# 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 T0301 numbered 1 through 395 Created new target T0301 from T0301.a2m # command:CPU_time= 6.485 sec, elapsed time= 6.527 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gkeA/T0301-2gkeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gkeA expands to /projects/compbio/data/pdb/2gke.pdb.gz 2gkeA:Skipped atom 758, because occupancy 0.5 <= existing 0.500 in 2gkeA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 2gkeA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 2gkeA # T0301 read from 2gkeA/T0301-2gkeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkeA read from 2gkeA/T0301-2gkeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gkeA to template set # found chain 2gkeA in template set Warning: unaligning (T0301)G21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)V22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTSK 2gkeA 2 :QFSKMHGLGND # choosing archetypes in rotamer library T0301 23 :FFR 2gkeA 15 :VVD T0301 28 :DLPESCRVPGEARDRLF 2gkeA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAH 2gkeA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 2gkeA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 2gkeA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 2gkeA 94 :DISVS T0301 151 :VSGGQVQET 2gkeA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGA 2gkeA 108 :VKDDNQIRVNMGEPIWEPAKIPF T0301 193 :PTGNLVDDLEVP 2gkeA 131 :TANKFEKNYILR T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 261 :GL 2gkeA 184 :RF T0301 273 :QHTPKIAFVA 2gkeA 186 :PERVNAGFMQ T0301 294 :LVAAG 2gkeA 196 :IINKE T0301 301 :DLLVRALSMG 2gkeA 201 :HIKLRVYERG T0301 311 :KLHHAMMGTAAVAIGTAAA 2gkeA 212 :GETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 2gkeA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 21 number of extra gaps= 2 total=21 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 2gkeA/T0301-2gkeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 2gkeA/T0301-2gkeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkeA read from 2gkeA/T0301-2gkeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gkeA in template set Warning: unaligning (T0301)G21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)V22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTSK 2gkeA 2 :QFSKMHGLGND T0301 23 :FFR 2gkeA 15 :VVD T0301 28 :DLPESCRVPGEARDRLF 2gkeA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAH 2gkeA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 2gkeA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 2gkeA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 2gkeA 94 :DISVS T0301 140 :NIGKTIIAH 2gkeA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 2gkeA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 261 :GL 2gkeA 181 :SH T0301 268 :EAA 2gkeA 183 :ERF T0301 273 :QHTPKIAFV 2gkeA 186 :PERVNAGFM T0301 293 :KLVAAG 2gkeA 195 :QIINKE T0301 301 :DLLVRALSMGK 2gkeA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAA 2gkeA 213 :ETQACGSGACAAVAVGI T0301 339 :AGGGERSAVRFGHPSGTLRV 2gkeA 230 :MQGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 21 number of extra gaps= 2 total=42 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 2gkeA/T0301-2gkeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 2gkeA/T0301-2gkeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gkeA read from 2gkeA/T0301-2gkeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gkeA in template set Warning: unaligning (T0301)F23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)V14 Warning: unaligning (T0301)F24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)V14 Warning: unaligning (T0301)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gkeA)G151 Warning: unaligning (T0301)T212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gkeA)G151 T0301 10 :PATYLRGGTS 2gkeA 2 :QFSKMHGLGN T0301 22 :V 2gkeA 12 :D T0301 25 :RLEDLPESCRVPGEARDRLF 2gkeA 15 :VVDGVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 2gkeA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 2gkeA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 2gkeA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDP 2gkeA 71 :SQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 2gkeA 93 :KDISVS T0301 140 :NIGKTIIAHV 2gkeA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGG 2gkeA 109 :KDDNQIRVNMGEPIWEPAKIP T0301 192 :FPTGNLVDDLEVP 2gkeA 130 :FTANKFEKNYILR T0301 205 :GVGTFK 2gkeA 144 :DIQTVL T0301 213 :MINAGIPTVFVNAEEIGYRG 2gkeA 152 :AVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 2gkeA 173 :EQLGPLLE T0301 272 :RQHTPKIAFV 2gkeA 185 :FPERVNAGFM T0301 293 :KLVAAGDIDLLVRALSMGKL 2gkeA 195 :QIINKEHIKLRVYERGAGET T0301 314 :HAMMGTAAVAIGTAA 2gkeA 215 :QACGSGACAAVAVGI T0301 339 :AGGGERSAVRFGHPSGTLRV 2gkeA 230 :MQGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 2gkeA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 2 total=61 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 1gqzA/T0301-1gqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gqzA expands to /projects/compbio/data/pdb/1gqz.pdb.gz 1gqzA:# T0301 read from 1gqzA/T0301-1gqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gqzA read from 1gqzA/T0301-1gqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gqzA to template set # found chain 1gqzA in template set T0301 10 :PATYLRGGTSKGVFFR 1gqzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1gqzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 1gqzA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDPA 1gqzA 71 :SQCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 1gqzA 94 :DISVS T0301 151 :VSGGQVQET 1gqzA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 1gqzA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 261 :GL 1gqzA 184 :RF T0301 273 :QHTPKIAFVA 1gqzA 186 :PERVNAGFMQ T0301 294 :LVAAG 1gqzA 196 :IINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAI 1gqzA 213 :ETQACGSGACAAVAVGIMQ T0301 341 :GGERSAVRFGHPSGTLRV 1gqzA 232 :GLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 18 number of extra gaps= 0 total=79 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 1gqzA/T0301-1gqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1gqzA/T0301-1gqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gqzA read from 1gqzA/T0301-1gqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gqzA in template set T0301 10 :PATYLRGGTSKGVFFR 1gqzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1gqzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFVD 1gqzA 65 :ADGSEVS T0301 103 :NCGNLSTGAGAFALHAGLVDPA 1gqzA 72 :QCGNGARCFARFVTLKGLTNKK T0301 131 :ICEVR 1gqzA 94 :DISVS T0301 140 :NIGKTIIAH 1gqzA 99 :TQKGNMVLT T0301 168 :TFPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEV 1gqzA 108 :VKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRT T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 261 :GL 1gqzA 181 :SH T0301 268 :EAA 1gqzA 183 :ERF T0301 273 :QHTPKIAFV 1gqzA 186 :PERVNAGFM T0301 293 :KLVAAG 1gqzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAI 1gqzA 213 :ETQACGSGACAAVAVGIMQ T0301 341 :GGERSAVRFGHPSGTLRV 1gqzA 232 :GLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 0 total=98 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 1gqzA/T0301-1gqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1gqzA/T0301-1gqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gqzA read from 1gqzA/T0301-1gqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gqzA in template set T0301 10 :PATYLRGG 1gqzA 2 :QFSKMHGL T0301 20 :KGVFFRLEDLPESCRVPGEARDRLF 1gqzA 10 :GNDFVVVDGVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1gqzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1gqzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDKPFV 1gqzA 65 :ADGSEV T0301 102 :GNCGNLSTGAGAFALHAGLVDP 1gqzA 71 :SQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 1gqzA 93 :KDISVS T0301 140 :NIGKTIIAHV 1gqzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGG 1gqzA 109 :KDDNQIRVNMGEPIWEPAKIP T0301 192 :FPTGNLVDDLEVP 1gqzA 130 :FTANKFEKNYILR T0301 205 :GVGTFKATMINAGIPTVFVNAEEIGYRG 1gqzA 144 :DIQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1gqzA 173 :EQLGPLLE T0301 272 :RQHTPKIAFVA 1gqzA 185 :FPERVNAGFMQ T0301 294 :LVAAG 1gqzA 196 :IINKE T0301 301 :DLLVRALSMGK 1gqzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAAIP 1gqzA 213 :ETQACGSGACAAVAVGIMQG T0301 342 :GERSAVRFGHPSGTLRV 1gqzA 233 :LLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1gqzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 18 number of extra gaps= 0 total=116 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 1w61A/T0301-1w61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w61A expands to /projects/compbio/data/pdb/1w61.pdb.gz 1w61A:# T0301 read from 1w61A/T0301-1w61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w61A read from 1w61A/T0301-1w61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w61A to template set # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSKGVFF 1w61A 53 :TEGEAARIV T0301 26 :LEDLPE 1w61A 62 :TSGLPH T0301 33 :CRVPG 1w61A 68 :IPGSN T0301 38 :EARDRLFMRVIGSPDPYAAH 1w61A 82 :ENMDYLRRGIMLEPRGHDDM T0301 70 :KCVILSKSSQPGHDVDYLYGQV 1w61A 102 :FGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQVQET 1w61A 163 :PAGLVRGTAHLQSGTESEV T0301 172 :AEIVLEFLDP 1w61A 182 :SNASIINVPS T0301 195 :GNLVDDLEV 1w61A 194 :YQQDVVVVL T0301 204 :PGVGTFKATMINA 1w61A 204 :KPYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 264 :KT 1w61A 258 :QH T0301 272 :RQHTPKIAFVAPPRD 1w61A 265 :INTVDCVEIYGPPTN T0301 291 :SGK 1w61A 280 :PEA T0301 300 :IDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTL 1w61A 283 :NYKNVVIFGNRQADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGA 1w61A 332 :LFQGRV T0301 361 :EASQANG 1w61A 339 :GEERIPG Number of specific fragments extracted= 24 number of extra gaps= 6 total=140 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 1w61A/T0301-1w61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1w61A/T0301-1w61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w61A read from 1w61A/T0301-1w61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSKGV 1w61A 53 :TEGEAAR T0301 24 :FRLEDLPE 1w61A 60 :IVTSGLPH T0301 33 :CRVPG 1w61A 68 :IPGSN T0301 38 :EARDRLFMRVIGSPDPYAA 1w61A 82 :ENMDYLRRGIMLEPRGHDD T0301 69 :SKCVILSKSSQPGHDVDYLYGQV 1w61A 101 :MFGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQV 1w61A 163 :PAGLVRGTAHLQSGTE T0301 169 :FPAAEIVLEFLDP 1w61A 179 :SEVSNASIINVPS T0301 192 :F 1w61A 194 :Y T0301 196 :NLVDDLEV 1w61A 195 :QQDVVVVL T0301 204 :PGVGTFKATMINA 1w61A 204 :KPYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 268 :EAATRQHT 1w61A 258 :QHPQLPHI T0301 276 :PKIAFVAPPRD 1w61A 269 :DCVEIYGPPTN T0301 298 :GDIDLLVRALSMGK 1w61A 280 :PEANYKNVVIFGNR T0301 312 :LHHAMMGTAAVAIGTAAAIPGTL 1w61A 295 :ADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGAEA 1w61A 332 :LFQGRVLG T0301 363 :SQ 1w61A 341 :ER Number of specific fragments extracted= 25 number of extra gaps= 6 total=165 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 1w61A/T0301-1w61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1w61A/T0301-1w61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w61A read from 1w61A/T0301-1w61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w61A in template set Warning: unaligning (T0301)P5 because first residue in template chain is (1w61A)F42 Warning: unaligning (T0301)A11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)I49 Warning: unaligning (T0301)T12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)I49 Warning: unaligning (T0301)L14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)H52 Warning: unaligning (T0301)R15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)H52 Warning: unaligning (T0301)S182 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w61A)L193 Warning: unaligning (T0301)I191 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w61A)L193 Warning: unaligning (T0301)G217 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)N218 Warning: unaligning (T0301)I218 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)N218 Warning: unaligning (T0301)T220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w61A)A221 Warning: unaligning (T0301)V221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w61A)A221 Warning: unaligning (T0301)L258 because of BadResidue code BAD_PEPTIDE in next template residue (1w61A)S254 Warning: unaligning (T0301)R259 because of BadResidue code BAD_PEPTIDE at template residue (1w61A)S254 T0301 6 :QIRIP 1w61A 43 :KKSFT T0301 13 :Y 1w61A 50 :D T0301 16 :GGTSK 1w61A 53 :TEGEA T0301 22 :VFFRLEDLPES 1w61A 58 :ARIVTSGLPHI T0301 36 :PG 1w61A 69 :PG T0301 38 :EARDRLFMRVIGSPDPYAAH 1w61A 82 :ENMDYLRRGIMLEPRGHDDM T0301 70 :KCVILSKSSQPGHDVDYLYGQV 1w61A 102 :FGAFLFDPIEEGADLGIVFMDT T0301 98 :VDWSGNCGNLSTGAGAFALHAGLVDPA 1w61A 124 :GGYLNMCGHNSIAAVTAAVETGIVSVP T0301 127 :PEDGICEVRIWQ 1w61A 151 :AKATNVPVVLDT T0301 141 :IGKTIIAHVPVSGGQ 1w61A 163 :PAGLVRGTAHLQSGT T0301 168 :TFPAAEIVLEFLDP 1w61A 178 :ESEVSNASIINVPS T0301 195 :GNLVDDLEVP 1w61A 194 :YQQDVVVVLP T0301 205 :GVGTFKATMINA 1w61A 205 :PYGEVRVDIAFG T0301 219 :P 1w61A 219 :F T0301 222 :FVNAEEIGYRGTE 1w61A 222 :IVPAEQLGIDISV T0301 240 :NGDPQQLARFERIRVAGA 1w61A 235 :QNLSRLQEAGELLRTEIN T0301 260 :MGL 1w61A 255 :VKV T0301 263 :IKTP 1w61A 260 :PQLP T0301 272 :RQHTPKIAFVAPPRDYRT 1w61A 265 :INTVDCVEIYGPPTNPEA T0301 300 :IDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTL 1w61A 283 :NYKNVVIFGNRQADRSPCGTGTSAKMATLYAKGQL T0301 342 :GERSAVRFGHPSG 1w61A 318 :RIGETFVYESILG T0301 355 :TLRVGAEAS 1w61A 332 :LFQGRVLGE Number of specific fragments extracted= 22 number of extra gaps= 6 total=187 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 1bwzA/T0301-1bwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bwzA expands to /projects/compbio/data/pdb/1bwz.pdb.gz 1bwzA:# T0301 read from 1bwzA/T0301-1bwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bwzA read from 1bwzA/T0301-1bwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bwzA to template set # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFRL 1bwzA 2 :QFSKMHGLGNDFVVVDG T0301 29 :LPESCRVPGEARDRLF 1bwzA 19 :VTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1bwzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1bwzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 93 :IDK 1bwzA 65 :ADG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVD 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTN T0301 129 :DGICEVR 1bwzA 92 :KKDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVPGV 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQ T0301 208 :TFKATMINAGIPTVFVNAEEIGYRG 1bwzA 147 :TVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 261 :GL 1bwzA 184 :RF T0301 273 :QHTPKIAFV 1bwzA 186 :PERVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLR 1bwzA 231 :QGLLNNNVQVDLPGGSLM T0301 360 :AEASQANGEWTV 1bwzA 249 :IEWNGVGHPLYM Number of specific fragments extracted= 18 number of extra gaps= 0 total=205 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 1bwzA/T0301-1bwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1bwzA/T0301-1bwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bwzA read from 1bwzA/T0301-1bwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFRL 1bwzA 2 :QFSKMHGLGNDFVVVDG T0301 29 :LPESCRVPGEARDRLF 1bwzA 19 :VTQNVFFTPETIRRLA T0301 51 :PDPYAAH 1bwzA 35 :NRHCGIG T0301 68 :TSKCVILSKSSQPGHDVDYLYGQ 1bwzA 42 :FDQLLIVEAPYDPELDFHYRIFN T0301 94 :DK 1bwzA 66 :DG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVD 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTN T0301 129 :DGICEVR 1bwzA 92 :KKDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVP 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTD T0301 206 :VGTFKATMINAGIPTVFVNAEEIGYRG 1bwzA 145 :IQTVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 261 :GL 1bwzA 181 :SH T0301 268 :EAATR 1bwzA 183 :ERFPE T0301 275 :TPKIAFV 1bwzA 188 :RVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 1bwzA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTVT 1bwzA 250 :EWNGVGHPLYMT Number of specific fragments extracted= 19 number of extra gaps= 0 total=224 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 1bwzA/T0301-1bwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1bwzA/T0301-1bwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bwzA read from 1bwzA/T0301-1bwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bwzA in template set T0301 10 :PATYLRGGTSKGVFFR 1bwzA 2 :QFSKMHGLGNDFVVVD T0301 28 :DLPESCRVPGEARDRLF 1bwzA 18 :GVTQNVFFTPETIRRLA T0301 51 :PDPYAAHI 1bwzA 35 :NRHCGIGF T0301 69 :SKCVILSKSSQPGHDVDYLYGQ 1bwzA 43 :DQLLIVEAPYDPELDFHYRIFN T0301 94 :DK 1bwzA 66 :DG T0301 99 :DWSGNCGNLSTGAGAFALHAGLVDP 1bwzA 68 :SEVSQCGNGARCFARFVTLKGLTNK T0301 130 :GICEVR 1bwzA 93 :KDISVS T0301 140 :NIGKTIIAHV 1bwzA 99 :TQKGNMVLTV T0301 169 :FPAAEIVLEFLDPSDDGEDGGAIFPTGNLVDDLEVPGV 1bwzA 109 :KDMNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQ T0301 208 :TFKATMINAGIPTVFVNAEEIGYRG 1bwzA 147 :TVLCGAVSMGNPHCVVQVDDIQTAN T0301 243 :PQQLARFE 1bwzA 173 :EQLGPLLE T0301 272 :RQHTPKIAFV 1bwzA 185 :FPERVNAGFM T0301 293 :KLVAAG 1bwzA 195 :QIINKE T0301 301 :DLLVRALSMGK 1bwzA 201 :HIKLRVYERGA T0301 312 :LHHAMMGTAAVAIGTAAA 1bwzA 213 :ETQACGSGACAAVAVGIM T0301 340 :GGGERSAVRFGHPSGTLRV 1bwzA 231 :QGLLNNNVQVDLPGGSLMI T0301 361 :EASQANGEWTV 1bwzA 250 :EWNGVGHPLYM Number of specific fragments extracted= 17 number of extra gaps= 0 total=241 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 1tm0A/T0301-1tm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tm0A expands to /projects/compbio/data/pdb/1tm0.pdb.gz 1tm0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0301 read from 1tm0A/T0301-1tm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tm0A read from 1tm0A/T0301-1tm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tm0A to template set # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFRLEDL 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIVGGVA T0301 34 :RVPGEARDRLFMRVI 1tm0A 28 :PPPGETVWEQSRFIA T0301 51 :PDPY 1tm0A 53 :NKPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 57 :GGVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDPA 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAMQ T0301 129 :DGICEVRIW 1tm0A 111 :EPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQE 1tm0A 120 :APGGIIEVEAECRNGKAER T0301 174 :IVLEFLDPS 1tm0A 139 :ISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 242 :DPQQLARFER 1tm0A 188 :PGQARELAEI T0301 252 :IRVA 1tm0A 199 :VKIT T0301 265 :TPEEA 1tm0A 212 :RHPER T0301 271 :TRQHTPKIAFVAPPRD 1tm0A 217 :DWRHISFCQITEPVTR T0301 291 :SGK 1tm0A 233 :EGD T0301 302 :LLVR 1tm0A 236 :VLTG T0301 317 :MGTAAVAIGTAAAIPGT 1tm0A 255 :TGTGCSARMAVLHAKGQ T0301 341 :GGERSAVRFGH 1tm0A 272 :MKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 19 number of extra gaps= 0 total=260 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 1tm0A/T0301-1tm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1tm0A/T0301-1tm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tm0A read from 1tm0A/T0301-1tm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFR 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIV T0301 27 :EDL 1tm0A 24 :GGV T0301 33 :CRVPGEARDRLFMRVI 1tm0A 27 :APPPGETVWEQSRFIA T0301 51 :PDPY 1tm0A 53 :NKPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 57 :GGVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDP 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAM T0301 128 :EDGICEVRIW 1tm0A 110 :QEPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQE 1tm0A 120 :APGGIIEVEAECRNGKAER T0301 174 :IVLEFLDPS 1tm0A 139 :ISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 242 :DPQQLARFERIRVA 1tm0A 188 :PGQARELAEIGVKI T0301 263 :I 1tm0A 212 :R T0301 267 :EEAATRQHTPKIAFVAPPRD 1tm0A 213 :HPERDWRHISFCQITEPVTR T0301 291 :SG 1tm0A 233 :EG T0301 301 :DLLVR 1tm0A 235 :DVLTG T0301 317 :MGTAAVAIGTAAAIPGT 1tm0A 255 :TGTGCSARMAVLHAKGQ T0301 341 :GGERSAVRFGH 1tm0A 272 :MKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 19 number of extra gaps= 0 total=279 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 1tm0A/T0301-1tm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1tm0A/T0301-1tm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tm0A read from 1tm0A/T0301-1tm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tm0A in template set Warning: unaligning (T0301)H3 because first residue in template chain is (1tm0A)M1 Warning: unaligning (T0301)G229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)E187 Warning: unaligning (T0301)T233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)E187 Warning: unaligning (T0301)L262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)F211 Warning: unaligning (T0301)M316 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)P254 Warning: unaligning (T0301)P352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tm0A)T286 Warning: unaligning (T0301)T355 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tm0A)T286 T0301 4 :PPQIRIPATYLRGGTSKGVFFRLEDLPESCRVPGEARDRL 1tm0A 2 :RSTKVIHIVGCHAEGEVGDVIVGGVAPPPGETVWEQSRFI T0301 44 :FMRVIGSPDP 1tm0A 48 :RNFVLNKPRG T0301 66 :SSTSKCVILSKSSQPGHDVDYLYGQ 1tm0A 58 :GVFRHVNLLVPPKDPRAQMGFIIME T0301 97 :FVDWSGNCGNLSTGAGAFALHAGLVDP 1tm0A 83 :PADTPPMSGSNSICVSTVLLDSGIIAM T0301 128 :EDGICEVRIW 1tm0A 110 :QEPVTHMVLE T0301 140 :NIGKTIIAHVPVSGGQVQ 1tm0A 120 :APGGIIEVEAECRNGKAE T0301 173 :EIVLEFLDPS 1tm0A 138 :RISVRNVPSF T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEI 1tm0A 148 :ADRLDAPLDVTGLGTIMVDTAYGGDSFVIVDAAQI T0301 234 :E 1tm0A 188 :P T0301 243 :PQQLARFERIRVA 1tm0A 189 :GQARELAEIGVKI T0301 263 :I 1tm0A 212 :R T0301 272 :RQHTPKIAFVAPPRDYRT 1tm0A 218 :WRHISFCQITEPVTREGD T0301 301 :DLLV 1tm0A 236 :VLTG T0301 317 :MGTAAVAIGTAAAIPG 1tm0A 255 :TGTGCSARMAVLHAKG T0301 340 :GGGERSAVRFGH 1tm0A 271 :QMKAGERFIGKS T0301 356 :LRVGA 1tm0A 288 :FHCRL T0301 361 :EASQANGEWTVT 1tm0A 294 :KVLELGGKPAIS Number of specific fragments extracted= 17 number of extra gaps= 0 total=296 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 1sdjA/T0301-1sdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sdjA expands to /projects/compbio/data/pdb/1sdj.pdb.gz 1sdjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0301 read from 1sdjA/T0301-1sdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdjA read from 1sdjA/T0301-1sdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sdjA to template set # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAFALH 1sdjA 70 :PICGHATVAAHYVRAK T0301 118 :AGL 1sdjA 87 :LGL T0301 129 :DGIC 1sdjA 90 :GNCT T0301 136 :IWQANIGKTIIAHVPVSGGQVQETGDFEL 1sdjA 94 :IWQTSLAGKHRVTIEKHNDDYRISLEQGT T0301 176 :LEFLDPSDD 1sdjA 123 :PGFEPPLEG T0301 186 :E 1sdjA 132 :E T0301 187 :DGGAIFP 1sdjA 144 :TEDDILP T0301 208 :TFKATMINAGIPTVFVNAE 1sdjA 151 :GLPIQVATTGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 242 :D 1sdjA 180 :D T0301 246 :LARFERIRV 1sdjA 181 :LNALTAISK T0301 259 :RMGL 1sdjA 190 :KIGC T0301 275 :TPKIAFVAPP 1sdjA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGKLHHA 1sdjA 204 :GKNETDGRMFSPAIGIVE T0301 316 :MMGTAAVAIGTAAA 1sdjA 224 :VTGNANGPMGAWLV T0301 336 :NLAAG 1sdjA 238 :HHNVL T0301 341 :GGERSAVRFGHPS 1sdjA 245 :DGNVLRVKGHQGR T0301 354 :GTLRVGAEASQA 1sdjA 263 :GMIEVTVTIRDN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 23 number of extra gaps= 0 total=319 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 1sdjA/T0301-1sdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1sdjA/T0301-1sdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdjA read from 1sdjA/T0301-1sdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAF 1sdjA 70 :PICGHATVAAHYV T0301 115 :ALHAGL 1sdjA 84 :AKVLGL T0301 128 :EDGIC 1sdjA 90 :GNCTI T0301 137 :WQANIGKTIIAHVPVSGGQVQETGDFELD 1sdjA 95 :WQTSLAGKHRVTIEKHNDDYRISLEQGTP T0301 177 :EFLDPSDD 1sdjA 124 :GFEPPLEG T0301 186 :E 1sdjA 132 :E T0301 187 :DGGAI 1sdjA 144 :TEDDI T0301 203 :VPGV 1sdjA 149 :LPGL T0301 210 :KATMINAGIPTVFVNAE 1sdjA 153 :PIQVATTGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 246 :LARFERIR 1sdjA 181 :LNALTAIS T0301 258 :LRMGL 1sdjA 189 :KKIGC T0301 275 :TPKIAFVAPP 1sdjA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGKLHHA 1sdjA 204 :GKNETDGRMFSPAIGIVE T0301 316 :MMGTAAVAIGTAA 1sdjA 224 :VTGNANGPMGAWL T0301 335 :VNLAAG 1sdjA 237 :VHHNVL T0301 341 :GGERSAVRFGHPS 1sdjA 245 :DGNVLRVKGHQGR T0301 354 :GTLRVGAEAS 1sdjA 263 :GMIEVTVTIR T0301 366 :NG 1sdjA 273 :DN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 24 number of extra gaps= 0 total=343 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 1sdjA/T0301-1sdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1sdjA/T0301-1sdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdjA read from 1sdjA/T0301-1sdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sdjA in template set T0301 17 :GTSKGVFFRLEDLP 1sdjA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1sdjA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1sdjA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFV 1sdjA 64 :TPTVEV T0301 102 :GNCGNLSTGAGAFALH 1sdjA 70 :PICGHATVAAHYVRAK T0301 118 :AGL 1sdjA 87 :LGL T0301 128 :EDGICEVR 1sdjA 90 :GNCTIWQT T0301 140 :NIGKTIIAHVPVSGGQVQETGDFEL 1sdjA 98 :SLAGKHRVTIEKHNDDYRISLEQGT T0301 176 :LEFLDPSD 1sdjA 123 :PGFEPPLE T0301 185 :GEDGGAIFP 1sdjA 142 :HLTEDDILP T0301 195 :GNLVDDLE 1sdjA 151 :GLPIQVAT T0301 216 :AGIPTVFVNAE 1sdjA 159 :TGHSKVMIPLK T0301 227 :EIGYRGTEL 1sdjA 171 :EVDIDALSP T0301 246 :LARFERIRVAG 1sdjA 181 :LNALTAISKKI T0301 273 :QHTPKIAFVAPPRDY 1sdjA 192 :GCNGFFPFQIRPGKN T0301 301 :DLLVRALSMGKLHH 1sdjA 207 :ETDGRMFSPAIGIV T0301 315 :AMMGTAAVAIGTAAA 1sdjA 223 :PVTGNANGPMGAWLV T0301 336 :NLAAG 1sdjA 238 :HHNVL T0301 341 :GGERSAVRFGH 1sdjA 245 :DGNVLRVKGHQ T0301 352 :PSGTLRVGAEASQA 1sdjA 261 :RDGMIEVTVTIRDN T0301 370 :TVTKA 1sdjA 275 :QPEKV Number of specific fragments extracted= 21 number of extra gaps= 0 total=364 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 1xubA/T0301-1xubA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xubA expands to /projects/compbio/data/pdb/1xub.pdb.gz 1xubA:Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 42, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 44, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 46, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 48, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 50, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 52, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 54, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 56, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 58, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 60, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 62, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 64, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 66, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 68, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 286, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 288, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 290, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 292, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 294, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 296, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 298, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 300, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 302, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 304, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 306, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 535, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 537, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 539, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 541, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 543, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 545, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 547, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 914, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 916, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 918, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 920, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 922, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 924, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 958, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 960, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 962, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 964, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 966, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 968, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 970, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 972, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1404, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1406, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1408, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1410, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1412, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1414, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1416, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1418, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1441, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1443, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1445, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1447, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1449, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1451, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1453, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1455, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1532, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1534, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1536, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1538, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1540, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1542, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1544, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1546, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1548, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1550, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1552, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1579, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1581, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1583, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1585, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1587, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1589, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1957, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1959, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1961, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1963, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1965, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1967, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1969, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 1971, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2173, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2175, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2177, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2179, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2181, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2183, because occupancy 0.300 <= existing 0.700 in 1xubA Skipped atom 2185, because occupancy 0.300 <= existing 0.700 in 1xubA # T0301 read from 1xubA/T0301-1xubA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xubA read from 1xubA/T0301-1xubA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xubA to template set # found chain 1xubA in template set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGHD 1xubA 47 :TFVLKPRNGGDA T0301 88 :YGQV 1xubA 59 :LIRI T0301 94 :DKPFVDW 1xubA 65 :PVNELPF T0301 104 :CGNLSTGAGAFALHAG 1xubA 72 :AGAPLLGTAIALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 185 :GE 1xubA 128 :GR T0301 205 :GVG 1xubA 138 :GIS T0301 208 :TFKATMINAGIPTVFVNAEEI 1xubA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1xubA 164 :DALSA T0301 262 :LIKTPEEAATRQHT 1xubA 169 :LHPDHRALSNFHDM T0301 277 :KIAFVAP 1xubA 183 :AINCFAG T0301 290 :ASG 1xubA 190 :AGR T0301 301 :DLLVRALSM 1xubA 193 :RWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWT 1xubA 245 :PSLMFAKAEGRAEQLT Number of specific fragments extracted= 23 number of extra gaps= 4 total=387 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 1xubA/T0301-1xubA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1xubA/T0301-1xubA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xubA read from 1xubA/T0301-1xubA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xubA in template set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGH 1xubA 47 :TFVLKPRNGGD T0301 87 :LYGQV 1xubA 58 :ALIRI T0301 94 :DKPFVDW 1xubA 65 :PVNELPF T0301 104 :CGNLSTGAGAFALHAG 1xubA 72 :AGAPLLGTAIALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 185 :GE 1xubA 128 :GR T0301 201 :LEVPGV 1xubA 137 :LGISDS T0301 208 :TFKATMINAGIPTVFVNAEEI 1xubA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 234 :ELREE 1xubA 164 :DALSA T0301 263 :IKTPEEAATRQHTPKIAFVAPP 1xubA 169 :LHPDHRALSNFHDMAINCFAGA T0301 291 :SG 1xubA 191 :GR T0301 301 :DLLVRALSM 1xubA 193 :RWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWT 1xubA 245 :PSLMFAKAEGRAEQLT T0301 373 :K 1xubA 261 :R Number of specific fragments extracted= 23 number of extra gaps= 4 total=410 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 1xubA/T0301-1xubA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1xubA/T0301-1xubA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xubA read from 1xubA/T0301-1xubA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xubA in template set Warning: unaligning (T0301)R8 because first residue in template chain is (1xubA)M1 Warning: unaligning (T0301)K70 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)S46 Warning: unaligning (T0301)C71 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)S46 Warning: unaligning (T0301)S92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1xubA)T64 Warning: unaligning (T0301)I93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1xubA)T64 Warning: unaligning (T0301)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1xubA)E104 Warning: unaligning (T0301)H148 because of BadResidue code BAD_PEPTIDE at template residue (1xubA)E104 Warning: unaligning (T0301)S353 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xubA)R244 Warning: unaligning (T0301)G354 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xubA)R244 T0301 9 :IPATYLRG 1xubA 2 :HNYVIIDA T0301 17 :GTSKGVFFRLEDLP 1xubA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1xubA 31 :PAQMQRIAREM T0301 67 :STS 1xubA 42 :NLS T0301 72 :VILSKSSQPGHD 1xubA 47 :TFVLKPRNGGDA T0301 88 :YGQV 1xubA 59 :LIRI T0301 94 :DKPFVDWS 1xubA 65 :PVNELPFA T0301 105 :GNLSTGAGA 1xubA 73 :GAPLLGTAI T0301 115 :ALHAGL 1xubA 82 :ALGAHT T0301 128 :EDGICEVRI 1xubA 88 :DNHRLYLET T0301 141 :IGKTII 1xubA 97 :QMGTIA T0301 149 :VPVSGGQVQE 1xubA 105 :LERQNGSVIA T0301 162 :FELDGVTFPAAEI 1xubA 115 :ASMDQPIPTWTAL T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1xubA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 237 :E 1xubA 164 :D T0301 248 :RFER 1xubA 165 :ALSA T0301 262 :LIKTPEEAATRQHTPKIAFVA 1xubA 169 :LHPDHRALSNFHDMAINCFAG T0301 298 :GDIDLLVRALSM 1xubA 190 :AGRRWRSRMFSP T0301 310 :GKLHHAMMGTAAVAIGTAAAIPGTL 1xubA 204 :GVVEDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1xubA 229 :EFGQPVEILQG T0301 355 :TLRVGAEASQANGEWTV 1xubA 245 :PSLMFAKAEGRAEQLTR Number of specific fragments extracted= 21 number of extra gaps= 4 total=431 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 1qyaA/T0301-1qyaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qyaA expands to /projects/compbio/data/pdb/1qya.pdb.gz 1qyaA:Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2148, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 1qyaA Skipped atom 2154, because occupancy 0.500 <= existing 0.500 in 1qyaA # T0301 read from 1qyaA/T0301-1qyaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyaA read from 1qyaA/T0301-1qyaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qyaA to template set # found chain 1qyaA in template set Warning: unaligning (T0301)N103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LSTGAGAFALH 1qyaA 75 :ATVAAHYVRAK T0301 118 :AGL 1qyaA 87 :LGL T0301 125 :RI 1qyaA 93 :TI T0301 132 :CEVRIWQANIGKTIIAHV 1qyaA 103 :HRVTIEKHNDDYRISLEQ T0301 154 :GQVQETG 1qyaA 121 :GTPGFEP T0301 181 :PSD 1qyaA 128 :PLE T0301 185 :GE 1qyaA 131 :GE T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 208 :TFKATMINAGI 1qyaA 160 :GHSKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRV 1qyaA 181 :LNALTAISK T0301 259 :RMGL 1qyaA 190 :KIGC T0301 275 :TPKIAFVAPP 1qyaA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGK 1qyaA 204 :GKNETDGRMFSPAI T0301 314 :HAMMGTAAVAIGTAAAIP 1qyaA 222 :DPVTGNANGPMGAWLVHH T0301 338 :AAG 1qyaA 240 :NVL T0301 341 :GGERSAVRFGH 1qyaA 245 :DGNVLRVKGHQ T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 370 :TVTK 1qyaA 275 :QPEK Number of specific fragments extracted= 25 number of extra gaps= 2 total=456 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 1qyaA/T0301-1qyaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1qyaA/T0301-1qyaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyaA read from 1qyaA/T0301-1qyaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyaA in template set Warning: unaligning (T0301)W100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)K102 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LS 1qyaA 75 :AT T0301 109 :TGAGAFALHAGL 1qyaA 78 :AAHYVRAKVLGL T0301 127 :P 1qyaA 98 :S T0301 132 :CEVRIWQANIGKTIIAHV 1qyaA 103 :HRVTIEKHNDDYRISLEQ T0301 154 :GQVQ 1qyaA 121 :GTPG T0301 178 :FLDPSD 1qyaA 125 :FEPPLE T0301 185 :GE 1qyaA 131 :GE T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 204 :PG 1qyaA 160 :GH T0301 210 :KATMINAGI 1qyaA 162 :SKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRV 1qyaA 181 :LNALTAISK T0301 259 :RMGL 1qyaA 190 :KIGC T0301 275 :TPKIAFVAPP 1qyaA 194 :NGFFPFQIRP T0301 298 :GDIDLLVRALSMGK 1qyaA 204 :GKNETDGRMFSPAI T0301 315 :AMMGTAAVAIGTAA 1qyaA 223 :PVTGNANGPMGAWL T0301 335 :VNLAAGGGERS 1qyaA 237 :VHHNVLPHDGN T0301 346 :AVRFGH 1qyaA 250 :RVKGHQ T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 368 :E 1qyaA 275 :Q T0301 371 :VTKA 1qyaA 276 :PEKV Number of specific fragments extracted= 27 number of extra gaps= 2 total=483 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 1qyaA/T0301-1qyaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1qyaA/T0301-1qyaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyaA read from 1qyaA/T0301-1qyaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyaA in template set Warning: unaligning (T0301)W100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)H74 Warning: unaligning (T0301)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)H74 Warning: unaligning (T0301)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qyaA)K102 Warning: unaligning (T0301)I131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qyaA)K102 Warning: unaligning (T0301)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)I154 Warning: unaligning (T0301)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)I154 Warning: unaligning (T0301)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qyaA)T159 Warning: unaligning (T0301)V203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qyaA)T159 T0301 17 :GTSKGVFFRLEDLP 1qyaA 18 :GNSAGVVFPADNLS T0301 37 :GEARDRLFMRV 1qyaA 32 :EAQMQLIAREL T0301 67 :STSKCVILSKSSQPGHDVDYL 1qyaA 43 :GHSETAFLLHSDDSDVRIRYF T0301 93 :IDKPFVD 1qyaA 64 :TPTVEVP T0301 107 :LSTGAGAFALH 1qyaA 75 :ATVAAHYVRAK T0301 118 :AGL 1qyaA 87 :LGL T0301 123 :P 1qyaA 98 :S T0301 132 :CEVRIWQANIGKTIIAHVP 1qyaA 103 :HRVTIEKHNDDYRISLEQG T0301 155 :QVQ 1qyaA 122 :TPG T0301 178 :FLDPSDD 1qyaA 125 :FEPPLEG T0301 187 :DGGAIFP 1qyaA 144 :TEDDILP T0301 195 :GN 1qyaA 151 :GL T0301 199 :DDL 1qyaA 155 :QVA T0301 208 :TFKATMINAGI 1qyaA 160 :GHSKVMIPLKP T0301 223 :VNAEEIGYR 1qyaA 172 :VDIDALSPD T0301 246 :LARFERIRVAG 1qyaA 181 :LNALTAISKKI T0301 273 :QHTPKIAFVAPPRDY 1qyaA 192 :GCNGFFPFQIRPGKN T0301 301 :DLLVRALSMGK 1qyaA 207 :ETDGRMFSPAI T0301 315 :AMMGTAAVAIGTAAAI 1qyaA 223 :PVTGNANGPMGAWLVH T0301 337 :LAAGGGERSAVRFG 1qyaA 239 :HNVLPHDGNVLRVK T0301 351 :H 1qyaA 255 :Q T0301 352 :PSGTLRVGAEASQA 1qyaA 261 :RDGMIEVTVTIRDN T0301 370 :TVTKA 1qyaA 275 :QPEKV Number of specific fragments extracted= 23 number of extra gaps= 2 total=506 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 1u1wA/T0301-1u1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u1wA expands to /projects/compbio/data/pdb/1u1w.pdb.gz 1u1wA:Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 99, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 101, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 103, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 105, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 107, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 109, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 616, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 618, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 620, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 622, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 624, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 626, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 628, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 630, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 632, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 634, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 636, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 638, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 640, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 642, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 644, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 646, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 677, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 679, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 681, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 683, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 685, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 687, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 689, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 691, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 1u1wA Skipped atom 764, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 766, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 768, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 770, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 772, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 774, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 776, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 778, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 816, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 818, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 820, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 822, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 824, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 826, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 828, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 830, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 832, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 935, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 937, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 939, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 941, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 943, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 945, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1046, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1048, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1050, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1052, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1054, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1056, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1058, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1455, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1457, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1459, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1461, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1463, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1465, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1467, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1469, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1471, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1475, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1477, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1479, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1481, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1525, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1527, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1529, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1531, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1533, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1535, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1537, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1539, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1631, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1633, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1635, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1637, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1639, because occupancy 0.300 <= existing 0.700 in 1u1wA Skipped atom 1641, because occupancy 0.300 <= existing 0.700 in 1u1wA # T0301 read from 1u1wA/T0301-1u1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1wA read from 1u1wA/T0301-1u1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u1wA to template set # found chain 1u1wA in template set T0301 7 :I 1u1wA 16 :E T0301 17 :GTSKGVFFRLEDLP 1u1wA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGH 1u1wA 42 :NLSESTFVLKPRNGGD T0301 87 :LYGQVSIDKPFVDW 1u1wA 58 :ALIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHA 1u1wA 72 :AGHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 204 :P 1u1wA 128 :G T0301 205 :GVG 1u1wA 138 :GIS T0301 208 :TFKATMINAGIPTVFVNAEE 1u1wA 143 :TFPIEIYHNGPRHVFVGLPS T0301 236 :R 1u1wA 163 :I T0301 247 :ARFER 1u1wA 164 :DALSA T0301 262 :LIKTPEEAATRQHTPKIAF 1u1wA 169 :LHPDHRALSNFHDMAINCF T0301 282 :AP 1u1wA 188 :AG T0301 290 :ASG 1u1wA 190 :AGR T0301 301 :DLLVRALSMGKL 1u1wA 193 :RWRSRMFSPAYG T0301 313 :HHAMMGTAAVAIGTAAAIPGTL 1u1wA 207 :EDAATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1u1wA 229 :EFGQPVEILQG T0301 353 :SG 1u1wA 242 :IG T0301 355 :TLRVGAEASQANGEWT 1u1wA 245 :PSLMFAKAEGRAEQLT Number of specific fragments extracted= 22 number of extra gaps= 0 total=528 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 1u1wA/T0301-1u1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1u1wA/T0301-1u1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1wA read from 1u1wA/T0301-1u1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1wA in template set Warning: unaligning (T0301)P4 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1u1wA)V13 Warning: unaligning (T0301)G205 because of BadResidue code BAD_PEPTIDE in next template residue (1u1wA)S142 Warning: unaligning (T0301)V206 because of BadResidue code BAD_PEPTIDE at template residue (1u1wA)S142 T0301 5 :PQIRIPA 1u1wA 14 :PLEGNPV T0301 21 :GVFFRLEDLP 1u1wA 21 :AVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGH 1u1wA 42 :NLSESTFVLKPRNGGD T0301 87 :LYGQVSIDKPFVDW 1u1wA 58 :ALIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHA 1u1wA 72 :AGHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 185 :GE 1u1wA 128 :GR T0301 201 :LEVP 1u1wA 137 :LGIS T0301 208 :TFKATMINAGIPTVFVNAEEI 1u1wA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 234 :ELREEINGDPQQL 1u1wA 164 :DALSALHPDHRAL T0301 260 :MGL 1u1wA 177 :SNF T0301 274 :HTPKIAFVAPP 1u1wA 180 :HDMAINCFAGA T0301 291 :SG 1u1wA 191 :GR T0301 301 :DLLVRALSMGKL 1u1wA 193 :RWRSRMFSPAYG T0301 315 :AMMGTAAVAIGTAAAIPGTL 1u1wA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1u1wA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGEWT 1u1wA 245 :PSLMFAKAEGRAEQLT T0301 373 :K 1u1wA 261 :R Number of specific fragments extracted= 21 number of extra gaps= 2 total=549 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 1u1wA/T0301-1u1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1u1wA/T0301-1u1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1wA read from 1u1wA/T0301-1u1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1wA in template set Warning: unaligning (T0301)R8 because first residue in template chain is (1u1wA)M1 Warning: unaligning (T0301)S19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1u1wA)V13 Warning: unaligning (T0301)K20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1u1wA)V13 Warning: unaligning (T0301)V206 because of BadResidue code BAD_PEPTIDE in next template residue (1u1wA)S142 Warning: unaligning (T0301)G207 because of BadResidue code BAD_PEPTIDE at template residue (1u1wA)S142 T0301 9 :IPATYLRGGT 1u1wA 2 :HNYVIIDAFA T0301 21 :GVFFRLEDLP 1u1wA 21 :AVFFDADDLP T0301 37 :GEARDRLFMRV 1u1wA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1u1wA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDWS 1u1wA 59 :LIRIFTPVNELPFA T0301 105 :GNLSTGAGAFALHA 1u1wA 73 :GHPLLGTAIALGAH T0301 127 :PEDGICEVRI 1u1wA 87 :TDNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1u1wA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1u1wA 115 :ASMDQPIPTWTAL T0301 204 :P 1u1wA 128 :G T0301 205 :G 1u1wA 140 :S T0301 208 :TFKATMINAGIPTVFVNAEE 1u1wA 143 :TFPIEIYHNGPRHVFVGLPS T0301 236 :REE 1u1wA 163 :IDA T0301 249 :FER 1u1wA 166 :LSA T0301 262 :LIKTPEEAATRQHTPKIAFVA 1u1wA 169 :LHPDHRALSNFHDMAINCFAG T0301 298 :GDIDLLVRALSMGKL 1u1wA 190 :AGRRWRSRMFSPAYG T0301 315 :AMMGTAAVAIGTAAAIPGTL 1u1wA 209 :AATGSAAGPLAIHLARHGQI T0301 342 :GERSAVRFGHP 1u1wA 229 :EFGQPVEILQG T0301 353 :SGTLRVGAEASQANGEWTV 1u1wA 243 :GRPSLMFAKAEGRAEQLTR Number of specific fragments extracted= 19 number of extra gaps= 2 total=568 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 1t6kA/T0301-1t6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t6kA expands to /projects/compbio/data/pdb/1t6k.pdb.gz 1t6kA:# T0301 read from 1t6kA/T0301-1t6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6kA read from 1t6kA/T0301-1t6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t6kA to template set # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDW 1t6kA 59 :LIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHAG 1t6kA 72 :AGHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 185 :GE 1t6kA 128 :GR T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1t6kA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 262 :LIKTPEEAATRQHT 1t6kA 169 :LHPDHRALSNFHDM T0301 277 :KIAFVAP 1t6kA 183 :AINCFAG T0301 290 :ASG 1t6kA 190 :AGR T0301 301 :DLLVRALSMGKL 1t6kA 193 :RWRSRMFSPAYG T0301 313 :HHAMMGTAAVAIGTAAAIPGTL 1t6kA 207 :EDAATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGEW 1t6kA 245 :PSLMFAKAEGRAEQL T0301 372 :TK 1t6kA 260 :TR Number of specific fragments extracted= 19 number of extra gaps= 0 total=587 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 1t6kA/T0301-1t6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1t6kA/T0301-1t6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6kA read from 1t6kA/T0301-1t6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDW 1t6kA 59 :LIRIFTPVNELPF T0301 104 :CGNLSTGAGAFALHAG 1t6kA 72 :AGHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 185 :GE 1t6kA 128 :GR T0301 201 :LEVPGV 1t6kA 137 :LGISDS T0301 208 :TFKATMINAGIPTVFVNAEEI 1t6kA 143 :TFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 263 :IKTPEEAATRQHTPKIAFVAPP 1t6kA 169 :LHPDHRALSNFHDMAINCFAGA T0301 291 :SG 1t6kA 191 :GR T0301 301 :DLLVRALSMG 1t6kA 193 :RWRSRMFSPA T0301 315 :AMMGTAAVAIGTAAAIPGTL 1t6kA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGE 1t6kA 245 :PSLMFAKAEGRAEQ T0301 371 :VTKA 1t6kA 259 :LTRV Number of specific fragments extracted= 19 number of extra gaps= 0 total=606 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 1t6kA/T0301-1t6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1t6kA/T0301-1t6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6kA read from 1t6kA/T0301-1t6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6kA in template set T0301 17 :GTSKGVFFRLEDLP 1t6kA 17 :GNPVAVFFDADDLP T0301 37 :GEARDRLFMRV 1t6kA 31 :PAQMQRIAREM T0301 67 :STSKCVILSKSSQPGHD 1t6kA 42 :NLSESTFVLKPRNGGDA T0301 88 :YGQVSIDKPFVDWS 1t6kA 59 :LIRIFTPVNELPFA T0301 105 :GNLSTGAGAFALHAG 1t6kA 73 :GHPLLGTAIALGAHT T0301 128 :EDGICEVRI 1t6kA 88 :DNHRLYLET T0301 141 :IGKTIIAHVPVSGGQVQE 1t6kA 97 :QMGTIAFELERQNGSVIA T0301 162 :FELDGVTFPAAEI 1t6kA 115 :ASMDQPIPTWTAL T0301 204 :P 1t6kA 128 :G T0301 205 :GVGTFKATMINAGIPTVFVNAEEI 1t6kA 140 :SDSTFPIEIYHNGPRHVFVGLPSI T0301 247 :ARFER 1t6kA 164 :DALSA T0301 262 :LIKTPEEAATRQHTPKIAFVAP 1t6kA 169 :LHPDHRALSNFHDMAINCFAGA T0301 299 :DIDLLVRALSMG 1t6kA 191 :GRRWRSRMFSPA T0301 315 :AMMGTAAVAIGTAAAIPGTL 1t6kA 209 :AATGSAAGPLAIHLARHGQI T0301 340 :GGGERSAVRFGHPSG 1t6kA 229 :EFGQPVEILQGVEIG T0301 355 :TLRVGAEASQANGE 1t6kA 245 :PSLMFAKAEGRAEQ T0301 371 :VTKA 1t6kA 259 :LTRV Number of specific fragments extracted= 17 number of extra gaps= 0 total=623 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 1ym5A/T0301-1ym5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ym5A expands to /projects/compbio/data/pdb/1ym5.pdb.gz 1ym5A:# T0301 read from 1ym5A/T0301-1ym5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ym5A read from 1ym5A/T0301-1ym5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ym5A to template set # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 19 :SKGVFFRLEDLPES 1ym5A 21 :NPVAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYLY 1ym5A 49 :NLSETTFLFKPSDKKYDYKLRI T0301 92 :SIDKPFVDW 1ym5A 71 :FTPRSELPF T0301 104 :CGNLSTGAGAFALHAG 1ym5A 80 :AGHPTIGSCKAFLEFT T0301 125 :RIPEDGICEVRI 1ym5A 96 :KNTTATSLVQEC T0301 140 :NI 1ym5A 108 :KI T0301 143 :KTIIAH 1ym5A 110 :GAVPIT T0301 151 :VSGGQVQET 1ym5A 116 :INEGLISFK T0301 160 :GDFELDGVT 1ym5A 126 :PMADYESIS T0301 176 :LEFLDPS 1ym5A 147 :LKFIKPP T0301 199 :DDLE 1ym5A 154 :ALLH T0301 216 :AGIPTVFVN 1ym5A 158 :TGPEWIVAL T0301 227 :EI 1ym5A 169 :DA T0301 234 :ELREEINGDPQQ 1ym5A 171 :ETCFNANPNFAM T0301 249 :FER 1ym5A 183 :LAH T0301 268 :EAATRQH 1ym5A 186 :QTKQNDH T0301 276 :PKIAFVAPPRDY 1ym5A 193 :VGIILAGPKKEA T0301 297 :AGDID 1ym5A 205 :AIKNS T0301 304 :VRALSM 1ym5A 212 :MRAFAP T0301 310 :GKLHHAMMGTAAVAIGTAA 1ym5A 220 :NVYEDPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 24 number of extra gaps= 3 total=647 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 1ym5A/T0301-1ym5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1ym5A/T0301-1ym5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ym5A read from 1ym5A/T0301-1ym5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 19 :SKGVFFRLEDLPES 1ym5A 21 :NPVAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYL 1ym5A 49 :NLSETTFLFKPSDKKYDYKLR T0301 91 :VSIDKPFVDW 1ym5A 70 :IFTPRSELPF T0301 104 :CGNLSTGAGAFALH 1ym5A 80 :AGHPTIGSCKAFLE T0301 118 :AGL 1ym5A 95 :TKN T0301 127 :PEDGICEVRI 1ym5A 98 :TTATSLVQEC T0301 140 :NI 1ym5A 108 :KI T0301 143 :KTI 1ym5A 110 :GAV T0301 148 :HVPVSGGQVQET 1ym5A 113 :PITINEGLISFK T0301 160 :GDFELD 1ym5A 126 :PMADYE T0301 166 :GVT 1ym5A 146 :GLK T0301 178 :FLD 1ym5A 149 :FIK T0301 210 :KATMINAGIPTVFVN 1ym5A 152 :PPALLHTGPEWIVAL T0301 227 :EI 1ym5A 169 :DA T0301 236 :REEINGD 1ym5A 171 :ETCFNAN T0301 243 :PQQLARFERI 1ym5A 181 :AMLAHQTKQN T0301 274 :HTPKIAFVAPPRDYR 1ym5A 191 :DHVGIILAGPKKEAA T0301 298 :GDID 1ym5A 206 :IKNS T0301 304 :VRALSMGK 1ym5A 212 :MRAFAPVI T0301 313 :HHAMMGTAAVAIGTAA 1ym5A 223 :EDPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 24 number of extra gaps= 3 total=671 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 1ym5A/T0301-1ym5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1ym5A/T0301-1ym5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ym5A read from 1ym5A/T0301-1ym5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ym5A in template set Warning: unaligning (T0301)A225 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E168 Warning: unaligning (T0301)E226 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E168 Warning: unaligning (T0301)L302 because of BadResidue code BAD_PEPTIDE in next template residue (1ym5A)E211 Warning: unaligning (T0301)L303 because of BadResidue code BAD_PEPTIDE at template residue (1ym5A)E211 Warning: unaligning (T0301)H351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ym5A)G255 Warning: unaligning (T0301)P352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ym5A)G255 T0301 7 :IRIPATYLRGGTSK 1ym5A 3 :LMVPFKQVDVFTEK T0301 21 :GVFFRLEDLPES 1ym5A 23 :VAVINFLEIDEN T0301 34 :RVPGEARDRLFMRV 1ym5A 35 :EVSQEELQAIANWT T0301 67 :STSKCVILSKSSQPGHDVDYLY 1ym5A 49 :NLSETTFLFKPSDKKYDYKLRI T0301 92 :SIDKPFVDWS 1ym5A 71 :FTPRSELPFA T0301 105 :GNLSTGAGAFALHA 1ym5A 81 :GHPTIGSCKAFLEF T0301 124 :ARIPEDGICEVRI 1ym5A 95 :TKNTTATSLVQEC T0301 143 :KTII 1ym5A 110 :GAVP T0301 149 :VPVSGGQVQET 1ym5A 114 :ITINEGLISFK T0301 160 :GDFELD 1ym5A 126 :PMADYE T0301 166 :GVT 1ym5A 146 :GLK T0301 178 :FLDPS 1ym5A 149 :FIKPP T0301 199 :DDLE 1ym5A 154 :ALLH T0301 216 :AGIPTVFVN 1ym5A 158 :TGPEWIVAL T0301 227 :E 1ym5A 169 :D T0301 235 :LREEINGD 1ym5A 170 :AETCFNAN T0301 243 :P 1ym5A 180 :F T0301 247 :ARFER 1ym5A 181 :AMLAH T0301 268 :EAATRQHT 1ym5A 186 :QTKQNDHV T0301 277 :KIAFVAPPRDYRT 1ym5A 194 :GIILAGPKKEAAI T0301 299 :DID 1ym5A 207 :KNS T0301 304 :VRALSMGK 1ym5A 212 :MRAFAPVI T0301 314 :HAMMGTAAVAIGTAA 1ym5A 224 :DPVCGSGSVALARYL T0301 336 :NLAAGGGERSAVRFG 1ym5A 239 :QEVYKFEKTTDITIS T0301 353 :SGTLRVGAE 1ym5A 261 :NGLMLASIK T0301 363 :SQANGEWTVT 1ym5A 270 :KEADNSTSYY Number of specific fragments extracted= 26 number of extra gaps= 3 total=697 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 2azpA/T0301-2azpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2azpA expands to /projects/compbio/data/pdb/2azp.pdb.gz 2azpA:# T0301 read from 2azpA/T0301-2azpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2azpA read from 2azpA/T0301-2azpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2azpA to template set # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSKGVFF 2azpA -1 :HMQRIRIIDSHTGGEPTRLV T0301 26 :LEDLPES 2azpA 20 :IGGFPDL T0301 34 :RVPG 2azpA 27 :GQGD T0301 38 :EARDRLFMRVIGSPD 2azpA 40 :ERHDAWRAACILEPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYG 2azpA 55 :GSDVLVGALLCAPVDPEACAGVIFF T0301 93 :IDKPF 2azpA 80 :NNSGY T0301 101 :SGNCGNLSTGAGAFALHAGLVD 2azpA 85 :LGMCGHGTIGLVASLAHLGRIG T0301 129 :DGICEV 2azpA 107 :PGVHRI T0301 150 :PVSGGQVQET 2azpA 113 :ETPVGEVEAT T0301 164 :L 2azpA 123 :L T0301 169 :FPAAEIVLEFLDPS 2azpA 124 :HEDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVNAEEIGYRG 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVAGHGQRLAG T0301 240 :NGDPQQLARFERIRVAGA 2azpA 177 :DNLDALTAYTVAVQQALD T0301 259 :RMGLIK 2azpA 195 :DQDIRG T0301 270 :ATRQHTPKIAFVA 2azpA 201 :EDGGAIDHIELFA T0301 296 :AAGDIDLLVRALSMGK 2azpA 214 :DDPHADSRNFVLCPGK T0301 312 :LHHAMMGTAAVAIGTAAAIPGT 2azpA 231 :YDRSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSG 2azpA 253 :LLPGQPWRQASVIG T0301 355 :TLRVGAEA 2azpA 268 :QFEGRYEW T0301 363 :SQANGEWTV 2azpA 278 :GQPGGPIVP Number of specific fragments extracted= 20 number of extra gaps= 0 total=717 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 2azpA/T0301-2azpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 2azpA/T0301-2azpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2azpA read from 2azpA/T0301-2azpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSKGVFF 2azpA -1 :HMQRIRIIDSHTGGEPTRLV T0301 26 :LEDLPES 2azpA 20 :IGGFPDL T0301 34 :RVPG 2azpA 27 :GQGD T0301 38 :EARDRLFMRVIGSPD 2azpA 40 :ERHDAWRAACILEPR T0301 65 :TSSTSKCVILSKSSQPGHDVDYLYG 2azpA 55 :GSDVLVGALLCAPVDPEACAGVIFF T0301 93 :IDKPFV 2azpA 80 :NNSGYL T0301 102 :GNCGNLSTGAGAFALHAGLVD 2azpA 86 :GMCGHGTIGLVASLAHLGRIG T0301 129 :DGICEVR 2azpA 107 :PGVHRIE T0301 139 :ANIG 2azpA 114 :TPVG T0301 144 :TIIAHV 2azpA 118 :EVEATL T0301 169 :FPAAEIVLEFLDPS 2azpA 124 :HEDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVN 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVA T0301 229 :GYRGTELR 2azpA 169 :GHGQRLAG T0301 240 :NGDPQQLARFERIRVAGAL 2azpA 177 :DNLDALTAYTVAVQQALDD T0301 260 :MGL 2azpA 196 :QDI T0301 264 :KTPEEA 2azpA 199 :RGEDGG T0301 274 :HTPKIAFVA 2azpA 205 :AIDHIELFA T0301 296 :AAGDIDLLVRALSMGKLH 2azpA 214 :DDPHADSRNFVLCPGKAY T0301 314 :HAMMGTAAVAIGTAAAIPGT 2azpA 233 :RSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSG 2azpA 253 :LLPGQPWRQASVIG T0301 355 :TLRVGAEA 2azpA 268 :QFEGRYEW T0301 363 :SQANGEWTVT 2azpA 278 :GQPGGPIVPT Number of specific fragments extracted= 22 number of extra gaps= 0 total=739 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 2azpA/T0301-2azpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 2azpA/T0301-2azpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2azpA read from 2azpA/T0301-2azpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2azpA in template set T0301 5 :PQIRIPATYLRGGTSK 2azpA -1 :HMQRIRIIDSHTGGEP T0301 22 :VFFRLEDLPESCRVP 2azpA 16 :TRLVIGGFPDLGQGD T0301 37 :GEARDRLFMRVIGSPDPYAAHI 2azpA 39 :GERHDAWRAACILEPRGSDVLV T0301 71 :CVILSKSSQPGHDVDYLYG 2azpA 61 :GALLCAPVDPEACAGVIFF T0301 93 :IDKPFV 2azpA 80 :NNSGYL T0301 102 :GNCGNLSTGAGAFALHAGLVDP 2azpA 86 :GMCGHGTIGLVASLAHLGRIGP T0301 130 :GICEVR 2azpA 108 :GVHRIE T0301 139 :ANIG 2azpA 114 :TPVG T0301 144 :TIIAHVP 2azpA 118 :EVEATLH T0301 170 :PAAEIVLEFLDPS 2azpA 125 :EDGSVSVRNVPAY T0301 194 :TGNLVDDLEVPGVGTFKATMINAGIPTVFVN 2azpA 138 :RYRRQVSVEVPGIGRVSGDIAWGGNWFFLVA T0301 229 :GYRGTELR 2azpA 169 :GHGQRLAG T0301 240 :NGDPQQLARFERIRVAGALR 2azpA 177 :DNLDALTAYTVAVQQALDDQ T0301 261 :GLIK 2azpA 197 :DIRG T0301 270 :ATRQHTPKIAFV 2azpA 201 :EDGGAIDHIELF T0301 295 :VAAGDIDLLVRALSMGKLH 2azpA 213 :ADDPHADSRNFVLCPGKAY T0301 314 :HAMMGTAAVAIGTAAAIPGT 2azpA 233 :RSPCGTGTSAKLACLAADGK T0301 341 :GGERSAVRFGHPSGT 2azpA 253 :LLPGQPWRQASVIGS T0301 357 :RVGAEASQ 2azpA 268 :QFEGRYEW T0301 365 :ANGEWTVT 2azpA 280 :PGGPIVPT Number of specific fragments extracted= 20 number of extra gaps= 0 total=759 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 1oe4A/T0301-1oe4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oe4A expands to /projects/compbio/data/pdb/1oe4.pdb.gz 1oe4A:Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2098, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2100, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2103, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2105, because occupancy 0.500 <= existing 0.500 in 1oe4A Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 1oe4A # T0301 read from 1oe4A/T0301-1oe4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oe4A read from 1oe4A/T0301-1oe4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oe4A to template set # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVN 1oe4A 170 :CFVHNHCPLIFMN T0301 225 :AEEIG 1oe4A 190 :PTDLP T0301 237 :EEIN 1oe4A 195 :KAQR T0301 243 :PQQLARFERIRVAGALRMGL 1oe4A 199 :DTLLEICDEALCQAVRVLGV T0301 264 :K 1oe4A 219 :K T0301 266 :PEEAATRQHTPKIAFVAPP 1oe4A 233 :RKALMAEGIDVTVKGIMHP T0301 309 :M 1oe4A 252 :S Number of specific fragments extracted= 7 number of extra gaps= 0 total=766 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 1oe4A/T0301-1oe4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1oe4A/T0301-1oe4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oe4A read from 1oe4A/T0301-1oe4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVNAEEIGYRGTELREEIN 1oe4A 170 :CFVHNHCPLIFMNHSGKNLTPTDLPKAQR T0301 243 :PQQLARFERIRVAGALRMGL 1oe4A 199 :DTLLEICDEALCQAVRVLGV T0301 276 :PKIAFVA 1oe4A 219 :KLVIGVG Number of specific fragments extracted= 3 number of extra gaps= 0 total=769 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 1oe4A/T0301-1oe4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0301 read from 1oe4A/T0301-1oe4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oe4A read from 1oe4A/T0301-1oe4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oe4A in template set T0301 212 :TMINAGIPTVFVNAEEIGYRGTELREEIN 1oe4A 170 :CFVHNHCPLIFMNHSGKNLTPTDLPKAQR T0301 243 :PQQLARFERIRVAGALRMGLI 1oe4A 199 :DTLLEICDEALCQAVRVLGVK T0301 266 :PEEAATRQHTPKIAFVAPPRD 1oe4A 233 :RKALMAEGIDVTVKGIMHPSP Number of specific fragments extracted= 3 number of extra gaps= 0 total=772 Will force an alignment to be made, even if fragment is small Number of alignments=39 # command:CPU_time= 19.008 sec, elapsed time= 20.158 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 39 Adding 77815 constraints to all_contacts Done adding distance constraints # command:CPU_time= 19.219 sec, elapsed time= 20.403 sec. # command:Reading probabilities from T0301.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 18.810 Optimizing... Probability sum: -807.260, CN propb: -807.260 weights: 0.305 constraints: 1350 # command:CPU_time= 326.003 sec, elapsed time= 327.366 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1350 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1350 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1927 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1927 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 71414 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 71414 # command:CPU_time= 327.360 sec, elapsed time= 329.587 sec. # command: