# 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 T0507 numbered 1 through 148 Created new target T0507 from T0507.a2m # command:CPU_time= 6.507 sec, elapsed time= 6.646 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qjcA/T0507-1qjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qjcA expands to /projects/compbio/data/pdb/1qjc.pdb.gz 1qjcA:# T0507 read from 1qjcA/T0507-1qjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjcA read from 1qjcA/T0507-1qjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qjcA to template set # found chain 1qjcA in template set Warning: unaligning (T0507)K2 because first residue in template chain is (1qjcA)K3 Warning: unaligning (T0507)I45 because of BadResidue code BAD_PEPTIDE in next template residue (1qjcA)K43 Warning: unaligning (T0507)R46 because of BadResidue code BAD_PEPTIDE at template residue (1qjcA)K43 T0507 3 :VAL 1qjcA 4 :RAI # choosing archetypes in rotamer library T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1qjcA 8 :PGTFDPITNGHIDIVTRATQMF T0507 29 :RDITIGVTS 1qjcA 30 :DHVILAIAA T0507 42 :RAR 1qjcA 39 :SPS T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKI 1qjcA 44 :PMFTLEERVALAQQATAHLGNVEVVGFSD T0507 77 :NPYG 1qjcA 73 :LMAN T0507 81 :KTLDVD 1qjcA 79 :RNQHAT T0507 89 :YLVVSPETYEMALKINQKREELGKR 1qjcA 85 :VLIRGLRAVADFEYEMQLAHMNRHL T0507 114 :KITIVKVDW 1qjcA 112 :ELESVFLMP T0507 125 :AEDGKPISSTRIKR 1qjcA 121 :SKEWSFISSSLVKE T0507 139 :GEIDRY 1qjcA 140 :GDVTHF Number of specific fragments extracted= 11 number of extra gaps= 1 total=11 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 1qjcA/T0507-1qjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1qjcA/T0507-1qjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjcA read from 1qjcA/T0507-1qjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qjcA in template set Warning: unaligning (T0507)I45 because of BadResidue code BAD_PEPTIDE in next template residue (1qjcA)K43 Warning: unaligning (T0507)R46 because of BadResidue code BAD_PEPTIDE at template residue (1qjcA)K43 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1qjcA 4 :RAIYPGTFDPITNGHIDIVTRATQMF T0507 29 :RDITIGVT 1qjcA 30 :DHVILAIA T0507 41 :ARAR 1qjcA 38 :ASPS T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1qjcA 44 :PMFTLEERVALAQQATAHLGNVEVVGFSDL T0507 78 :PYGKTLDVDFEYLVVSPETYEMALKINQKREELGKR 1qjcA 74 :MANFARNQHATVLIRGLRAVADFEYEMQLAHMNRHL T0507 114 :KITIVKVDW 1qjcA 112 :ELESVFLMP T0507 125 :AEDGKPISSTRIK 1qjcA 121 :SKEWSFISSSLVK T0507 140 :EIDRYG 1qjcA 134 :EVARHQ T0507 147 :II 1qjcA 141 :DV Number of specific fragments extracted= 9 number of extra gaps= 1 total=20 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 1qjcA/T0507-1qjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1qjcA/T0507-1qjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjcA read from 1qjcA/T0507-1qjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qjcA in template set Warning: unaligning (T0507)S47 because of BadResidue code BAD_PEPTIDE in next template residue (1qjcA)K43 Warning: unaligning (T0507)V48 because of BadResidue code BAD_PEPTIDE at template residue (1qjcA)K43 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1qjcA 3 :KRAIYPGTFDPITNGHIDIVTRATQMFD T0507 30 :DITIGVTS 1qjcA 31 :HVILAIAA T0507 44 :RIR 1qjcA 39 :SPS T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVKITNPYGKT 1qjcA 44 :PMFTLEERVALAQQATAHLGNVEVVGFSDLMANF T0507 83 :LDVDFEYLVVSPE 1qjcA 79 :RNQHATVLIRGLR T0507 96 :TYEMALKINQKREEL 1qjcA 95 :DFEYEMQLAHMNRHL T0507 112 :KRKITIVKV 1qjcA 110 :MPELESVFL Number of specific fragments extracted= 7 number of extra gaps= 1 total=27 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 1tfuA/T0507-1tfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tfuA expands to /projects/compbio/data/pdb/1tfu.pdb.gz 1tfuA:# T0507 read from 1tfuA/T0507-1tfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tfuA read from 1tfuA/T0507-1tfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tfuA to template set # found chain 1tfuA in template set T0507 1 :MKVAL 1tfuA 1 :MTGAV T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1tfuA 7 :PGSFDPVTLGHVDIFERAAAQF T0507 29 :RDITIGVTS 1tfuA 29 :DEVVVAILV T0507 42 :RARIRSVLPFAIRAENVKRYVMRKYGFEPEIVKI 1tfuA 38 :NPAKTGMFDLDERIAMVKESTTHLPNLRVQVGHG T0507 77 :NPYG 1tfuA 72 :LVVD T0507 81 :KTLDVD 1tfuA 78 :RSCGMT T0507 89 :YLVVSPETYEMALKINQKREELGKR 1tfuA 84 :AIVKGLRTGTDFEYELQMAQMNKHI T0507 114 :KITIVKVDW 1tfuA 110 :GVDTFFVAT T0507 125 :AEDGKPISSTRIKR 1tfuA 119 :APRYSFVSSSLAKE T0507 139 :GEIDRY 1tfuA 138 :GDVSEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=37 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 1tfuA/T0507-1tfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1tfuA/T0507-1tfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tfuA read from 1tfuA/T0507-1tfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tfuA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1tfuA 3 :GAVCPGSFDPVTLGHVDIFERAAAQF T0507 29 :RDITIGVT 1tfuA 29 :DEVVVAIL T0507 41 :ARARIRSVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1tfuA 37 :VNPAKTGMFDLDERIAMVKESTTHLPNLRVQVGHGL T0507 78 :PYGKTLDVDFEYLVVSPETYEMALKINQKREELGKR 1tfuA 73 :VVDFVRSCGMTAIVKGLRTGTDFEYELQMAQMNKHI T0507 114 :KITIVKV 1tfuA 112 :DTFFVAT T0507 125 :AEDGKPISSTRIK 1tfuA 119 :APRYSFVSSSLAK T0507 140 :EIDRYGGII 1tfuA 132 :EVAMLGGDV Number of specific fragments extracted= 7 number of extra gaps= 0 total=44 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 1tfuA/T0507-1tfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1tfuA/T0507-1tfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tfuA read from 1tfuA/T0507-1tfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tfuA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1tfuA 2 :TGAVCPGSFDPVTLGHVDIFERAAAQFD T0507 30 :DITIGVTSD 1tfuA 30 :EVVVAILVN T0507 45 :IRSVLPFAIRAENVKRYVMRKYGFEPEIVKITNPYGKT 1tfuA 39 :PAKTGMFDLDERIAMVKESTTHLPNLRVQVGHGLVVDF T0507 83 :LDVDFEYLVVS 1tfuA 78 :RSCGMTAIVKG T0507 96 :TYEMALKINQKREELGKRKITIVK 1tfuA 94 :DFEYELQMAQMNKHIAGVDTFFVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=49 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 1yumA/T0507-1yumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yumA expands to /projects/compbio/data/pdb/1yum.pdb.gz 1yumA:Skipped atom 69, because occupancy 0.43 <= existing 0.570 in 1yumA Skipped atom 71, because occupancy 0.430 <= existing 0.570 in 1yumA Skipped atom 73, because occupancy 0.430 <= existing 0.570 in 1yumA Skipped atom 612, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 613, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 615, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 616, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 618, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 619, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 621, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 622, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 624, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 625, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 627, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 628, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 630, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 631, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 868, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 870, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 872, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 874, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1216, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1218, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1220, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1222, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1224, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1226, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1228, because occupancy 0.330 <= existing 0.670 in 1yumA # T0507 read from 1yumA/T0507-1yumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yumA read from 1yumA/T0507-1yumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yumA to template set # found chain 1yumA in template set Warning: unaligning (T0507)V22 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)M26 Warning: unaligning (T0507)A23 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)M26 Warning: unaligning (T0507)M40 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)H45 Warning: unaligning (T0507)A41 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)H45 Warning: unaligning (T0507)S47 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)Q50 Warning: unaligning (T0507)V48 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)Q50 Warning: unaligning (T0507)I117 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)L132 Warning: unaligning (T0507)V118 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)L132 Warning: unaligning (T0507)D142 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)A159 Warning: unaligning (T0507)R143 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)A159 T0507 1 :MKVAL 1yumA 3 :KRIGL T0507 6 :GGTFEPLHEGHKKLID 1yumA 9 :GGTFDPVHIGHMRSAV T0507 24 :IKLG 1yumA 27 :AEQF T0507 28 :GRDITIGVTSDR 1yumA 32 :LDELRLLPNARP T0507 42 :RA 1yumA 46 :RE T0507 46 :R 1yumA 48 :T T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVKITNPYG 1yumA 51 :VSAAQRLAMVERAVAGVERLTVDPRELQRDKP T0507 81 :KTLDVDFE 1yumA 94 :AELAADDQ T0507 89 :YLVVSPETYEMALKINQKREELGKRKIT 1yumA 103 :FMLIGWDAFCGLPTWHRWEALLDHCHIV T0507 119 :KVDWMMAE 1yumA 133 :QRPDADSE T0507 128 :GKPISSTRIKR 1yumA 141 :PPESLRDLLAA T0507 139 :GEI 1yumA 155 :ADP T0507 144 :YGGI 1yumA 160 :LKGP Number of specific fragments extracted= 13 number of extra gaps= 5 total=62 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 1yumA/T0507-1yumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1yumA/T0507-1yumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yumA read from 1yumA/T0507-1yumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yumA in template set Warning: unaligning (T0507)V22 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)M26 Warning: unaligning (T0507)A23 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)M26 Warning: unaligning (T0507)M40 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)H45 Warning: unaligning (T0507)A43 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)H45 Warning: unaligning (T0507)S47 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)Q50 Warning: unaligning (T0507)V48 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)Q50 Warning: unaligning (T0507)I117 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)L132 Warning: unaligning (T0507)V118 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)L132 T0507 2 :KVALGGTFEPLHEGHKKLID 1yumA 5 :IGLFGGTFDPVHIGHMRSAV T0507 24 :IK 1yumA 27 :AE T0507 26 :LGGRDITIGVTSDR 1yumA 30 :FALDELRLLPNARP T0507 44 :RIR 1yumA 46 :RET T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVKIT 1yumA 51 :VSAAQRLAMVERAVAGVERLTVDPRELQ T0507 77 :NPYGKTLDV 1yumA 84 :YTIDTLESV T0507 86 :DFE 1yumA 99 :DDQ T0507 89 :YLVVSPETYEMALKINQKREELGKRKIT 1yumA 103 :FMLIGWDAFCGLPTWHRWEALLDHCHIV T0507 119 :KVDWMMAED 1yumA 133 :QRPDADSEP T0507 128 :GKPISSTRIK 1yumA 174 :PLAVSATQIR T0507 140 :EIDRYG 1yumA 184 :ALLGAG T0507 146 :G 1yumA 191 :S Number of specific fragments extracted= 12 number of extra gaps= 4 total=74 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 1yumA/T0507-1yumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1yumA/T0507-1yumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yumA read from 1yumA/T0507-1yumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yumA in template set Warning: unaligning (T0507)V22 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)M26 Warning: unaligning (T0507)A23 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)M26 Warning: unaligning (T0507)R44 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)H45 Warning: unaligning (T0507)I45 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)H45 Warning: unaligning (T0507)L49 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)Q50 Warning: unaligning (T0507)P50 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)Q50 T0507 1 :MKVALGGTFEPLHEGHKKLID 1yumA 4 :RIGLFGGTFDPVHIGHMRSAV T0507 24 :IKLGGRDITIGVTS 1yumA 27 :AEQFALDELRLLPN T0507 46 :RSV 1yumA 46 :RET T0507 51 :FAIRAEN 1yumA 51 :VSAAQRL T0507 58 :VKRYVMRKYGFEP 1yumA 90 :ESVRAELAADDQL T0507 89 :YLVVSPET 1yumA 103 :FMLIGWDA Number of specific fragments extracted= 6 number of extra gaps= 3 total=80 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 1od6A/T0507-1od6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1od6A expands to /projects/compbio/data/pdb/1od6.pdb.gz 1od6A:Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1od6A Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1od6A # T0507 read from 1od6A/T0507-1od6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1od6A read from 1od6A/T0507-1od6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1od6A to template set # found chain 1od6A in template set Warning: unaligning (T0507)D38 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1od6A)Q43 Warning: unaligning (T0507)R46 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1od6A)Q43 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLG 1od6A 1 :MHVVYPGSFDPLTNGHLDVIQRASRLF T0507 29 :RDITIGVTS 1od6A 28 :EKVTVAVLE T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKI 1od6A 44 :YLFSAEERLAIIREATAHLANVEAATFSG T0507 77 :NPYG 1od6A 73 :LLVD T0507 81 :KTLDVD 1od6A 79 :RRVGAQ T0507 89 :YLVVSPETYEMALKINQKREELGKR 1od6A 85 :AIVKGLRAVSDYEYELQMAHLNRQL T0507 114 :KITIVKVDW 1od6A 112 :GLETLFILA T0507 125 :AEDGKPISSTRIKR 1od6A 121 :ATRYSFVSSTMVKE T0507 139 :GEIDR 1od6A 140 :GDVSK Number of specific fragments extracted= 9 number of extra gaps= 0 total=89 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 1od6A/T0507-1od6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1od6A/T0507-1od6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1od6A read from 1od6A/T0507-1od6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1od6A in template set Warning: unaligning (T0507)D38 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1od6A)Q43 Warning: unaligning (T0507)R44 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1od6A)Q43 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1od6A 2 :HVVYPGSFDPLTNGHLDVIQRASRLF T0507 29 :RDITIGVTS 1od6A 28 :EKVTVAVLE T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1od6A 44 :YLFSAEERLAIIREATAHLANVEAATFSGL T0507 78 :PYGKTLDVDFEYLVVSPETYEMALKINQKREEL 1od6A 74 :LVDFVRRVGAQAIVKGLRAVSDYEYELQMAHLN T0507 111 :GKRKITIVKVDW 1od6A 109 :LYPGLETLFILA T0507 125 :AEDGKPISSTRIK 1od6A 121 :ATRYSFVSSTMVK T0507 140 :EIDRYG 1od6A 134 :EIARYG T0507 147 :I 1od6A 141 :D Number of specific fragments extracted= 8 number of extra gaps= 0 total=97 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 1od6A/T0507-1od6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1od6A/T0507-1od6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1od6A read from 1od6A/T0507-1od6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1od6A in template set Warning: unaligning (T0507)D38 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1od6A)Q43 Warning: unaligning (T0507)V48 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1od6A)Q43 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1od6A 1 :MHVVYPGSFDPLTNGHLDVIQRASRLFE T0507 30 :DITIGVTS 1od6A 29 :KVTVAVLE T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVKITNPYGKT 1od6A 44 :YLFSAEERLAIIREATAHLANVEAATFSGLLVDF T0507 83 :LDVDFEYLVVS 1od6A 79 :RRVGAQAIVKG T0507 94 :PETYEMALKINQKREELGK 1od6A 93 :VSDYEYELQMAHLNRQLYP T0507 114 :KITIVKVD 1od6A 112 :GLETLFIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=103 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 1f9aA/T0507-1f9aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f9aA expands to /projects/compbio/data/pdb/1f9a.pdb.gz 1f9aA:# T0507 read from 1f9aA/T0507-1f9aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9aA read from 1f9aA/T0507-1f9aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f9aA to template set # found chain 1f9aA in template set Warning: unaligning (T0507)L5 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1f9aA)I5 Warning: unaligning (T0507)P11 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)F12 Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)F12 Warning: unaligning (T0507)G15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)H16 Warning: unaligning (T0507)H16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)H16 Warning: unaligning (T0507)V62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)K61 Warning: unaligning (T0507)M63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)K61 Warning: unaligning (T0507)R64 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)D62 Warning: unaligning (T0507)P78 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)E76 Warning: unaligning (T0507)Y79 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)E76 Warning: unaligning (T0507)I103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)P100 Warning: unaligning (T0507)N104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)P100 Warning: unaligning (T0507)V118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1f9aA)R115 Warning: unaligning (T0507)K119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1f9aA)R115 Warning: unaligning (T0507)M123 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)N120 Warning: unaligning (T0507)M124 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)N120 T0507 3 :VA 1f9aA 2 :RG T0507 6 :GGTFE 1f9aA 6 :IGRFQ T0507 13 :HE 1f9aA 13 :HK T0507 17 :KKLIDVAIKLG 1f9aA 17 :LEVIKKIAEEV T0507 29 :RDITIGVTSDRMARARI 1f9aA 28 :DEIIIGIGSAQKSHTLE T0507 47 :SVLPFAIRAENVKRY 1f9aA 45 :NPFTAGERILMITQS T0507 66 :YGFEPEIVKITN 1f9aA 63 :YDLTYYPIPIKD T0507 80 :G 1f9aA 77 :F T0507 81 :KTLDVD 1f9aA 88 :LTPPFD T0507 89 :YLV 1f9aA 94 :IVY T0507 93 :S 1f9aA 97 :S T0507 102 :K 1f9aA 98 :G T0507 105 :QKREELGKRKITI 1f9aA 101 :LVRVLFEERGYEV T0507 120 :VDW 1f9aA 116 :PEM T0507 125 :A 1f9aA 121 :R T0507 129 :KPISSTRIKR 1f9aA 122 :KEYSGTEIRR T0507 139 :GEIDRY 1f9aA 137 :EKWEHL Number of specific fragments extracted= 17 number of extra gaps= 8 total=120 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 1f9aA/T0507-1f9aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1f9aA/T0507-1f9aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9aA read from 1f9aA/T0507-1f9aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f9aA in template set Warning: unaligning (T0507)A4 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1f9aA)I5 Warning: unaligning (T0507)L5 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1f9aA)I5 Warning: unaligning (T0507)P11 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)F12 Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)F12 Warning: unaligning (T0507)G15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)H16 Warning: unaligning (T0507)H16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)H16 Warning: unaligning (T0507)V62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)K61 Warning: unaligning (T0507)M63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)K61 Warning: unaligning (T0507)R64 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)D62 Warning: unaligning (T0507)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)E76 Warning: unaligning (T0507)N77 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)E76 Warning: unaligning (T0507)E95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)P100 Warning: unaligning (T0507)T96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)P100 Warning: unaligning (T0507)V118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1f9aA)R115 Warning: unaligning (T0507)K119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1f9aA)R115 Warning: unaligning (T0507)M123 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)N120 Warning: unaligning (T0507)M124 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)N120 T0507 1 :MKV 1f9aA 1 :LRG T0507 6 :GGTFE 1f9aA 6 :IGRFQ T0507 13 :HE 1f9aA 13 :HK T0507 17 :KKLIDVAIKLG 1f9aA 17 :LEVIKKIAEEV T0507 29 :RDITIGVTSDRMARAR 1f9aA 28 :DEIIIGIGSAQKSHTL T0507 46 :RSVLPFAIRAENVKRY 1f9aA 44 :ENPFTAGERILMITQS T0507 65 :KY 1f9aA 63 :YD T0507 67 :GFEPEIVKI 1f9aA 66 :TYYPIPIKD T0507 78 :PYGK 1f9aA 77 :FNSI T0507 82 :TLDV 1f9aA 85 :VESL T0507 86 :DFE 1f9aA 91 :PFD T0507 90 :LVVSP 1f9aA 94 :IVYSG T0507 98 :EMALKINQ 1f9aA 101 :LVRVLFEE T0507 113 :RKITI 1f9aA 109 :RGYEV T0507 120 :VDW 1f9aA 116 :PEM T0507 125 :AED 1f9aA 121 :RKE T0507 131 :ISSTRIK 1f9aA 124 :YSGTEIR T0507 140 :EIDRYGGII 1f9aA 131 :RRMLNGEKW Number of specific fragments extracted= 18 number of extra gaps= 8 total=138 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 1f9aA/T0507-1f9aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1f9aA/T0507-1f9aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f9aA read from 1f9aA/T0507-1f9aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f9aA in template set Warning: unaligning (T0507)A4 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1f9aA)I5 Warning: unaligning (T0507)L5 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1f9aA)I5 Warning: unaligning (T0507)P11 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)F12 Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)F12 Warning: unaligning (T0507)G15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)H16 Warning: unaligning (T0507)H16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)H16 Warning: unaligning (T0507)M63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)K61 Warning: unaligning (T0507)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)K61 Warning: unaligning (T0507)K65 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)D62 Warning: unaligning (T0507)P78 because of BadResidue code BAD_PEPTIDE in next template residue (1f9aA)E76 Warning: unaligning (T0507)Y79 because of BadResidue code BAD_PEPTIDE at template residue (1f9aA)E76 Warning: unaligning (T0507)E95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f9aA)P100 Warning: unaligning (T0507)L101 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f9aA)P100 T0507 1 :MKV 1f9aA 1 :LRG T0507 6 :GGTFE 1f9aA 6 :IGRFQ T0507 13 :HE 1f9aA 13 :HK T0507 17 :KKLIDVAIKLGG 1f9aA 17 :LEVIKKIAEEVD T0507 30 :DITIGVTSDR 1f9aA 29 :EIIIGIGSAQ T0507 43 :ARIRSVLPFAIRAEN 1f9aA 39 :KSHTLENPFTAGERI T0507 58 :VKRYV 1f9aA 55 :MITQS T0507 66 :YGFEPEIVKITN 1f9aA 63 :YDLTYYPIPIKD T0507 80 :GKT 1f9aA 77 :FNS T0507 83 :LDVDFEYLV 1f9aA 88 :LTPPFDIVY T0507 93 :SP 1f9aA 97 :SG T0507 102 :KINQKREELGKR 1f9aA 101 :LVRVLFEERGYE Number of specific fragments extracted= 12 number of extra gaps= 6 total=150 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 2h29A/T0507-2h29A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h29A expands to /projects/compbio/data/pdb/2h29.pdb.gz 2h29A:# T0507 read from 2h29A/T0507-2h29A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h29A read from 2h29A/T0507-2h29A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h29A to template set # found chain 2h29A in template set Warning: unaligning (T0507)P11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2h29A)I14 Warning: unaligning (T0507)L12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2h29A)I14 T0507 1 :M 2h29A 1 :M T0507 2 :KVAL 2h29A 3 :KIVL T0507 6 :GGTFE 2h29A 8 :GGQFN T0507 13 :HEGHKKLIDVAIKLG 2h29A 15 :HTAHMIVASEVFHEL T0507 28 :GRDITIGVTSDRMARARI 2h29A 31 :PDEFYFLPSFMSPLKKHH T0507 47 :SVLPFAIRAENVKRYVMRKYGFEP 2h29A 49 :DFIDVQHRLTMIQMIIDELGFGDI T0507 75 :IT 2h29A 73 :CD T0507 85 :VDFE 2h29A 97 :KDSE T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAED 2h29A 102 :YFVIGTDQYNQLEKWYQIEYLKEMVTFVVVNRDKNSQNV T0507 128 :GKPISSTRIKR 2h29A 151 :RVDISSTMIRQ T0507 139 :GEIDR 2h29A 167 :KSIQV Number of specific fragments extracted= 11 number of extra gaps= 1 total=161 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 2h29A/T0507-2h29A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2h29A/T0507-2h29A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h29A read from 2h29A/T0507-2h29A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h29A in template set Warning: unaligning (T0507)P11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2h29A)I14 Warning: unaligning (T0507)L12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2h29A)I14 T0507 1 :M 2h29A 1 :M T0507 2 :KVALGGTFE 2h29A 4 :IVLYGGQFN T0507 13 :HEGHKKLIDVAIK 2h29A 15 :HTAHMIVASEVFH T0507 26 :LGGRDITIGVTSDRM 2h29A 29 :LQPDEFYFLPSFMSP T0507 42 :RARIRSVLPFAIRAENVKRYVMRKYGFEPEI 2h29A 44 :LKKHHDFIDVQHRLTMIQMIIDELGFGDICD T0507 77 :NPYGKTLDV 2h29A 87 :DTIKAFKEQ T0507 86 :DFE 2h29A 98 :DSE T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAE 2h29A 102 :YFVIGTDQYNQLEKWYQIEYLKEMVTFVVVNRDKNSQN T0507 128 :GKPISSTRIK 2h29A 151 :RVDISSTMIR T0507 140 :EIDRYG 2h29A 161 :QRVSEG T0507 147 :I 2h29A 168 :S Number of specific fragments extracted= 11 number of extra gaps= 1 total=172 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 2h29A/T0507-2h29A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2h29A/T0507-2h29A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h29A read from 2h29A/T0507-2h29A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h29A in template set Warning: unaligning (T0507)P11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2h29A)I14 Warning: unaligning (T0507)L12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2h29A)I14 T0507 1 :MKVALGGTFE 2h29A 3 :KIVLYGGQFN T0507 13 :HEGHKKLIDVAIKLGGRDITIGVTSDRMARARIRSVLPFAIRAEN 2h29A 15 :HTAHMIVASEVFHELQPDEFYFLPSFMSPLKKHHDFIDVQHRLTM T0507 58 :VKRYVMRKYGFEP 2h29A 89 :IKAFKEQHKDSEL T0507 89 :YLVVSPE 2h29A 102 :YFVIGTD T0507 96 :TYEMALKINQK 2h29A 115 :KWYQIEYLKEM T0507 115 :ITIVKV 2h29A 126 :VTFVVV Number of specific fragments extracted= 6 number of extra gaps= 1 total=178 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 1k4mA/T0507-1k4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k4mA expands to /projects/compbio/data/pdb/1k4m.pdb.gz 1k4mA:# T0507 read from 1k4mA/T0507-1k4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k4mA read from 1k4mA/T0507-1k4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k4mA to template set # found chain 1k4mA in template set T0507 2 :KVAL 1k4mA 4 :LQAL T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1k4mA 9 :GGTFDPVHYGHLKPVETLANLI T0507 28 :GRDITIGVTSDRMARARIR 1k4mA 32 :LTRVTIIPNNVPPHRPQPE T0507 49 :LPFAIRAENVKRYVMRKYGFEPEI 1k4mA 51 :ANSVQRKHMLELAIADKPLFTLDE T0507 81 :KTLDVDFE 1k4mA 94 :QEQGPDVP T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAED 1k4mA 103 :AFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLEM T0507 128 :GKPISSTRIKR 1k4mA 176 :WFNISATIIRE T0507 139 :GEID 1k4mA 192 :ESCE Number of specific fragments extracted= 8 number of extra gaps= 0 total=186 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 1k4mA/T0507-1k4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1k4mA/T0507-1k4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k4mA read from 1k4mA/T0507-1k4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k4mA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIK 1k4mA 5 :QALFGGTFDPVHYGHLKPVETLAN T0507 26 :LGGRDITIGVTSDRMARAR 1k4mA 30 :IGLTRVTIIPNNVPPHRPQ T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEI 1k4mA 49 :PEANSVQRKHMLELAIADKPLFTLDE T0507 77 :NPYGKT 1k4mA 84 :YTAQTL T0507 83 :LDVDFE 1k4mA 94 :QEQGPD T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAE 1k4mA 103 :AFIIGQDSLLTFPTWYEYETILDNAHLIVCRRPGYPLE T0507 128 :GKPISSTRIK 1k4mA 176 :WFNISATIIR T0507 140 :EIDRYGGI 1k4mA 186 :ERLQNGES Number of specific fragments extracted= 8 number of extra gaps= 0 total=194 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 1k4mA/T0507-1k4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1k4mA/T0507-1k4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k4mA read from 1k4mA/T0507-1k4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k4mA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1k4mA 4 :LQALFGGTFDPVHYGHLKPVETLANLIG T0507 29 :RDITIGVTS 1k4mA 33 :TRVTIIPNN T0507 39 :R 1k4mA 42 :V T0507 43 :ARIRSVLPFAIRAEN 1k4mA 43 :PPHRPQPEANSVQRK T0507 58 :VKRYVMRKYGFEP 1k4mA 90 :KEWRQEQGPDVPL T0507 89 :YLVVSPETYEM 1k4mA 103 :AFIIGQDSLLT T0507 100 :ALKINQK 1k4mA 120 :YETILDN T0507 115 :ITIVKVD 1k4mA 127 :AHLIVCR Number of specific fragments extracted= 8 number of extra gaps= 0 total=202 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 1cozA/T0507-1cozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cozA expands to /projects/compbio/data/pdb/1coz.pdb.gz 1cozA:# T0507 read from 1cozA/T0507-1cozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cozA read from 1cozA/T0507-1cozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cozA to template set # found chain 1cozA in template set T0507 1 :MKVAL 1cozA 1 :MKKVI T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1cozA 7 :YGTFDLLHWGHIKLLERAKQLG T0507 29 :RDITIGVTSDRMA 1cozA 29 :DYLVVAISTDEFN T0507 42 :RARIRSVLPFAIRAENVKRY 1cozA 43 :QKQKKAYHSYEHRKLILETI T0507 64 :RKYGF 1cozA 63 :RYVDE T0507 70 :PEIVKIT 1cozA 68 :VIPEKNW T0507 77 :NPY 1cozA 76 :QKK T0507 81 :KTLDVD 1cozA 82 :IDHNID T0507 89 :YLVVSPETYEMA 1cozA 88 :VFVMGDDWEGKF T0507 107 :REELGKRKITIVKV 1cozA 100 :DFLKDQCEVVYLPR T0507 128 :GKPISSTRIKR 1cozA 114 :TEGISTTKIKE Number of specific fragments extracted= 11 number of extra gaps= 0 total=213 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 1cozA/T0507-1cozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1cozA/T0507-1cozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cozA read from 1cozA/T0507-1cozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cozA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1cozA 3 :KVITYGTFDLLHWGHIKLLERAKQLG T0507 29 :RDITIGVTSDRMA 1cozA 29 :DYLVVAISTDEFN T0507 42 :RARIRSVLPFAIRAENVKR 1cozA 43 :QKQKKAYHSYEHRKLILET T0507 62 :VMRKYGF 1cozA 62 :IRYVDEV T0507 70 :PEIVKITNPYGKTLDVDFEYLVVSPETYEMA 1cozA 69 :IPEKNWEQKKQDIIDHNIDVFVMGDDWEGKF T0507 108 :EELGK 1cozA 100 :DFLKD T0507 114 :KITIVKVDWMMA 1cozA 105 :QCEVVYLPRTEG T0507 131 :ISSTRIKRG 1cozA 117 :ISTTKIKEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=221 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 1cozA/T0507-1cozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1cozA/T0507-1cozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cozA read from 1cozA/T0507-1cozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cozA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1cozA 2 :KKVITYGTFDLLHWGHIKLLERAKQLGD T0507 30 :DITIGVTSDRMARARIR 1cozA 30 :YLVVAISTDEFNLQKQK T0507 48 :VLPFAIRAENVKRYVMRKYGFEPEIVKITNPYGKTLDVDFEYLVVSPETYEMAL 1cozA 47 :KAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFD T0507 110 :LGK 1cozA 103 :KDQ T0507 115 :ITIVK 1cozA 106 :CEVVY Number of specific fragments extracted= 5 number of extra gaps= 0 total=226 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 1ej2A/T0507-1ej2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ej2A expands to /projects/compbio/data/pdb/1ej2.pdb.gz 1ej2A:# T0507 read from 1ej2A/T0507-1ej2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej2A read from 1ej2A/T0507-1ej2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ej2A to template set # found chain 1ej2A in template set Warning: unaligning (T0507)K2 because first residue in template chain is (1ej2A)M4 T0507 3 :VAL 1ej2A 5 :RGL T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1ej2A 9 :VGRMQPFHRGHLQVIKSILEEV T0507 29 :RDITIGVTSDRMARARI 1ej2A 31 :DELIICIGSAQLSHSIR T0507 47 :SVLPFAIRAENVKRYVMRK 1ej2A 48 :DPFTAGERVMMLTKALSEN T0507 66 :YGFEPEIVKIT 1ej2A 71 :SRYYIIPVQDI T0507 79 :YG 1ej2A 82 :EC T0507 81 :KTLDVD 1ej2A 92 :KMLTPP T0507 89 :YLVVSPETYEMALKINQ 1ej2A 98 :FDRVYSGNPLVQRLFSE T0507 113 :RKITIVKVDWMMAED 1ej2A 115 :DGYEVTAPPLFYRDR T0507 131 :ISSTRIKR 1ej2A 130 :YSGTEVRR T0507 139 :GEIDRY 1ej2A 143 :GDWRSL Number of specific fragments extracted= 11 number of extra gaps= 0 total=237 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 1ej2A/T0507-1ej2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1ej2A/T0507-1ej2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej2A read from 1ej2A/T0507-1ej2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ej2A in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1ej2A 5 :RGLLVGRMQPFHRGHLQVIKSILEEV T0507 29 :RDITIGVTSDRMARAR 1ej2A 31 :DELIICIGSAQLSHSI T0507 46 :RSVLPFAIRAENVKRYVMRKY 1ej2A 47 :RDPFTAGERVMMLTKALSENG T0507 67 :GFEPEIVKIT 1ej2A 72 :RYYIIPVQDI T0507 77 :NPYGKTLDV 1ej2A 83 :CNALWVGHI T0507 86 :DFEY 1ej2A 97 :PFDR T0507 91 :VVSPE 1ej2A 101 :VYSGN T0507 104 :NQKREELGKRKITIVKVDWMMAED 1ej2A 106 :PLVQRLFSEDGYEVTAPPLFYRDR T0507 131 :ISSTRIK 1ej2A 130 :YSGTEVR T0507 140 :EIDRYGGI 1ej2A 137 :RRMLDDGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=247 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 1ej2A/T0507-1ej2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1ej2A/T0507-1ej2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej2A read from 1ej2A/T0507-1ej2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ej2A in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1ej2A 4 :MRGLLVGRMQPFHRGHLQVIKSILEEVD T0507 30 :DITIGVTSD 1ej2A 32 :ELIICIGSA T0507 42 :RARIRSVLPFAIRAEN 1ej2A 41 :QLSHSIRDPFTAGERV T0507 58 :VKRYVMRKYGFEPEIVKITNPYG 1ej2A 61 :KALSENGIPASRYYIIPVQDIEC T0507 85 :VDFEYLVVSP 1ej2A 96 :PPFDRVYSGN T0507 101 :LKINQKREELGKR 1ej2A 106 :PLVQRLFSEDGYE Number of specific fragments extracted= 6 number of extra gaps= 0 total=253 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 1m8jA/T0507-1m8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m8jA expands to /projects/compbio/data/pdb/1m8j.pdb.gz 1m8jA:# T0507 read from 1m8jA/T0507-1m8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m8jA read from 1m8jA/T0507-1m8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m8jA to template set # found chain 1m8jA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLG 1m8jA 4 :MRGLLVGRMQPFHRGHLQVIKSILEEV T0507 29 :RDITIGVT 1m8jA 31 :DELIICIG T0507 38 :DRMARARIRSVLPFAIRAENVKRYVMRK 1m8jA 39 :SAQLSHSIRDPFTAGERVMMLTKALSEN T0507 66 :YGFEPEIVKITNPYG 1m8jA 71 :SRYYIIPVQDIECNA T0507 81 :KTLDVD 1m8jA 94 :LTPPFD T0507 89 :Y 1m8jA 100 :R T0507 91 :VVSPETY 1m8jA 101 :VYSGNPL T0507 106 :KREELGKRKITIVKVDWMMAED 1m8jA 108 :VQRLFSEDGYEVTAPPLFYRDR T0507 131 :ISSTRIKR 1m8jA 130 :YSGTEVAR T0507 139 :GEIDRY 1m8jA 143 :GDWRSL Number of specific fragments extracted= 10 number of extra gaps= 0 total=263 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 1m8jA/T0507-1m8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1m8jA/T0507-1m8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m8jA read from 1m8jA/T0507-1m8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m8jA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1m8jA 5 :RGLLVGRMQPFHRGHLQVIKSILEEV T0507 29 :RDITIGVTSDRMARAR 1m8jA 31 :DELIICIGSAQLSHSI T0507 46 :RSVLPFAIRAENVKRYVMRKY 1m8jA 47 :RDPFTAGERVMMLTKALSENG T0507 67 :GFEPEIVKIT 1m8jA 72 :RYYIIPVQDI T0507 77 :NPYGKTLDV 1m8jA 83 :CNALWVGHI T0507 86 :DFE 1m8jA 97 :PFD T0507 90 :LVVSP 1m8jA 100 :RVYSG T0507 103 :INQKREELGKRKITIVKVDWMMAED 1m8jA 105 :NPLVQRLFSEDGYEVTAPPLFYRDR T0507 131 :ISSTRIK 1m8jA 130 :YSGTEVA T0507 140 :EIDRYGGI 1m8jA 137 :RRMLDDGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=273 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 1m8jA/T0507-1m8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1m8jA/T0507-1m8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m8jA read from 1m8jA/T0507-1m8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m8jA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1m8jA 4 :MRGLLVGRMQPFHRGHLQVIKSILEEVD T0507 30 :DITIGVTSD 1m8jA 32 :ELIICIGSA T0507 42 :RARIRSVLPFAIRAEN 1m8jA 41 :QLSHSIRDPFTAGERV T0507 58 :VKRYVMRKYGFEPEIVKITNPYGKT 1m8jA 61 :KALSENGIPASRYYIIPVQDIECNA T0507 83 :LDVDFEYLVVSP 1m8jA 94 :LTPPFDRVYSGN T0507 101 :LKINQKREELGKR 1m8jA 106 :PLVQRLFSEDGYE Number of specific fragments extracted= 6 number of extra gaps= 0 total=279 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 1kamA/T0507-1kamA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kamA expands to /projects/compbio/data/pdb/1kam.pdb.gz 1kamA:# T0507 read from 1kamA/T0507-1kamA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kamA read from 1kamA/T0507-1kamA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kamA to template set # found chain 1kamA in template set Warning: unaligning (T0507)M40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kamA)D52 Warning: unaligning (T0507)P50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kamA)D52 T0507 1 :MKVAL 1kamA 2 :KKIGI T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1kamA 8 :GGTFDPPHNGHLLMANEVLYQA T0507 28 :GRDITIGV 1kamA 31 :LDEIWFMP T0507 37 :SDR 1kamA 39 :NQI T0507 51 :FAIRAENVKRYVMRKYGFEPEIVKIT 1kamA 53 :SFHRVEMLKLAIQSNPSFKLELVEME T0507 85 :VDFE 1kamA 97 :PNDQ T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAED 1kamA 102 :FFIIGADMIEYLPKWYKLDELLNLIQFIGVKRPGFHVET T0507 128 :GKPISSTRIKR 1kamA 151 :EFEVSSTMIRE T0507 139 :GEIDR 1kamA 167 :KPTDY Number of specific fragments extracted= 9 number of extra gaps= 0 total=288 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 1kamA/T0507-1kamA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1kamA/T0507-1kamA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kamA read from 1kamA/T0507-1kamA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kamA in template set Warning: unaligning (T0507)M40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kamA)D52 Warning: unaligning (T0507)P50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kamA)D52 T0507 1 :M 1kamA 2 :K T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDR 1kamA 4 :IGIFGGTFDPPHNGHLLMANEVLYQAGLDEIWFMPNQI T0507 51 :FAIRAENVKRYVMRKYGFEPEIVKIT 1kamA 53 :SFHRVEMLKLAIQSNPSFKLELVEME T0507 77 :NPYGKTLDV 1kamA 87 :DTVSLLKQR T0507 86 :DFE 1kamA 98 :NDQ T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAED 1kamA 102 :FFIIGADMIEYLPKWYKLDELLNLIQFIGVKRPGFHVET T0507 128 :GKPISSTRIK 1kamA 151 :EFEVSSTMIR T0507 140 :EIDRYGGI 1kamA 161 :ERFKSKKP Number of specific fragments extracted= 8 number of extra gaps= 0 total=296 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 1kamA/T0507-1kamA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1kamA/T0507-1kamA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kamA read from 1kamA/T0507-1kamA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kamA in template set Warning: unaligning (T0507)M40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kamA)D52 Warning: unaligning (T0507)A52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kamA)D52 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDR 1kamA 3 :KIGIFGGTFDPPHNGHLLMANEVLYQAGLDEIWFMPNQI T0507 53 :IRAEN 1kamA 53 :SFHRV T0507 58 :VKRYVMRKYGFEP 1kamA 89 :VSLLKQRYPNDQL T0507 89 :YLVVSPE 1kamA 102 :FFIIGAD T0507 96 :TYEMALKINQK 1kamA 115 :KWYKLDELLNL T0507 115 :ITIVKVD 1kamA 126 :IQFIGVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=302 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 1mrzA/T0507-1mrzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mrzA expands to /projects/compbio/data/pdb/1mrz.pdb.gz 1mrzA:# T0507 read from 1mrzA/T0507-1mrzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrzA read from 1mrzA/T0507-1mrzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mrzA to template set # found chain 1mrzA in template set Warning: unaligning (T0507)V3 because first residue in template chain is (1mrzA)V2 T0507 4 :ALGGTFEPLHEGHKKLIDVAIKLG 1mrzA 3 :VSIGVFDGVHIGHQKVLRTMKEIA T0507 28 :GRDITIGVTSDRMA 1mrzA 30 :KDDSLIYTISYPPE T0507 42 :RARIRSVLPFAIRAENVK 1mrzA 47 :PDFPGLLMTVESRVEMLS T0507 64 :RKYGF 1mrzA 65 :RYART T0507 71 :EIVKIT 1mrzA 70 :VVLDFF T0507 77 :NPYG 1mrzA 78 :KDLT T0507 81 :KTLDVD 1mrzA 89 :YLSGVS T0507 89 :YLVVSPETYEMALKINQKREELGK 1mrzA 95 :AVVVGRDFRFGKNASGNASFLRKK T0507 114 :KITIVKVDWMMAED 1mrzA 119 :GVEVYEIEDVVVQG T0507 129 :KPISSTRIKR 1mrzA 133 :KRVSSSLIRN T0507 139 :GEIDRYG 1mrzA 147 :GRVEEIP Number of specific fragments extracted= 11 number of extra gaps= 0 total=313 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 1mrzA/T0507-1mrzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1mrzA/T0507-1mrzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrzA read from 1mrzA/T0507-1mrzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mrzA in template set Warning: unaligning (T0507)V3 because first residue in template chain is (1mrzA)V2 T0507 4 :ALGGTFEPLHEGHKKLIDVAIK 1mrzA 3 :VSIGVFDGVHIGHQKVLRTMKE T0507 26 :LGGR 1mrzA 29 :RKDD T0507 30 :DITIGVTSDRMARARI 1mrzA 34 :LIYTISYPPEYFLPDF T0507 46 :RSVLPFAIRAENV 1mrzA 51 :GLLMTVESRVEML T0507 63 :MRKYG 1mrzA 64 :SRYAR T0507 70 :PEIVKIT 1mrzA 69 :TVVLDFF T0507 77 :NPYGKT 1mrzA 80 :LTPEGF T0507 84 :DV 1mrzA 88 :RY T0507 86 :DFEYLVVSPETYEMALKINQ 1mrzA 92 :GVSAVVVGRDFRFGKNASGN T0507 107 :REELGKRKITIVKVDWMMA 1mrzA 112 :ASFLRKKGVEVYEIEDVVV T0507 127 :DGKPISSTRIK 1mrzA 131 :QGKRVSSSLIR T0507 140 :EIDRYG 1mrzA 142 :NLVQEG Number of specific fragments extracted= 12 number of extra gaps= 0 total=325 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 1mrzA/T0507-1mrzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1mrzA/T0507-1mrzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrzA read from 1mrzA/T0507-1mrzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mrzA in template set Warning: unaligning (T0507)V3 because first residue in template chain is (1mrzA)V2 T0507 4 :ALGGTFEPLHEGHKKLIDVAIKLG 1mrzA 3 :VSIGVFDGVHIGHQKVLRTMKEIA T0507 29 :RDITIGVTSDRMARARIRSVLPFAIRAEN 1mrzA 32 :DSLIYTISYPPEYFLPDFPGLLMTVESRV T0507 58 :VKR 1mrzA 87 :ERY T0507 63 :M 1mrzA 90 :L T0507 85 :VDFEYLVVSPETY 1mrzA 91 :SGVSAVVVGRDFR T0507 104 :NQKREELG 1mrzA 112 :ASFLRKKG T0507 115 :ITIVKVDWMMAEDG 1mrzA 120 :VEVYEIEDVVVQGK Number of specific fragments extracted= 7 number of extra gaps= 0 total=332 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 1nuuA/T0507-1nuuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nuuA expands to /projects/compbio/data/pdb/1nuu.pdb.gz 1nuuA:# T0507 read from 1nuuA/T0507-1nuuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nuuA read from 1nuuA/T0507-1nuuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nuuA to template set # found chain 1nuuA in template set Warning: unaligning (T0507)L83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nuuA)A126 T0507 2 :KVAL 1nuuA 7 :VVLL T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1nuuA 12 :CGSFNPITNMHLRMFEVARDHL T0507 28 :GRDITI 1nuuA 36 :TGMYQV T0507 34 :GVTSDRMARARIR 1nuuA 45 :IISPVNDTYGKKD T0507 48 :VLPFAIRAENVKRYVMRKYGFEP 1nuuA 58 :LAASHHRVAMARLALQTSDWIRV T0507 75 :IT 1nuuA 81 :DP T0507 84 :DVD 1nuuA 127 :VPE T0507 89 :YLVVSPETYEMALKINQ 1nuuA 131 :KLLCGADVLKTFQTPNL T0507 106 :KREELGKRKITIVKVDWMMAED 1nuuA 153 :IQEIVEKFGLVCVGRVSHDPKG T0507 128 :GKPISSTRIKR 1nuuA 197 :QNEISATYIRR T0507 139 :GEIDR 1nuuA 213 :QSVKY Number of specific fragments extracted= 11 number of extra gaps= 0 total=343 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 1nuuA/T0507-1nuuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1nuuA/T0507-1nuuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nuuA read from 1nuuA/T0507-1nuuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nuuA in template set T0507 1 :M 1nuuA 5 :I T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1nuuA 8 :VLLACGSFNPITNMHLRMFEVARDHL T0507 28 :GRDI 1nuuA 38 :MYQV T0507 32 :TIGVTSDRMARA 1nuuA 44 :GIISPVNDTYGK T0507 46 :RSVLPFAIRAENVKRYVMRKYGFEPEI 1nuuA 56 :KDLAASHHRVAMARLALQTSDWIRVDP T0507 89 :YLVVSPETYEMALK 1nuuA 131 :KLLCGADVLKTFQT T0507 103 :INQKREELGKRKITIVKVDWMMAED 1nuuA 150 :DAHIQEIVEKFGLVCVGRVSHDPKG T0507 128 :GKPISSTRIK 1nuuA 197 :QNEISATYIR T0507 140 :EIDRYGGI 1nuuA 207 :RALGQGQS Number of specific fragments extracted= 9 number of extra gaps= 0 total=352 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 1nuuA/T0507-1nuuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1nuuA/T0507-1nuuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nuuA read from 1nuuA/T0507-1nuuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nuuA in template set Warning: unaligning (T0507)R64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nuuA)A126 Warning: unaligning (T0507)V85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nuuA)A126 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGG 1nuuA 8 :VLLACGSFNPITNMHLRMFEVARDHLH T0507 29 :RDITIGVTSD 1nuuA 42 :IQGIISPVND T0507 44 :RIRSVLPFAIRAEN 1nuuA 52 :TYGKKDLAASHHRV T0507 58 :VKRYVM 1nuuA 99 :HHHSKL T0507 86 :DFE 1nuuA 127 :VPE T0507 89 :YLVVSPETYEM 1nuuA 131 :KLLCGADVLKT Number of specific fragments extracted= 6 number of extra gaps= 0 total=358 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 1lw7A/T0507-1lw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lw7A expands to /projects/compbio/data/pdb/1lw7.pdb.gz 1lw7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0507 read from 1lw7A/T0507-1lw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lw7A read from 1lw7A/T0507-1lw7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lw7A to template set # found chain 1lw7A in template set T0507 2 :KVAL 1lw7A 59 :KVGV T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1lw7A 64 :FGKFYPVHTGHINMIYEAFSKV T0507 29 :RDITIGVTSDRMA 1lw7A 86 :DELHVIVCSDTVR T0507 42 :RARIRSVLPFAIRAENVKRYVMRK 1lw7A 105 :DSKMKRMPTVQDRLRWMQQIFKYQ T0507 66 :YGFEPEIVKIT 1lw7A 130 :NQIFIHHLVED T0507 77 :NPYG 1lw7A 143 :PSYP T0507 81 :KTLDVD 1lw7A 163 :KHFEPS T0507 89 :YLVVSPET 1lw7A 169 :IVFSSEPQ T0507 105 :QKREELGKRKITIVKVDWMM 1lw7A 177 :DKAPYEKYLGLEVSLVDPDR T0507 126 :E 1lw7A 197 :T T0507 128 :GKPISSTRIKRGEIDRYG 1lw7A 198 :FFNVSATKIRTTPFQYWK Number of specific fragments extracted= 11 number of extra gaps= 0 total=369 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 1lw7A/T0507-1lw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1lw7A/T0507-1lw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lw7A read from 1lw7A/T0507-1lw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lw7A in template set T0507 1 :M 1lw7A 57 :E T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1lw7A 60 :VGVIFGKFYPVHTGHINMIYEAFSKV T0507 29 :RDITIGVTSDRMA 1lw7A 86 :DELHVIVCSDTVR T0507 42 :RARIRSVLPFAIRAENVKRYVMRKY 1lw7A 105 :DSKMKRMPTVQDRLRWMQQIFKYQK T0507 67 :GFEPEIVKIT 1lw7A 131 :QIFIHHLVED T0507 77 :NPYGKTLDV 1lw7A 151 :SWSEAVKTL T0507 86 :DFEY 1lw7A 166 :EPSI T0507 91 :VVSPETYE 1lw7A 170 :VFSSEPQD T0507 100 :A 1lw7A 178 :K T0507 107 :REELGKRKITIV 1lw7A 179 :APYEKYLGLEVS T0507 121 :DWMMAEDGKPISSTRIK 1lw7A 191 :LVDPDRTFFNVSATKIR T0507 140 :EIDRYG 1lw7A 208 :TTPFQY Number of specific fragments extracted= 12 number of extra gaps= 0 total=381 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 1lw7A/T0507-1lw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1lw7A/T0507-1lw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lw7A read from 1lw7A/T0507-1lw7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lw7A in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDRMARA 1lw7A 59 :KVGVIFGKFYPVHTGHINMIYEAFSKVDELHVIVCSDTVRDLK T0507 44 :RIRSVLPFAIRAEN 1lw7A 105 :DSKMKRMPTVQDRL T0507 58 :VKRYVMRKYGFEPEIVKITNPYGKTLD 1lw7A 120 :WMQQIFKYQKNQIFIHHLVEDGIPSYP T0507 94 :PETYEMALKINQKREELGKRKITIV 1lw7A 147 :NGWQSWSEAVKTLFHEKHFEPSIVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=385 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 1kqnA/T0507-1kqnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kqnA expands to /projects/compbio/data/pdb/1kqn.pdb.gz 1kqnA:# T0507 read from 1kqnA/T0507-1kqnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqnA read from 1kqnA/T0507-1kqnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kqnA to template set # found chain 1kqnA in template set Warning: unaligning (T0507)D84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kqnA)A147 T0507 1 :MKVAL 1kqnA 7 :TEVVL T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1kqnA 14 :CGSFNPITNMHLRLFELAKDYM T0507 28 :GRDI 1kqnA 38 :TGRY T0507 32 :TIGVTSDRMAR 1kqnA 46 :GIISPVGDAYK T0507 45 :IRSVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1kqnA 57 :KKGLIPAYHRVIMAELATKNSKWVEVDTWESL T0507 85 :VDFEYLVVSPETYEMALKIN 1kqnA 148 :VPKVKLLCGADLLESFAVPN T0507 105 :QKREELGKRKITIVKVDWMMAED 1kqnA 173 :DITQIVANYGLICVTRAGNDAQK T0507 128 :GKPISSTRIKR 1kqnA 218 :ANDISSTKIRR T0507 139 :GEIDR 1kqnA 234 :QSIRY Number of specific fragments extracted= 9 number of extra gaps= 0 total=394 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 1kqnA/T0507-1kqnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1kqnA/T0507-1kqnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqnA read from 1kqnA/T0507-1kqnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kqnA in template set T0507 1 :M 1kqnA 8 :E T0507 2 :KVALGGTFEPLHEGHKKLIDVAIK 1kqnA 10 :VLLACGSFNPITNMHLRLFELAKD T0507 28 :GRDI 1kqnA 38 :TGRY T0507 32 :TIGVTSDRMARAR 1kqnA 46 :GIISPVGDAYKKK T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1kqnA 59 :GLIPAYHRVIMAELATKNSKWVEVDTWESL T0507 89 :YLVVSPETYEMAL 1kqnA 152 :KLLCGADLLESFA T0507 102 :KINQKREELGKRKITIVKVD 1kqnA 170 :KSEDITQIVANYGLICVTRA T0507 128 :GKPISSTRIK 1kqnA 218 :ANDISSTKIR T0507 140 :EIDRYGGI 1kqnA 228 :RALRRGQS Number of specific fragments extracted= 9 number of extra gaps= 0 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kqnA/T0507-1kqnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1kqnA/T0507-1kqnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqnA read from 1kqnA/T0507-1kqnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kqnA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGG 1kqnA 10 :VLLACGSFNPITNMHLRLFELAKDYMN T0507 29 :RDITIGVTSDRM 1kqnA 44 :VKGIISPVGDAY T0507 46 :RSVLPFAIRAEN 1kqnA 56 :KKKGLIPAYHRV Number of specific fragments extracted= 3 number of extra gaps= 0 total=406 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 2qjoA/T0507-2qjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qjoA expands to /projects/compbio/data/pdb/2qjo.pdb.gz 2qjoA:# T0507 read from 2qjoA/T0507-2qjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjoA read from 2qjoA/T0507-2qjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qjoA to template set # found chain 2qjoA in template set Warning: unaligning (T0507)E126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qjoA)D136 Warning: unaligning (T0507)D127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjoA)D136 T0507 1 :MKVAL 2qjoA 5 :YQYGI T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 2qjoA 11 :IGRFQPFHLGHLRTLNLALEKA T0507 29 :RDITIGVTSDRMARARIRS 2qjoA 33 :EQVIIILGSHRVAADTRNP T0507 49 :LPFAIRAENVKRYVMRK 2qjoA 52 :WRSPERMAMIEACLSPQ T0507 66 :YGFEPEIVKIT 2qjoA 71 :KRVHFLTVRDW T0507 77 :NPYG 2qjoA 101 :GGSN T0507 89 :YLVVSPETYEMALK 2qjoA 107 :VVLGHRKDASSYYL T0507 111 :GKR 2qjoA 121 :NLF T0507 114 :KITIVKVDW 2qjoA 125 :QWDYLETGH T0507 125 :A 2qjoA 134 :Y T0507 131 :ISSTRIKR 2qjoA 137 :FSSTAIRG T0507 139 :GEIDRYGGI 2qjoA 149 :GKEGDYLDK Number of specific fragments extracted= 12 number of extra gaps= 1 total=418 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qjoA/T0507-2qjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2qjoA/T0507-2qjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjoA read from 2qjoA/T0507-2qjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qjoA in template set Warning: unaligning (T0507)K129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qjoA)D136 Warning: unaligning (T0507)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjoA)D136 T0507 1 :M 2qjoA 5 :Y T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKL 2qjoA 7 :YGIYIGRFQPFHLGHLRTLNLALEK T0507 28 :GRDITIGVTSDR 2qjoA 32 :AEQVIIILGSHR T0507 41 :ARARIRSVLPFAIRAENVKRYVMRKY 2qjoA 44 :VAADTRNPWRSPERMAMIEACLSPQI T0507 67 :GFEPEIVKIT 2qjoA 72 :RVHFLTVRDW T0507 95 :ETYEMALKINQKREELGKRKITIVKVDWMMAED 2qjoA 86 :NLWLAAVQQQVLKITGGSNSVVVLGHRKDASSY T0507 128 :G 2qjoA 134 :Y T0507 131 :ISSTRIK 2qjoA 137 :FSSTAIR T0507 140 :EIDRYG 2qjoA 144 :GAYFEG Number of specific fragments extracted= 9 number of extra gaps= 1 total=427 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 2qjoA/T0507-2qjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2qjoA/T0507-2qjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjoA read from 2qjoA/T0507-2qjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qjoA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSD 2qjoA 6 :QYGIYIGRFQPFHLGHLRTLNLALEKAEQVIIILGSHR T0507 43 :ARIRSVLPFAIRAENVKRYVMRK 2qjoA 44 :VAADTRNPWRSPERMAMIEACLS T0507 66 :YG 2qjoA 71 :KR T0507 70 :PEIVKITNPYGK 2qjoA 73 :VHFLTVRDWLYS T0507 96 :TYEMALKINQKREEL 2qjoA 85 :DNLWLAAVQQQVLKI T0507 111 :GKRKITIVK 2qjoA 102 :GSNSVVVLG Number of specific fragments extracted= 6 number of extra gaps= 0 total=433 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 2qjtA/T0507-2qjtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qjtA expands to /projects/compbio/data/pdb/2qjt.pdb.gz 2qjtA:# T0507 read from 2qjtA/T0507-2qjtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjtA read from 2qjtA/T0507-2qjtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qjtA to template set # found chain 2qjtA in template set Warning: unaligning (T0507)K65 because of BadResidue code BAD_PEPTIDE in next template residue (2qjtA)G66 Warning: unaligning (T0507)L83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qjtA)N102 Warning: unaligning (T0507)D84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjtA)N102 Warning: unaligning (T0507)S93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qjtA)S114 Warning: unaligning (T0507)E98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qjtA)S114 T0507 1 :MKVAL 2qjtA 2 :YDISV T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 2qjtA 8 :IGRFQPFHKGHLHNIIIALQNS T0507 29 :RDITIGVTSDRM 2qjtA 30 :KKVIINIGSCFN T0507 42 :RARIRSVLPFAIRAENVKRYVMR 2qjtA 42 :TPNIKNPFSFEQRKQMIESDLQV T0507 66 :YGFEPEIVKI 2qjtA 70 :DTVVIEPLAD T0507 77 :NPYG 2qjtA 80 :YFYQ T0507 81 :KT 2qjtA 99 :AK T0507 85 :VD 2qjtA 103 :NS T0507 89 :YLVV 2qjtA 105 :IAIV T0507 99 :M 2qjtA 115 :S T0507 107 :REELGKR 2qjtA 116 :SYYIRSF T0507 114 :KITIVKVDW 2qjtA 124 :EWDYIGVDN T0507 125 :AED 2qjtA 133 :YKN T0507 131 :ISSTRIKR 2qjtA 304 :NAADDAKD Number of specific fragments extracted= 14 number of extra gaps= 2 total=447 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 2qjtA/T0507-2qjtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2qjtA/T0507-2qjtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjtA read from 2qjtA/T0507-2qjtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qjtA in template set Warning: unaligning (T0507)K65 because of BadResidue code BAD_PEPTIDE in next template residue (2qjtA)G66 Warning: unaligning (T0507)Y66 because of BadResidue code BAD_PEPTIDE at template residue (2qjtA)G66 Warning: unaligning (T0507)D86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjtA)N102 Warning: unaligning (T0507)S93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qjtA)S114 Warning: unaligning (T0507)E98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qjtA)S114 T0507 1 :M 2qjtA 1 :M T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 2qjtA 4 :ISVFIGRFQPFHKGHLHNIIIALQNS T0507 29 :RDITIGVTSDRMA 2qjtA 30 :KKVIINIGSCFNT T0507 43 :ARIRSVLPFAIRAENVKRYVMR 2qjtA 43 :PNIKNPFSFEQRKQMIESDLQV T0507 67 :GFEPEIVKIT 2qjtA 71 :TVVIEPLADY T0507 87 :FEYLVV 2qjtA 103 :NSIAIV T0507 99 :MAL 2qjtA 115 :SSY T0507 106 :KREELG 2qjtA 118 :YIRSFP T0507 114 :KITIVKVDW 2qjtA 124 :EWDYIGVDN T0507 128 :GKPISSTRIK 2qjtA 133 :YKNFNATEFR T0507 140 :EIDRYGGII 2qjtA 143 :QKFYNGIIS Number of specific fragments extracted= 11 number of extra gaps= 2 total=458 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 2qjtA/T0507-2qjtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 2qjtA/T0507-2qjtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjtA read from 2qjtA/T0507-2qjtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qjtA in template set Warning: unaligning (T0507)G67 because of BadResidue code BAD_PEPTIDE in next template residue (2qjtA)G66 Warning: unaligning (T0507)F68 because of BadResidue code BAD_PEPTIDE at template residue (2qjtA)G66 Warning: unaligning (T0507)E69 because of BadResidue code BAD_PEPTIDE at template residue (2qjtA)I67 Warning: unaligning (T0507)R113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qjtA)N102 Warning: unaligning (T0507)K114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjtA)N102 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGG 2qjtA 4 :ISVFIGRFQPFHKGHLHNIIIALQNSK T0507 30 :DITIGVTS 2qjtA 31 :KVIINIGS T0507 45 :IRSVLPFAIRAENVKRYVMRKY 2qjtA 43 :PNIKNPFSFEQRKQMIESDLQV T0507 70 :PEIVKITNPYGK 2qjtA 72 :VVIEPLADYFYQ T0507 96 :TYEMALKINQKREELGK 2qjtA 84 :EQKWQDELRKNVYKHAK T0507 115 :ITIVKV 2qjtA 103 :NSIAIV Number of specific fragments extracted= 6 number of extra gaps= 2 total=464 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 1ihoA/T0507-1ihoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ihoA expands to /projects/compbio/data/pdb/1iho.pdb.gz 1ihoA:Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 1ihoA # T0507 read from 1ihoA/T0507-1ihoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihoA read from 1ihoA/T0507-1ihoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ihoA to template set # found chain 1ihoA in template set Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)H34 Warning: unaligning (T0507)H13 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)H34 Warning: unaligning (T0507)E14 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)G36 Warning: unaligning (T0507)G15 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)G36 T0507 2 :KVALGGTFEP 1ihoA 23 :RVALVPTMGN T0507 16 :HKKLIDVAIKLG 1ihoA 37 :HMKLVDEAKARA T0507 29 :RDITIGVTSDRMA 1ihoA 49 :DVVVVSIFVNPMQ T0507 42 :RAR 1ihoA 64 :RPE T0507 45 :IR 1ihoA 71 :YP T0507 49 :LPFAIRAENVKRY 1ihoA 73 :RTLQEDCEKLNKR T0507 64 :RK 1ihoA 86 :KV T0507 66 :YGFEP 1ihoA 104 :ETHTY T0507 73 :VKIT 1ihoA 109 :VDVP T0507 84 :DVD 1ihoA 142 :QPD T0507 89 :YLVVSPETYEMALKINQKREELGK 1ihoA 145 :IACFGEKDFQQLALIRKMVADMGF T0507 114 :KITIVKVDWMMAEDGKPISS 1ihoA 169 :DIEIVGVPIMRAKDGLALSS T0507 143 :RY 1ihoA 189 :RN Number of specific fragments extracted= 13 number of extra gaps= 1 total=477 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 1ihoA/T0507-1ihoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1ihoA/T0507-1ihoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihoA read from 1ihoA/T0507-1ihoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ihoA in template set Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)H34 Warning: unaligning (T0507)H13 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)H34 Warning: unaligning (T0507)E14 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)G36 Warning: unaligning (T0507)G15 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)G36 T0507 2 :KVALGGTFEP 1ihoA 23 :RVALVPTMGN T0507 16 :HKKLIDVAIKLG 1ihoA 37 :HMKLVDEAKARA T0507 29 :RDITIGVTSDRMA 1ihoA 49 :DVVVVSIFVNPMQ T0507 43 :AR 1ihoA 64 :RP T0507 46 :RSVLPFAIRAENVKRY 1ihoA 70 :RYPRTLQEDCEKLNKR T0507 64 :RKY 1ihoA 86 :KVD T0507 69 :EPEIVKIT 1ihoA 89 :LVFAPSVK T0507 77 :NPYGKTLDVDFEYLVVSPETYEMALKINQKREELG 1ihoA 133 :IVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMG T0507 113 :RKITIVKVDWMMAEDGKPISSTR 1ihoA 168 :FDIEIVGVPIMRAKDGLALSSRN Number of specific fragments extracted= 9 number of extra gaps= 1 total=486 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 1ihoA/T0507-1ihoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1ihoA/T0507-1ihoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihoA read from 1ihoA/T0507-1ihoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ihoA in template set Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)H34 Warning: unaligning (T0507)H13 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)H34 Warning: unaligning (T0507)E14 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)G36 Warning: unaligning (T0507)G15 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)G36 T0507 1 :MKVALGGTFEP 1ihoA 22 :KRVALVPTMGN T0507 16 :HKKLIDVAIKLGG 1ihoA 37 :HMKLVDEAKARAD T0507 30 :DITIGVTS 1ihoA 50 :VVVVSIFV T0507 38 :DRMARAR 1ihoA 65 :PEDLARY T0507 50 :PFAIRAEN 1ihoA 72 :PRTLQEDC T0507 58 :V 1ihoA 139 :N T0507 86 :DFEYLVVSPETYEMALKINQKREELGKR 1ihoA 142 :QPDIACFGEKDFQQLALIRKMVADMGFD T0507 115 :ITIVKVDWMMAEDGKPISST 1ihoA 170 :IEIVGVPIMRAKDGLALSSR Number of specific fragments extracted= 8 number of extra gaps= 1 total=494 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 1v8fA/T0507-1v8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v8fA expands to /projects/compbio/data/pdb/1v8f.pdb.gz 1v8fA:# T0507 read from 1v8fA/T0507-1v8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8fA read from 1v8fA/T0507-1v8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v8fA to template set # found chain 1v8fA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1v8fA 18 :GVGFVPTMGYLHRGHLALVERARREN T0507 29 :RDITIGVTSDRMA 1v8fA 44 :PFVVVSVFVNPLQ T0507 42 :RAR 1v8fA 59 :PGE T0507 45 :IRSVLPFAIRAENVKRY 1v8fA 64 :HRYPRDLERDRALLQEA T0507 64 :RK 1v8fA 81 :GV T0507 66 :YGFEPEIVKIT 1v8fA 96 :EGFATRVQVEG T0507 84 :DVD 1v8fA 136 :QPQ T0507 89 :YLVVSPETYEMALKINQKREELG 1v8fA 139 :RAYFGEKDYQQLLVVRRMVRDLG T0507 113 :RKITIVKVDWMMAEDGKPISSTR 1v8fA 162 :FPVEVVGVPTVREEDGLALSSRN Number of specific fragments extracted= 9 number of extra gaps= 0 total=503 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 1v8fA/T0507-1v8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1v8fA/T0507-1v8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8fA read from 1v8fA/T0507-1v8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8fA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1v8fA 18 :GVGFVPTMGYLHRGHLALVERARREN T0507 29 :RDITIGVTSDRMA 1v8fA 44 :PFVVVSVFVNPLQ T0507 42 :RARIRS 1v8fA 58 :GPGEDY T0507 48 :VLPFAIRAENVKRY 1v8fA 67 :PRDLERDRALLQEA T0507 64 :RKY 1v8fA 81 :GVD T0507 69 :EPEIVKIT 1v8fA 84 :LLFAPGVE T0507 77 :NPYGKTLDVDFEYLVVSPETYEMALKINQKREELG 1v8fA 127 :VVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLG T0507 113 :RKITIVKVDWMMAEDGKPISSTR 1v8fA 162 :FPVEVVGVPTVREEDGLALSSRN Number of specific fragments extracted= 8 number of extra gaps= 0 total=511 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 1v8fA/T0507-1v8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1v8fA/T0507-1v8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8fA read from 1v8fA/T0507-1v8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8fA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGG 1v8fA 18 :GVGFVPTMGYLHRGHLALVERARRENP T0507 30 :DITIGVTSDRMAR 1v8fA 45 :FVVVSVFVNPLQF T0507 43 :ARIRSVLPFAIRAEN 1v8fA 60 :GEDYHRYPRDLERDR T0507 58 :VKRYVMRKYGFEPEIVKIT 1v8fA 88 :PGVEEMYPEGFATRVQVEG T0507 86 :DFEYLVVSPETYEMALKINQKREELGKR 1v8fA 136 :QPQRAYFGEKDYQQLLVVRRMVRDLGFP T0507 115 :ITIVKVDWMMAEDGKPISS 1v8fA 164 :VEVVGVPTVREEDGLALSS Number of specific fragments extracted= 6 number of extra gaps= 0 total=517 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n2eA/T0507-1n2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n2eA expands to /projects/compbio/data/pdb/1n2e.pdb.gz 1n2eA:Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1n2eA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1n2eA # T0507 read from 1n2eA/T0507-1n2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n2eA read from 1n2eA/T0507-1n2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n2eA to template set # found chain 1n2eA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1n2eA 33 :RVMLVPTMGALHEGHLALVRAAKRVP T0507 29 :RDITIGVTSDRMA 1n2eA 59 :GSVVVVSIFVNPM T0507 42 :RAR 1n2eA 75 :AGG T0507 45 :IRS 1n2eA 81 :AYP T0507 49 :LPFAIRAENVKRY 1n2eA 84 :RTPDDDLAQLRAE T0507 64 :RK 1n2eA 97 :GV T0507 66 :YGFEPEIVKIT 1n2eA 114 :LRTTVQPGPLA T0507 84 :DVD 1n2eA 151 :RPD T0507 89 :YLVVSPETYEMALKINQKREELGK 1n2eA 154 :RVFFGEKDYQQLVLIRQLVADFNL T0507 114 :KITIVKVDWMMAEDGKPISSTRI 1n2eA 178 :DVAVVGVPTVREADGLAMSSRNR Number of specific fragments extracted= 10 number of extra gaps= 0 total=527 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n2eA/T0507-1n2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1n2eA/T0507-1n2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n2eA read from 1n2eA/T0507-1n2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n2eA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDRMA 1n2eA 33 :RVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQ T0507 43 :ARIR 1n2eA 74 :GAGG T0507 47 :SVLPFAIRAENVKRY 1n2eA 82 :YPRTPDDDLAQLRAE T0507 67 :GFEPEIV 1n2eA 97 :GVEIAFT T0507 75 :IT 1n2eA 104 :PT T0507 77 :NPYGKTLDVDFEYLVVSPETYEMALKINQKREELG 1n2eA 142 :VVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFN T0507 113 :RKITIVKVDWMMAEDGKPISSTR 1n2eA 177 :LDVAVVGVPTVREADGLAMSSRN Number of specific fragments extracted= 7 number of extra gaps= 0 total=534 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n2eA/T0507-1n2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1n2eA/T0507-1n2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n2eA read from 1n2eA/T0507-1n2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n2eA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDRMA 1n2eA 32 :RRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQ T0507 49 :LPFAIRAEN 1n2eA 82 :YPRTPDDDL T0507 63 :M 1n2eA 109 :M T0507 65 :KYGFEPEIVKITNPYGKT 1n2eA 110 :YPDGLRTTVQPGPLAAEL T0507 83 :LDV 1n2eA 130 :GPR T0507 86 :DFEYLVVSPETYEMALKINQKREELGKR 1n2eA 151 :RPDRVFFGEKDYQQLVLIRQLVADFNLD T0507 115 :ITIVKVDWMMAEDGKPISS 1n2eA 179 :VAVVGVPTVREADGLAMSS Number of specific fragments extracted= 7 number of extra gaps= 0 total=541 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jhdA/T0507-1jhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jhdA expands to /projects/compbio/data/pdb/1jhd.pdb.gz 1jhdA:# T0507 read from 1jhdA/T0507-1jhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jhdA read from 1jhdA/T0507-1jhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jhdA to template set # found chain 1jhdA in template set T0507 3 :VALGGTFEPLHEGHKKLIDVAIKLG 1jhdA 195 :VVAFQTRNPMHRAHEELCRMAMESL T0507 28 :GRDITIGVTSD 1jhdA 221 :ADGVVVHMLLG T0507 43 :ARIRSVLPFAIRAENVKRYVMRK 1jhdA 232 :KLKKGDIPAPVRDAAIRTMAEVY T0507 66 :YGFEPEIVKIT 1jhdA 258 :NTVMVTGYGFD T0507 85 :VD 1jhdA 289 :AT T0507 89 :YLVVSPET 1jhdA 291 :HFIIGRDH T0507 97 :YEMALKINQKREELGKR 1jhdA 301 :VGDYYGAFDAQTIFDDE T0507 114 :KITIVK 1jhdA 324 :EIEIFR T0507 120 :VDWMMAEDGKPISSTRIKR 1jhdA 331 :DHTAYSKKLNKIVMMRDVP T0507 139 :GE 1jhdA 354 :ED Number of specific fragments extracted= 10 number of extra gaps= 0 total=551 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jhdA/T0507-1jhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1jhdA/T0507-1jhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jhdA read from 1jhdA/T0507-1jhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jhdA in template set T0507 3 :VALGGTFEPLHEGHKKLIDVAIK 1jhdA 195 :VVAFQTRNPMHRAHEELCRMAME T0507 26 :LGGRDITIGVTSDRM 1jhdA 219 :LDADGVVVHMLLGKL T0507 42 :RAR 1jhdA 234 :KKG T0507 48 :VLPFAIRAENVKRYVMRK 1jhdA 237 :DIPAPVRDAAIRTMAEVY T0507 66 :YGFEPEIVKIT 1jhdA 258 :NTVMVTGYGFD T0507 78 :PYGKTLDV 1jhdA 271 :YAGPREAV T0507 86 :DFEYLVVSPETY 1jhdA 288 :GATHFIIGRDHA T0507 101 :LKINQKREEL 1jhdA 308 :FDAQTIFDDE T0507 111 :GKRKITIVKVDWMMAED 1jhdA 321 :GAMEIEIFRADHTAYSK T0507 128 :GKPISSTRIK 1jhdA 356 :FVLLSGTKVR T0507 140 :EIDRYGGII 1jhdA 366 :EMLGQGIAP Number of specific fragments extracted= 11 number of extra gaps= 0 total=562 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jhdA/T0507-1jhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1jhdA/T0507-1jhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jhdA read from 1jhdA/T0507-1jhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jhdA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGG 1jhdA 194 :KVVAFQTRNPMHRAHEELCRMAMESLD T0507 29 :RDITIGVTS 1jhdA 223 :GVVVHMLLG T0507 43 :ARIRSVL 1jhdA 232 :KLKKGDI T0507 52 :AIRAEN 1jhdA 239 :PAPVRD T0507 60 :RYVMRKYGFEPEIVKITNPYGKT 1jhdA 250 :MAEVYFPPNTVMVTGYGFDMLYA T0507 87 :FEYLVVSPETY 1jhdA 289 :ATHFIIGRDHA T0507 98 :EMALKINQK 1jhdA 308 :FDAQTIFDD T0507 111 :GKRKITIVKVD 1jhdA 321 :GAMEIEIFRAD T0507 122 :WMMAEDGKPISS 1jhdA 333 :TAYSKKLNKIVM Number of specific fragments extracted= 9 number of extra gaps= 0 total=571 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b6tA/T0507-1b6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b6tA expands to /projects/compbio/data/pdb/1b6t.pdb.gz 1b6tA:# T0507 read from 1b6tA/T0507-1b6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b6tA read from 1b6tA/T0507-1b6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b6tA to template set # found chain 1b6tA in template set Warning: unaligning (T0507)K2 because first residue in template chain is (1b6tA)K3 T0507 3 :VAL 1b6tA 4 :RAI T0507 6 :GGTFEPLHEGHKKLIDVAIKLG 1b6tA 8 :PGTFDPITNGHIDIVTRATQMF T0507 29 :RDITIGVTS 1b6tA 30 :DHVILAIAA T0507 42 :RARIRSVLPFAIRAENVKRYVMRKYGFEPEIVKI 1b6tA 39 :SPSKKPMFTLEERVALAQQATAHLGNVEVVGFSD T0507 77 :NPYG 1b6tA 73 :LMAN T0507 81 :KTLDVD 1b6tA 79 :RNQHAT T0507 89 :YLVVSPETYEMALKINQKREELGKR 1b6tA 85 :VLIRGLRAVADFEYEMQLAHMNRHL T0507 114 :KITIVKVDW 1b6tA 112 :ELESVFLMP T0507 125 :AEDGKPISSTRIKR 1b6tA 121 :SKEWSFISSSLVKE T0507 139 :GEIDRY 1b6tA 140 :GDVTHF Number of specific fragments extracted= 10 number of extra gaps= 0 total=581 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b6tA/T0507-1b6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1b6tA/T0507-1b6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b6tA read from 1b6tA/T0507-1b6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b6tA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKL 1b6tA 4 :RAIYPGTFDPITNGHIDIVTRATQM T0507 28 :GRDITIGVT 1b6tA 29 :FDHVILAIA T0507 41 :ARARIRSVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1b6tA 38 :ASPSKKPMFTLEERVALAQQATAHLGNVEVVGFSDL T0507 78 :PYGKTLDVDFEYLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAEDGKPISSTRIK 1b6tA 74 :MANFARNQHATVLIRGLRAVADFEYEMQLAHMNRHLMPELESVFLMPSKEWSFISSSLVK T0507 140 :EIDRYGGI 1b6tA 134 :EVARHQGD Number of specific fragments extracted= 5 number of extra gaps= 0 total=586 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b6tA/T0507-1b6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1b6tA/T0507-1b6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b6tA read from 1b6tA/T0507-1b6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b6tA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1b6tA 3 :KRAIYPGTFDPITNGHIDIVTRATQMFD T0507 30 :DITIGVTSD 1b6tA 31 :HVILAIAAS T0507 45 :IRSVLPFAIRAENVKRYVMRKYGFEPEIVKITNP 1b6tA 40 :PSKKPMFTLEERVALAQQATAHLGNVEVVGFSDL T0507 83 :LDVDFEYLVVSPE 1b6tA 79 :RNQHATVLIRGLR T0507 96 :TYEMALKINQKREEL 1b6tA 95 :DFEYEMQLAHMNRHL T0507 112 :KRKITIVKV 1b6tA 110 :MPELESVFL Number of specific fragments extracted= 6 number of extra gaps= 0 total=592 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hybA/T0507-1hybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hybA expands to /projects/compbio/data/pdb/1hyb.pdb.gz 1hybA:# T0507 read from 1hybA/T0507-1hybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hybA read from 1hybA/T0507-1hybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hybA to template set # found chain 1hybA in template set Warning: unaligning (T0507)D121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hybA)Y130 Warning: unaligning (T0507)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hybA)Y130 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLG 1hybA 4 :MRGLLVGRMQPFHRGALQVIKSILEEV T0507 29 :RDITIGVTSDRMARARIRS 1hybA 31 :DELIICIGSAQLSHSIRDP T0507 49 :LPFAIRAENVKRYVMRK 1hybA 50 :FTAGERVMMLTKALSEN T0507 68 :FEPEIVKITNPYG 1hybA 71 :SRYYIIPVQDIEC T0507 81 :KTLDVD 1hybA 94 :LTPPFD T0507 89 :YLVVSPET 1hybA 100 :RVYSGNPL T0507 106 :KREELGKRKITIVKV 1hybA 108 :VQRLFSEDGYEVTAP T0507 132 :SSTRIKR 1hybA 131 :SGTEVRR T0507 139 :GEIDRY 1hybA 143 :GDWRSL Number of specific fragments extracted= 9 number of extra gaps= 0 total=601 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hybA/T0507-1hybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1hybA/T0507-1hybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hybA read from 1hybA/T0507-1hybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hybA in template set Warning: unaligning (T0507)D121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hybA)Y130 Warning: unaligning (T0507)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hybA)Y130 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIK 1hybA 4 :MRGLLVGRMQPFHRGALQVIKSILE T0507 28 :GRDITIGVTSDRMARAR 1hybA 30 :VDELIICIGSAQLSHSI T0507 46 :RSVLPFAIRAENVKRYVMRKY 1hybA 47 :RDPFTAGERVMMLTKALSENG T0507 67 :GFEPEIVKIT 1hybA 72 :RYYIIPVQDI T0507 77 :NPYGKTLDV 1hybA 86 :LWVGHIKML T0507 86 :DFEYLVVSPET 1hybA 97 :PFDRVYSGNPL T0507 106 :KREELGKRKITIVKV 1hybA 108 :VQRLFSEDGYEVTAP T0507 132 :SSTRIK 1hybA 131 :SGTEVR T0507 140 :EIDRYGG 1hybA 137 :RRMLDDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=610 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hybA/T0507-1hybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1hybA/T0507-1hybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hybA read from 1hybA/T0507-1hybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hybA in template set T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGG 1hybA 4 :MRGLLVGRMQPFHRGALQVIKSILEEVD T0507 30 :DITIGVTSD 1hybA 32 :ELIICIGSA T0507 42 :RARIRSVLPFAIRAEN 1hybA 41 :QLSHSIRDPFTAGERV T0507 58 :VKRYVMRKYGFEPEIVKITNPYGK 1hybA 61 :KALSENGIPASRYYIIPVQDIECN T0507 85 :VDFEYLVVSP 1hybA 96 :PPFDRVYSGN T0507 101 :LKINQKREELGKR 1hybA 106 :PLVQRLFSEDGYE Number of specific fragments extracted= 6 number of extra gaps= 0 total=616 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g8fA/T0507-1g8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g8fA expands to /projects/compbio/data/pdb/1g8f.pdb.gz 1g8fA:# T0507 read from 1g8fA/T0507-1g8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g8fA read from 1g8fA/T0507-1g8fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g8fA to template set # found chain 1g8fA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1g8fA 190 :RVVAFQTRNPMHRAHRELTVRAAREA T0507 29 :RDITIGVTSDRMARARI 1g8fA 216 :NAKVLIHPVVGLTKPGD T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVKIT 1g8fA 233 :IDHHTRVRVYQEIIKRYPNGIAFLSLLP T0507 104 :NQKREELGKR 1g8fA 308 :YDAQELVESY T0507 114 :KITIVKVDWM 1g8fA 322 :DIEVVPFRMV T0507 124 :MAED 1g8fA 335 :PDED Number of specific fragments extracted= 6 number of extra gaps= 0 total=622 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g8fA/T0507-1g8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1g8fA/T0507-1g8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g8fA read from 1g8fA/T0507-1g8fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g8fA in template set T0507 3 :VALGGTFEPLHEGHKKLIDVAIK 1g8fA 191 :VVAFQTRNPMHRAHRELTVRAAR T0507 26 :LGGRDITIGVTS 1g8fA 215 :ANAKVLIHPVVG T0507 43 :ARIRSVLPFAIRAENVKRYVMRKY 1g8fA 227 :LTKPGDIDHHTRVRVYQEIIKRYP T0507 67 :GFEPEIVKIT 1g8fA 253 :IAFLSLLPLA T0507 82 :T 1g8fA 277 :I T0507 83 :LDVDFEYLVVSPETY 1g8fA 279 :KNYGASHFIVGRDHA T0507 100 :ALKINQKREELG 1g8fA 307 :PYDAQELVESYK T0507 112 :KRKITIVKVD 1g8fA 320 :ELDIEVVPFR T0507 122 :WMMAED 1g8fA 333 :YLPDED T0507 128 :GKPISSTRIK 1g8fA 353 :TLNISGTELR T0507 140 :EIDRYGGII 1g8fA 363 :RRLRVGGEI Number of specific fragments extracted= 11 number of extra gaps= 0 total=633 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g8fA/T0507-1g8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0507 read from 1g8fA/T0507-1g8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g8fA read from 1g8fA/T0507-1g8fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g8fA in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTS 1g8fA 190 :RVVAFQTRNPMHRAHRELTVRAAREANAKVLIHPVV T0507 44 :RIRSV 1g8fA 228 :TKPGD T0507 51 :FAIRAEN 1g8fA 233 :IDHHTRV T0507 58 :VKRYVMRKYGFEPEIVKITNPYGKTLDVD 1g8fA 329 :RMVTYLPDEDRYAPIDQIDTTKTRTLNIS T0507 100 :ALKINQKREEL 1g8fA 358 :GTELRRRLRVG Number of specific fragments extracted= 5 number of extra gaps= 0 total=638 Will force an alignment to be made, even if fragment is small Number of alignments=72 # command:CPU_time= 19.708 sec, elapsed time= 41.724 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 72 Adding 1416 constraints to all_contacts Done adding distance constraints # command:CPU_time= 19.766 sec, elapsed time= 41.783 sec. # command:Reading probabilities from T0507.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 64.832 Optimizing... Probability sum: -251.644, CN propb: -251.644 weights: 0.336 constraints: 367 # command:CPU_time= 31.731 sec, elapsed time= 53.755 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 367 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 367 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1049 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1049 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 31.756 sec, elapsed time= 55.415 sec. # command: