# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0574 numbered 1 through 126 Created new target T0574 from T0574.a2m # command:CPU_time= 5.756 sec, elapsed time= 6.642 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvsA/T0574-1xvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xvsA expands to /projects/compbio/data/pdb/1xvs.pdb.gz 1xvsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0574 read from 1xvsA/T0574-1xvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvsA read from 1xvsA/T0574-1xvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xvsA to template set # found chain 1xvsA in template set Warning: unaligning (T0574)S74 because of BadResidue code BAD_PEPTIDE in next template residue (1xvsA)A56 Warning: unaligning (T0574)A75 because of BadResidue code BAD_PEPTIDE at template residue (1xvsA)A56 T0574 43 :DKHFRTQAFKVRLVNAAKSEISLKNSCLVAQ 1xvsA 24 :EYQRFVFAYLITIKNLSSQTVQLMSRRWLIT # choosing archetypes in rotamer library T0574 76 :AGQSFRLDT 1xvsA 57 :DGKQTVVEG T0574 87 :EELTAD 1xvsA 66 :DGVVGE T0574 93 :TLKPGASVE 1xvsA 74 :RIKANDEYT T0574 102 :GDAIFASEDDAVYGASL 1xvsA 98 :GQYLMIDEQGESFTVEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvsA/T0574-1xvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1xvsA/T0574-1xvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvsA read from 1xvsA/T0574-1xvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xvsA in template set Warning: unaligning (T0574)S74 because of BadResidue code BAD_PEPTIDE in next template residue (1xvsA)A56 Warning: unaligning (T0574)A75 because of BadResidue code BAD_PEPTIDE at template residue (1xvsA)A56 T0574 43 :DKHFRTQAFKVRLVNAAKSEISLKNSCLVAQ 1xvsA 24 :EYQRFVFAYLITIKNLSSQTVQLMSRRWLIT T0574 76 :AGQSFRLDT 1xvsA 57 :DGKQTVVEG T0574 87 :EELTAD 1xvsA 66 :DGVVGE T0574 93 :TLKPGASVE 1xvsA 74 :RIKANDEYT T0574 102 :GDAIFASEDDAVYGASLVR 1xvsA 98 :GQYLMIDEQGESFTVEIEP Number of specific fragments extracted= 5 number of extra gaps= 1 total=10 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvsA/T0574-1xvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1xvsA/T0574-1xvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvsA read from 1xvsA/T0574-1xvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xvsA in template set Warning: unaligning (T0574)S74 because of BadResidue code BAD_PEPTIDE in next template residue (1xvsA)A56 Warning: unaligning (T0574)A75 because of BadResidue code BAD_PEPTIDE at template residue (1xvsA)A56 T0574 26 :AVMVFARQGDKGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQ 1xvsA 7 :CIKIQVQTRYIEEQSNPEYQRFVFAYLITIKNLSSQTVQLMSRRWLIT T0574 76 :AGQSFRLDT 1xvsA 57 :DGKQTVVEG T0574 87 :EELTAD 1xvsA 66 :DGVVGE T0574 93 :TLKPGASVE 1xvsA 74 :RIKANDEYT T0574 102 :GDAIFASEDDAVYGASLVRL 1xvsA 98 :GQYLMIDEQGESFTVEIEPF Number of specific fragments extracted= 5 number of extra gaps= 1 total=15 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cfuA/T0574-3cfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cfuA expands to /projects/compbio/data/pdb/3cfu.pdb.gz 3cfuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0574 read from 3cfuA/T0574-3cfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfuA read from 3cfuA/T0574-3cfuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cfuA to template set # found chain 3cfuA in template set Warning: unaligning (T0574)K44 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3cfuA)T103 T0574 26 :AVMVFAR 3cfuA 74 :HTNFTVN T0574 33 :Q 3cfuA 84 :R T0574 34 :GDKGSVSVGD 3cfuA 86 :QKGEYMNVGG T0574 51 :FKVRLVNAAKSEISLKNSCLVAQSAAGQSFRL 3cfuA 113 :IEVTMENIGEDSISYNFIGFDLRDKNDQSVRP T0574 89 :LTADTLKPGASVEGDAIFASEDDAVYGASLV 3cfuA 155 :LMGGTLVSGKKVTGVLSYVIPKGEQKHYTLV Number of specific fragments extracted= 5 number of extra gaps= 0 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cfuA/T0574-3cfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3cfuA/T0574-3cfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfuA read from 3cfuA/T0574-3cfuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cfuA in template set T0574 26 :AVMVFARQ 3cfuA 74 :HTNFTVNK T0574 34 :GDKGSVSVG 3cfuA 86 :QKGEYMNVG T0574 43 :DKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRL 3cfuA 105 :KDDEERLIIEVTMENIGEDSISYNFIGFDLRDKNDQSVRP T0574 89 :LTADTLKPGASVEGDAIFASEDDAVYGASLV 3cfuA 155 :LMGGTLVSGKKVTGVLSYVIPKGEQKHYTLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 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 3cfuA/T0574-3cfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3cfuA/T0574-3cfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cfuA read from 3cfuA/T0574-3cfuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cfuA in template set Warning: unaligning (T0574)V41 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cfuA)T103 T0574 42 :GDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFR 3cfuA 104 :IKDDEERLIIEVTMENIGEDSISYNFIGFDLRDKNDQSVR T0574 83 :DTVDEELTADTL 3cfuA 144 :PVFSIEEKGRIL T0574 95 :KPGASVEGDAIFASEDDAVYGASLV 3cfuA 161 :VSGKKVTGVLSYVIPKGEQKHYTLV Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hn9A/T0574-3hn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hn9A expands to /projects/compbio/data/pdb/3hn9.pdb.gz 3hn9A:# T0574 read from 3hn9A/T0574-3hn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hn9A read from 3hn9A/T0574-3hn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hn9A to template set # found chain 3hn9A in template set T0574 33 :QGDKGSVSVGDKHFRTQA 3hn9A 436 :ASATGNVCIEEIDVDGKF T0574 53 :VRLVNAAKSEISLKNSCLVAQS 3hn9A 454 :IRLKNTSEQDQPMGGWEMIRKI T0574 76 :AGQSFRLDT 3hn9A 476 :GDTSVSYKY T0574 86 :DEEL 3hn9A 485 :TSRY T0574 93 :TLKPGASVEGDA 3hn9A 489 :VLKAGQTVTIWA Number of specific fragments extracted= 5 number of extra gaps= 0 total=32 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 3hn9A/T0574-3hn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3hn9A/T0574-3hn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hn9A read from 3hn9A/T0574-3hn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hn9A in template set T0574 32 :RQGDKGSVSVGDKHFRTQA 3hn9A 435 :SASATGNVCIEEIDVDGKF T0574 53 :VRLVNAAKSEISLKNSCLVAQSA 3hn9A 454 :IRLKNTSEQDQPMGGWEMIRKIG T0574 77 :GQSFRLDT 3hn9A 477 :DTSVSYKY T0574 90 :TAD 3hn9A 485 :TSR T0574 93 :TLKPGASVEGD 3hn9A 489 :VLKAGQTVTIW Number of specific fragments extracted= 5 number of extra gaps= 0 total=37 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 3hn9A/T0574-3hn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3hn9A/T0574-3hn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hn9A read from 3hn9A/T0574-3hn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hn9A in template set T0574 32 :RQGDKGSVSVGDKHFRTQA 3hn9A 435 :SASATGNVCIEEIDVDGKF T0574 53 :VRLVNAAKSEISLKNSCLVAQSA 3hn9A 454 :IRLKNTSEQDQPMGGWEMIRKIG T0574 77 :GQSFRLDT 3hn9A 477 :DTSVSYKY T0574 90 :TAD 3hn9A 485 :TSR T0574 93 :TLKPGASVEGD 3hn9A 489 :VLKAGQTVTIW Number of specific fragments extracted= 5 number of extra gaps= 0 total=42 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 1ifrA/T0574-1ifrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ifrA expands to /projects/compbio/data/pdb/1ifr.pdb.gz 1ifrA:# T0574 read from 1ifrA/T0574-1ifrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ifrA read from 1ifrA/T0574-1ifrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ifrA to template set # found chain 1ifrA in template set T0574 33 :QGDKGSVSVGDKHFR 1ifrA 434 :HRTSGRVAVEEVDEE T0574 53 :VRLVNAAKSEISLKNSCLVAQSAAGQSFRLDT 1ifrA 452 :VRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRF T0574 90 :TA 1ifrA 484 :PP T0574 93 :TLKPGASVEGDA 1ifrA 488 :TLKAGQVVTIWA Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 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 1ifrA/T0574-1ifrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1ifrA/T0574-1ifrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ifrA read from 1ifrA/T0574-1ifrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ifrA in template set T0574 32 :RQGDKGSVSVGDKHFRTQ 1ifrA 433 :SHRTSGRVAVEEVDEEGK T0574 53 :VRLVNAAKSEISLKNSCLVAQSAAGQSFRLDT 1ifrA 452 :VRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRF T0574 90 :TAD 1ifrA 484 :PPK T0574 93 :TLKPGASVEGDA 1ifrA 488 :TLKAGQVVTIWA Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 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 1ifrA/T0574-1ifrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1ifrA/T0574-1ifrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ifrA read from 1ifrA/T0574-1ifrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ifrA in template set T0574 34 :GDKGSVSVGDKHFRTQ 1ifrA 435 :RTSGRVAVEEVDEEGK T0574 53 :VRLVNAAKSEISLKNSCLVAQSAAGQSFRLDT 1ifrA 452 :VRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRF T0574 90 :TAD 1ifrA 484 :PPK T0574 93 :TLKPGASVEGDA 1ifrA 488 :TLKAGQVVTIWA Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 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 1tzaA/T0574-1tzaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tzaA expands to /projects/compbio/data/pdb/1tza.pdb.gz 1tzaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0574 read from 1tzaA/T0574-1tzaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tzaA read from 1tzaA/T0574-1tzaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tzaA to template set # found chain 1tzaA in template set T0574 26 :AVMVFARQGDKGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLD 1tzaA 7 :SIRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEVQ T0574 89 :LTAD 1tzaA 68 :VVGE T0574 93 :TLKPGASVE 1tzaA 74 :TIPPNTAYQ T0574 102 :GDAIFASEDDA 1tzaA 98 :GTYGMVSESGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=58 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 1tzaA/T0574-1tzaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1tzaA/T0574-1tzaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tzaA read from 1tzaA/T0574-1tzaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tzaA in template set T0574 36 :KGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLDT 1tzaA 17 :IEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEVQG T0574 87 :EELTAD 1tzaA 66 :AGVVGE T0574 93 :TLKPGASVE 1tzaA 74 :TIPPNTAYQ T0574 102 :GDAIFASEDDAVYGASL 1tzaA 98 :GTYGMVSESGEHFNAII Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 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 1tzaA/T0574-1tzaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1tzaA/T0574-1tzaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tzaA read from 1tzaA/T0574-1tzaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tzaA in template set T0574 27 :VMVFARQGDKGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLDT 1tzaA 8 :IRVEVKTEYIEQQSSPEDEKYLFSYTITIINLGEQAAKLETRHWIITDANGKTSEVQG T0574 87 :EELTAD 1tzaA 66 :AGVVGE T0574 93 :TLKPGASVE 1tzaA 74 :TIPPNTAYQ T0574 102 :GDAIFASEDDAVYGASLV 1tzaA 98 :GTYGMVSESGEHFNAIIK Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 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 1v84A/T0574-1v84A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v84A expands to /projects/compbio/data/pdb/1v84.pdb.gz 1v84A:# T0574 read from 1v84A/T0574-1v84A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v84A read from 1v84A/T0574-1v84A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v84A to template set # found chain 1v84A in template set T0574 92 :DTLKPGASVEGDAIFASEDD 1v84A 179 :ETFPRNSSQPGVVYFADDDN Number of specific fragments extracted= 1 number of extra gaps= 0 total=67 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 1v84A/T0574-1v84A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1v84A/T0574-1v84A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v84A read from 1v84A/T0574-1v84A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v84A in template set T0574 89 :LTA 1v84A 177 :LRE T0574 93 :TLKPGASVEGDAIFASEDD 1v84A 180 :TFPRNSSQPGVVYFADDDN Number of specific fragments extracted= 2 number of extra gaps= 0 total=69 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 1v84A/T0574-1v84A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1v84A/T0574-1v84A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v84A read from 1v84A/T0574-1v84A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v84A in template set T0574 89 :LT 1v84A 177 :LR T0574 92 :DTLKPGASVEGDAIFASEDD 1v84A 179 :ETFPRNSSQPGVVYFADDDN Number of specific fragments extracted= 2 number of extra gaps= 0 total=71 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 1ejpA/T0574-1ejpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ejpA expands to /projects/compbio/data/pdb/1ejp.pdb.gz 1ejpA:# T0574 read from 1ejpA/T0574-1ejpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejpA read from 1ejpA/T0574-1ejpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ejpA to template set # found chain 1ejpA in template set T0574 33 :QGDKGSVSVGDKHFR 1ejpA 4 :KKDEGSYDLGKKPIY Number of specific fragments extracted= 1 number of extra gaps= 0 total=72 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 1ejpA/T0574-1ejpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1ejpA/T0574-1ejpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejpA read from 1ejpA/T0574-1ejpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejpA in template set T0574 33 :QGDKGSVSVGDKHF 1ejpA 4 :KKDEGSYDLGKKPI Number of specific fragments extracted= 1 number of extra gaps= 0 total=73 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 1ejpA/T0574-1ejpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1ejpA/T0574-1ejpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejpA read from 1ejpA/T0574-1ejpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejpA in template set T0574 33 :QGDKGSVSVGDKHFR 1ejpA 4 :KKDEGSYDLGKKPIY Number of specific fragments extracted= 1 number of extra gaps= 0 total=74 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zvfA/T0574-1zvfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zvfA expands to /projects/compbio/data/pdb/1zvf.pdb.gz 1zvfA:Skipped atom 297, because occupancy 0.43 <= existing 0.570 in 1zvfA Skipped atom 299, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 301, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 303, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 305, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 307, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 309, because occupancy 0.430 <= existing 0.570 in 1zvfA Skipped atom 311, because occupancy 0.430 <= existing 0.570 in 1zvfA # T0574 read from 1zvfA/T0574-1zvfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvfA read from 1zvfA/T0574-1zvfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zvfA to template set # found chain 1zvfA in template set T0574 22 :AAPDAVMVFARQGDK 1zvfA 59 :QKKGSMLLKVVDETD T0574 38 :SVSVGDKHFRTQ 1zvfA 80 :DIIINEGDSYLL T0574 53 :VRLVN 1zvfA 107 :GIVVE T0574 92 :DTLKPGAS 1zvfA 112 :QDRPGGEN T0574 102 :GDAIFASEDD 1zvfA 120 :DKIRWYCSHC Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 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 1zvfA/T0574-1zvfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1zvfA/T0574-1zvfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvfA read from 1zvfA/T0574-1zvfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zvfA in template set Warning: unaligning (T0574)P96 because of BadResidue code BAD_PEPTIDE in next template residue (1zvfA)D104 Warning: unaligning (T0574)G97 because of BadResidue code BAD_PEPTIDE at template residue (1zvfA)D104 T0574 28 :MVFARQGDKGSVSVG 1zvfA 37 :MIVGGPNERTDYHIN T0574 43 :DKHFRTQA 1zvfA 54 :PEWFYQKK T0574 51 :FKVRLVNAAKSEISLKNSCL 1zvfA 64 :MLLKVVDETDAEPKFIDIII T0574 75 :AAGQSFRLDT 1zvfA 84 :NEGDSYLLPG T0574 92 :DT 1zvfA 94 :NV T0574 95 :K 1zvfA 102 :F T0574 98 :AS 1zvfA 105 :TV T0574 102 :GDAIF 1zvfA 107 :GIVVE Number of specific fragments extracted= 8 number of extra gaps= 1 total=87 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 1zvfA/T0574-1zvfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 1zvfA/T0574-1zvfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvfA read from 1zvfA/T0574-1zvfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zvfA in template set Warning: unaligning (T0574)P96 because of BadResidue code BAD_PEPTIDE in next template residue (1zvfA)D104 Warning: unaligning (T0574)G97 because of BadResidue code BAD_PEPTIDE at template residue (1zvfA)D104 T0574 26 :AVMVFARQGDK 1zvfA 33 :GFTVMIVGGPN T0574 37 :GSVSVGDKHFRTQA 1zvfA 48 :YHINPTPEWFYQKK T0574 51 :FKVRLVNAAKSEISLKNSCL 1zvfA 64 :MLLKVVDETDAEPKFIDIII T0574 75 :AAGQSFRLDT 1zvfA 84 :NEGDSYLLPG T0574 92 :DTL 1zvfA 94 :NVP T0574 95 :K 1zvfA 102 :F T0574 98 :A 1zvfA 105 :T T0574 101 :EGDAIFA 1zvfA 106 :VGIVVEQ T0574 108 :SEDDAVYGASL 1zvfA 114 :RPGGENDKIRW Number of specific fragments extracted= 9 number of extra gaps= 1 total=96 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 3gvkA/T0574-3gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gvkA expands to /projects/compbio/data/pdb/3gvk.pdb.gz 3gvkA:Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1331, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1333, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1335, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2399, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2613, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2617, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2619, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2621, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2623, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2837, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2841, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2843, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2845, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2847, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 2849, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3592, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3596, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3598, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3600, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3602, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3837, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3841, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3843, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3875, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3879, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 3881, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4045, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4049, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4051, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4053, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4055, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4057, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4059, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4061, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4244, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4248, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4250, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4252, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4254, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4649, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4653, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4655, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4657, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4659, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4661, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4687, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4691, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4693, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4695, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 4998, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 5002, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 5004, because occupancy 0.500 <= existing 0.500 in 3gvkA Skipped atom 5006, because occupancy 0.500 <= existing 0.500 in 3gvkA # T0574 read from 3gvkA/T0574-3gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvkA read from 3gvkA/T0574-3gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gvkA to template set # found chain 3gvkA in template set T0574 25 :DAVMVFARQGDK 3gvkA 414 :TNCALWDRPMSR T0574 38 :SVSVG 3gvkA 426 :SLHLT T0574 43 :DKHFRTQAF 3gvkA 438 :NQRYATIHV T0574 52 :KVRLVN 3gvkA 456 :FVNFSN T0574 58 :AAKSEISLKNS 3gvkA 466 :GVSGDMTVATV T0574 69 :CLVAQSAAGQSFRLDT 3gvkA 481 :NFTVLTPNQQTSDLNN T0574 96 :PGASV 3gvkA 497 :AGKNW Number of specific fragments extracted= 7 number of extra gaps= 0 total=103 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 3gvkA/T0574-3gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3gvkA/T0574-3gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvkA read from 3gvkA/T0574-3gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gvkA in template set T0574 25 :DAVMVFAR 3gvkA 414 :TNCALWDR T0574 57 :NAA 3gvkA 422 :PMS T0574 61 :SEISLKNSCL 3gvkA 425 :RSLHLTGGIT T0574 73 :QSAAGQSFRLDT 3gvkA 435 :KAANQRYATIHV T0574 90 :TADTLKPGASVE 3gvkA 447 :PDHGLFVGDFVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=108 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 3gvkA/T0574-3gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3gvkA/T0574-3gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvkA read from 3gvkA/T0574-3gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gvkA in template set Warning: unaligning (T0574)L82 because of BadResidue code BAD_PEPTIDE in next template residue (3gvkA)G504 Warning: unaligning (T0574)D83 because of BadResidue code BAD_PEPTIDE at template residue (3gvkA)G504 Warning: unaligning (T0574)G97 because of BadResidue code BAD_PEPTIDE in next template residue (3gvkA)R513 Warning: unaligning (T0574)A98 because of BadResidue code BAD_PEPTIDE at template residue (3gvkA)R513 T0574 36 :KGSVSVGDKHFRTQAF 3gvkA 431 :GGITKAANQRYATIHV T0574 52 :KVRLVN 3gvkA 456 :FVNFSN T0574 58 :AAKSEISLKNS 3gvkA 466 :GVSGDMTVATV T0574 69 :CLVAQSA 3gvkA 481 :NFTVLTP T0574 76 :AGQSFR 3gvkA 497 :AGKNWH T0574 84 :T 3gvkA 505 :T T0574 96 :P 3gvkA 511 :P T0574 99 :SVE 3gvkA 514 :KTD T0574 102 :GDAIFASEDDAVYGASLVRLS 3gvkA 537 :FAMGYHQGDVAPREVGLFYFP Number of specific fragments extracted= 9 number of extra gaps= 2 total=117 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 3gvjA/T0574-3gvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gvjA expands to /projects/compbio/data/pdb/3gvj.pdb.gz 3gvjA:Skipped atom 67, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 69, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 71, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 73, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 75, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 77, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 79, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 137, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 142, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 145, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 177, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 179, because occupancy 0.250 <= existing 0.450 in 3gvjA Skipped atom 180, because occupancy 0.300 <= existing 0.450 in 3gvjA Skipped atom 182, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 184, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 186, because occupancy 0.250 <= existing 0.450 in 3gvjA Skipped atom 187, because occupancy 0.300 <= existing 0.450 in 3gvjA Skipped atom 189, because occupancy 0.250 <= existing 0.450 in 3gvjA Skipped atom 190, because occupancy 0.300 <= existing 0.450 in 3gvjA Skipped atom 192, because occupancy 0.250 <= existing 0.450 in 3gvjA Skipped atom 193, because occupancy 0.300 <= existing 0.450 in 3gvjA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 934, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 938, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 940, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 942, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 944, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1529, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1531, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1533, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2090, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2091, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2095, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2096, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2098, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2099, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2101, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2102, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2104, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2105, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2107, because occupancy 0.200 <= existing 0.400 in 3gvjA Skipped atom 2108, because occupancy 0.400 <= existing 0.400 in 3gvjA Skipped atom 2150, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2154, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2156, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2500, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2505, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2508, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2511, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2514, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2517, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2520, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2523, because occupancy 0.250 <= existing 0.250 in 3gvjA Skipped atom 2646, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2648, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2650, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2652, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2654, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2656, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2734, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2738, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2740, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2742, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2744, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2746, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 2878, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 2882, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 2884, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 2886, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 2888, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 3040, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3042, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3044, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3046, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3048, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3050, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3052, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3054, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3056, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3058, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3060, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3612, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3614, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3616, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3618, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3620, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3622, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3624, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3626, because occupancy 0.400 <= existing 0.600 in 3gvjA Skipped atom 3864, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 3868, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 3870, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 3872, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 3874, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4311, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4315, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4317, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4319, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4321, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4323, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4325, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4327, because occupancy 0.500 <= existing 0.500 in 3gvjA Skipped atom 4432, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4436, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4438, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4440, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4442, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4915, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4919, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4921, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4923, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4925, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4927, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4953, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4957, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4959, because occupancy 0.300 <= existing 0.700 in 3gvjA Skipped atom 4961, because occupancy 0.300 <= existing 0.700 in 3gvjA # T0574 read from 3gvjA/T0574-3gvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvjA read from 3gvjA/T0574-3gvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gvjA to template set # found chain 3gvjA in template set Warning: unaligning (T0574)A104 because of BadResidue code BAD_PEPTIDE in next template residue (3gvjA)G504 Warning: unaligning (T0574)I105 because of BadResidue code BAD_PEPTIDE at template residue (3gvjA)G504 Warning: unaligning (T0574)F106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gvjA)T505 T0574 24 :PDAVMVFARQGD 3gvjA 413 :LTNCALWDRPMS T0574 36 :KGSVSVG 3gvjA 430 :TGGITKA T0574 43 :DKHFRTQAF 3gvjA 438 :NQRYATIHV T0574 52 :KVRLVN 3gvjA 456 :FVNFSN T0574 58 :AAKSEISLKNS 3gvjA 466 :GVSGDMTVATV T0574 69 :CLVAQSAAGQSFRLDT 3gvjA 481 :NFTVLTPNQQTSDLNN T0574 96 :PGASV 3gvjA 497 :AGKNW T0574 103 :D 3gvjA 502 :H T0574 107 :ASEDD 3gvjA 506 :SFHKS Number of specific fragments extracted= 9 number of extra gaps= 1 total=126 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 3gvjA/T0574-3gvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3gvjA/T0574-3gvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvjA read from 3gvjA/T0574-3gvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gvjA in template set T0574 20 :FAAAPDAVMVF 3gvjA 392 :MGVCRNRLFAM T0574 38 :SVSVGDKHFRTQAFKVRLVNAA 3gvjA 403 :IETRTLAKNALTNCALWDRPMS T0574 61 :SEISLKNSCL 3gvjA 425 :RSLHLTGGIT T0574 73 :QSAAGQSFRLDT 3gvjA 435 :KAANQRYATIHV T0574 90 :TADTLKPGASVE 3gvjA 447 :PDHGLFVGDFVN T0574 106 :F 3gvjA 459 :F Number of specific fragments extracted= 6 number of extra gaps= 0 total=132 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 3gvjA/T0574-3gvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0574 read from 3gvjA/T0574-3gvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gvjA read from 3gvjA/T0574-3gvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gvjA in template set Warning: unaligning (T0574)L82 because of BadResidue code BAD_PEPTIDE in next template residue (3gvjA)G504 Warning: unaligning (T0574)D83 because of BadResidue code BAD_PEPTIDE at template residue (3gvjA)G504 Warning: unaligning (T0574)T84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gvjA)T505 T0574 25 :DAVMVFAR 3gvjA 414 :TNCALWDR T0574 33 :QGDKGSVSVGDKHFRTQAF 3gvjA 428 :HLTGGITKAANQRYATIHV T0574 52 :KVRLVN 3gvjA 456 :FVNFSN T0574 58 :AAKSEISLKNS 3gvjA 466 :GVSGDMTVATV T0574 69 :CLVAQSA 3gvjA 481 :NFTVLTP T0574 76 :AGQSFR 3gvjA 497 :AGKNWH T0574 93 :TL 3gvjA 506 :SF T0574 96 :PGASVE 3gvjA 511 :PWRKTD T0574 102 :GDAIFASEDD 3gvjA 525 :EVHSFATIDN Number of specific fragments extracted= 9 number of extra gaps= 1 total=141 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.290 sec, elapsed time= 13.776 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 762 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.308 sec, elapsed time= 13.794 sec. # command:Reading probabilities from T0574.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 14.398 Optimizing... Probability sum: -257.015, CN propb: -257.015 weights: 0.251 constraints: 292 # command:CPU_time= 18.582 sec, elapsed time= 22.076 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 292 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 292 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 470 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 470 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 18.595 sec, elapsed time= 23.869 sec. # command: