1amp/T0318-1amp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1amp/T0318-1amp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1amp read from 1amp/T0318-1amp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1amp in template set Warning: unaligning (T0318)N198 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)S59 Warning: unaligning (T0318)A199 because of BadResidue code BAD_PEPTIDE at template residue (1amp)S59 Warning: unaligning (T0318)D275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1amp)D118 Warning: unaligning (T0318)A361 because of BadResidue code BAD_PEPTIDE in next template residue (1amp)M180 Warning: unaligning (T0318)T362 because of BadResidue code BAD_PEPTIDE at template residue (1amp)M180 T0318 166 :LSESVRETARLIDTPANILT 1amp 19 :ASQITGTISSLESFTNRFYT T0318 186 :TDALVDEAVKVG 1amp 46 :SDWIASEWQALS T0318 200 :T 1amp 60 :L T0318 201 :GSKITVIR 1amp 62 :NASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 1amp 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTKTGMPNMKR 1amp 98 :LDSTIGSHTNEQSV T0318 276 :MGGAAGMLEAYSALVKHGFS 1amp 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QTLHACLCIVEN 1amp 141 :RSIAFMAYAAEE T0318 309 :VSPI 1amp 153 :VGLR T0318 343 :DGVFYAKET 1amp 160 :DLANQYKSE T0318 352 :LKATTIFDM 1amp 170 :KNVVSALQL T0318 363 :LT 1amp 181 :TN T0318 371 :SGRLHGAAMTND 1amp 184 :KGSAQDVVFITD T0318 383 :EQLENEIIKAGKA 1amp 199 :SNFTQYLTQLMDE T0318 413 :DLKSSIADMKNSNL 1amp 212 :YLPSLTYGFDTCGY T0318 430 :DGPPS 1amp 226 :ACSDH T0318 438 :GLLIG 1amp 231 :ASWHN T0318 449 :EGLRWLHLDI 1amp 236 :AGYPAAMPFE T0318 459 :AAPAEVGDRGTGYGPALFSTLLGKYTSV 1amp 251 :YNPRIHTTQDTLANSDPTGSHAKKFTQL Number of specific fragments extracted= 19 number of extra gaps= 3 total=744 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 2anpA/T0318-2anpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2anpA expands to /projects/compbio/data/pdb/2anp.pdb.gz 2anpA:# T0318 read from 2anpA/T0318-2anpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anpA read from 2anpA/T0318-2anpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2anpA to template set # found chain 2anpA in template set Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (2anpA)D118 T0318 157 :NEDAVFLTD 2anpA 7 :QATVTAWLP T0318 166 :LSESVRETARLIDTPANILTTDALV 2anpA 19 :ASQITGTISSLESFTNRFYTTTSGA T0318 191 :DEAVKVGNAT 2anpA 47 :DWIASEWQAL T0318 201 :G 2anpA 61 :P T0318 202 :SKITVIR 2anpA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 2anpA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTKTGMPNMKR 2anpA 98 :LDSTIGSHTNEQSV T0318 276 :MGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSPI 2anpA 119 :ASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAHEVGL T0318 343 :DGVFYAKET 2anpA 160 :DLANQYKSE T0318 352 :LKATTIFDMATLT 2anpA 170 :KNVVSALQLDMTN T0318 370 :LSGRLHGAAMTND 2anpA 183 :YKGSAQDVVFITD T0318 383 :EQLENEIIKAGKA 2anpA 199 :SNFTQYLTQLMDE T0318 413 :DLKSSIADMKNS 2anpA 212 :YLPSLTYGFDTC T0318 428 :KMDGPPSAVAG 2anpA 224 :GYACSDHASWH T0318 448 :GEGLRWL 2anpA 235 :NAGYPAA T0318 461 :PAEVGD 2anpA 242 :MPFESK T0318 467 :RGTGYGPALFSTLLGK 2anpA 266 :DPTGSHAKKFTQLGLA Number of specific fragments extracted= 17 number of extra gaps= 1 total=761 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 2anpA/T0318-2anpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 2anpA/T0318-2anpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anpA read from 2anpA/T0318-2anpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2anpA in template set Warning: unaligning (T0318)R274 because of BadResidue code BAD_PEPTIDE in next template residue (2anpA)D118 Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (2anpA)D118 T0318 166 :LSESVRETARLIDTPANILT 2anpA 19 :ASQITGTISSLESFTNRFYT T0318 186 :TDALVDEAVKVGNATG 2anpA 46 :SDWIASEWQALSASLP T0318 202 :SKITVIR 2anpA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 2anpA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTKTGMPN 2anpA 98 :LDSTIGSHTNE T0318 272 :MK 2anpA 115 :AD T0318 276 :MGGAAGMLEAYSALVKHGFSQTLHACLCIVENNVSP 2anpA 119 :ASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAHEVG T0318 342 :A 2anpA 158 :S T0318 343 :DGVFYAKET 2anpA 160 :DLANQYKSE T0318 352 :LKATTIFDMATLT 2anpA 170 :KNVVSALQLDMTN T0318 370 :LSGRLHGAAMTND 2anpA 183 :YKGSAQDVVFITD T0318 383 :EQLENEIIKAGKAS 2anpA 199 :SNFTQYLTQLMDEY T0318 411 :FGDLK 2anpA 213 :LPSLT T0318 424 :SNLGKMDGPPSAVAGLL 2anpA 218 :YGFDTCGYACSDHASWH T0318 448 :GEGLRWLHLDIAAP 2anpA 235 :NAGYPAAMPFESKF T0318 467 :RGTGYGPALFSTLLGK 2anpA 266 :DPTGSHAKKFTQLGLA Number of specific fragments extracted= 16 number of extra gaps= 1 total=777 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 2anpA/T0318-2anpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 2anpA/T0318-2anpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anpA read from 2anpA/T0318-2anpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2anpA in template set Warning: unaligning (T0318)D275 because of BadResidue code BAD_PEPTIDE at template residue (2anpA)D118 T0318 166 :LSESVRETARLIDTPANILT 2anpA 19 :ASQITGTISSLESFTNRFYT T0318 186 :TDALVDEAVKVGNATG 2anpA 46 :SDWIASEWQALSASLP T0318 202 :SKITVIR 2anpA 63 :ASVKQVS T0318 226 :AGPTPPAFVVLSHEVPGSTEHIALVGKG 2anpA 70 :HSGYNQKSVVMTITGSEAPDEWIVIGGH T0318 261 :LQIKTKTGMPNMKR 2anpA 98 :LDSTIGSHTNEQSV T0318 276 :MGGAAGMLEAYSALVKHGFS 2anpA 119 :ASGIAAVTEVIRVLSENNFQ T0318 296 :QT 2anpA 141 :RS T0318 299 :HACLCIVENNVSPI 2anpA 143 :IAFMAYAAHEVGLR T0318 343 :DGVFYAKET 2anpA 160 :DLANQYKSE T0318 352 :LKATTIFDMATLT 2anpA 170 :KNVVSALQLDMTN T0318 372 :GRLHGAAMTND 2anpA 185 :GSAQDVVFITD T0318 383 :EQLENEIIKAG 2anpA 199 :SNFTQYLTQLM T0318 411 :FGDLKSSIADMKNSNL 2anpA 210 :DEYLPSLTYGFDTCGY T0318 430 :DGPPS 2anpA 226 :ACSDH T0318 438 :GLLIG 2anpA 231 :ASWHN T0318 449 :EGLRWLHLDIAAPAE 2anpA 236 :AGYPAAMPFESKFND T0318 464 :VGDRGTGYGPALFSTLLGKYTSV 2anpA 256 :HTTQDTLANSDPTGSHAKKFTQL Number of specific fragments extracted= 17 number of extra gaps= 1 total=794 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 1cs0A/T0318-1cs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cs0A expands to /projects/compbio/data/pdb/1cs0.pdb.gz 1cs0A:Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 4294, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 4296, because occupancy 0.500 <= existing 0.500 in 1cs0A Skipped atom 7661, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7663, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7665, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7667, because occupancy 0.500 <= existing 1.000 in 1cs0A Skipped atom 7669, because occupancy 0.500 <= existing 1.000 in 1cs0A # T0318 read from 1cs0A/T0318-1cs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0A read from 1cs0A/T0318-1cs0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cs0A to template set # found chain 1cs0A in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0A)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 T0318 84 :GNTPTNAHSIYKELK 1cs0A 418 :PEALTKIRRELKDAG T0318 114 :FAEYPDVLSHVA 1cs0A 433 :ADRIWYIADAFR T0318 153 :DKLTNEDA 1cs0A 445 :AGLSVDGV T0318 161 :VFLTDLSESVRETARLIDTPANILTTDALVD 1cs0A 461 :WFLVQIEELVRLEEKVAEVGITGLNADFLRQ T0318 192 :EAVKVGNATGSKITVIR 1cs0A 512 :EIRKLRDQYDLHPVYKR T0318 223 :VGKAGP 1cs0A 529 :VDTCAA T0318 229 :TPPAFVVLSHEVP 1cs0A 538 :TDTAYMYSTYEEE T0318 244 :TEHIALVGKG 1cs0A 559 :REKIMVLGGG T0318 262 :QIKTKT 1cs0A 569 :PNRIGQ T0318 275 :DMGGAAGMLEAYSALVKHGF 1cs0A 575 :GIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNVSPIANK 1cs0A 595 :ETIMVNCNPETVSTDYDTS T0318 326 :KTVEIN 1cs0A 614 :DRLYFE T0318 338 :RLILADGVFYA 1cs0A 620 :PVTLEDVLEIV T0318 350 :ETLKATTIFDMAT 1cs0A 631 :RIEKPKGVIVQYG T0318 363 :LTGAQ 1cs0A 650 :LARAL T0318 369 :WLSG 1cs0A 655 :EAAG T0318 375 :HGAAMTNDEQL 1cs0A 659 :VPVIGTSPDAI T0318 386 :ENEIIKAGKASG 1cs0A 675 :RERFQHAVERLK Number of specific fragments extracted= 18 number of extra gaps= 1 total=812 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 1cs0A/T0318-1cs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1cs0A/T0318-1cs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0A read from 1cs0A/T0318-1cs0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs0A in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0A)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 T0318 15 :DGLTSLIIV 1cs0A 352 :IDYVVTKIP T0318 24 :GKKSVLK 1cs0A 363 :NFEKFAG T0318 56 :ISRIPASGRHPLHYELAHLIT 1cs0A 370 :ANDRLTTQMKSVGEVMAIGRT T0318 77 :VPDASSRGN 1cs0A 409 :FDPKVSLDD T0318 87 :PTNAHSIYKELKPIN 1cs0A 418 :PEALTKIRRELKDAG T0318 117 :YPDVLSHVAAIAR 1cs0A 433 :ADRIWYIADAFRA T0318 154 :KLTNED 1cs0A 446 :GLSVDG T0318 160 :AVFLTDLSESVRETARLIDTPANILTTDALVD 1cs0A 460 :RWFLVQIEELVRLEEKVAEVGITGLNADFLRQ T0318 192 :EAVKVGNATGSKITVIR 1cs0A 512 :EIRKLRDQYDLHPVYKR T0318 223 :VGKAG 1cs0A 529 :VDTCA T0318 228 :PTPPAFVVLSHEVP 1cs0A 537 :ATDTAYMYSTYEEE T0318 244 :TEHIALVGKG 1cs0A 559 :REKIMVLGGG T0318 262 :QIKTK 1cs0A 569 :PNRIG T0318 274 :RDMGGAAGMLEAYSALVKHGF 1cs0A 574 :QGIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNVSPIA 1cs0A 595 :ETIMVNCNPETVSTDYD T0318 335 :AEG 1cs0A 612 :TSD T0318 338 :RLILADGVFYA 1cs0A 620 :PVTLEDVLEIV T0318 350 :ETLKATTIFDMAT 1cs0A 631 :RIEKPKGVIVQYG T0318 363 :LTGA 1cs0A 650 :LARA T0318 368 :AWLSG 1cs0A 654 :LEAAG T0318 375 :HGAAMTNDEQL 1cs0A 659 :VPVIGTSPDAI T0318 386 :ENEIIKAGKASG 1cs0A 675 :RERFQHAVERLK Number of specific fragments extracted= 22 number of extra gaps= 1 total=834 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 1cs0A/T0318-1cs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1cs0A/T0318-1cs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs0A read from 1cs0A/T0318-1cs0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs0A in template set Warning: unaligning (T0318)G242 because of BadResidue code BAD_PEPTIDE in next template residue (1cs0A)D558 Warning: unaligning (T0318)S243 because of BadResidue code BAD_PEPTIDE at template residue (1cs0A)D558 T0318 74 :LITVPDASSRGNTPTNAHSI 1cs0A 446 :GLSVDGVFNLTNIDRWFLVQ T0318 117 :YPDVLSHVAAIART 1cs0A 466 :IEELVRLEEKVAEV T0318 151 :VCDKLTNEDAVFLTDLSESVRETARLIDTP 1cs0A 480 :GITGLNADFLRQLKRKGFADARLAKLAGVR T0318 190 :VDEAVKVGNATGSKITVIR 1cs0A 510 :EAEIRKLRDQYDLHPVYKR T0318 223 :VGKAG 1cs0A 529 :VDTCA T0318 228 :PTPPAFVVLSHEVP 1cs0A 537 :ATDTAYMYSTYEEE T0318 244 :TEHIALVGKG 1cs0A 559 :REKIMVLGGG T0318 262 :QIKTK 1cs0A 569 :PNRIG T0318 274 :RDMGGAAGMLEAYSALVKHGF 1cs0A 574 :QGIEFDYCCVHASLALREDGY T0318 297 :TLHACLCIVENNVSPIA 1cs0A 595 :ETIMVNCNPETVSTDYD T0318 335 :AEGR 1cs0A 612 :TSDR T0318 339 :LILADGVFYA 1cs0A 621 :VTLEDVLEIV T0318 350 :ETLKATTIF 1cs0A 631 :RIEKPKGVI T0318 363 :LTGAQAWL 1cs0A 650 :LARALEAA T0318 374 :LHGAAMTNDEQL 1cs0A 658 :GVPVIGTSPDAI T0318 386 :ENEIIKAGKASG 1cs0A 675 :RERFQHAVERLK Number of specific fragments extracted= 16 number of extra gaps= 1 total=850 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 1ysjA/T0318-1ysjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ysjA expands to /projects/compbio/data/pdb/1ysj.pdb.gz 1ysjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 1ysjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1686, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1688, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1690, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 1ysjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1898, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1900, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1902, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1904, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1906, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1910, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 1ysjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2167, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2169, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2171, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2173, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2175, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2177, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2179, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 1ysjA Skipped atom 2183, because occupancy 0.500 <= existing 0.500 in 1ysjA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0318 read from 1ysjA/T0318-1ysjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysjA read from 1ysjA/T0318-1ysjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ysjA to template set # found chain 1ysjA in template set Warning: unaligning (T0318)T156 because first residue in template chain is (1ysjA)A2 Warning: unaligning (T0318)M360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ysjA)H158 Warning: unaligning (T0318)A361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ysjA)H158 T0318 157 :NEDAV 1ysjA 3 :DKAFH T0318 167 :SESVRETARLIDTPANILTTDALVDEAVKVGNATGSKI 1ysjA 8 :TRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEI T0318 227 :GPTPPAFVVLSH 1ysjA 50 :QLKTGVIAEIKG T0318 242 :GSTEHIAL 1ysjA 62 :REDGPVIA T0318 254 :VVYDTGGLQIKTKTGMPNMKR 1ysjA 70 :IRADIDALPIQEQTNLPFASK T0318 275 :DMGG 1ysjA 96 :HACG T0318 279 :AAGMLEAYSALVK 1ysjA 104 :TASIIGTAMLLNQ T0318 315 :KPDDI 1ysjA 117 :RRAEL T0318 324 :SG 1ysjA 122 :KG T0318 327 :TVEINNTDAE 1ysjA 124 :TVRFIFQPAE T0318 344 :GVFYAKET 1ysjA 138 :GARKVLEA T0318 352 :LKATTIFD 1ysjA 149 :NGVSAIFG T0318 362 :T 1ysjA 159 :N Number of specific fragments extracted= 13 number of extra gaps= 1 total=863 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 1ysjA/T0318-1ysjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1ysjA/T0318-1ysjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysjA read from 1ysjA/T0318-1ysjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ysjA in template set Warning: unaligning (T0318)T156 because first residue in template chain is (1ysjA)A2 Warning: unaligning (T0318)M360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ysjA)H158 Warning: unaligning (T0318)A361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ysjA)H158 T0318 157 :NEDAV 1ysjA 3 :DKAFH T0318 167 :SESVRETARLIDTPANILTTDALVDEAVKVGNATGSKI 1ysjA 8 :TRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEI T0318 227 :GPTPPAFVVLSH 1ysjA 50 :QLKTGVIAEIKG T0318 242 :GSTEHIAL 1ysjA 62 :REDGPVIA T0318 254 :VVYDTGGLQIKTKTGMPNMKR 1ysjA 70 :IRADIDALPIQEQTNLPFASK T0318 275 :DMGG 1ysjA 96 :HACG T0318 279 :AAGMLEAYSALVK 1ysjA 104 :TASIIGTAMLLNQ T0318 315 :KPDDI 1ysjA 117 :RRAEL T0318 324 :SG 1ysjA 122 :KG T0318 327 :TVEINNTDAEG 1ysjA 124 :TVRFIFQPAEE T0318 342 :ADGVFYAKET 1ysjA 136 :AAGARKVLEA T0318 353 :KATTIFD 1ysjA 150 :GVSAIFG T0318 362 :T 1ysjA 159 :N Number of specific fragments extracted= 13 number of extra gaps= 1 total=876 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 1ysjA/T0318-1ysjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1ysjA/T0318-1ysjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysjA read from 1ysjA/T0318-1ysjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ysjA in template set Warning: unaligning (T0318)L155 because first residue in template chain is (1ysjA)A2 Warning: unaligning (T0318)M360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ysjA)H158 Warning: unaligning (T0318)A361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ysjA)H158 T0318 156 :TNEDA 1ysjA 3 :DKAFH T0318 167 :SESVRETARLIDTPANILTTDALVDEAVKVGNATGSKI 1ysjA 8 :TRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEI T0318 227 :GPTPPAFVVLSH 1ysjA 50 :QLKTGVIAEIKG T0318 241 :PGS 1ysjA 62 :RED T0318 245 :EHIAL 1ysjA 65 :GPVIA T0318 254 :VVYDTGGLQIKTKTGMPNMKR 1ysjA 70 :IRADIDALPIQEQTNLPFASK T0318 275 :DMGG 1ysjA 96 :HACG T0318 279 :AAGMLEAYSALVK 1ysjA 104 :TASIIGTAMLLNQ T0318 315 :KPDDI 1ysjA 117 :RRAEL T0318 324 :S 1ysjA 122 :K T0318 326 :KTVEINNTDAE 1ysjA 123 :GTVRFIFQPAE T0318 344 :GVFYAKET 1ysjA 138 :GARKVLEA T0318 352 :LKATTIFD 1ysjA 149 :NGVSAIFG T0318 362 :TLTG 1ysjA 159 :NKPD T0318 383 :EQLENEIIKA 1ysjA 203 :IAAAGQIISG Number of specific fragments extracted= 15 number of extra gaps= 1 total=891 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 1u9yA/T0318-1u9yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u9yA expands to /projects/compbio/data/pdb/1u9y.pdb.gz 1u9yA:# T0318 read from 1u9yA/T0318-1u9yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9yA read from 1u9yA/T0318-1u9yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u9yA to template set # found chain 1u9yA in template set Warning: unaligning (T0318)R208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9yA)I196 Warning: unaligning (T0318)H238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9yA)I196 T0318 33 :TFEGKFKEVAQKF 1u9yA 12 :LAFKVAKLLNTKL T0318 46 :VTDGDSWNSMISRIPASGRHPLHYE 1u9yA 32 :FPDNEIYVRIVDEINDDEAVIINTQ T0318 75 :ITVPDASSRGNTPTNAHSIYKELKP 1u9yA 57 :KNQNDAIVETILLCDALRDEGVKKI T0318 100 :INYPEDTKNVHFVLFA 1u9yA 85 :APYLAYARQDKKFNPG T0318 116 :EYPDVLSHVAAIARTF 1u9yA 104 :SIRALAKIYSNIVDKL T0318 134 :FSMKTSGIRELNVNIDVV 1u9yA 125 :HETHIKDFFTIPFIYGDA T0318 170 :VRETARLIDTPANIL 1u9yA 143 :VPKLAEYVKDKLNDP T0318 185 :TTDALVDEAVKVG 1u9yA 165 :GALEFAKTASKIL T0318 201 :GSKITVI 1u9yA 178 :NAEYDYL T0318 239 :EVPG 1u9yA 197 :APKT T0318 243 :STEHIALVGKGV 1u9yA 204 :KDRDVFIVDDII T0318 266 :KT 1u9yA 217 :TG T0318 280 :AGMLEAYSALVKHGFS 1u9yA 219 :GTMATAVKLLKEQGAK T0318 298 :LHACLCI 1u9yA 236 :IIAACVH T0318 307 :NNVSPI 1u9yA 243 :PVLIGD T0318 344 :GVFYAKET 1u9yA 249 :ALNKLYSA T0318 353 :KATTIFDMAT 1u9yA 257 :GVEEVVGTDT Number of specific fragments extracted= 17 number of extra gaps= 0 total=908 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 1u9yA/T0318-1u9yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1u9yA/T0318-1u9yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9yA read from 1u9yA/T0318-1u9yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u9yA in template set Warning: unaligning (T0318)R208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9yA)I196 Warning: unaligning (T0318)H238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9yA)I196 T0318 19 :SLIIVGK 1u9yA 2 :IVVSGSQ T0318 38 :FKEVAQKFVTDGDSWNSMISRIPASGRH 1u9yA 9 :SQNLAFKVAKLLNTKLTRVEYKRFPDNE T0318 66 :PLHYELAHLITV 1u9yA 46 :NDDEAVIINTQK T0318 82 :SRGNTPTNAHSIYKELKPINYPEDTKNVHFVL 1u9yA 58 :NQNDAIVETILLCDALRDEGVKKITLVAPYLA T0318 117 :YPDVLSHVAAIARTFCK 1u9yA 102 :AISIRALAKIYSNIVDK T0318 134 :FSMKTS 1u9yA 126 :ETHIKD T0318 143 :ELNVNIDVVC 1u9yA 132 :FFTIPFIYGD T0318 166 :LSESVRETARLIDTP 1u9yA 143 :VPKLAEYVKDKLNDP T0318 182 :NILTTDALVDEAVKVG 1u9yA 162 :PDKGALEFAKTASKIL T0318 201 :GSKITVI 1u9yA 178 :NAEYDYL T0318 239 :EVPG 1u9yA 197 :APKT T0318 243 :STEHIALVGKGV 1u9yA 204 :KDRDVFIVDDII T0318 266 :KT 1u9yA 217 :TG T0318 280 :AGMLEAYSALVKHGFS 1u9yA 219 :GTMATAVKLLKEQGAK T0318 298 :LHACLCI 1u9yA 236 :IIAACVH T0318 307 :NNVSPI 1u9yA 243 :PVLIGD T0318 344 :GVFYAKET 1u9yA 249 :ALNKLYSA T0318 353 :KATTIFDMA 1u9yA 257 :GVEEVVGTD Number of specific fragments extracted= 18 number of extra gaps= 0 total=926 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 1u9yA/T0318-1u9yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0318 read from 1u9yA/T0318-1u9yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u9yA read from 1u9yA/T0318-1u9yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u9yA in template set Warning: unaligning (T0318)R208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u9yA)I196 Warning: unaligning (T0318)H238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u9yA)I196 T0318 43 :QKFVTDGDSWNSMISRIPASGRHPLHY 1u9yA 29 :YKRFPDNEIYVRIVDEINDDEAVIINT T0318 74 :LITVPDASSRGNTPTNAHSIYKELKP 1u9yA 56 :QKNQNDAIVETILLCDALRDEGVKKI T0318 100 :INYPEDTKNVHFVLFAEYPDVLSHVAAIARTFCK 1u9yA 85 :APYLAYARQDKKFNPGEAISIRALAKIYSNIVDK T0318 134 :FSMKTSGIRELNVNIDVV 1u9yA 125 :HETHIKDFFTIPFIYGDA T0318 170 :VRETARLIDTPANIL 1u9yA 143 :VPKLAEYVKDKLNDP T0318 185 :TTDALVDEAVKVG 1u9yA 165 :GALEFAKTASKIL T0318 201 :GSKITVI 1u9yA 178 :NAEYDYL T0318 239 :EVPGS 1u9yA 197 :APKTL T0318 244 :TEHIALVGKGV 1u9yA 205 :DRDVFIVDDII T0318 266 :KT 1u9yA 217 :TG T0318 280 :AGMLEAYSALVKHGFS 1u9yA 219 :GTMATAVKLLKEQGAK T0318 298 :LHACLCI 1u9yA 236 :IIAACVH T0318 307 :NNVSPI 1u9yA 243 :PVLIGD T0318 344 :GVFYA 1u9yA 249 :ALNKL T0318 350 :ETLKATTIFDM 1u9yA 254 :YSAGVEEVVGT Number of specific fragments extracted= 15 number of extra gaps= 0 total=941 Will force an alignment to be made, even if fragment is small Number of alignments=57 # command:CPU_time= 24.670 sec, elapsed time= 26.740 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 57 Adding 7205 constraints to all_contacts Done adding distance constraints # command:CPU_time= 24.882 sec, elapsed time= 26.979 sec. # command:Reading probabilities from T0318.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 8.285 Optimizing... Probability sum: -878.366, CN propb: -878.366 weights: 0.314 constraints: 1641 # command:CPU_time= 1070.922 sec, elapsed time= 1075.317 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1641 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1641 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 5564 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 5564 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 1071.031 sec, elapsed time= 1075.498 sec. # command: