# 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 T0290 numbered 1 through 173 Created new target T0290 from T0290.a2m # command:CPU_time= 6.455 sec, elapsed time= 6.548 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dywA/T0290-1dywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dywA expands to /projects/compbio/data/pdb/1dyw.pdb.gz 1dywA:# T0290 read from 1dywA/T0290-1dywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dywA read from 1dywA/T0290-1dywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dywA to template set # found chain 1dywA in template set Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1dywA 3 :RSKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGIG # choosing archetypes in rotamer library T0290 47 :STQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 48 :KSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESNG T0290 154 :DAASKPFAE 1dywA 154 :SQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dywA/T0290-1dywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1dywA/T0290-1dywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dywA read from 1dywA/T0290-1dywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dywA in template set Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1dywA 6 :VFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGI T0290 46 :KSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 47 :GKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESNG T0290 154 :DAASKPFAE 1dywA 154 :SQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=10 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 1dywA/T0290-1dywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1dywA/T0290-1dywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dywA read from 1dywA/T0290-1dywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dywA in template set Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1dywA 3 :RSKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGE T0290 43 :GTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 44 :NGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESN T0290 153 :TDAASKPFAE 1dywA 153 :GSQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=15 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 1ihgA/T0290-1ihgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ihgA expands to /projects/compbio/data/pdb/1ihg.pdb.gz 1ihgA:# T0290 read from 1ihgA/T0290-1ihgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihgA read from 1ihgA/T0290-1ihgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ihgA to template set # found chain 1ihgA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKT 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEV T0290 155 :AASKPFAEVRILSCGELI 1ihgA 168 :KGEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=17 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 1ihgA/T0290-1ihgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1ihgA/T0290-1ihgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihgA read from 1ihgA/T0290-1ihgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ihgA in template set T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTD 1ihgA 18 :VFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK T0290 156 :ASKPFAEVRILSCGELI 1ihgA 169 :GEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=19 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 1ihgA/T0290-1ihgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1ihgA/T0290-1ihgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihgA read from 1ihgA/T0290-1ihgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ihgA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVKGE T0290 158 :KPFAEVRILSCGELI 1ihgA 171 :KPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=21 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 1yndA/T0290-1yndA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yndA expands to /projects/compbio/data/pdb/1ynd.pdb.gz 1yndA:# T0290 read from 1yndA/T0290-1yndA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yndA read from 1yndA/T0290-1yndA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yndA to template set # found chain 1yndA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1yndA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1yndA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 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 1yndA/T0290-1yndA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1yndA/T0290-1yndA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yndA read from 1yndA/T0290-1yndA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yndA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1yndA 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1yndA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 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 1yndA/T0290-1yndA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1yndA/T0290-1yndA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yndA read from 1yndA/T0290-1yndA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yndA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1yndA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1yndA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=30 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 1h0pA/T0290-1h0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h0pA expands to /projects/compbio/data/pdb/1h0p.pdb.gz 1h0pA:Skipped atom 983, because occupancy 0.46 <= existing 0.540 in 1h0pA Skipped atom 985, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 987, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 989, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 991, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1106, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1108, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1110, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1112, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1114, because occupancy 0.460 <= existing 0.540 in 1h0pA # T0290 read from 1h0pA/T0290-1h0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0pA read from 1h0pA/T0290-1h0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h0pA to template set # found chain 1h0pA in template set Warning: unaligning (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1h0pA 31 :YFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 72 :YPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=33 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 1h0pA/T0290-1h0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1h0pA/T0290-1h0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0pA read from 1h0pA/T0290-1h0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h0pA in template set Warning: unaligning (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1h0pA 32 :FDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGE T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 71 :GYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=36 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 1h0pA/T0290-1h0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1h0pA/T0290-1h0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h0pA read from 1h0pA/T0290-1h0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h0pA in template set Warning: unaligning (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1h0pA 29 :RVYFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGE T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 71 :GYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=39 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 1lopA/T0290-1lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lopA expands to /projects/compbio/data/pdb/1lop.pdb.gz 1lopA:# T0290 read from 1lopA/T0290-1lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lopA read from 1lopA/T0290-1lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lopA to template set # found chain 1lopA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1lopA)E164 T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGF T0290 54 :YKSCLFHRVVKDFMVQGGDF 1lopA 36 :YNNTIFHRVINGFMIQGGGF T0290 76 :GNGRGGESI 1lopA 56 :EPGMKQKAT T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0290 111 :KDTNGSQFFITTKPTPHLDGH 1lopA 91 :PHSATAQFFINVVDNDFLNFS T0290 132 :HVVFGQVISGQEVVREIENQKTDA 1lopA 120 :YCVFAEVVDGMDEVDKIKGVATGR T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS Number of specific fragments extracted= 7 number of extra gaps= 0 total=46 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 1lopA/T0290-1lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1lopA/T0290-1lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lopA read from 1lopA/T0290-1lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lopA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1lopA)E164 T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLC 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYC T0290 41 :EKG 1lopA 32 :REG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGE 1lopA 35 :FYNNTIFHRVINGFMIQGGGFEPGMKQKAT T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0290 111 :KDTNGSQFFITTKPTPHLD 1lopA 91 :PHSATAQFFINVVDNDFLN T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVAT T0290 155 :A 1lopA 146 :M T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS Number of specific fragments extracted= 8 number of extra gaps= 0 total=54 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 1lopA/T0290-1lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1lopA/T0290-1lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lopA read from 1lopA/T0290-1lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lopA in template set T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGES 1lopA 35 :FYNNTIFHRVINGFMIQGGGFEPGMKQKATK T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1lopA 66 :EPIKNEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLN T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVATGR T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 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 1a58/T0290-1a58-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a58 expands to /projects/compbio/data/pdb/1a58.pdb.gz 1a58:Warning: there is no chain 1a58 will retry with 1a58A # T0290 read from 1a58/T0290-1a58-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a58 read from 1a58/T0290-1a58-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a58 to template set # found chain 1a58 in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1a58)V177 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 9 :VFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=60 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 1a58/T0290-1a58-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1a58/T0290-1a58-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a58 read from 1a58/T0290-1a58-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a58 in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1a58)V177 T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 11 :LDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=61 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 1a58/T0290-1a58-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1a58/T0290-1a58-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a58 read from 1a58/T0290-1a58-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a58 in template set T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 8 :RVFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=62 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 2bitX/T0290-2bitX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bitX expands to /projects/compbio/data/pdb/2bit.pdb.gz 2bitX:# T0290 read from 2bitX/T0290-2bitX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bitX read from 2bitX/T0290-2bitX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bitX to template set # found chain 2bitX in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFG T0290 54 :YKSC 2bitX 48 :YKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFG T0290 154 :DAASKPFAEVRILSCGEL 2bitX 147 :SKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=66 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 2bitX/T0290-2bitX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2bitX/T0290-2bitX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bitX read from 2bitX/T0290-2bitX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bitX in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2bitX 4 :PLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGF T0290 53 :HYKSC 2bitX 47 :GYKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFG T0290 154 :DAASKPFAEVRILSCGEL 2bitX 147 :SKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=70 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 2bitX/T0290-2bitX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2bitX/T0290-2bitX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bitX read from 2bitX/T0290-2bitX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bitX in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGE T0290 50 :KPLHYKSC 2bitX 44 :KGFGYKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESF T0290 153 :TDAASKPFAEVRILSCGEL 2bitX 146 :GSKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=74 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 1awqA/T0290-1awqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1awqA expands to /projects/compbio/data/pdb/1awq.pdb.gz 1awqA:# T0290 read from 1awqA/T0290-1awqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awqA read from 1awqA/T0290-1awqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1awqA to template set # found chain 1awqA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awqA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=77 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 1awqA/T0290-1awqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1awqA/T0290-1awqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awqA read from 1awqA/T0290-1awqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1awqA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awqA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=80 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 1awqA/T0290-1awqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1awqA/T0290-1awqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awqA read from 1awqA/T0290-1awqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1awqA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1awqA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1awqA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=83 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 1xo7A/T0290-1xo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xo7A expands to /projects/compbio/data/pdb/1xo7.pdb.gz 1xo7A:# T0290 read from 1xo7A/T0290-1xo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo7A read from 1xo7A/T0290-1xo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xo7A to template set # found chain 1xo7A in template set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 6 :DKVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 43 :GTG 1xo7A 47 :GFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKH 1xo7A 50 :YKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0290 100 :AAFLL 1xo7A 95 :FVGAV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=88 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 1xo7A/T0290-1xo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1xo7A/T0290-1xo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo7A read from 1xo7A/T0290-1xo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xo7A in template set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 9 :YFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 43 :GT 1xo7A 47 :GF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKH 1xo7A 49 :GYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0290 100 :AAFLL 1xo7A 95 :FVGAV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=93 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 1xo7A/T0290-1xo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1xo7A/T0290-1xo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo7A read from 1xo7A/T0290-1xo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xo7A in template set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K50 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 6 :DKVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 51 :PLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAA 1xo7A 47 :GFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKHFVG T0290 103 :LL 1xo7A 98 :AV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 4 number of extra gaps= 2 total=97 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 2rmcA/T0290-2rmcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rmcA expands to /projects/compbio/data/pdb/2rmc.pdb.gz 2rmcA:# T0290 read from 2rmcA/T0290-2rmcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rmcA read from 2rmcA/T0290-2rmcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rmcA to template set # found chain 2rmcA in template set T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2rmcA 41 :FFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 2rmcA 82 :YKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=99 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 2rmcA/T0290-2rmcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2rmcA/T0290-2rmcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rmcA read from 2rmcA/T0290-2rmcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rmcA in template set T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2rmcA 42 :FDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 2rmcA 82 :YKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=101 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 2rmcA/T0290-2rmcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2rmcA/T0290-2rmcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rmcA read from 2rmcA/T0290-2rmcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rmcA in template set T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2rmcA 40 :VFFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 2rmcA 78 :KGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=103 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 1qoiA/T0290-1qoiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qoiA expands to /projects/compbio/data/pdb/1qoi.pdb.gz 1qoiA:# T0290 read from 1qoiA/T0290-1qoiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qoiA read from 1qoiA/T0290-1qoiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qoiA to template set # found chain 1qoiA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEF T0290 46 :KSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 52 :RKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 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 1qoiA/T0290-1qoiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1qoiA/T0290-1qoiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qoiA read from 1qoiA/T0290-1qoiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qoiA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKG 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFR T0290 47 :STQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 53 :KDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=107 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 1qoiA/T0290-1qoiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1qoiA/T0290-1qoiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qoiA read from 1qoiA/T0290-1qoiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qoiA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGE T0290 45 :GKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 51 :FRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 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 1zcxA/T0290-1zcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zcxA expands to Error: no filename for 1zcxA # T0290 read from 1zcxA/T0290-1zcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zcxA read from 1zcxA/T0290-1zcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zcxA/T0290-1zcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zcxA expands to Error: no filename for 1zcxA # T0290 read from 1zcxA/T0290-1zcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zcxA read from 1zcxA/T0290-1zcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zcxA/T0290-1zcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zcxA expands to Error: no filename for 1zcxA # T0290 read from 1zcxA/T0290-1zcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zcxA read from 1zcxA/T0290-1zcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfeA/T0290-2cfeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cfeA expands to /projects/compbio/data/pdb/2cfe.pdb.gz 2cfeA:Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2cfeA # T0290 read from 2cfeA/T0290-2cfeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfeA read from 2cfeA/T0290-2cfeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cfeA to template set # found chain 2cfeA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (2cfeA)C162 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cfeA 46 :YAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAEG T0290 154 :DAASKPFAEVRILSCGE 2cfeA 145 :SGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=112 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 2cfeA/T0290-2cfeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2cfeA/T0290-2cfeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfeA read from 2cfeA/T0290-2cfeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cfeA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (2cfeA)C162 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cfeA 45 :GYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAEG T0290 154 :DAASKPFAEVRILSCGE 2cfeA 145 :SGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=115 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 2cfeA/T0290-2cfeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2cfeA/T0290-2cfeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfeA read from 2cfeA/T0290-2cfeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cfeA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2cfeA 42 :KGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAE T0290 153 :TDAASKPFAEVRILSCGE 2cfeA 144 :GSGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=118 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 1vdnA/T0290-1vdnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vdnA expands to /projects/compbio/data/pdb/1vdn.pdb.gz 1vdnA:# T0290 read from 1vdnA/T0290-1vdnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdnA read from 1vdnA/T0290-1vdnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vdnA to template set # found chain 1vdnA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1vdnA 46 :YAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLG T0290 154 :DAASKPFAEVRILSCGE 1vdnA 145 :SPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=121 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 1vdnA/T0290-1vdnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1vdnA/T0290-1vdnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdnA read from 1vdnA/T0290-1vdnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdnA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1vdnA 5 :YFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1vdnA 45 :GYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLG T0290 154 :DAASKPFAEVRILSCGE 1vdnA 145 :SPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=124 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 1vdnA/T0290-1vdnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1vdnA/T0290-1vdnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdnA read from 1vdnA/T0290-1vdnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdnA in template set Warning: unaligning (T0290)P2 because first residue in template chain is (1vdnA)S2 Warning: unaligning (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1vdnA 42 :KGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESL T0290 153 :TDAASKPFAEVRILSCGE 1vdnA 144 :GSPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=127 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 1zkcA/T0290-1zkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zkcA expands to /projects/compbio/data/pdb/1zkc.pdb.gz 1zkcA:# T0290 read from 1zkcA/T0290-1zkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkcA read from 1zkcA/T0290-1zkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zkcA to template set # found chain 1zkcA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1zkcA 280 :GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1zkcA 316 :YDGTIFHRSIRNFVIQGGDPT T0290 76 :GNGRGGESIYGGFFEDES 1zkcA 337 :GTGTGGESYWGKPFKDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 356 :PNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELI 1zkcA 420 :DRPKEEIRIDATTVFV Number of specific fragments extracted= 5 number of extra gaps= 0 total=132 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 1zkcA/T0290-1zkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1zkcA/T0290-1zkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkcA read from 1zkcA/T0290-1zkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkcA in template set T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLC 1zkcA 281 :YVRLHTNKGDLNLELHCDLTPKTCENFIRLC T0290 41 :EKG 1zkcA 312 :KKH T0290 53 :HYKSCLFHRVVKDFMVQGGD 1zkcA 315 :YYDGTIFHRSIRNFVIQGGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 1zkcA 335 :PTGTGTGGESYWGKPFKDEFRP T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 358 :LSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELIP 1zkcA 420 :DRPKEEIRIDATTVFVD Number of specific fragments extracted= 6 number of extra gaps= 0 total=138 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 1zkcA/T0290-1zkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1zkcA/T0290-1zkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkcA read from 1zkcA/T0290-1zkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkcA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1zkcA 280 :GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKH T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 315 :YYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELI 1zkcA 420 :DRPKEEIRIDATTVFV Number of specific fragments extracted= 3 number of extra gaps= 0 total=141 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 2a2nA/T0290-2a2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a2nA expands to /projects/compbio/data/pdb/2a2n.pdb.gz 2a2nA:# T0290 read from 2a2nA/T0290-2a2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2nA read from 2a2nA/T0290-2a2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a2nA to template set # found chain 2a2nA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 2a2nA 528 :YNGHTFHRIIKGFMIQTGDPT T0290 76 :GNGRGGESIYGGFFEDES 2a2nA 549 :GTGMGGESIWGGEFEDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDA 2a2nA 568 :STLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNP T0290 156 :ASKPFAEVRILSCGE 2a2nA 631 :TDKPYEDVSIINITV Number of specific fragments extracted= 5 number of extra gaps= 0 total=146 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 2a2nA/T0290-2a2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2a2nA/T0290-2a2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2nA read from 2a2nA/T0290-2a2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2nA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHS T0290 41 :EKG 2a2nA 524 :RNG T0290 53 :HYKSCLFHRVVKDFMVQGGD 2a2nA 527 :YYNGHTFHRIIKGFMIQTGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 2a2nA 547 :PTGTGMGGESIWGGEFEDEFHS T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 2a2nA 570 :LRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0290 157 :SKPFAEVRILSCGE 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 6 number of extra gaps= 0 total=152 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 2a2nA/T0290-2a2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2a2nA/T0290-2a2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2nA read from 2a2nA/T0290-2a2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2nA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2a2nA 492 :DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 2a2nA 527 :YYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0290 157 :SKPFAEVRILSCGE 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 3 number of extra gaps= 0 total=155 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 2cpl/T0290-2cpl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cpl expands to /projects/compbio/data/pdb/2cpl.pdb.gz 2cpl:Warning: there is no chain 2cpl will retry with 2cplA # T0290 read from 2cpl/T0290-2cpl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cpl read from 2cpl/T0290-2cpl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cpl to template set # found chain 2cpl in template set Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cpl 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 2cpl 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=158 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 2cpl/T0290-2cpl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2cpl/T0290-2cpl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cpl read from 2cpl/T0290-2cpl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cpl in template set Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cpl 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 2cpl 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=161 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 2cpl/T0290-2cpl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2cpl/T0290-2cpl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cpl read from 2cpl/T0290-2cpl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cpl in template set Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2cpl 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 2cpl 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=164 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 1awsA/T0290-1awsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1awsA expands to /projects/compbio/data/pdb/1aws.pdb.gz 1awsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0290 read from 1awsA/T0290-1awsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awsA read from 1awsA/T0290-1awsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1awsA to template set # found chain 1awsA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awsA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=167 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 1awsA/T0290-1awsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1awsA/T0290-1awsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awsA read from 1awsA/T0290-1awsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1awsA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awsA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=170 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 1awsA/T0290-1awsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1awsA/T0290-1awsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1awsA read from 1awsA/T0290-1awsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1awsA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1awsA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1awsA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 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 1xwnA/T0290-1xwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xwnA expands to /projects/compbio/data/pdb/1xwn.pdb.gz 1xwnA:# T0290 read from 1xwnA/T0290-1xwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwnA read from 1xwnA/T0290-1xwnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xwnA to template set # found chain 1xwnA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1xwnA 7 :DSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1xwnA 48 :YNGTKFHRIIKDFMIQGGDPT T0290 76 :GNGRGGESIYGGFFEDES 1xwnA 69 :GTGRGGASIYGKQFEDEL T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1xwnA 88 :PDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPS Number of specific fragments extracted= 4 number of extra gaps= 0 total=177 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 1xwnA/T0290-1xwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1xwnA/T0290-1xwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwnA read from 1xwnA/T0290-1xwnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwnA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1xwnA 7 :DSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELA T0290 41 :EKG 1xwnA 44 :RRG T0290 53 :HYKSCLFHRVVKDFMVQGGD 1xwnA 47 :YYNGTKFHRIIKDFMIQGGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 1xwnA 67 :PTGTGRGGASIYGKQFEDELHP T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1xwnA 90 :LKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPS Number of specific fragments extracted= 5 number of extra gaps= 0 total=182 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 1xwnA/T0290-1xwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1xwnA/T0290-1xwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwnA read from 1xwnA/T0290-1xwnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwnA in template set T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1xwnA 13 :NVYLETSMGIIVLELYWKHAPKTCKNFAELARRG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xwnA 47 :YYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYP Number of specific fragments extracted= 2 number of extra gaps= 0 total=184 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 2fu0A/T0290-2fu0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fu0A expands to /projects/compbio/data/pdb/2fu0.pdb.gz 2fu0A:# T0290 read from 2fu0A/T0290-2fu0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fu0A read from 2fu0A/T0290-2fu0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fu0A to template set # found chain 2fu0A in template set Warning: unaligning (T0290)F6 because first residue in template chain is (2fu0A)P5 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 2fu0A 42 :YNNCIFHRVIKHFMVQTGDPS T0290 76 :GNGRGGESIYGGFFEDES 2fu0A 63 :GDGTGGESIWGNEFEDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 82 :DHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=188 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 2fu0A/T0290-2fu0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2fu0A/T0290-2fu0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fu0A read from 2fu0A/T0290-2fu0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fu0A in template set Warning: unaligning (T0290)F6 because first residue in template chain is (2fu0A)P5 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHS T0290 41 :EKG 2fu0A 38 :ING T0290 53 :HYKSCLFHRVVKDFMVQGGD 2fu0A 41 :YYNNCIFHRVIKHFMVQTGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 2fu0A 61 :PSGDGTGGESIWGNEFEDEFFD T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 84 :LNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=193 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 2fu0A/T0290-2fu0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2fu0A/T0290-2fu0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fu0A read from 2fu0A/T0290-2fu0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fu0A in template set T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2fu0A 7 :SAIIYTTMGDIHISLFYKECKKTVQNFSVHSING T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 41 :YYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWGNEFEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=195 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 2b71A/T0290-2b71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b71A expands to /projects/compbio/data/pdb/2b71.pdb.gz 2b71A:# T0290 read from 2b71A/T0290-2b71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b71A read from 2b71A/T0290-2b71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b71A to template set # found chain 2b71A in template set Warning: unaligning (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0290)E170 because last residue in template chain is (2b71A)T191 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2b71A 39 :GYITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGF T0290 54 :YKSCLFHRVVKDF 2b71A 75 :YDNTIFHRVIPNF T0290 69 :QGGDFS 2b71A 90 :QGGDPT T0290 76 :GNGRGGESIY 2b71A 96 :GTGKGGKSIY T0290 88 :FFEDES 2b71A 108 :YFEDEI T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQF 2b71A 115 :KELKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 7 number of extra gaps= 3 total=202 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 2b71A/T0290-2b71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2b71A/T0290-2b71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b71A read from 2b71A/T0290-2b71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b71A in template set Warning: unaligning (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0290)E170 because last residue in template chain is (2b71A)T191 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2b71A 39 :GYITIYTNLGDFEVELYWYHSPKTCLNFYTLC T0290 41 :EKG 2b71A 71 :EMG T0290 53 :HYKSCLFHRVVKDF 2b71A 74 :FYDNTIFHRVIPNF T0290 69 :QGGD 2b71A 90 :QGGD T0290 74 :SEGNGRGGESIY 2b71A 94 :PTGTGKGGKSIY T0290 88 :FFEDESFA 2b71A 108 :YFEDEINK T0290 96 :VKHNAAFLLSMANRGKDTNGSQF 2b71A 117 :LKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 8 number of extra gaps= 3 total=210 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 2b71A/T0290-2b71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 2b71A/T0290-2b71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b71A read from 2b71A/T0290-2b71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b71A in template set Warning: unaligning (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2b71A 40 :YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMG T0290 53 :HYKSCLFHRVVKDF 2b71A 74 :FYDNTIFHRVIPNF T0290 69 :QGGDFSEGNGRGGESI 2b71A 90 :QGGDPTGTGKGGKSIY T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQF 2b71A 108 :YFEDEINKELKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 5 number of extra gaps= 3 total=215 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 1v9tA/T0290-1v9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v9tA expands to /projects/compbio/data/pdb/1v9t.pdb.gz 1v9tA:# T0290 read from 1v9tA/T0290-1v9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v9tA read from 1v9tA/T0290-1v9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v9tA to template set # found chain 1v9tA in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 Warning: unaligning (T0290)I172 because last residue in template chain is (1v9tA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1v9tA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSC 1v9tA 41 :YNNT T0290 60 :HRVVKDFMVQGGDFS 1v9tA 47 :HRVIPGFMIQGGGFT T0290 77 :NGRGGESI 1v9tA 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1v9tA 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1v9tA 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :DA 1v9tA 147 :GP T0290 156 :ASKPFAEVRILSCGEL 1v9tA 150 :QNVPSKPVVILSATVL Number of specific fragments extracted= 9 number of extra gaps= 1 total=224 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 1v9tA/T0290-1v9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1v9tA/T0290-1v9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v9tA read from 1v9tA/T0290-1v9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v9tA in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 Warning: unaligning (T0290)I172 because last residue in template chain is (1v9tA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1v9tA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1v9tA 37 :NSG T0290 53 :HYKSC 1v9tA 40 :FYNNT T0290 60 :HRVVKDFMVQGGDFSEGNGRGGE 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1v9tA 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1v9tA 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCGEL 1v9tA 148 :PYQNVPSKPVVILSATVL Number of specific fragments extracted= 8 number of extra gaps= 1 total=232 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 1v9tA/T0290-1v9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1v9tA/T0290-1v9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v9tA read from 1v9tA/T0290-1v9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v9tA in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1v9tA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSC 1v9tA 40 :FYNNT T0290 60 :HRVVKDFMVQGGDFSEGNGRGGES 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1v9tA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1v9tA 120 :FGYAVFGKVVKGMDVADKISQVPTHD T0290 156 :ASKPFAEVRILSCGEL 1v9tA 150 :QNVPSKPVVILSATVL Number of specific fragments extracted= 6 number of extra gaps= 1 total=238 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 1j2aA/T0290-1j2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j2aA expands to /projects/compbio/data/pdb/1j2a.pdb.gz 1j2aA:# T0290 read from 1j2aA/T0290-1j2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j2aA read from 1j2aA/T0290-1j2aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j2aA to template set # found chain 1j2aA in template set Warning: unaligning (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 Warning: unaligning (T0290)I172 because last residue in template chain is (1j2aA)P166 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1j2aA 41 :YNNTTFHRVIPGFMIQGGGFT T0290 76 :GNGRGGES 1j2aA 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1j2aA 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1j2aA 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 7 number of extra gaps= 1 total=245 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 1j2aA/T0290-1j2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1j2aA/T0290-1j2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j2aA read from 1j2aA/T0290-1j2aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j2aA in template set Warning: unaligning (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 Warning: unaligning (T0290)I172 because last residue in template chain is (1j2aA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1j2aA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1j2aA 37 :NSG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGE 1j2aA 40 :FYNNTTFHRVIPGFMIQGGGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1j2aA 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1j2aA 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 7 number of extra gaps= 1 total=252 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 1j2aA/T0290-1j2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1j2aA/T0290-1j2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j2aA read from 1j2aA/T0290-1j2aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j2aA in template set Warning: unaligning (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGES 1j2aA 40 :FYNNTTFHRVIPGFMIQGGGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1j2aA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDAAS 1j2aA 120 :FGYAVFGKVVKGMDVADKISQVPTHDVG T0290 158 :KPFAEVRILSCG 1j2aA 152 :VPSKPVVILSAT Number of specific fragments extracted= 5 number of extra gaps= 1 total=257 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 1cwoA/T0290-1cwoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cwoA expands to /projects/compbio/data/pdb/1cwo.pdb.gz 1cwoA:# T0290 read from 1cwoA/T0290-1cwoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwoA read from 1cwoA/T0290-1cwoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cwoA to template set # found chain 1cwoA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1cwoA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1cwoA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=260 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 1cwoA/T0290-1cwoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1cwoA/T0290-1cwoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwoA read from 1cwoA/T0290-1cwoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cwoA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1cwoA 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1cwoA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=263 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 1cwoA/T0290-1cwoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1cwoA/T0290-1cwoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwoA read from 1cwoA/T0290-1cwoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cwoA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1cwoA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1cwoA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=266 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 1clh/T0290-1clh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1clh expands to /projects/compbio/data/pdb/1clh.pdb.gz 1clh:Warning: there is no chain 1clh will retry with 1clhA # T0290 read from 1clh/T0290-1clh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1clh read from 1clh/T0290-1clh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1clh to template set # found chain 1clh in template set Warning: unaligning (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1clh 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSCLFHR 1clh 41 :YNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFS 1clh 58 :GGFT T0290 76 :GNGRGGES 1clh 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1clh 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1clh 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1clh 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :D 1clh 148 :P T0290 156 :ASKPFAEVRILSCGEL 1clh 150 :QNVPSKPVVILSAKVL Number of specific fragments extracted= 10 number of extra gaps= 2 total=276 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 1clh/T0290-1clh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1clh/T0290-1clh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1clh read from 1clh/T0290-1clh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1clh in template set Warning: unaligning (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1clh 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1clh 37 :NSG T0290 53 :HYKSCLFHR 1clh 40 :FYNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFSEGNGRGGE 1clh 58 :GGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1clh 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1clh 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1clh 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCGEL 1clh 148 :PYQNVPSKPVVILSAKVL Number of specific fragments extracted= 9 number of extra gaps= 2 total=285 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 1clh/T0290-1clh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0290 read from 1clh/T0290-1clh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1clh read from 1clh/T0290-1clh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1clh in template set Warning: unaligning (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1clh 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSCLFHR 1clh 40 :FYNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFSEGNGRGGES 1clh 58 :GGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1clh 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1clh 120 :FGYAVFGKVVKGMDVADKISQVPTHD T0290 156 :ASKPFAEVRILSCGEL 1clh 150 :QNVPSKPVVILSAKVL Number of specific fragments extracted= 7 number of extra gaps= 2 total=292 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cynA/T0290-1cynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cynA/T0290-1cynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cynA/T0290-1cynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m9eA/T0290-1m9eA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m9eA expands to /projects/compbio/data/pdb/1m9e.pdb.gz 1m9eA:# T0290 read from 1m9eA/T0290-1m9eA-t06-local-adpstyle5.a2m # 1m9eA read from 1m9eA/T0290-1m9eA-t06-local-adpstyle5.a2m # adding 1m9eA to template set # found chain 1m9eA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1m9eA)L164 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1m9eA 4 :PTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1m9eA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGE 1m9eA 147 :SRNGKTSKKITIADCGQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=295 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2alfA/T0290-2alfA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2alfA expands to /projects/compbio/data/pdb/2alf.pdb.gz 2alfA:# T0290 read from 2alfA/T0290-2alfA-t06-local-adpstyle5.a2m # 2alfA read from 2alfA/T0290-2alfA-t06-local-adpstyle5.a2m # adding 2alfA to template set # found chain 2alfA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2alfA 4 :PTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2alfA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTKWLDGKHVVFGAVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 2alfA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=298 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qngA/T0290-1qngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qngA/T0290-1qngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qngA/T0290-1qngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmfA/T0290-1zmfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmfA/T0290-1zmfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmfA/T0290-1zmfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qnhA/T0290-1qnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qnhA/T0290-1qnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qnhA/T0290-1qnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eslA/T0290-2eslA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2eslA expands to /projects/compbio/data/pdb/2esl.pdb.gz 2eslA:# T0290 read from 2eslA/T0290-2eslA-t06-local-adpstyle5.a2m # 2eslA read from 2eslA/T0290-2eslA-t06-local-adpstyle5.a2m # adding 2eslA to template set # found chain 2eslA in template set T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2eslA 39 :KVFFDVRIGDKDVGRIVIGLFGKVVPKTVENFVALATGEKGYG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 2eslA 82 :YKGSKFHRVIKDFMIQGGDITTGDGTGGVSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVIDGMTVVHSIELQATDGHDRPLTNCSIINSGKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=300 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xyhA/T0290-1xyhA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xyhA expands to /projects/compbio/data/pdb/1xyh.pdb.gz 1xyhA:# T0290 read from 1xyhA/T0290-1xyhA-t06-local-adpstyle5.a2m # 1xyhA read from 1xyhA/T0290-1xyhA-t06-local-adpstyle5.a2m # adding 1xyhA to template set # found chain 1xyhA in template set T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1xyhA 3 :VTLHTDVGDIKIEVFCERTPKTCENFLALCASNY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1xyhA 37 :YNGCIFHRNIKGFMVQTGDPT T0290 76 :GNGRGGESIYGGFFEDES 1xyhA 58 :GTGRGGNSIWGKKFEDEY T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDA 1xyhA 77 :EYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPHLDMKYTVFGKVIDGLETLDELEKLPVNE T0290 156 :ASKPFAEVRILSCGEL 1xyhA 140 :TYRPLNDVHIKDITIH Number of specific fragments extracted= 5 number of extra gaps= 0 total=305 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z81A/T0290-1z81A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z81A expands to /projects/compbio/data/pdb/1z81.pdb.gz 1z81A:# T0290 read from 1z81A/T0290-1z81A-t06-local-adpstyle5.a2m # 1z81A read from 1z81A/T0290-1z81A-t06-local-adpstyle5.a2m # adding 1z81A to template set # found chain 1z81A in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1z81A)L210 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1z81A 41 :PVVFMDINLGNNFLGKFKFELFQNIVPKTSENFRQFCTGEY T0290 46 :KSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISG 1z81A 82 :KVNNLPVGYKNTIFHRVIKEFMIQGGDFINHNGSGSLSIYGEKFDDENFDIKHDKEGLLSMANSGPNTNGCQFFITTKKCEWLDGKNVVFGRIIDN T0290 142 :QEVVREIENQKT 1z81A 180 :LLLLKKIENVSV T0290 154 :DAASKPFAEVRILSCGE 1z81A 193 :PYIYKPKIPINVVECGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=309 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3bA/T0290-2c3bA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c3bA expands to /projects/compbio/data/pdb/2c3b.pdb.gz 2c3bA:Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2c3bA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2c3bA # T0290 read from 2c3bA/T0290-2c3bA-t06-local-adpstyle5.a2m # 2c3bA read from 2c3bA/T0290-2c3bA-t06-local-adpstyle5.a2m # adding 2c3bA to template set # found chain 2c3bA in template set Warning: unaligning (T0290)D72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3bA)S92 Warning: unaligning (T0290)A95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3bA)S92 Warning: unaligning (T0290)A107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3bA)Q114 Warning: unaligning (T0290)Q117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3bA)Q114 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2c3bA 10 :YAPVGTAETKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEG T0290 54 :YKSCLFHRVVKDFMVQGG 2c3bA 51 :YRESTFHRIIPNFMIQGG T0290 96 :VKHNAAFLLSM 2c3bA 93 :RKHDKKGILSM T0290 118 :FFITTKPTPHLDGHHVVFGQVIS 2c3bA 115 :FFITTAVTSWLDGKHVVFGEVAD T0290 141 :GQEVVREIENQKTDAASKPF 2c3bA 140 :SYSVVKEIEALGSSSGSVRS T0290 161 :AEVRILSCGE 2c3bA 161 :TRPKIVNCGE Number of specific fragments extracted= 6 number of extra gaps= 0 total=315 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w74A/T0290-1w74A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w74A expands to /projects/compbio/data/pdb/1w74.pdb.gz 1w74A:# T0290 read from 1w74A/T0290-1w74A-t06-local-adpstyle5.a2m # 1w74A read from 1w74A/T0290-1w74A-t06-local-adpstyle5.a2m # adding 1w74A to template set # found chain 1w74A in template set T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKP 1w74A 14 :TATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASG T0290 52 :LHYKSCLFHRVVKDFMVQGGDFS 1w74A 64 :PFYDGAVFHRVIQGFMIQGGDPT T0290 76 :GNGRGGE 1w74A 87 :GTGRGGP T0290 86 :GGFFEDES 1w74A 94 :GYKFADEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVI 1w74A 103 :PELQFDKPYLLAMANAGPGTNGSQFFITVGKTPHLNRRHTIFGEVI T0290 140 :SGQEVVREIENQKTDAASKPFAEVRILSCGE 1w74A 151 :ESQRVVEAISKTATDGNDRPTDPVVIESITI Number of specific fragments extracted= 6 number of extra gaps= 0 total=321 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nul/T0290-2nul-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2nul expands to /projects/compbio/data/pdb/2nul.pdb.gz 2nul:Warning: there is no chain 2nul will retry with 2nulA # T0290 read from 2nul/T0290-2nul-t06-local-adpstyle5.a2m # 2nul read from 2nul/T0290-2nul-t06-local-adpstyle5.a2m # adding 2nul to template set # found chain 2nul in template set Warning: unaligning (T0290)I8 because first residue in template chain is (2nul)M1 Warning: unaligning (T0290)E170 because of BadResidue code BAD_PEPTIDE in next template residue (2nul)S163 T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2nul 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGF T0290 54 :YKSCLFHRVVKDFMVQGGDF 2nul 36 :YNNTIFHRVINGFMIQGGGF T0290 76 :GNGRGGESI 2nul 56 :EPGMKQKAT T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 2nul 65 :KEPIKNEANNGLKNTRGTLAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 2nul 90 :APHSATAQFFINVVDNDFLNFS T0290 132 :HVVFGQVISGQEVVREIENQKTDA 2nul 120 :YCVFAEVVDGMDVVDKIKGVATGR T0290 156 :ASKPFAEVRILSCG 2nul 148 :QDVPKEDVIIESVT Number of specific fragments extracted= 7 number of extra gaps= 1 total=328 Will force an alignment to be made, even if fragment is small Number of alignments=80 # command:CPU_time= 18.551 sec, elapsed time= 96.640 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 80 Adding 14878 constraints to all_contacts Done adding distance constraints # command:CPU_time= 18.636 sec, elapsed time= 96.729 sec. # command:Reading probabilities from T0290.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 49.414 Optimizing... Probability sum: -328.882, CN propb: -328.882 weights: 0.632 constraints: 428 # command:CPU_time= 24.546 sec, elapsed time= 102.676 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 428 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 428 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 533 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 533 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 12569 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 12569 # command:CPU_time= 24.789 sec, elapsed time= 103.116 sec. # command: