# 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 T0627 numbered 1 through 261 Created new target T0627 from T0627.a2m # command:CPU_time= 5.752 sec, elapsed time= 10.909 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qcxA/T0627-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qcxA expands to /projects/compbio/data/pdb/2qcx.pdb.gz 2qcxA:Skipped atom 1239, because occupancy 0.5 <= existing 0.500 in 2qcxA Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2qcxA Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 2qcxA # T0627 read from 2qcxA/T0627-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0627-2qcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qcxA to template set # found chain 2qcxA in template set Warning: unaligning (T0627)S16 because first residue in template chain is (2qcxA)Q-1 Warning: unaligning (T0627)S251 because last residue in template chain is (2qcxA)D220 T0627 17 :YPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2qcxA 0 :GMKFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA # choosing archetypes in rotamer library T0627 85 :P 2qcxA 63 :K T0627 87 :EDMARRWLMRNIRVEL 2qcxA 64 :DLYTTGRMASHAQGTY T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 2qcxA 81 :AEMALHREFAELLEISEEERKAFKPSPTAYSFTSHMYRSVLSGNFAEILAALLPC T0627 159 :EGATGEWSAVVC 2qcxA 136 :YWLYYEVGEKLL T0627 173 :G 2qcxA 148 :H T0627 180 :AEETRKKSMKWLKMHAQYD 2qcxA 149 :CDPGHPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 2qcxA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 2qcxA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 9 number of extra gaps= 0 total=9 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 2qcxA/T0627-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2qcxA/T0627-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0627-2qcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qcxA in template set Warning: unaligning (T0627)S16 because first residue in template chain is (2qcxA)Q-1 Warning: unaligning (T0627)S251 because last residue in template chain is (2qcxA)D220 T0627 17 :YPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2qcxA 0 :GMKFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 82 :GRHPGEDMARRWLMRNIRVE 2qcxA 63 :KDLYTTGRMASHAQGTYEAE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 2qcxA 83 :MALHREFAELLEISEEERKAFKPSPTAYSFTSHMYRSVLSGNFAEILAALLPCY T0627 165 :WSAVVCSTGV 2qcxA 137 :WLYYEVGEKL T0627 176 :AE 2qcxA 147 :LH T0627 180 :AEETRKKSMKWLKMHAQYD 2qcxA 149 :CDPGHPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 2qcxA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 2qcxA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=17 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 2qcxA/T0627-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2qcxA/T0627-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qcxA read from 2qcxA/T0627-2qcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qcxA in template set Warning: unaligning (T0627)S251 because last residue in template chain is (2qcxA)D220 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 2qcxA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAK T0627 84 :HPGEDMARRWLMRNI 2qcxA 64 :DLYTTGRMASHAQGT T0627 101 :ELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 2qcxA 79 :YEAEMALHREFAELLEISEEERKAFKPSPTAYSFTSHMYRSVLSGNFAEILAALLPCYWL T0627 162 :TGEWSAVVCST 2qcxA 139 :YYEVGEKLLHC T0627 178 :AFA 2qcxA 150 :DPG T0627 184 :RKKSMKWLKMHAQYDDAHP 2qcxA 153 :HPIYQKWIGTYGGDWFRQQ T0627 203 :WEALEIICTLVGNK 2qcxA 173 :EEQINRFDELAENS T0627 218 :SLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 2qcxA 187 :TEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=25 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 1yakA/T0627-1yakA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yakA expands to /projects/compbio/data/pdb/1yak.pdb.gz 1yakA:# T0627 read from 1yakA/T0627-1yakA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yakA read from 1yakA/T0627-1yakA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yakA to template set # found chain 1yakA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1yakA)K2 Warning: unaligning (T0627)S251 because last residue in template chain is (1yakA)D220 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1yakA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 85 :P 1yakA 63 :K T0627 87 :EDMARRWLMRNIRVEL 1yakA 64 :DLYTTGRMASHAQGTY T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1yakA 81 :AEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPC T0627 159 :EGATGEWSAVVC 1yakA 136 :YWLYYEVGEKLL T0627 173 :G 1yakA 148 :H T0627 180 :AEETRKKSMKWLKMHAQYD 1yakA 149 :CDPGHPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 1yakA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 1yakA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 9 number of extra gaps= 0 total=34 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 1yakA/T0627-1yakA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1yakA/T0627-1yakA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yakA read from 1yakA/T0627-1yakA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yakA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1yakA)K2 Warning: unaligning (T0627)S251 because last residue in template chain is (1yakA)D220 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1yakA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 82 :GRHPGEDMARRWLMRNIRVE 1yakA 63 :KDLYTTGRMASHAQGTYEAE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1yakA 83 :MALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCY T0627 165 :WSAVVCSTGV 1yakA 137 :WLYYEVGEKL T0627 176 :AEAFAE 1yakA 147 :LHCDPG T0627 184 :RKKSMKWLKMHAQYD 1yakA 153 :HPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 1yakA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 1yakA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=42 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 1yakA/T0627-1yakA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1yakA/T0627-1yakA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yakA read from 1yakA/T0627-1yakA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yakA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1yakA)K2 Warning: unaligning (T0627)S251 because last residue in template chain is (1yakA)D220 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 1yakA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAK T0627 84 :HPGEDMARRWLMRNI 1yakA 64 :DLYTTGRMASHAQGT T0627 101 :ELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1yakA 79 :YEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPC T0627 159 :EGATGEWSAVV 1yakA 136 :YWLYYEVGEKL T0627 177 :EAFA 1yakA 147 :LHCD T0627 183 :TRKKSMKWLKMHAQYDDAHP 1yakA 152 :GHPIYQKWIGTYGGDWFRQQ T0627 203 :WEALEIICTLVGN 1yakA 173 :EEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVK 1yakA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=50 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 1tyhA/T0627-1tyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tyhA expands to /projects/compbio/data/pdb/1tyh.pdb.gz 1tyhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 1tyhA/T0627-1tyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyhA read from 1tyhA/T0627-1tyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tyhA to template set # found chain 1tyhA in template set Warning: unaligning (T0627)P18 because first residue in template chain is (1tyhA)L1 Warning: unaligning (T0627)P252 because last residue in template chain is (1tyhA)S221 T0627 19 :AWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1tyhA 2 :KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 85 :P 1tyhA 63 :K T0627 87 :EDMARRWLMRNIRVEL 1tyhA 64 :DLYTTGRMASHAQGTY T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1tyhA 81 :AEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPC T0627 159 :EGATGEWSAVVC 1tyhA 136 :YWLYYEVGEKLL T0627 173 :G 1tyhA 148 :H T0627 180 :AEETRKKSMKWLKMHAQYD 1tyhA 149 :CDPGHPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 1tyhA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKS 1tyhA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD Number of specific fragments extracted= 9 number of extra gaps= 0 total=59 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 1tyhA/T0627-1tyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1tyhA/T0627-1tyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyhA read from 1tyhA/T0627-1tyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tyhA in template set Warning: unaligning (T0627)P252 because last residue in template chain is (1tyhA)S221 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1tyhA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYA T0627 82 :GRHPGEDMARRWLMRNIRVE 1tyhA 63 :KDLYTTGRMASHAQGTYEAE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1tyhA 83 :MALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCY T0627 165 :WSAVVCSTG 1tyhA 137 :WLYYEVGEK T0627 175 :YAEAFAE 1tyhA 146 :LLHCDPG T0627 184 :RKKSMKWLKMHAQYD 1tyhA 153 :HPIYQKWIGTYGGDW T0627 199 :DAHPWEALEIICTLVGN 1tyhA 169 :RQQVEEQINRFDELAEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKS 1tyhA 186 :STEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD Number of specific fragments extracted= 8 number of extra gaps= 0 total=67 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 1tyhA/T0627-1tyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1tyhA/T0627-1tyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyhA read from 1tyhA/T0627-1tyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tyhA in template set Warning: unaligning (T0627)P252 because last residue in template chain is (1tyhA)S221 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 1tyhA 3 :FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAK T0627 87 :EDMARRWLMRNIRV 1tyhA 64 :DLYTTGRMASHAQG T0627 101 :ELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1tyhA 79 :YEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPC T0627 159 :EGATGEWSAVVCST 1tyhA 136 :YWLYYEVGEKLLHC T0627 178 :AF 1tyhA 150 :DP T0627 183 :TRKKSMKWLKMHAQYDDAHP 1tyhA 152 :GHPIYQKWIGTYGGDWFRQQ T0627 203 :WEALEIICTLVGNKP 1tyhA 173 :EEQINRFDELAENST T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDKVKS 1tyhA 188 :EEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD Number of specific fragments extracted= 8 number of extra gaps= 0 total=75 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 2rd3A/T0627-2rd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rd3A expands to /projects/compbio/data/pdb/2rd3.pdb.gz 2rd3A:# T0627 read from 2rd3A/T0627-2rd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rd3A read from 2rd3A/T0627-2rd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rd3A to template set # found chain 2rd3A in template set Warning: unaligning (T0627)E13 because first residue in template chain is (2rd3A)D-3 Warning: unaligning (T0627)A14 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)P-2 Warning: unaligning (T0627)Y57 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)I41 Warning: unaligning (T0627)L58 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)I41 Warning: unaligning (T0627)H104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)E82 Warning: unaligning (T0627)D106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)S84 T0627 15 :SS 2rd3A -1 :FT T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQ 2rd3A 1 :MQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRF T0627 59 :IGGWPVVEQFAVYMAKNLTKT 2rd3A 42 :IQDYLFLLEYAKVFALGVVKA T0627 85 :P 2rd3A 63 :C T0627 87 :EDMARRWLMRNIRVELN 2rd3A 64 :DEAVMREFSNAIQDILN T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 2rd3A 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSC T0627 159 :EGATGEWSAVVC 2rd3A 136 :GWSYLVIAQNLS T0627 173 :G 2rd3A 148 :Q T0627 180 :AEETR 2rd3A 149 :IPNAL T0627 185 :KKSMKWLKMHAQYD 2rd3A 156 :AFYGHWIKGYSSKE T0627 199 :DAHPWEALEIICTLVGN 2rd3A 171 :QACVNWNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCI 2rd3A 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAY Number of specific fragments extracted= 12 number of extra gaps= 3 total=87 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 2rd3A/T0627-2rd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2rd3A/T0627-2rd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rd3A read from 2rd3A/T0627-2rd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rd3A in template set Warning: unaligning (T0627)A14 because first residue in template chain is (2rd3A)D-3 Warning: unaligning (T0627)S15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)P-2 Warning: unaligning (T0627)Y57 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)I41 Warning: unaligning (T0627)L58 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)I41 Warning: unaligning (T0627)V100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)E82 Warning: unaligning (T0627)E101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)E82 Warning: unaligning (T0627)A105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)M83 Warning: unaligning (T0627)D106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)S84 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQ 2rd3A -1 :FTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRF T0627 59 :IGGWPVVEQFAVYMAKNLTKT 2rd3A 42 :IQDYLFLLEYAKVFALGVVKA T0627 82 :GRHPGEDMARRWLMRNIR 2rd3A 63 :CDEAVMREFSNAIQDILN T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 2rd3A 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCG T0627 165 :WSAVVCSTGV 2rd3A 137 :WSYLVIAQNL T0627 175 :YAEAFA 2rd3A 149 :IPNALE T0627 184 :RKKSMKWLKMHAQYDDAHPWE 2rd3A 155 :HAFYGHWIKGYSSKEFQACVN T0627 205 :ALEIICTLVGN 2rd3A 177 :NINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCI 2rd3A 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAY Number of specific fragments extracted= 9 number of extra gaps= 2 total=96 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 2rd3A/T0627-2rd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2rd3A/T0627-2rd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rd3A read from 2rd3A/T0627-2rd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rd3A in template set Warning: unaligning (T0627)Y57 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)I41 Warning: unaligning (T0627)L58 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)I41 Warning: unaligning (T0627)N103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)E82 Warning: unaligning (T0627)H104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)E82 Warning: unaligning (T0627)A105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)M83 Warning: unaligning (T0627)D106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rd3A)S84 Warning: unaligning (T0627)Q245 because of BadResidue code HAS_OXT+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rd3A)S217 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQ 2rd3A 3 :VSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRF T0627 59 :IGGWPVVEQFAVYMAKNLTKTRF 2rd3A 42 :IQDYLFLLEYAKVFALGVVKACD T0627 85 :PGEDMARRWLMRNIR 2rd3A 65 :EAVMREFSNAIQDIL T0627 102 :L 2rd3A 80 :N T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 2rd3A 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWS T0627 162 :TGEWSAVVCSTGVYA 2rd3A 139 :YLVIAQNLSQIPNAL T0627 183 :TRKKSMKWLKMHAQYDDA 2rd3A 154 :EHAFYGHWIKGYSSKEFQ T0627 201 :HPWEALEIICTLVGNKP 2rd3A 173 :CVNWNINLLDSLTLASS T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCI 2rd3A 190 :KQEIEKLKEIFITTSEYEYLFWDMAY Number of specific fragments extracted= 9 number of extra gaps= 3 total=105 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 1rcwA/T0627-1rcwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rcwA expands to /projects/compbio/data/pdb/1rcw.pdb.gz 1rcwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 1rcwA/T0627-1rcwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcwA read from 1rcwA/T0627-1rcwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rcwA to template set # found chain 1rcwA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1rcwA)N7 Warning: unaligning (T0627)E101 because of BadResidue code BAD_PEPTIDE in next template residue (1rcwA)E82 Warning: unaligning (T0627)L102 because of BadResidue code BAD_PEPTIDE at template residue (1rcwA)E82 T0627 20 :WAQQLINDCSPAKA 1rcwA 8 :FLDQLDLIIQNKHM T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMA 1rcwA 22 :LEHTFYVKWSKGELTKEQLQAYAKDYYLHIKAFPKYLS T0627 79 :TRFGRHP 1rcwA 60 :AIHSRCD T0627 87 :EDMARRWLMRNIRV 1rcwA 67 :DLEARKLLLDNLMD T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1rcwA 87 :NHIDLWKQFVFALGVTPEELEAHEPSEAAKAKVATFMRWCTGDSLAAGVAALYSY T0627 159 :EGATGEWSAVVC 1rcwA 142 :ESQIPRIAREKI T0627 173 :GVYAEAFAEE 1rcwA 154 :RGLTEYFGFS T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLVGNK 1rcwA 164 :NPEDYAYFTEHEEADVRHAREEKALIEMLLKDD T0627 222 :QAELRQAVTKSYDYMYLFLER 1rcwA 197 :ADKVLEASQEVTQSLYGFLDS Number of specific fragments extracted= 9 number of extra gaps= 1 total=114 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 1rcwA/T0627-1rcwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1rcwA/T0627-1rcwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcwA read from 1rcwA/T0627-1rcwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcwA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1rcwA)N7 Warning: unaligning (T0627)N97 because of BadResidue code BAD_PEPTIDE in next template residue (1rcwA)E82 Warning: unaligning (T0627)I98 because of BadResidue code BAD_PEPTIDE at template residue (1rcwA)E82 T0627 20 :WAQQLINDCSPAK 1rcwA 8 :FLDQLDLIIQNKH T0627 35 :VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1rcwA 21 :MLEHTFYVKWSKGELTKEQLQAYAKDYYLHIKAFPKYLSAIHSRC T0627 82 :GRHPGEDMARRWLMR 1rcwA 66 :DDLEARKLLLDNLMD T0627 99 :RVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1rcwA 83 :NGYPNHIDLWKQFVFALGVTPEELEAHEPSEAAKAKVATFMRWCTGDSLAAGVAALYSY T0627 159 :EGATGEWSAVVCST 1rcwA 142 :ESQIPRIAREKIRG T0627 175 :YAEAFAE 1rcwA 156 :LTEYFGF T0627 183 :TRKKSMKWLKMHAQYDDAHPWEALEIICTLVGNK 1rcwA 163 :SNPEDYAYFTEHEEADVRHAREEKALIEMLLKDD T0627 219 :LQ 1rcwA 197 :AD T0627 224 :ELRQAVTKSYDYMYLFLE 1rcwA 199 :KVLEASQEVTQSLYGFLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=123 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 1rcwA/T0627-1rcwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1rcwA/T0627-1rcwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcwA read from 1rcwA/T0627-1rcwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcwA in template set Warning: unaligning (T0627)N97 because of BadResidue code BAD_PEPTIDE in next template residue (1rcwA)E82 Warning: unaligning (T0627)I98 because of BadResidue code BAD_PEPTIDE at template residue (1rcwA)E82 Warning: unaligning (T0627)I244 because last residue in template chain is (1rcwA)L219 T0627 20 :WAQQLINDCSPAK 1rcwA 8 :FLDQLDLIIQNKH T0627 35 :VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRH 1rcwA 21 :MLEHTFYVKWSKGELTKEQLQAYAKDYYLHIKAFPKYLSAIHSRCDDLEA T0627 87 :EDMARRWLMR 1rcwA 71 :RKLLLDNLMD T0627 99 :RVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 1rcwA 83 :NGYPNHIDLWKQFVFALGVTPEELEAHEPSEAAKAKVATFMRWCTGDSLAAGVAALYSYESQ T0627 162 :TGEWSAVVCSTGVYAEAFA 1rcwA 145 :IPRIAREKIRGLTEYFGFS T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLVGNKPS 1rcwA 164 :NPEDYAYFTEHEEADVRHAREEKALIEMLLKDDAD T0627 224 :ELRQAVTKSYDYMYLFLERC 1rcwA 199 :KVLEASQEVTQSLYGFLDSF Number of specific fragments extracted= 7 number of extra gaps= 1 total=130 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 3ibxA/T0627-3ibxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ibxA expands to /projects/compbio/data/pdb/3ibx.pdb.gz 3ibxA:# T0627 read from 3ibxA/T0627-3ibxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ibxA read from 3ibxA/T0627-3ibxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ibxA to template set # found chain 3ibxA in template set Warning: unaligning (T0627)A14 because first residue in template chain is (3ibxA)D-3 Warning: unaligning (T0627)S15 because of BadResidue code BAD_PEPTIDE at template residue (3ibxA)P-2 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ibxA -1 :FTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLYLLEYAKVFALGVVKA T0627 85 :P 3ibxA 63 :C T0627 87 :EDMARRWLMRNIRVELNH 3ibxA 64 :DEAVMREFSNAIQDILNN T0627 106 :DYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 3ibxA 84 :SIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSC T0627 159 :EGATGEWSAVVC 3ibxA 136 :GWSYLVIAQNLS T0627 173 :GVY 3ibxA 148 :QIP T0627 180 :AEETRKKSMKWLKMHAQYD 3ibxA 151 :NALEHAFYGHWIKGYSSKE T0627 199 :DAHPWEALEIICTLVGN 3ibxA 171 :QACVNWNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQ 3ibxA 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAYQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=139 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 3ibxA/T0627-3ibxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3ibxA/T0627-3ibxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ibxA read from 3ibxA/T0627-3ibxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ibxA in template set Warning: unaligning (T0627)S15 because of BadResidue code BAD_PEPTIDE at template residue (3ibxA)P-2 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ibxA -1 :FTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLYLLEYAKVFALGVVKA T0627 82 :GRHPGEDMARRWLMRNIRVE 3ibxA 63 :CDEAVMREFSNAIQDILNNE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 3ibxA 83 :MSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCG T0627 165 :WSAVVCSTG 3ibxA 137 :WSYLVIAQN T0627 175 :YAEAFAEETRKKSMKWLKMHAQYD 3ibxA 146 :LSQIPNALEHAFYGHWIKGYSSKE T0627 199 :DAHPWEALEIICTLVGN 3ibxA 171 :QACVNWNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQ 3ibxA 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAYQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=146 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 3ibxA/T0627-3ibxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3ibxA/T0627-3ibxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ibxA read from 3ibxA/T0627-3ibxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ibxA in template set T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 3ibxA 3 :VSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLYLLEYAKVFALGVVKAC T0627 87 :EDMARRWLMRNIRVELNH 3ibxA 64 :DEAVMREFSNAIQDILNN T0627 107 :YWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 3ibxA 85 :IHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSC T0627 159 :EGATGEWSAVVCSTGV 3ibxA 136 :GWSYLVIAQNLSQIPN T0627 182 :ETRKKSMKWLKMHAQYDDAHP 3ibxA 153 :LEHAFYGHWIKGYSSKEFQAC T0627 203 :WEALEIICTLVGN 3ibxA 175 :NWNINLLDSLTLA T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQ 3ibxA 188 :SSKQEIEKLKEIFITTSEYEYLFWDMAYQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=153 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 3mvuA/T0627-3mvuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3mvuA expands to /projects/compbio/data/pdb/3mvu.pdb.gz 3mvuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 610, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 614, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 616, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 618, because occupancy 0.300 <= existing 0.450 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 620, because occupancy 0.400 <= existing 0.600 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 721, because occupancy 0.370 <= existing 0.380 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1549, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1553, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 3mvuA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 3mvuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 3mvuA/T0627-3mvuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mvuA read from 3mvuA/T0627-3mvuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3mvuA to template set # found chain 3mvuA in template set T0627 14 :ASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3mvuA 2 :SEPYGKAFSLMRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKS T0627 85 :P 3mvuA 68 :E T0627 87 :EDMARRWLMRNIRVEL 3mvuA 69 :THSEMLAAVGTVNALV T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 3mvuA 86 :EEMQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPC T0627 159 :EGATGEWSAVVC 3mvuA 141 :VMGYGEIGKRLT T0627 173 :G 3mvuA 153 :A T0627 180 :AEE 3mvuA 154 :EAT T0627 184 :RKKSMKWLKMHAQYDDAHPW 3mvuA 157 :STLYGDWIDTYGGDDYQAAC T0627 204 :EALEIICTLVGN 3mvuA 178 :AVGTLLDDALER T0627 217 :P 3mvuA 190 :R T0627 218 :SLQLQAELRQAVTKSYDYMYLFLERCI 3mvuA 197 :SSPRWSRLCQTFHTATELEVGFWQMGL Number of specific fragments extracted= 11 number of extra gaps= 0 total=164 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 3mvuA/T0627-3mvuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3mvuA/T0627-3mvuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mvuA read from 3mvuA/T0627-3mvuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3mvuA in template set Warning: unaligning (T0627)E13 because first residue in template chain is (3mvuA)M1 T0627 14 :ASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3mvuA 2 :SEPYGKAFSLMRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKS T0627 82 :GRHPGEDMARRWLMRNIRVE 3mvuA 68 :ETHSEMLAAVGTVNALVAEE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 3mvuA 88 :MQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPCV T0627 165 :WSAVVCSTG 3mvuA 142 :MGYGEIGKR T0627 175 :YAEAFA 3mvuA 151 :LTAEAT T0627 184 :RKKSMKWLKMHAQYD 3mvuA 157 :STLYGDWIDTYGGDD T0627 199 :DAHPWEALEIICTLVGN 3mvuA 173 :QAACKAVGTLLDDALER T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCI 3mvuA 195 :FTSSPRWSRLCQTFHTATELEVGFWQMGL Number of specific fragments extracted= 8 number of extra gaps= 0 total=172 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 3mvuA/T0627-3mvuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3mvuA/T0627-3mvuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mvuA read from 3mvuA/T0627-3mvuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3mvuA in template set T0627 19 :AWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRF 3mvuA 7 :KAFSLMRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKSET T0627 85 :PGEDMARRWLMRNI 3mvuA 70 :HSEMLAAVGTVNAL T0627 101 :ELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 3mvuA 84 :VAEEMQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPCV T0627 160 :GATGEWSAVVCST 3mvuA 142 :MGYGEIGKRLTAE T0627 179 :F 3mvuA 155 :A T0627 183 :TRKKSMKWLKMHAQYD 3mvuA 156 :TSTLYGDWIDTYGGDD T0627 202 :PWEALEIICTLV 3mvuA 172 :YQAACKAVGTLL T0627 214 :GNKPSLQLQAELRQAVTKSYDYMYLFLERCIQ 3mvuA 193 :AEFTSSPRWSRLCQTFHTATELEVGFWQMGLT Number of specific fragments extracted= 8 number of extra gaps= 0 total=180 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 1z72A/T0627-1z72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z72A expands to /projects/compbio/data/pdb/1z72.pdb.gz 1z72A:Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 441, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1z72A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1z72A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1409, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1411, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1413, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1415, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1423, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1755, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1757, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1759, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1761, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1763, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1765, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1771, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1773, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1775, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1777, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1779, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1781, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1783, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1785, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1804, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1z72A # T0627 read from 1z72A/T0627-1z72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z72A read from 1z72A/T0627-1z72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z72A to template set # found chain 1z72A in template set Warning: unaligning (T0627)M12 because first residue in template chain is (1z72A)Q4 Warning: unaligning (T0627)G214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z72A)R195 Warning: unaligning (T0627)K216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z72A)R195 T0627 13 :E 1z72A 5 :D T0627 14 :ASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1z72A 7 :AFQPGLTVGELLKSSQKDWQAAINHRFVKELFAGTIENKVLKDYLIQDYHFFDAFLSMLGACVAHA T0627 85 :P 1z72A 73 :D T0627 87 :EDMARRWLMRNIRVEL 1z72A 74 :KLESKLRFAKQLGFLE T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1z72A 91 :DEDGYFQKAFKELKVAENDYLEVTLHPVTKAFQDLMYSAVASSDYAHLLVMLVIA T0627 159 :EGATGEWSAVVC 1z72A 146 :EGLYLDWGSKDL T0627 180 :AEETRKKSMKWLKMHAQYD 1z72A 158 :ALPEVYIHSEWINLHRGPF T0627 199 :DAHPWEALEIICTLV 1z72A 178 :AEWVQFLVDELNRVG T0627 217 :PSLQ 1z72A 196 :EDLT T0627 224 :ELRQAVTKSYDYMYLFL 1z72A 200 :ELQQRWNQAVALELAFF Number of specific fragments extracted= 10 number of extra gaps= 0 total=190 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 1z72A/T0627-1z72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1z72A/T0627-1z72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z72A read from 1z72A/T0627-1z72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z72A in template set Warning: unaligning (T0627)G214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z72A)R195 Warning: unaligning (T0627)K216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z72A)R195 T0627 14 :ASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1z72A 7 :AFQPGLTVGELLKSSQKDWQAAINHRFVKELFAGTIENKVLKDYLIQDYHFFDAFLSMLGACVAHA T0627 82 :GRHPGEDMARRWLMRNIRVE 1z72A 73 :DKLESKLRFAKQLGFLEADE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1z72A 93 :DGYFQKAFKELKVAENDYLEVTLHPVTKAFQDLMYSAVASSDYAHLLVMLVIAE T0627 165 :WSAVVCSTGV 1z72A 147 :GLYLDWGSKD T0627 180 :AE 1z72A 159 :LP T0627 183 :TRKKSMKWLKMHAQYDDAHPWE 1z72A 161 :EVYIHSEWINLHRGPFFAEWVQ T0627 205 :ALEIICTLV 1z72A 184 :LVDELNRVG T0627 217 :PSLQ 1z72A 196 :EDLT T0627 224 :ELRQAVTKSYDYMYLFL 1z72A 200 :ELQQRWNQAVALELAFF Number of specific fragments extracted= 9 number of extra gaps= 0 total=199 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 1z72A/T0627-1z72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1z72A/T0627-1z72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z72A read from 1z72A/T0627-1z72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z72A in template set Warning: unaligning (T0627)G214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z72A)R195 Warning: unaligning (T0627)K216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z72A)R195 T0627 16 :SYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 1z72A 9 :QPGLTVGELLKSSQKDWQAAINHRFVKELFAGTIENKVLKDYLIQDYHFFDAFLSMLGACVAHAD T0627 84 :HPGEDMARRWLMRNI 1z72A 74 :KLESKLRFAKQLGFL T0627 101 :ELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 1z72A 89 :EADEDGYFQKAFKELKVAENDYLEVTLHPVTKAFQDLMYSAVASSDYAHLLVMLVIAEGL T0627 162 :TGEWSAV 1z72A 149 :YLDWGSK T0627 172 :TG 1z72A 156 :DL T0627 180 :AEETRKKSMKWLKMHAQYDDAHP 1z72A 158 :ALPEVYIHSEWINLHRGPFFAEW T0627 203 :WEALEIICTLV 1z72A 182 :QFLVDELNRVG T0627 217 :PS 1z72A 196 :ED T0627 222 :QAELRQAVTKSYDYMYLFLE 1z72A 198 :LTELQQRWNQAVALELAFFD Number of specific fragments extracted= 9 number of extra gaps= 0 total=208 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 1uddA/T0627-1uddA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uddA expands to /projects/compbio/data/pdb/1udd.pdb.gz 1uddA:# T0627 read from 1uddA/T0627-1uddA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uddA read from 1uddA/T0627-1uddA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uddA to template set # found chain 1uddA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (1uddA)G215 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1uddA 3 :VMITDKLRRDSEQIWKKIFEHPFVVQLYSGTLPLEKFKFYVLQDFNYLVGLTRALAVISSKA T0627 87 :EDMARRWLMRNIRVEL 1uddA 65 :EYPLMAELIELARDEV T0627 103 :NHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 1uddA 82 :VEVENYVKLLKELDLTLEDAIKTEPTLVNSAYMDFMLATAYKGNIIEGLTALLPC T0627 159 :EGATGEWSAVVC 1uddA 137 :FWSYAEIAEYHK T0627 173 :GVY 1uddA 149 :DKL T0627 180 :AEETRKKSMKWLKMHAQYD 1uddA 152 :RDNPIKIYREWGKVYLSNE T0627 199 :DAHPWEALEIICT 1uddA 172 :LNLVGRLRKIIDS T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQL 1uddA 185 :SGHSGYDRLRRIFITGSKFELAFWEMAWRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=216 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 1uddA/T0627-1uddA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1uddA/T0627-1uddA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uddA read from 1uddA/T0627-1uddA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uddA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (1uddA)G215 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1uddA 5 :ITDKLRRDSEQIWKKIFEHPFVVQLYSGTLPLEKFKFYVLQDFNYLVGLTRALAVISSKA T0627 82 :GR 1uddA 65 :EY T0627 85 :PGEDMARRWLMRNIRVE 1uddA 67 :PLMAELIELARDEVTVE T0627 105 :ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1uddA 84 :VENYVKLLKELDLTLEDAIKTEPTLVNSAYMDFMLATAYKGNIIEGLTALLPCF T0627 165 :WSAVVCSTG 1uddA 138 :WSYAEIAEY T0627 175 :YAEAFAEETRKKSMKWLKMHAQYD 1uddA 147 :HKDKLRDNPIKIYREWGKVYLSNE T0627 199 :DAHPWEALEIICT 1uddA 172 :LNLVGRLRKIIDS T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQL 1uddA 185 :SGHSGYDRLRRIFITGSKFELAFWEMAWRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=224 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 1uddA/T0627-1uddA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1uddA/T0627-1uddA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uddA read from 1uddA/T0627-1uddA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uddA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (1uddA)G215 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 1uddA 5 :ITDKLRRDSEQIWKKIFEHPFVVQLYSGTLPLEKFKFYVLQDFNYLVGLTRALAVISSKAEYP T0627 87 :EDMARRWLMRN 1uddA 68 :LMAELIELARD T0627 100 :VELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNY 1uddA 79 :EVTVEVENYVKLLKELDLTLEDAIKTEPTLVNSAYMDFMLATAYKGNIIEGLTALLP T0627 158 :IEGATGEWSAVV 1uddA 136 :CFWSYAEIAEYH T0627 173 :GVYAEAFA 1uddA 148 :KDKLRDNP T0627 184 :RKKSMKWLKMHAQ 1uddA 156 :IKIYREWGKVYLS T0627 200 :AHPWEALEIICTLVGNKPS 1uddA 169 :NEYLNLVGRLRKIIDSSGH T0627 220 :QLQAELRQAVTKSYDYMYLFLERCIQL 1uddA 188 :SGYDRLRRIFITGSKFELAFWEMAWRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=232 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 2qzcA/T0627-2qzcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qzcA expands to /projects/compbio/data/pdb/2qzc.pdb.gz 2qzcA:Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 305, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 310, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 313, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 316, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 319, because occupancy 0.250 <= existing 0.250 in 2qzcA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 2qzcA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1502, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1545, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1546, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1550, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1551, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1553, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1554, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1556, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1557, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1559, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1560, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1562, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1563, because occupancy 0.330 <= existing 0.330 in 2qzcA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1720, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2qzcA Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2qzcA # T0627 read from 2qzcA/T0627-2qzcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzcA read from 2qzcA/T0627-2qzcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qzcA to template set # found chain 2qzcA in template set Warning: unaligning (T0627)Y17 because first residue in template chain is (2qzcA)I3 Warning: unaligning (T0627)V100 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qzcA)K83 Warning: unaligning (T0627)S251 because last residue in template chain is (2qzcA)Y213 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2qzcA 4 :VGNVENLINGVGELWNKYVKHEFILKMRDGSLPLDIFRYYLIQDGKYVEDMLRALLIASSKG T0627 85 :P 2qzcA 66 :P T0627 87 :EDMARR 2qzcA 67 :IDKVTK T0627 94 :LMRNIR 2qzcA 73 :ILNLVF T0627 101 :EL 2qzcA 84 :GL T0627 106 :DYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSS 2qzcA 86 :ETHGKLYSKLDISRDVIVKTGYNLINYAYTRHLYYYANL T0627 146 :SLAVAMAATNYA 2qzcA 125 :DWNKFLVAWTPC T0627 159 :EGATGEWSAVVC 2qzcA 137 :MFGYSIVGDYVI T0627 180 :AEE 2qzcA 149 :DSP T0627 184 :RKKSMKWLKMHAQY 2qzcA 152 :NEVYKTWASFYAST T0627 201 :HPWEALEIICTLVGN 2qzcA 166 :EYKKRIEAILYALDE T0627 216 :KPSLQL 2qzcA 182 :SITEDL T0627 226 :RQAVTKSYDYMYLFLERCIQLDKVK 2qzcA 188 :LNIFINSVRFEIGFWDASLRKDPTV Number of specific fragments extracted= 13 number of extra gaps= 0 total=245 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 2qzcA/T0627-2qzcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2qzcA/T0627-2qzcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzcA read from 2qzcA/T0627-2qzcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qzcA in template set Warning: unaligning (T0627)Y17 because first residue in template chain is (2qzcA)I3 Warning: unaligning (T0627)E101 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qzcA)K83 Warning: unaligning (T0627)N103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qzcA)K83 Warning: unaligning (T0627)S251 because last residue in template chain is (2qzcA)Y213 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2qzcA 4 :VGNVENLINGVGELWNKYVKHEFILKMRDGSLPLDIFRYYLIQDGKYVEDMLRALLIASSKG T0627 82 :G 2qzcA 66 :P T0627 84 :HPGEDMARRWL 2qzcA 67 :IDKVTKILNLV T0627 99 :RV 2qzcA 78 :FS T0627 104 :HADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTS 2qzcA 84 :GLETHGKLYSKLDISRDVIVKTGYNLINYAYTRHLYYYA T0627 144 :SDSLAVAMAATNYAI 2qzcA 123 :NLDWNKFLVAWTPCM T0627 165 :WSAVVCSTGV 2qzcA 138 :FGYSIVGDYV T0627 177 :EAFA 2qzcA 148 :IDSP T0627 184 :RKKSMKWLKMHAQ 2qzcA 152 :NEVYKTWASFYAS T0627 200 :AHPWEALEIICTLVGN 2qzcA 165 :TEYKKRIEAILYALDE T0627 216 :KPSLQL 2qzcA 182 :SITEDL T0627 226 :RQAVTKSYDYMYLFLERCIQLDKVK 2qzcA 188 :LNIFINSVRFEIGFWDASLRKDPTV Number of specific fragments extracted= 12 number of extra gaps= 0 total=257 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 2qzcA/T0627-2qzcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2qzcA/T0627-2qzcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qzcA read from 2qzcA/T0627-2qzcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qzcA in template set Warning: unaligning (T0627)N103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qzcA)K83 T0627 19 :AWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 2qzcA 5 :GNVENLINGVGELWNKYVKHEFILKMRDGSLPLDIFRYYLIQDGKYVEDMLRALLIASSKGP T0627 88 :DMARRWLMRNIRV 2qzcA 67 :IDKVTKILNLVFS T0627 104 :HADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSS 2qzcA 84 :GLETHGKLYSKLDISRDVIVKTGYNLINYAYTRHLYYYANL T0627 146 :SLAVAMAATNYA 2qzcA 125 :DWNKFLVAWTPC T0627 159 :EGATGEWSAV 2qzcA 137 :MFGYSIVGDY T0627 176 :AEAFA 2qzcA 147 :VIDSP T0627 184 :RKKSMKWLKMHA 2qzcA 152 :NEVYKTWASFYA T0627 199 :DAHPWEALEIICTLVGNKPSLQ 2qzcA 164 :STEYKKRIEAILYALDEVSITE T0627 224 :ELRQAVTKSYDYMYLFLERCIQLDKV 2qzcA 186 :DLLNIFINSVRFEIGFWDASLRKDPT Number of specific fragments extracted= 9 number of extra gaps= 0 total=266 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 3hlxA/T0627-3hlxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hlxA expands to /projects/compbio/data/pdb/3hlx.pdb.gz 3hlxA:Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 283, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 287, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 289, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 291, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 293, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 324, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 326, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 328, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 330, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 332, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 334, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 336, because occupancy 0.300 <= existing 0.700 in 3hlxA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1830, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 3hlxA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 3hlxA # T0627 read from 3hlxA/T0627-3hlxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hlxA read from 3hlxA/T0627-3hlxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hlxA to template set # found chain 3hlxA in template set Warning: unaligning (T0627)P10 because first residue in template chain is (3hlxA)L2 Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3hlxA)R185 Warning: unaligning (T0627)A200 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3hlxA)R185 T0627 11 :LMEASSY 3hlxA 3 :ITDTLSP T0627 22 :QQLINDCSPAKAR 3hlxA 10 :QAFEEALRAKGDF T0627 35 :VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMA 3hlxA 24 :HIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDA T0627 79 :TRFGRHP 3hlxA 63 :AIMANCP T0627 87 :EDMARRWLMRNIRVEL 3hlxA 70 :DAQTRRKWVQRILDHD T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 3hlxA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATN 3hlxA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSL T0627 158 :IEGATGEWSAVVC 3hlxA 146 :TELFAPQIHQSRL T0627 173 :GVYAEAFAEE 3hlxA 159 :DSWPQHYPWI T0627 184 :RKKSMKWLKMHAQYD 3hlxA 169 :KEEGYFFFRSRLSQA T0627 201 :HPWEALEIICTLVGN 3hlxA 186 :DVEHGLALAKAYCDS T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVAALE 3hlxA 201 :AEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTDK Number of specific fragments extracted= 12 number of extra gaps= 1 total=278 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 3hlxA/T0627-3hlxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hlxA/T0627-3hlxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hlxA read from 3hlxA/T0627-3hlxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hlxA in template set Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3hlxA)R185 Warning: unaligning (T0627)A200 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3hlxA)R185 T0627 11 :LMEASSYPAWAQQLINDCSPAK 3hlxA 3 :ITDTLSPQAFEEALRAKGDFYH T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3hlxA 25 :IHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :GRHPGEDMARRWLMRNIR 3hlxA 69 :PDAQTRRKWVQRILDHDG T0627 100 :VELNHADYWVNWCAAHDVTLEDLHDQR 3hlxA 89 :GEDGGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 3hlxA 117 :VLPGVRFAVDAYLNFARRACWQEAACSS T0627 156 :YA 3hlxA 145 :LT T0627 159 :EGATGEWSAVVCST 3hlxA 147 :ELFAPQIHQSRLDS T0627 175 :YAEAFAE 3hlxA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHAQYD 3hlxA 168 :IKEEGYFFFRSRLSQA T0627 201 :HPWEALEIICTLV 3hlxA 186 :DVEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVAA 3hlxA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVT Number of specific fragments extracted= 11 number of extra gaps= 1 total=289 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 3hlxA/T0627-3hlxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hlxA/T0627-3hlxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hlxA read from 3hlxA/T0627-3hlxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hlxA in template set Warning: unaligning (T0627)R99 because of BadResidue code BAD_PEPTIDE at template residue (3hlxA)H88 Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3hlxA)R185 Warning: unaligning (T0627)A200 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3hlxA)R185 T0627 18 :PAWAQQLINDC 3hlxA 9 :PQAFEEALRAK T0627 31 :AKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 3hlxA 20 :GDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCP T0627 87 :EDMARRWLMRNI 3hlxA 70 :DAQTRRKWVQRI T0627 100 :VELNHADYWVNWCAAHDVTLEDLHDQRV 3hlxA 89 :GEDGGIEAWLRLGEAVGLSRDDLLSERH T0627 128 :APELHALSHWCWQTSSSDSLAVAMAAT 3hlxA 118 :LPGVRFAVDAYLNFARRACWQEAACSS T0627 157 :AIEGATGEWSAVVCSTGVYAEAF 3hlxA 145 :LTELFAPQIHQSRLDSWPQHYPW T0627 183 :TRKKSMKWLKMHAQYD 3hlxA 168 :IKEEGYFFFRSRLSQA T0627 201 :HPWEALEIICTLVG 3hlxA 186 :DVEHGLALAKAYCD T0627 218 :SLQLQAELRQAVTKSYDYMYLFLERCIQ 3hlxA 200 :SAEKQNRMLEILQFKLDILWSMLDAMTM Number of specific fragments extracted= 9 number of extra gaps= 2 total=298 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 3hmlA/T0627-3hmlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hmlA expands to /projects/compbio/data/pdb/3hml.pdb.gz 3hmlA:Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 3hmlA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 3hmlA # T0627 read from 3hmlA/T0627-3hmlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hmlA read from 3hmlA/T0627-3hmlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hmlA to template set # found chain 3hmlA in template set Warning: unaligning (T0627)P10 because first residue in template chain is (3hmlA)L2 Warning: unaligning (T0627)N103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)G92 Warning: unaligning (T0627)T162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)P151 Warning: unaligning (T0627)G163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)P151 Warning: unaligning (T0627)V174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)S160 Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)D186 Warning: unaligning (T0627)H201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)D186 T0627 11 :LMEASS 3hmlA 3 :ITDTLS T0627 21 :AQQLINDCSPAKAR 3hmlA 9 :PQAFEEALRAKGDF T0627 35 :VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMA 3hmlA 24 :HIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDA T0627 79 :TRFGRHP 3hmlA 63 :AIMANCP T0627 87 :EDMARRWLMRNIRVEL 3hmlA 70 :DAQTRRKWVQRILDHD T0627 104 :HADYWVNWCAAHDVTLEDLHDQR 3hmlA 93 :GIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATN 3hmlA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSL T0627 158 :IEGA 3hmlA 146 :TELF T0627 175 :YAEAFAEE 3hmlA 161 :WPQHYPWI T0627 184 :RKKSMKWLKMHA 3hmlA 169 :KEEGYFYFRSRL T0627 202 :PWEALEIICTLVGN 3hmlA 187 :VEHGLALAKAYCDS T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVA 3hmlA 201 :AEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTV Number of specific fragments extracted= 12 number of extra gaps= 2 total=310 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 3hmlA/T0627-3hmlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hmlA/T0627-3hmlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hmlA read from 3hmlA/T0627-3hmlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hmlA in template set Warning: unaligning (T0627)V100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)D91 Warning: unaligning (T0627)N103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)G92 Warning: unaligning (T0627)T162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)P151 Warning: unaligning (T0627)G163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)P151 Warning: unaligning (T0627)T172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)S160 Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)D186 Warning: unaligning (T0627)H201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)D186 T0627 15 :SSYPAWAQQLINDCSPAKARV 3hmlA 3 :ITDTLSPQAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3hmlA 25 :IHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :GRHPGEDMARRWLMRNIR 3hmlA 69 :PDAQTRRKWVQRILDHDG T0627 104 :HADYWVNWCAAHDVTLEDLHDQR 3hmlA 93 :GIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATNY 3hmlA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSLT T0627 159 :EGA 3hmlA 147 :ELF T0627 175 :YAEAFAE 3hmlA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHA 3hmlA 168 :IKEEGYFYFRSRL T0627 202 :PWEALEIICTLV 3hmlA 187 :VEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGR 3hmlA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYH Number of specific fragments extracted= 10 number of extra gaps= 2 total=320 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 3hmlA/T0627-3hmlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hmlA/T0627-3hmlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hmlA read from 3hmlA/T0627-3hmlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hmlA in template set Warning: unaligning (T0627)L102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)D91 Warning: unaligning (T0627)N103 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)G92 Warning: unaligning (T0627)T162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)P151 Warning: unaligning (T0627)G163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)P151 Warning: unaligning (T0627)T172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)S160 Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hmlA)D186 Warning: unaligning (T0627)H201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hmlA)D186 T0627 17 :YPAWAQQLINDC 3hmlA 8 :SPQAFEEALRAK T0627 31 :AKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRH 3hmlA 20 :GDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDAQT T0627 87 :EDMARRWLMRNI 3hmlA 74 :RRKWVQRILDHD T0627 104 :HADYWVNWCAAHDVTLEDLHDQR 3hmlA 93 :GIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 3hmlA 117 :VLPGVRFAVDAYLNFARRACWQEAACSS T0627 157 :AIEGA 3hmlA 145 :LTELF T0627 173 :GVYAEAF 3hmlA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHA 3hmlA 168 :IKEEGYFYFRSRL T0627 202 :PWEALEIICTLVG 3hmlA 187 :VEHGLALAKAYCD T0627 218 :SLQLQAELRQAVTKSYDYMYLFLERCI 3hmlA 200 :SAEKQNRMLEILQFKLDILWSMLDAMT Number of specific fragments extracted= 10 number of extra gaps= 1 total=330 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 1otvA/T0627-1otvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1otvA expands to /projects/compbio/data/pdb/1otv.pdb.gz 1otvA:# T0627 read from 1otvA/T0627-1otvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1otvA read from 1otvA/T0627-1otvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1otvA to template set # found chain 1otvA in template set Warning: unaligning (T0627)P10 because first residue in template chain is (1otvA)L2 T0627 11 :LMEASSYPAWAQQLINDCSPAK 1otvA 3 :ITDTLSPQAFEEALRAKGDFYH T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNL 1otvA 25 :IHHPYHIAMHNGDATRKQIQGWVANRFYYQTTIPLKDAAIM T0627 82 :GRHP 1otvA 66 :ANCP T0627 87 :EDMARRWLMRNIRVEL 1otvA 70 :DAQTRRKWVQRILDHD T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 1otvA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATN 1otvA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSL T0627 158 :IEGA 1otvA 146 :TELF T0627 173 :GVYAEAFAEE 1otvA 159 :DSWPQHYPWI T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLVGN 1otvA 169 :KEEGYFYFRSRLSQANRDVEHGLALAKAYCDS T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVAAL 1otvA 201 :AEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTVTD Number of specific fragments extracted= 10 number of extra gaps= 0 total=340 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 1otvA/T0627-1otvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1otvA/T0627-1otvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1otvA read from 1otvA/T0627-1otvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1otvA in template set Warning: unaligning (T0627)E101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1otvA)D91 Warning: unaligning (T0627)L102 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1otvA)D91 T0627 15 :SSYP 1otvA 4 :TDTL T0627 20 :WAQQLINDCSPAKARV 1otvA 8 :SPQAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1otvA 25 :IHHPYHIAMHNGDATRKQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :GRHPGEDMARRWLMRNIR 1otvA 69 :PDAQTRRKWVQRILDHDG T0627 100 :V 1otvA 89 :G T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 1otvA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATNY 1otvA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSLT T0627 159 :EGATGE 1otvA 147 :ELFAPQ T0627 171 :ST 1otvA 159 :DS T0627 175 :YAEAFAE 1otvA 161 :WPQHYPW T0627 183 :TRKKSMKWLKMHAQYDDAHPWEALEIICTLV 1otvA 168 :IKEEGYFYFRSRLSQANRDVEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRV 1otvA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHT Number of specific fragments extracted= 12 number of extra gaps= 1 total=352 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1otvA/T0627-1otvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1otvA/T0627-1otvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1otvA read from 1otvA/T0627-1otvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1otvA in template set Warning: unaligning (T0627)E101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1otvA)D91 Warning: unaligning (T0627)L102 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1otvA)D91 Warning: unaligning (T0627)T172 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1otvA)L158 Warning: unaligning (T0627)G173 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1otvA)L158 T0627 22 :QQLINDCSPAKARV 1otvA 10 :QAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRH 1otvA 25 :IHHPYHIAMHNGDATRKQIQGWVANRFYYQTTIPLKDAAIMANCPDAQT T0627 87 :EDMARRWLMRN 1otvA 74 :RRKWVQRILDH T0627 98 :IRV 1otvA 87 :SHG T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 1otvA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 1otvA 117 :VLPGVRFAVDAYLNFARRACWQEAACSS T0627 157 :AIEGATGEW 1otvA 145 :LTELFAPQI T0627 169 :VCS 1otvA 154 :HQS T0627 174 :VYAEAFAEETRKKSMKWLKMHAQYDDAHPWEALEIICTLV 1otvA 159 :DSWPQHYPWIKEEGYFYFRSRLSQANRDVEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCI 1otvA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMT Number of specific fragments extracted= 10 number of extra gaps= 2 total=362 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2gA/T0627-2f2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f2gA expands to /projects/compbio/data/pdb/2f2g.pdb.gz 2f2gA:Skipped atom 187, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 189, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 191, because occupancy 0.350 <= existing 0.650 in 2f2gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1217, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1219, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1221, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1223, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1345, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1347, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1349, because occupancy 0.350 <= existing 0.650 in 2f2gA Skipped atom 1351, because occupancy 0.350 <= existing 0.650 in 2f2gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 2f2gA/T0627-2f2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2gA read from 2f2gA/T0627-2f2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f2gA to template set # found chain 2f2gA in template set Warning: unaligning (T0627)P85 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2f2gA)G70 Warning: unaligning (T0627)G86 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2f2gA)G70 T0627 20 :WAQQLINDCSPAKARVVEH 2f2gA 6 :VIDTWIDKHRSIYTAATRH T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2f2gA 31 :RDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRA T0627 82 :GRH 2f2gA 66 :CKD T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDL 2f2gA 71 :ESSDMEVVLGGIASLNDEIEWFKREGSKWDVDFSTV T0627 126 :RVAPELHALSHWCWQTSSSD 2f2gA 107 :VPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAATNYA 2f2gA 128 :KYPVIMTAFWAI T0627 159 :EGATGEWSAVVC 2f2gA 140 :EAVYQESFAHCL T0627 173 :GV 2f2gA 152 :ED T0627 180 :AEETRKKSMKWLKMHAQYD 2f2gA 154 :GNKTPVELTGACHRWGNDG T0627 199 :DAHPWEALEIICTLVGN 2f2gA 174 :KQYCSSVKNIAERCLEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLE 2f2gA 191 :ASGEVLGEAEDVLVRVLELEVAFWE Number of specific fragments extracted= 11 number of extra gaps= 1 total=373 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2gA/T0627-2f2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2f2gA/T0627-2f2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2gA read from 2f2gA/T0627-2f2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f2gA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (2f2gA)G5 Warning: unaligning (T0627)F81 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2f2gA)G70 Warning: unaligning (T0627)G82 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2f2gA)G70 T0627 20 :WAQQLINDCSPAKARVVEH 2f2gA 6 :VIDTWIDKHRSIYTAATRH T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 2f2gA 31 :RDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRAC T0627 83 :RHPGEDMARR 2f2gA 71 :ESSDMEVVLG T0627 94 :LMRNIRVE 2f2gA 81 :GIASLNDE T0627 105 :ADYWVNWCAAHDVTLED 2f2gA 89 :IEWFKREGSKWDVDFST T0627 125 :QRVAPELHALSHWCWQTSSSD 2f2gA 106 :VVPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAATNYAI 2f2gA 128 :KYPVIMTAFWAIE T0627 165 :WSAVVCSTG 2f2gA 141 :AVYQESFAH T0627 175 :YAEAFAE 2f2gA 150 :CLEDGNK T0627 183 :TRKKSMKWLKMHAQYD 2f2gA 157 :TPVELTGACHRWGNDG T0627 199 :DAHPWEALEIICTLVGN 2f2gA 174 :KQYCSSVKNIAERCLEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLE 2f2gA 191 :ASGEVLGEAEDVLVRVLELEVAFWE Number of specific fragments extracted= 12 number of extra gaps= 1 total=385 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2gA/T0627-2f2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2f2gA/T0627-2f2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2gA read from 2f2gA/T0627-2f2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f2gA in template set Warning: unaligning (T0627)R83 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2f2gA)G70 Warning: unaligning (T0627)H84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2f2gA)G70 T0627 20 :WAQQLINDCSPAKARVVEHEL 2f2gA 6 :VIDTWIDKHRSIYTAATRHAF T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 2f2gA 31 :RDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKD T0627 85 :PG 2f2gA 71 :ES T0627 89 :MARRWLMRNIRVELNHADYWVNWCAAHDVTLED 2f2gA 73 :SDMEVVLGGIASLNDEIEWFKREGSKWDVDFST T0627 125 :QRVAPELHALSHWCWQTSSSD 2f2gA 106 :VVPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAATNYAIEGAT 2f2gA 128 :KYPVIMTAFWAIEAVYQ T0627 168 :VVCSTGVYAEAFAE 2f2gA 145 :ESFAHCLEDGNKTP T0627 185 :KKSMKWLKMHAQ 2f2gA 159 :VELTGACHRWGN T0627 200 :AHPWEALEIICTLVGN 2f2gA 171 :DGFKQYCSSVKNIAER T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLER 2f2gA 190 :NASGEVLGEAEDVLVRVLELEVAFWEM Number of specific fragments extracted= 10 number of extra gaps= 1 total=395 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ddeA/T0627-3ddeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ddeA expands to /projects/compbio/data/pdb/3dde.pdb.gz 3ddeA:Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 711, because occupancy 0.370 <= existing 0.380 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3ddeA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3ddeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 3ddeA/T0627-3ddeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ddeA read from 3ddeA/T0627-3ddeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ddeA to template set # found chain 3ddeA in template set T0627 15 :SSYPAWAQQLINDCSPAK 3ddeA 4 :IDLTKLEQKVATMWDSIL T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ddeA 22 :TNSPFIHEVLDGKATKALYAIYMTETYHYTKHNAKNQALVGIMG T0627 82 :GRH 3ddeA 66 :KDL T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYA 3ddeA 69 :PGKYLSFCFHHAHEEAGHELMALSDIASIGFDREDVLSSKPLPATETLIAYLYWISATGNPVQRLGYSYWA T0627 159 :EGATGEWSAVV 3ddeA 140 :ENVYGYIDPVL T0627 173 :GVYAEAFAEE 3ddeA 151 :KAIQSTLDLT T0627 185 :KKSMKWLKMHAQYDDAHPWEALEIICTLV 3ddeA 161 :PQSMKFFIAHSKIDAKHAEEVNEMLHEVC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKV 3ddeA 190 :KTQEDVDSVVAVMENSLVLTARILDDVWKEYQL Number of specific fragments extracted= 8 number of extra gaps= 0 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ddeA/T0627-3ddeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3ddeA/T0627-3ddeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ddeA read from 3ddeA/T0627-3ddeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ddeA in template set T0627 21 :AQQLINDCSPAKARV 3ddeA 6 :LTKLEQKVATMWDSI T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3ddeA 22 :TNSPFIHEVLDGKATKALYAIYMTETYHYTKHNAKNQALVGIMG T0627 82 :GRH 3ddeA 66 :KDL T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAAT 3ddeA 69 :PGKYLSFCFHHAHEEAGHELMALSDIASIGFDREDVLSSKPLPATETLIAYLYWISATGNPVQRLGYS T0627 156 :YAIEGAT 3ddeA 137 :YWAENVY T0627 165 :WSAVVCSTG 3ddeA 144 :GYIDPVLKA T0627 175 :YAEAFAE 3ddeA 153 :IQSTLDL T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLV 3ddeA 160 :TPQSMKFFIAHSKIDAKHAEEVNEMLHEVC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPR 3ddeA 190 :KTQEDVDSVVAVMENSLVLTARILDDVWKEYQLFQSG Number of specific fragments extracted= 9 number of extra gaps= 0 total=412 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ddeA/T0627-3ddeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3ddeA/T0627-3ddeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ddeA read from 3ddeA/T0627-3ddeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ddeA in template set T0627 21 :AQQLIND 3ddeA 9 :LEQKVAT T0627 30 :PAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 3ddeA 16 :MWDSILTNSPFIHEVLDGKATKALYAIYMTETYHYTKHNAKNQALVGIMGKDL T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAAT 3ddeA 69 :PGKYLSFCFHHAHEEAGHELMALSDIASIGFDREDVLSSKPLPATETLIAYLYWISATGNPVQRLGYS T0627 156 :YAIEGAT 3ddeA 137 :YWAENVY T0627 164 :EWSAVVCSTGVYAEAFA 3ddeA 144 :GYIDPVLKAIQSTLDLT T0627 185 :KKSMKWLKMHAQYDDAHPWEALEIICTLV 3ddeA 161 :PQSMKFFIAHSKIDAKHAEEVNEMLHEVC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQL 3ddeA 190 :KTQEDVDSVVAVMENSLVLTARILDDVWKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=419 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtwA/T0627-1rtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rtwA expands to /projects/compbio/data/pdb/1rtw.pdb.gz 1rtwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 1rtwA/T0627-1rtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtwA read from 1rtwA/T0627-1rtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rtwA to template set # found chain 1rtwA in template set T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1rtwA 2 :FSEELIKENENIWRRFLPHKFLIEMAENTIKKENFEKWLVNDYYFVKNALRFMALLMAKA T0627 87 :EDMARRWLMRNIRVELNHADYWVNWCAAHDVTL 1rtwA 62 :PDDLLPFFAESIYYISKELEMFEKKAQELGISL T0627 124 :DQRVAPELHALSHWCWQTSSSDSLAVAMAAT 1rtwA 95 :NGEIDWRAKSYVNYLLSVASLGSFLEGFTAL T0627 156 :YAIEGATGEWSAVVC 1rtwA 126 :YCEEKAYYEAWKWVR T0627 173 :G 1rtwA 141 :E T0627 180 :AEETRKKSMKWLKMHAQYD 1rtwA 142 :NLKERSPYQEFINHWSSQE T0627 199 :DAHPWEALEIICTLVGN 1rtwA 162 :GEYVKRIEKILNSLAEK T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 1rtwA 179 :HGEFEKERAREVFKEVSKFELIFWDIA Number of specific fragments extracted= 8 number of extra gaps= 0 total=427 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtwA/T0627-1rtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1rtwA/T0627-1rtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtwA read from 1rtwA/T0627-1rtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtwA in template set T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1rtwA 2 :FSEELIKENENIWRRFLPHKFLIEMAENTIKKENFEKWLVNDYYFVKNALRFMALLMAKA T0627 82 :GR 1rtwA 62 :PD T0627 85 :PGEDMARRWL 1rtwA 64 :DLLPFFAESI T0627 96 :RNIRVE 1rtwA 74 :YYISKE T0627 105 :ADYWVNWCAAHDVTLE 1rtwA 80 :LEMFEKKAQELGISLN T0627 125 :QRVAPELHALSHWCWQTSSSDSLAVAMAAT 1rtwA 96 :GEIDWRAKSYVNYLLSVASLGSFLEGFTAL T0627 156 :YAIE 1rtwA 126 :YCEE T0627 165 :WSAVVCSTG 1rtwA 130 :KAYYEAWKW T0627 175 :YAEAFAE 1rtwA 139 :VRENLKE T0627 184 :RKKSMKWLKMHAQYD 1rtwA 146 :RSPYQEFINHWSSQE T0627 199 :DAHPWEALEIICTLVGN 1rtwA 162 :GEYVKRIEKILNSLAEK T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 1rtwA 179 :HGEFEKERAREVFKEVSKFELIFWDIA Number of specific fragments extracted= 12 number of extra gaps= 0 total=439 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtwA/T0627-1rtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1rtwA/T0627-1rtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtwA read from 1rtwA/T0627-1rtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtwA in template set Warning: unaligning (T0627)I244 because last residue in template chain is (1rtwA)Y206 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGEDMARRWLMR 1rtwA 2 :FSEELIKENENIWRRFLPHKFLIEMAENTIKKENFEKWLVNDYYFVKNALRFMALLMAKAPDDLLPFFAESIYYISK T0627 104 :HADYWVNWCAAHDVTLE 1rtwA 79 :ELEMFEKKAQELGISLN T0627 125 :QRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 1rtwA 96 :GEIDWRAKSYVNYLLSVASLGSFLEGFTALYCEEKA T0627 162 :TGEWSAVVCST 1rtwA 132 :YYEAWKWVREN T0627 179 :FAEET 1rtwA 143 :LKERS T0627 186 :KSMKWLKMHAQYDD 1rtwA 148 :PYQEFINHWSSQEF T0627 200 :AHPWEALEIICTLVGNKP 1rtwA 163 :EYVKRIEKILNSLAEKHG T0627 219 :LQLQAELRQAVTKSYDYMYLFLERC 1rtwA 181 :EFEKERAREVFKEVSKFELIFWDIA Number of specific fragments extracted= 8 number of extra gaps= 0 total=447 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2q4xA/T0627-2q4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2q4xA expands to /projects/compbio/data/pdb/2q4x.pdb.gz 2q4xA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 2q4xA/T0627-2q4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2q4xA read from 2q4xA/T0627-2q4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2q4xA to template set # found chain 2q4xA in template set Warning: unaligning (T0627)T183 because of BadResidue code BAD_PEPTIDE in next template residue (2q4xA)P158 Warning: unaligning (T0627)R184 because of BadResidue code BAD_PEPTIDE at template residue (2q4xA)P158 T0627 20 :WAQQLINDCSPAKARVVEH 2q4xA 6 :VIDTWIDKHRSIYTAATRH T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2q4xA 31 :RDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRA T0627 82 :GRHPGEDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDL 2q4xA 66 :CKDSGESSDMEVVLGGIASLNDEIEWFKREGSKWDVDFSTV T0627 126 :RVAPELHALSHWCWQTSSSD 2q4xA 107 :VPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAAT 2q4xA 128 :KYPVIMTAF T0627 156 :YAIEGATGEWSAVVC 2q4xA 137 :WAIEAVYQESFAHCL T0627 173 :GV 2q4xA 152 :ED T0627 180 :AEE 2q4xA 154 :GNK T0627 185 :KKSMKWLKMHAQYD 2q4xA 159 :VELTGACHRWGNDG T0627 199 :DAHPWEALEIICTLVGN 2q4xA 174 :KQYCSSVKNIAERCLEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 2q4xA 191 :ASGEVLGEAEDVLVRVLELEVAFWEMS Number of specific fragments extracted= 11 number of extra gaps= 1 total=458 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2q4xA/T0627-2q4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2q4xA/T0627-2q4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2q4xA read from 2q4xA/T0627-2q4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2q4xA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (2q4xA)G5 Warning: unaligning (T0627)E181 because of BadResidue code BAD_PEPTIDE in next template residue (2q4xA)P158 Warning: unaligning (T0627)R184 because of BadResidue code BAD_PEPTIDE at template residue (2q4xA)P158 T0627 20 :WAQQLINDCSPAKARVVEH 2q4xA 6 :VIDTWIDKHRSIYTAATRH T0627 46 :DAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2q4xA 32 :DGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRA T0627 82 :GRHPGEDMARRWLMRNIRVELNHADYWVNWCAAHDVTLED 2q4xA 66 :CKDSGESSDMEVVLGGIASLNDEIEWFKREGSKWDVDFST T0627 125 :QRVAPELHALSHWCWQTSSSD 2q4xA 106 :VVPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAATNYAI 2q4xA 128 :KYPVIMTAFWAIE T0627 165 :WSAVVCSTGVYAEAFA 2q4xA 141 :AVYQESFAHCLEDGNK T0627 185 :KKSMKWLKMHAQYDDAHPWE 2q4xA 159 :VELTGACHRWGNDGFKQYCS T0627 205 :ALEIICTLVGN 2q4xA 180 :VKNIAERCLEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 2q4xA 191 :ASGEVLGEAEDVLVRVLELEVAFWEMS Number of specific fragments extracted= 9 number of extra gaps= 1 total=467 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2q4xA/T0627-2q4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2q4xA/T0627-2q4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2q4xA read from 2q4xA/T0627-2q4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2q4xA in template set Warning: unaligning (T0627)T183 because of BadResidue code BAD_PEPTIDE in next template residue (2q4xA)P158 Warning: unaligning (T0627)R184 because of BadResidue code BAD_PEPTIDE at template residue (2q4xA)P158 T0627 20 :WAQQLINDCSPAKARVVEHEL 2q4xA 6 :VIDTWIDKHRSIYTAATRHAF T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPG 2q4xA 31 :RDGSVDLSSFRTWLGQDYLFVRRFVPFVASVLIRACKDSGES T0627 87 :EDMARRWLMR 2q4xA 74 :DMEVVLGGIA T0627 100 :VELNHADYWVNWCAAHDVTLE 2q4xA 84 :SLNDEIEWFKREGSKWDVDFS T0627 124 :DQRVAPELHALSHWCWQTSSSD 2q4xA 105 :TVVPQRANQEYGRFLEDLMSSE T0627 146 :SLAVAMAATNYAIEGAT 2q4xA 128 :KYPVIMTAFWAIEAVYQ T0627 164 :EW 2q4xA 145 :ES T0627 170 :CST 2q4xA 147 :FAH T0627 176 :AEAFAEE 2q4xA 150 :CLEDGNK T0627 185 :KKSMKWLKMHAQYDDA 2q4xA 159 :VELTGACHRWGNDGFK T0627 201 :HPWEALEIICTLVGN 2q4xA 176 :YCSSVKNIAERCLEN T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERC 2q4xA 191 :ASGEVLGEAEDVLVRVLELEVAFWEMS Number of specific fragments extracted= 12 number of extra gaps= 1 total=479 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2mA/T0627-2a2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a2mA expands to /projects/compbio/data/pdb/2a2m.pdb.gz 2a2mA:Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 2a2mA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 2a2mA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2a2mA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2a2mA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2a2mA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 341, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 345, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 347, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 349, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 351, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 353, because occupancy 0.300 <= existing 0.700 in 2a2mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 697, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 701, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 703, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 705, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 707, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 709, because occupancy 0.400 <= existing 0.600 in 2a2mA Skipped atom 887, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 891, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 893, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 895, because occupancy 0.300 <= existing 0.700 in 2a2mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1314, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1318, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1320, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1322, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1324, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1404, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1408, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1410, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1412, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1414, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1540, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1544, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1546, because occupancy 0.300 <= existing 0.700 in 2a2mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1658, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1662, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1664, because occupancy 0.300 <= existing 0.700 in 2a2mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1784, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1788, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1790, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1792, because occupancy 0.300 <= existing 0.700 in 2a2mA Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2a2mA # T0627 read from 2a2mA/T0627-2a2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2mA read from 2a2mA/T0627-2a2mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a2mA to template set # found chain 2a2mA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (2a2mA)T240 T0627 5 :FERTGPLMEASS 2a2mA 26 :TTLKSDVPAADS T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2a2mA 38 :LFWKLWNGSLDTAVQVLQTDYFKGIAAGTLDPNAYGSLMVQDGYYCFRGRDDYATAATCA T0627 85 :P 2a2mA 98 :Q T0627 87 :EDMARRWLMRNIRVEL 2a2mA 99 :DETLREFFKAKAKSYD T0627 106 :DYWVNWCAAHDV 2a2mA 115 :EYNETYHQTWHL T0627 118 :TLEDL 2a2mA 128 :EASGL T0627 126 :RVAPELHALSHWCWQTSSSDSLAVAMAATNYA 2a2mA 133 :IPGTDIKDYADYEAYVAGSLASPYMCVVMLPC T0627 159 :EGATGEWSAVVC 2a2mA 165 :EYLWPWIANFLD T0627 173 :GVY 2a2mA 177 :GYT T0627 180 :AEE 2a2mA 180 :PTN T0627 185 :KKSMKWLKMHAQYD 2a2mA 183 :SLYRFWIEWNGGTP T0627 200 :AHPWEALEIICTLVGN 2a2mA 197 :NGAYQMGNMLEQYRDK T0627 217 :PSLQ 2a2mA 213 :IDED T0627 224 :ELRQAVTKSYDYMYLFLERCIQL 2a2mA 217 :KAVEIFNTAMNYELKVFTSSTIL Number of specific fragments extracted= 14 number of extra gaps= 0 total=493 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2mA/T0627-2a2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2a2mA/T0627-2a2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2mA read from 2a2mA/T0627-2a2mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2mA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (2a2mA)T240 T0627 11 :LMEASSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 2a2mA 29 :KSDVPAADSLFWKLWNGSLDTAVQVLQTDYFKGIAAGTLDPNAYGSLMVQDGYYCFRGRDDYATAATCA T0627 82 :GRH 2a2mA 98 :QDE T0627 89 :MARRWLMRNIRVE 2a2mA 101 :TLREFFKAKAKSY T0627 105 :ADYWVNWCAAHDV 2a2mA 114 :DEYNETYHQTWHL T0627 118 :TLED 2a2mA 128 :EASG T0627 125 :QRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 2a2mA 132 :LIPGTDIKDYADYEAYVAGSLASPYMCVVMLPCE T0627 165 :WSAVVCSTG 2a2mA 166 :YLWPWIANF T0627 175 :YAEAFAE 2a2mA 175 :LDGYTPT T0627 184 :RKKSMKWLKMHAQ 2a2mA 182 :NSLYRFWIEWNGG T0627 198 :DDAHPWEALEIICTLVGN 2a2mA 195 :TPNGAYQMGNMLEQYRDK T0627 217 :PSLQ 2a2mA 213 :IDED T0627 224 :ELRQAVTKSYDYMYLFLERCIQL 2a2mA 217 :KAVEIFNTAMNYELKVFTSSTIL Number of specific fragments extracted= 12 number of extra gaps= 0 total=505 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2mA/T0627-2a2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 2a2mA/T0627-2a2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2mA read from 2a2mA/T0627-2a2mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2mA in template set Warning: unaligning (T0627)D247 because last residue in template chain is (2a2mA)T240 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 2a2mA 38 :LFWKLWNGSLDTAVQVLQTDYFKGIAAGTLDPNAYGSLMVQDGYYCFRGRDDYATAATCAQ T0627 87 :EDMARRWLMR 2a2mA 99 :DETLREFFKA T0627 104 :HADYWVNWCAAH 2a2mA 109 :KAKSYDEYNETY T0627 123 :HDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEG 2a2mA 130 :SGLIPGTDIKDYADYEAYVAGSLASPYMCVVMLPCEYL T0627 162 :TGEWSAVVCS 2a2mA 168 :WPWIANFLDG T0627 178 :AFAE 2a2mA 178 :YTPT T0627 184 :RKKSMKWLKMHAQYDD 2a2mA 182 :NSLYRFWIEWNGGTPN T0627 202 :PWEALEIICTLVGNKPS 2a2mA 198 :GAYQMGNMLEQYRDKID T0627 222 :QAELRQAVTKSYDYMYLFLERCIQL 2a2mA 215 :EDKAVEIFNTAMNYELKVFTSSTIL Number of specific fragments extracted= 9 number of extra gaps= 0 total=514 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hnhA/T0627-3hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hnhA expands to /projects/compbio/data/pdb/3hnh.pdb.gz 3hnhA:Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1013, because occupancy 0.300 <= existing 0.700 in 3hnhA Skipped atom 1017, because occupancy 0.300 <= existing 0.700 in 3hnhA Skipped atom 1019, because occupancy 0.300 <= existing 0.700 in 3hnhA Skipped atom 1021, because occupancy 0.300 <= existing 0.700 in 3hnhA Skipped atom 1023, because occupancy 0.300 <= existing 0.700 in 3hnhA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 3hnhA Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 3hnhA # T0627 read from 3hnhA/T0627-3hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hnhA read from 3hnhA/T0627-3hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hnhA to template set # found chain 3hnhA in template set Warning: unaligning (T0627)P10 because first residue in template chain is (3hnhA)L2 Warning: unaligning (T0627)T162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hnhA)P162 Warning: unaligning (T0627)G163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)P162 Warning: unaligning (T0627)E164 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)Q163 Warning: unaligning (T0627)A180 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)H164 T0627 11 :LMEASSY 3hnhA 3 :ITDTLSP T0627 22 :QQLINDCSPAKAR 3hnhA 10 :QAFEEALRAKGDF T0627 35 :VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMA 3hnhA 24 :HIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDA T0627 79 :TRFGRHP 3hnhA 63 :AIMANCP T0627 87 :EDMARRWLMRNIRVEL 3hnhA 70 :DAQTRRKWVQRILDHD T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 3hnhA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATN 3hnhA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSL T0627 158 :IEGA 3hnhA 146 :TELF T0627 181 :EET 3hnhA 165 :YPW T0627 184 :RKKSMKWLKMHAQYDDAHPWEALEIICTLVGN 3hnhA 169 :KEEGYFSFRSSLSQANRDVEHGLALAKAYCDS T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRVA 3hnhA 201 :AEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHTV Number of specific fragments extracted= 11 number of extra gaps= 1 total=525 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hnhA/T0627-3hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hnhA/T0627-3hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hnhA read from 3hnhA/T0627-3hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hnhA in template set Warning: unaligning (T0627)V100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hnhA)D91 Warning: unaligning (T0627)G160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hnhA)P162 Warning: unaligning (T0627)A161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)P162 Warning: unaligning (T0627)T162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)Q163 Warning: unaligning (T0627)A178 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)H164 T0627 15 :SSYPAWAQQLINDCSPAKARV 3hnhA 3 :ITDTLSPQAFEEALRAKGDFY T0627 36 :VEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3hnhA 25 :IHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANC T0627 82 :GRHPGEDMARRWLMRNIR 3hnhA 69 :PDAQTRRKWVQRILDHDG T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 3hnhA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATNYAIE 3hnhA 117 :VLPGVRFAVDAYLNFARRACWQEAACSSLTELF T0627 179 :FAE 3hnhA 165 :YPW T0627 183 :TRKKSMKWLKMHAQYDDAHPWEALEIICTLV 3hnhA 168 :IKEEGYFSFRSSLSQANRDVEHGLALAKAYC T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPRGRV 3hnhA 199 :DSAEKQNRMLEILQFKLDILWSMLDAMTMAYALQRPPYHT Number of specific fragments extracted= 8 number of extra gaps= 1 total=533 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hnhA/T0627-3hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3hnhA/T0627-3hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hnhA read from 3hnhA/T0627-3hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hnhA in template set Warning: unaligning (T0627)E101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hnhA)D91 Warning: unaligning (T0627)L102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)D91 Warning: unaligning (T0627)A167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hnhA)P162 Warning: unaligning (T0627)V168 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)P162 Warning: unaligning (T0627)V169 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)Q163 Warning: unaligning (T0627)E181 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hnhA)H164 T0627 15 :SSYPAWAQQLINDC 3hnhA 6 :TLSPQAFEEALRAK T0627 31 :AKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 3hnhA 20 :GDFYHIHHPYHIAMHNGNATREQIQGWVANRFYYQTTIPLKDAAIMANCPDA T0627 86 :GEDMARRWLMRNIRV 3hnhA 72 :QTRRKWVQRILDHDG T0627 103 :NHADYWVNWCAAHDVTLEDLHDQR 3hnhA 92 :GGIEAWLRLGEAVGLSRDDLLSER T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 3hnhA 117 :VLPGVRFAVDAYLNFARRACWQEAACSS T0627 158 :IE 3hnhA 145 :LT T0627 164 :EWS 3hnhA 147 :ELF T0627 182 :ETRKKSMKWLKMHAQYDDAHPWEALEIICTLVG 3hnhA 167 :WIKEEGYFSFRSSLSQANRDVEHGLALAKAYCD T0627 218 :SLQLQAELRQAVTKSYDYMYLFLERCI 3hnhA 200 :SAEKQNRMLEILQFKLDILWSMLDAMT Number of specific fragments extracted= 9 number of extra gaps= 1 total=542 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bjdA/T0627-3bjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bjdA expands to /projects/compbio/data/pdb/3bjd.pdb.gz 3bjdA:Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 157, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 163, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 169, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 171, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 173, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 251, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 255, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 257, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 260, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 264, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 266, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 268, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 270, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 272, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 274, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 276, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 481, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 485, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 487, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 489, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 491, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 493, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 575, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 579, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 581, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 583, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 704, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 708, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 710, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 712, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 714, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 716, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 718, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 720, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 748, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 752, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 754, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 756, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 758, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 760, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 762, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 764, because occupancy 0.400 <= existing 0.600 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 803, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 807, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 809, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 811, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 813, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 854, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 858, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1036, because occupancy 0.370 <= existing 0.370 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3bjdA Skipped atom 1181, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1185, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1187, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1189, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1191, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1193, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1195, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1197, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1677, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1681, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1683, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1685, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1687, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1689, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1716, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1720, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1722, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1724, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1726, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 1728, because occupancy 0.400 <= existing 0.600 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2151, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2155, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2157, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2159, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2161, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2170, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2174, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2176, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2178, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2180, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2182, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2427, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2431, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2433, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2435, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2437, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2439, because occupancy 0.300 <= existing 0.700 in 3bjdA Skipped atom 2562, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2566, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2568, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2570, because occupancy 0.400 <= existing 0.600 in 3bjdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2692, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2696, because occupancy 0.400 <= existing 0.600 in 3bjdA Skipped atom 2698, because occupancy 0.400 <= existing 0.600 in 3bjdA # T0627 read from 3bjdA/T0627-3bjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bjdA read from 3bjdA/T0627-3bjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bjdA to template set # found chain 3bjdA in template set Warning: unaligning (T0627)A33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bjdA)E122 Warning: unaligning (T0627)V36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bjdA)E122 Warning: unaligning (T0627)V65 because of BadResidue code BAD_PEPTIDE in next template residue (3bjdA)F152 Warning: unaligning (T0627)E66 because of BadResidue code BAD_PEPTIDE at template residue (3bjdA)F152 Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bjdA)K283 Warning: unaligning (T0627)W203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bjdA)K283 T0627 7 :RTGPLMEASSYPAWAQQLINDCSP 3bjdA 95 :PAADLSRALSEEDFQKRLEQEIAA T0627 37 :EHELYQQMRDAKLSPQIMRQYLIGGWPV 3bjdA 123 :RHPMSQYVFSGSASRAQLQVFLRHQWFR T0627 67 :QFAVYMA 3bjdA 153 :RLYRDAA T0627 79 :TRFGRHP 3bjdA 160 :DLLVNLT T0627 87 :EDMARRWLMRNIRVEL 3bjdA 167 :DVDEAAALARYLYGEL T0627 103 :NHADYWVNWCAAHDVT 3bjdA 190 :SHPRLLAKLLEAIGLE T0627 122 :LHDQR 3bjdA 206 :ADFQA T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAATN 3bjdA 213 :TMPEEIAYLNNRARAFRHAEVGWGLAVFY T0627 157 :AIEGATGEWSAVVC 3bjdA 242 :ITELVVPGNHEKLY T0627 173 :GVYA 3bjdA 256 :RALL T0627 180 :AEETRKKSMKWLKMHAQYD 3bjdA 260 :QAGLSEDQAEYYKVHISLV T0627 204 :EALEIICTLVGN 3bjdA 284 :REWQLIARRIPD T0627 219 :LQLQAELRQAVTKSYDYMYLFLERCIQLDK 3bjdA 296 :VQFQNAFLTSLSQHFRVERAYYDAIWEEMQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=555 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bjdA/T0627-3bjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3bjdA/T0627-3bjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bjdA read from 3bjdA/T0627-3bjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bjdA in template set Warning: unaligning (T0627)V36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bjdA)E122 Warning: unaligning (T0627)V65 because of BadResidue code BAD_PEPTIDE in next template residue (3bjdA)F152 Warning: unaligning (T0627)E66 because of BadResidue code BAD_PEPTIDE at template residue (3bjdA)F152 Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bjdA)K283 Warning: unaligning (T0627)W203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bjdA)K283 T0627 8 :TGPLMEASSYPA 3bjdA 93 :FMPAADLSRALS T0627 21 :AQQLINDCSPAKA 3bjdA 105 :EEDFQKRLEQEIA T0627 37 :EHELYQQMRDAKLSPQIMRQYLIGGWPV 3bjdA 123 :RHPMSQYVFSGSASRAQLQVFLRHQWFR T0627 67 :QFAVYMAKNLTKT 3bjdA 153 :RLYRDAADLLVNL T0627 82 :GRHPGEDMARRWLMRNIR 3bjdA 166 :TDVDEAAALARYLYGELG T0627 100 :VELNHADYWVNWCAAHDVT 3bjdA 187 :EKGSHPRLLAKLLEAIGLE T0627 122 :LHDQR 3bjdA 206 :ADFQA T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 3bjdA 213 :TMPEEIAYLNNRARAFRHAEVGWGLAVF T0627 156 :YAIEGATGEWSAVVCST 3bjdA 241 :YITELVVPGNHEKLYRA T0627 175 :Y 3bjdA 258 :L T0627 177 :EAFAE 3bjdA 259 :LQAGL T0627 184 :RKKSMKWLKMHAQYD 3bjdA 264 :SEDQAEYYKVHISLV T0627 204 :EALEIICTLV 3bjdA 284 :REWQLIARRI T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDK 3bjdA 294 :PDVQFQNAFLTSLSQHFRVERAYYDAIWEEMQ Number of specific fragments extracted= 14 number of extra gaps= 1 total=569 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bjdA/T0627-3bjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3bjdA/T0627-3bjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bjdA read from 3bjdA/T0627-3bjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bjdA in template set Warning: unaligning (T0627)V36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bjdA)E122 Warning: unaligning (T0627)V65 because of BadResidue code BAD_PEPTIDE in next template residue (3bjdA)F152 Warning: unaligning (T0627)E66 because of BadResidue code BAD_PEPTIDE at template residue (3bjdA)F152 Warning: unaligning (T0627)D199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bjdA)K283 T0627 37 :EHELYQQMRDAKLSPQIMRQYLIGGWPV 3bjdA 123 :RHPMSQYVFSGSASRAQLQVFLRHQWFR T0627 67 :QFAVYMAKNLTKTR 3bjdA 153 :RLYRDAADLLVNLT T0627 87 :EDMARRWLMRNIRVE 3bjdA 167 :DVDEAAALARYLYGE T0627 102 :LNHADYWVNWCAAHDVT 3bjdA 189 :GSHPRLLAKLLEAIGLE T0627 127 :VAPELHALSHWCWQTSSSDSLAVAMAAT 3bjdA 213 :TMPEEIAYLNNRARAFRHAEVGWGLAVF T0627 156 :YAIEGATGEWSAVVCSTGVYA 3bjdA 241 :YITELVVPGNHEKLYRALLQA T0627 178 :AFAEET 3bjdA 262 :GLSEDQ T0627 188 :MKWLKMHAQYD 3bjdA 268 :AEYYKVHISLV T0627 203 :WE 3bjdA 286 :WQ T0627 209 :ICTLVG 3bjdA 288 :LIARRI T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQL 3bjdA 294 :PDVQFQNAFLTSLSQHFRVERAYYDAIWEE Number of specific fragments extracted= 11 number of extra gaps= 1 total=580 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwmA/T0627-1wwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wwmA expands to /projects/compbio/data/pdb/1wwm.pdb.gz 1wwmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0627 read from 1wwmA/T0627-1wwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwmA read from 1wwmA/T0627-1wwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wwmA to template set # found chain 1wwmA in template set Warning: unaligning (T0627)V36 because first residue in template chain is (1wwmA)E11 Warning: unaligning (T0627)E37 because of BadResidue code BAD_PEPTIDE at template residue (1wwmA)V12 Warning: unaligning (T0627)H38 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1wwmA)P13 T0627 39 :ELYQQMRD 1wwmA 14 :GLLEEIKA T0627 47 :AKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1wwmA 24 :LRLDEERFRFWLQQDYPFVEALYRYQVGLLLEA T0627 87 :EDMARRWLMRNIRV 1wwmA 57 :PQAHRAPLVQALMA T0627 102 :L 1wwmA 71 :T T0627 106 :DYWVNWCAAHDVT 1wwmA 72 :VEELDWLLLQGAS T0627 123 :HDQRVAPELHALSHWCWQTSSS 1wwmA 85 :PSAPVHPVRAGYIALLEEMGRL T0627 146 :SLAVAMAAT 1wwmA 107 :PYAYRVVFF T0627 156 :YAIEGATGEWSAVVC 1wwmA 116 :YFLNGLFLEAWAHHV T0627 180 :AEE 1wwmA 131 :PEE T0627 185 :KKSMKWLKMHAQYDDAHPW 1wwmA 134 :GPWAELSQHWFAPEFQAVL T0627 204 :EALEIICTLVGN 1wwmA 154 :DLEVLARGLWED T0627 217 :PSLQ 1wwmA 166 :LDPE T0627 224 :ELRQAVTKSYDYMYLFLER 1wwmA 170 :VVRTYLRRILEAEKATWSL Number of specific fragments extracted= 13 number of extra gaps= 0 total=593 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwmA/T0627-1wwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1wwmA/T0627-1wwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwmA read from 1wwmA/T0627-1wwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwmA in template set Warning: unaligning (T0627)V36 because first residue in template chain is (1wwmA)E11 Warning: unaligning (T0627)E37 because of BadResidue code BAD_PEPTIDE at template residue (1wwmA)V12 Warning: unaligning (T0627)H38 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1wwmA)P13 T0627 39 :ELYQQMRD 1wwmA 14 :GLLEEIKA T0627 47 :AKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 1wwmA 24 :LRLDEERFRFWLQQDYPFVEALYRYQVGLLLEA T0627 82 :G 1wwmA 57 :P T0627 84 :HPGEDMARR 1wwmA 58 :QAHRAPLVQ T0627 94 :LMRNIRVE 1wwmA 67 :ALMATVEE T0627 109 :VNWCAAHDVT 1wwmA 75 :LDWLLLQGAS T0627 123 :HDQRVAPELHALSHWCWQTS 1wwmA 85 :PSAPVHPVRAGYIALLEEMG T0627 144 :SDSLAVAMAATNYAI 1wwmA 105 :RLPYAYRVVFFYFLN T0627 165 :WSAVVCSTGVY 1wwmA 120 :GLFLEAWAHHV T0627 180 :AE 1wwmA 131 :PE T0627 184 :RKKSMKWLKMHAQYDDAHPWE 1wwmA 133 :EGPWAELSQHWFAPEFQAVLY T0627 205 :ALEIICTLVGN 1wwmA 155 :LEVLARGLWED T0627 217 :PSLQ 1wwmA 166 :LDPE T0627 224 :ELRQAVTKSYDYMYLFLER 1wwmA 170 :VVRTYLRRILEAEKATWSL Number of specific fragments extracted= 14 number of extra gaps= 0 total=607 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwmA/T0627-1wwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1wwmA/T0627-1wwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwmA read from 1wwmA/T0627-1wwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwmA in template set T0627 38 :HELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTR 1wwmA 15 :LLEEIKALPLRLDEERFRFWLQQDYPFVEALYRYQVGLLLEAP T0627 88 :DMARRWLMRNIRVELNHADYWV 1wwmA 58 :QAHRAPLVQALMATVEELDWLL T0627 114 :AHDVTL 1wwmA 80 :LQGASP T0627 124 :DQRVAPELHALSHWCWQTSSS 1wwmA 86 :SAPVHPVRAGYIALLEEMGRL T0627 146 :SLAVAMAAT 1wwmA 107 :PYAYRVVFF T0627 156 :YAIEGATGEWSAVVCST 1wwmA 116 :YFLNGLFLEAWAHHVPE T0627 180 :AEETRKKSMKW 1wwmA 133 :EGPWAELSQHW T0627 191 :LKMHA 1wwmA 148 :FQAVL T0627 203 :WEALEIICTLVGNKPS 1wwmA 153 :YDLEVLARGLWEDLDP T0627 223 :AELRQAVTKSYDYMYLFLER 1wwmA 169 :EVVRTYLRRILEAEKATWSL Number of specific fragments extracted= 10 number of extra gaps= 0 total=617 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b5oA/T0627-3b5oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3b5oA expands to /projects/compbio/data/pdb/3b5o.pdb.gz 3b5oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 468, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 985, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 987, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 989, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 991, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 993, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.300 <= existing 0.700 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.220 <= existing 0.530 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.300 <= existing 0.700 in 3b5oA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 3b5oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1887, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1889, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1891, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1897, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 3b5oA Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 3b5oA # T0627 read from 3b5oA/T0627-3b5oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b5oA read from 3b5oA/T0627-3b5oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3b5oA to template set # found chain 3b5oA in template set Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b5oA)A188 Warning: unaligning (T0627)G254 because of BadResidue code BAD_PEPTIDE in next template residue (3b5oA)S236 Warning: unaligning (T0627)R255 because of BadResidue code BAD_PEPTIDE at template residue (3b5oA)S236 T0627 16 :SYPAWAQQLINDCSPAKAR 3b5oA 2 :EFNHLTKQLNQLLAQDYVA T0627 35 :VVEHELYQQMR 3b5oA 23 :ITENPVVQMLS T0627 48 :KLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3b5oA 34 :QASFAQIAYVMQQYSIFPKELVGFTELARRKA T0627 82 :GRHP 3b5oA 66 :LGAG T0627 87 :EDMARRWLMRNIRVEL 3b5oA 70 :WNGVAQELQENIDEEM T0627 103 :NHADYWVNWCAAH 3b5oA 93 :SHYTLLADGLEEG T0627 116 :DVT 3b5oA 107 :GVA T0627 122 :LHDQRVAPELHALSHWCWQTSSS 3b5oA 110 :VKNTMPSVATSKLLRTVLSLFDR T0627 146 :SLAVAMAAT 3b5oA 133 :QVDYVLGAT T0627 156 :YAIEGATGE 3b5oA 142 :YAIEATSIP T0627 165 :WSAVVC 3b5oA 154 :LIVKLV T0627 173 :GVYA 3b5oA 160 :EWLH T0627 180 :AEETRKKSMKWLKMHA 3b5oA 164 :EGAIPKDLQYFFSKHL T0627 204 :EALEIICTL 3b5oA 189 :GLRTSVAAY T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDKVKSPR 3b5oA 198 :IQPEEFGEFAAGFRAMIDAMQVWWQELAQEAISSEVV Number of specific fragments extracted= 15 number of extra gaps= 1 total=632 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b5oA/T0627-3b5oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3b5oA/T0627-3b5oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b5oA read from 3b5oA/T0627-3b5oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b5oA in template set Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b5oA)A188 Warning: unaligning (T0627)E204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3b5oA)A188 T0627 17 :YPAWAQQLINDCSPAKARV 3b5oA 3 :FNHLTKQLNQLLAQDYVAF T0627 36 :VEHELYQ 3b5oA 24 :TENPVVQ T0627 45 :RDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKT 3b5oA 31 :MLSQASFAQIAYVMQQYSIFPKELVGFTELARRKA T0627 82 :GRHPG 3b5oA 66 :LGAGW T0627 88 :DMARRWLMRNIRVEL 3b5oA 71 :NGVAQELQENIDEEM T0627 103 :NHADYWVNWCAA 3b5oA 93 :SHYTLLADGLEE T0627 115 :HDVT 3b5oA 106 :LGVA T0627 122 :LHDQRVAPELHALSHWCWQTSSS 3b5oA 110 :VKNTMPSVATSKLLRTVLSLFDR T0627 146 :SLAVAMAAT 3b5oA 133 :QVDYVLGAT T0627 156 :YAIEGAT 3b5oA 142 :YAIEATS T0627 165 :WSAVVCSTGVYAEAFAEETRKKSMKWLKMHA 3b5oA 149 :IPELTLIVKLVEWLHEGAIPKDLQYFFSKHL T0627 205 :ALEIICTL 3b5oA 190 :LRTSVAAY T0627 217 :PSLQLQAELRQAVTKSYDYMYLFLERCIQLDK 3b5oA 198 :IQPEEFGEFAAGFRAMIDAMQVWWQELAQEAI Number of specific fragments extracted= 13 number of extra gaps= 0 total=645 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b5oA/T0627-3b5oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3b5oA/T0627-3b5oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b5oA read from 3b5oA/T0627-3b5oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b5oA in template set Warning: unaligning (T0627)Q196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b5oA)A188 T0627 21 :AQQLINDCSPAKAR 3b5oA 3 :FNHLTKQLNQLLAQ T0627 35 :VV 3b5oA 21 :FS T0627 37 :EHELY 3b5oA 25 :ENPVV T0627 47 :AKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRH 3b5oA 33 :SQASFAQIAYVMQQYSIFPKELVGFTELARRKALGAGW T0627 88 :DMARRWLMRNIRVE 3b5oA 71 :NGVAQELQENIDEE T0627 102 :LNHADYWVNWCAA 3b5oA 92 :ISHYTLLADGLEE T0627 115 :HDVT 3b5oA 106 :LGVA T0627 122 :LHDQRVAPELHALSHWCWQTSSSDSLAVAMAA 3b5oA 110 :VKNTMPSVATSKLLRTVLSLFDRQVDYVLGAT T0627 156 :YAIEG 3b5oA 142 :YAIEA T0627 162 :T 3b5oA 147 :T T0627 166 :SAVVCSTGVYAEA 3b5oA 148 :SIPELTLIVKLVE T0627 179 :FAEETRKKSMKWLKMHA 3b5oA 163 :HEGAIPKDLQYFFSKHL T0627 208 :IICTLVGNKPSLQLQAELRQAVTKSYDYMYLFLERCIQL 3b5oA 189 :GLRTSVAAYIQPEEFGEFAAGFRAMIDAMQVWWQELAQE Number of specific fragments extracted= 13 number of extra gaps= 0 total=658 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wzdA/T0627-1wzdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wzdA expands to /projects/compbio/data/pdb/1wzd.pdb.gz 1wzdA:Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1wzdA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1wzdA # T0627 read from 1wzdA/T0627-1wzdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wzdA read from 1wzdA/T0627-1wzdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wzdA to template set # found chain 1wzdA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1wzdA)G7 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTK 1wzdA 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRAS T0627 82 :GRHPG 1wzdA 67 :GFAES T0627 97 :NIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMA 1wzdA 72 :LLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVA T0627 154 :TNYAIEGATGEWSAVVC 1wzdA 128 :HHYVRYLGDLSGGQVIA T0627 173 :GVYAEAFAEE 1wzdA 145 :RMMQRHYGVD T0627 185 :KKSMKWLKMHAQYDDAHPW 1wzdA 155 :PEALGFYHFEGIAKLKVYK T0627 204 :EALEIICTL 1wzdA 175 :EYREKLNNL T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQ 1wzdA 184 :ELSDEQREHLLKEATDAFVFNHQVFADLGK Number of specific fragments extracted= 8 number of extra gaps= 0 total=666 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wzdA/T0627-1wzdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1wzdA/T0627-1wzdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wzdA read from 1wzdA/T0627-1wzdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wzdA in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1wzdA)G7 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 1wzdA 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAE T0627 85 :P 1wzdA 71 :S T0627 97 :NIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEGAT 1wzdA 72 :LLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDL T0627 165 :WSAVVCSTG 1wzdA 138 :SGGQVIARM T0627 175 :YAEAFAE 1wzdA 147 :MQRHYGV T0627 184 :RKKSMKW 1wzdA 154 :DPEALGF T0627 195 :AQYD 1wzdA 161 :YHFE T0627 199 :DAHPWEALEIICTLVGN 1wzdA 166 :IAKLKVYKDEYREKLNN T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQ 1wzdA 184 :ELSDEQREHLLKEATDAFVFNHQVFADLGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=675 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wzdA/T0627-1wzdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1wzdA/T0627-1wzdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wzdA read from 1wzdA/T0627-1wzdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wzdA in template set T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTK 1wzdA 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRAS T0627 79 :TRFGRH 1wzdA 74 :DPALNR T0627 87 :EDMARRW 1wzdA 80 :AEVLARD T0627 109 :VNWCAAHD 1wzdA 87 :LDKLNGSS T0627 119 :LE 1wzdA 97 :RS T0627 124 :DQRVAPELHALSHWCWQTSSSDSLAVAMAAT 1wzdA 99 :RITASPAVIDYVNRLEEIRDNVDGPALVAHH T0627 156 :YAIEGATGEWSAVVCSTGVYAEAFAEET 1wzdA 130 :YVRYLGDLSGGQVIARMMQRHYGVDPEA T0627 194 :HAQYDD 1wzdA 160 :FYHFEG T0627 200 :AHPWEALEIICTLVGN 1wzdA 167 :AKLKVYKDEYREKLNN T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCI 1wzdA 184 :ELSDEQREHLLKEATDAFVFNHQVFADLG Number of specific fragments extracted= 10 number of extra gaps= 0 total=685 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iw0A/T0627-1iw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iw0A expands to /projects/compbio/data/pdb/1iw0.pdb.gz 1iw0A:# T0627 read from 1iw0A/T0627-1iw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iw0A read from 1iw0A/T0627-1iw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iw0A to template set # found chain 1iw0A in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1iw0A)G7 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTK 1iw0A 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRAS T0627 82 :GRHPG 1iw0A 67 :GFAES T0627 97 :NIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAI 1iw0A 72 :LLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRY T0627 160 :GATGEWSAVVC 1iw0A 134 :LGDLSGGQVIA T0627 173 :GVYAEAFAEE 1iw0A 145 :RMMQRHYGVD T0627 185 :KKSMKWLKMHAQYDDAHPW 1iw0A 155 :PEALGFYHFEGIAKLKVYK T0627 204 :EALEIICTL 1iw0A 175 :EYREKLNNL T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCI 1iw0A 184 :ELSDEQREHLLKEATDAFVFNHQVFADLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=693 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iw0A/T0627-1iw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1iw0A/T0627-1iw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iw0A read from 1iw0A/T0627-1iw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iw0A in template set Warning: unaligning (T0627)A19 because first residue in template chain is (1iw0A)G7 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFG 1iw0A 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAE T0627 85 :P 1iw0A 71 :S T0627 97 :NIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMA 1iw0A 72 :LLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVA T0627 154 :TNYAI 1iw0A 128 :HHYVR T0627 165 :WSAVVCSTGV 1iw0A 133 :YLGDLSGGQV T0627 175 :YAEAFAE 1iw0A 147 :MQRHYGV T0627 184 :RKKSMKWLKM 1iw0A 154 :DPEALGFYHF T0627 197 :YDDAHPWEALEIICTLVGN 1iw0A 164 :EGIAKLKVYKDEYREKLNN T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCI 1iw0A 184 :ELSDEQREHLLKEATDAFVFNHQVFADLG Number of specific fragments extracted= 9 number of extra gaps= 0 total=702 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iw0A/T0627-1iw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1iw0A/T0627-1iw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iw0A read from 1iw0A/T0627-1iw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iw0A in template set Warning: unaligning (T0627)Q245 because last residue in template chain is (1iw0A)K213 T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTK 1iw0A 8 :LAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRAS T0627 79 :TRFGRH 1iw0A 74 :DPALNR T0627 87 :EDMARR 1iw0A 80 :AEVLAR T0627 104 :HADYWV 1iw0A 86 :DLDKLN T0627 116 :D 1iw0A 92 :G T0627 118 :TLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEGA 1iw0A 93 :SSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGD T0627 163 :GEWSAVVCSTGVYAEAFAEETRKKS 1iw0A 137 :LSGGQVIARMMQRHYGVDPEALGFY T0627 196 :QYDD 1iw0A 162 :HFEG T0627 200 :AHPWEALEIICTLVGN 1iw0A 167 :AKLKVYKDEYREKLNN T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCI 1iw0A 184 :ELSDEQREHLLKEATDAFVFNHQVFADLG Number of specific fragments extracted= 10 number of extra gaps= 0 total=712 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i9tA/T0627-3i9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i9tA expands to /projects/compbio/data/pdb/3i9t.pdb.gz 3i9tA:Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 3i9tA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3i9tA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3i9tA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3i9tA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3i9tA # T0627 read from 3i9tA/T0627-3i9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i9tA read from 3i9tA/T0627-3i9tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i9tA to template set # found chain 3i9tA in template set Warning: unaligning (T0627)P18 because first residue in template chain is (3i9tA)Q11 Warning: unaligning (T0627)E37 because of BadResidue code BAD_PEPTIDE in next template residue (3i9tA)S31 Warning: unaligning (T0627)H38 because of BadResidue code BAD_PEPTIDE at template residue (3i9tA)S31 Warning: unaligning (T0627)K248 because last residue in template chain is (3i9tA)T222 T0627 19 :AWAQQLINDCSPAKARVV 3i9tA 12 :DLSEALKEATKEVHIRAE T0627 39 :ELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGED 3i9tA 32 :EFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERNKQNPVYAPLYFPE T0627 101 :ELNHADYWVNWCAAH 3i9tA 82 :ELHRRAALEQDMAFW T0627 117 :VTLEDLHDQRVAPELHALSHWCWQTSSS 3i9tA 97 :YGPHWQEAIPYTPATQHYVKRLHEVGGT T0627 146 :SLAVAMAATNYAI 3i9tA 125 :HPELLVAHAYTRY T0627 160 :GATGEWSAVVC 3i9tA 138 :LGDLSGGQVLK T0627 173 :GVYAEAFAEET 3i9tA 149 :KIAQKAMALPS T0627 185 :KK 3i9tA 160 :SG T0627 191 :LKMHAQYDDAHPWEALEIICTLVGN 3i9tA 164 :LAFFTFPSIDNPTKFKQLYRARMNT T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQLD 3i9tA 190 :EMTPEVKHRVTEEAKTAFLLNIELFEELQALL Number of specific fragments extracted= 10 number of extra gaps= 1 total=722 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i9tA/T0627-3i9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3i9tA/T0627-3i9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i9tA read from 3i9tA/T0627-3i9tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i9tA in template set Warning: unaligning (T0627)P18 because first residue in template chain is (3i9tA)Q11 Warning: unaligning (T0627)E37 because of BadResidue code BAD_PEPTIDE in next template residue (3i9tA)S31 Warning: unaligning (T0627)H38 because of BadResidue code BAD_PEPTIDE at template residue (3i9tA)S31 Warning: unaligning (T0627)K248 because last residue in template chain is (3i9tA)T222 T0627 19 :AWAQQLINDCSPAKARVV 3i9tA 12 :DLSEALKEATKEVHIRAE T0627 39 :ELYQQMRDAKLSPQIMRQYLIGGWPV 3i9tA 32 :EFMRNFQKGQVSREGFKLVMASLYHI T0627 69 :AVYMAKNLTKT 3i9tA 58 :YTALEEEIERN T0627 82 :GRHPG 3i9tA 69 :KQNPV T0627 98 :IR 3i9tA 74 :YA T0627 100 :VELNHADYWVNWCAAH 3i9tA 81 :EELHRRAALEQDMAFW T0627 116 :DVTLEDL 3i9tA 98 :GPHWQEA T0627 125 :QRVAPELHALSHWCWQTSSSDS 3i9tA 105 :IPYTPATQHYVKRLHEVGGTHP T0627 147 :LAVAMAATNYAI 3i9tA 129 :LVAHAYTRYLGD T0627 163 :G 3i9tA 141 :L T0627 165 :WSAVVCSTG 3i9tA 142 :SGGQVLKKI T0627 175 :YAEAFAEETRKKSMKW 3i9tA 151 :AQKAMALPSSGEGLAF T0627 194 :HAQYDDAHPWEALEIICTLVGN 3i9tA 167 :FTFPSIDNPTKFKQLYRARMNT T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQLD 3i9tA 190 :EMTPEVKHRVTEEAKTAFLLNIELFEELQALL Number of specific fragments extracted= 14 number of extra gaps= 1 total=736 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i9tA/T0627-3i9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 3i9tA/T0627-3i9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i9tA read from 3i9tA/T0627-3i9tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i9tA in template set Warning: unaligning (T0627)E37 because of BadResidue code BAD_PEPTIDE in next template residue (3i9tA)S31 Warning: unaligning (T0627)H38 because of BadResidue code BAD_PEPTIDE at template residue (3i9tA)S31 Warning: unaligning (T0627)K248 because last residue in template chain is (3i9tA)T222 T0627 20 :WAQQLINDCSPAKARVV 3i9tA 13 :LSEALKEATKEVHIRAE T0627 39 :ELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKN 3i9tA 32 :EFMRNFQKGQVSREGFKLVMASLYHIYTALEEEIERN T0627 77 :TKTRFGRH 3i9tA 72 :PVYAPLYF T0627 87 :EDMA 3i9tA 80 :PEEL T0627 91 :R 3i9tA 86 :R T0627 103 :NHADYWVNWCAAHD 3i9tA 87 :AALEQDMAFWYGPH T0627 119 :LEDL 3i9tA 102 :QEAI T0627 126 :RVAPELHALSHWCWQTS 3i9tA 106 :PYTPATQHYVKRLHEVG T0627 143 :SSDSLAVAMAATNYAIE 3i9tA 125 :HPELLVAHAYTRYLGDL T0627 164 :EWSAVVCSTGVYAEAFAEET 3i9tA 142 :SGGQVLKKIAQKAMALPSSG T0627 195 :AQYD 3i9tA 167 :FTFP T0627 200 :AHPWEALEIICTLVGN 3i9tA 173 :DNPTKFKQLYRARMNT T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQLD 3i9tA 190 :EMTPEVKHRVTEEAKTAFLLNIELFEELQALL Number of specific fragments extracted= 13 number of extra gaps= 1 total=749 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xjzA/T0627-1xjzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xjzA expands to /projects/compbio/data/pdb/1xjz.pdb.gz 1xjzA:# T0627 read from 1xjzA/T0627-1xjzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjzA read from 1xjzA/T0627-1xjzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xjzA to template set # found chain 1xjzA in template set Warning: unaligning (T0627)Y17 because first residue in template chain is (1xjzA)P10 Warning: unaligning (T0627)V249 because last residue in template chain is (1xjzA)H223 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKN 1xjzA 11 :QDLSEALKEATKEVHTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVALEEEIERN T0627 76 :LTK 1xjzA 74 :FAP T0627 82 :GRH 1xjzA 77 :VYF T0627 87 :E 1xjzA 80 :P T0627 100 :VELNHADYWVNWCAAH 1xjzA 81 :EELHRKAALEQDLAFW T0627 117 :VTLEDLHDQRVAPELHALSHWCWQTSSSD 1xjzA 97 :YGPRWQEVIPYTPAMQRYVKRLHEVGRTE T0627 146 :SLAVAMAATN 1xjzA 127 :ELLVAHAYTR T0627 158 :I 1xjzA 137 :Y T0627 160 :GATGEWSAVVC 1xjzA 138 :LADLSGGQVLK T0627 173 :GVYAEAFAEETRKKSMKWLK 1xjzA 149 :KIAQKALDLPSSGEGLAFFT T0627 196 :QYDDAHPWEALEIICTLVGN 1xjzA 169 :FPNIASATKFKQLYRSRMNS T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQLDK 1xjzA 190 :EMTPAVRQRVIEEAKTAFLLNIQLFEELQELLT Number of specific fragments extracted= 12 number of extra gaps= 0 total=761 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xjzA/T0627-1xjzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1xjzA/T0627-1xjzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjzA read from 1xjzA/T0627-1xjzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjzA in template set Warning: unaligning (T0627)Y17 because first residue in template chain is (1xjzA)P10 Warning: unaligning (T0627)V249 because last residue in template chain is (1xjzA)H223 T0627 18 :PAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKN 1xjzA 11 :QDLSEALKEATKEVHTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVALEEEIERN T0627 76 :LTKTRF 1xjzA 74 :FAPVYF T0627 99 :RVELNHADYWVNWCAAH 1xjzA 80 :PEELHRKAALEQDLAFW T0627 117 :VTLEDLHDQRVAPELHALSHWCWQTSSS 1xjzA 97 :YGPRWQEVIPYTPAMQRYVKRLHEVGRT T0627 146 :SLAVAMAATNYAIEGATG 1xjzA 125 :EPELLVAHAYTRYLADLS T0627 165 :WSAVVCST 1xjzA 143 :GGQVLKKI T0627 175 :YAEAFAEETRKKSMKW 1xjzA 151 :AQKALDLPSSGEGLAF T0627 195 :AQYD 1xjzA 167 :FTFP T0627 199 :DAHPWEALEIICTLVGN 1xjzA 172 :IASATKFKQLYRSRMNS T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQLDK 1xjzA 190 :EMTPAVRQRVIEEAKTAFLLNIQLFEELQELLT Number of specific fragments extracted= 10 number of extra gaps= 0 total=771 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xjzA/T0627-1xjzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0627 read from 1xjzA/T0627-1xjzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xjzA read from 1xjzA/T0627-1xjzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xjzA in template set T0627 20 :WAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNL 1xjzA 13 :LSEALKEATKEVHTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVALEEEIERNK T0627 78 :KTRFGRHPGE 1xjzA 73 :VFAPVYFPEE T0627 88 :DMARRWLM 1xjzA 87 :AALEQDLA T0627 111 :W 1xjzA 95 :F T0627 114 :AHDVTLED 1xjzA 96 :WYGPRWQE T0627 124 :DQRVAPELHALSHWCWQTS 1xjzA 104 :VIPYTPAMQRYVKRLHEVG T0627 143 :SSDSLAVAMAATNYAIEG 1xjzA 125 :EPELLVAHAYTRYLADLS T0627 165 :WSAVVCSTGVYAEAFAE 1xjzA 143 :GGQVLKKIAQKALDLPS T0627 194 :HAQYDD 1xjzA 166 :FFTFPN T0627 200 :AHPWEALEIICTLVGN 1xjzA 173 :ASATKFKQLYRSRMNS T0627 216 :KPSLQLQAELRQAVTKSYDYMYLFLERCIQL 1xjzA 190 :EMTPAVRQRVIEEAKTAFLLNIQLFEELQEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=782 Will force an alignment to be made, even if fragment is small Number of alignments=78 # command:CPU_time= 28.111 sec, elapsed time= 77.044 sec. # command:DEBUG: alignment library has 78 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 78 # Adding 2187 constraints to all_contacts Done adding distance constraints # command:CPU_time= 28.236 sec, elapsed time= 77.177 sec. # command:Reading probabilities from T0627.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 75.300 Optimizing... Probability sum: -439.132, CN propb: -439.132 weights: 0.404 constraints: 423 # command:CPU_time= 64.379 sec, elapsed time= 113.332 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 423 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 423 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1764 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1764 # 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= 64.412 sec, elapsed time= 114.669 sec. # command: