# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0317 numbered 1 through 163 Created new target T0317 from T0317.a2m # command:CPU_time= 6.428 sec, elapsed time= 6.456 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wrmA/T0317-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wrmA expands to /projects/compbio/data/pdb/1wrm.pdb.gz 1wrmA:# T0317 read from 1wrmA/T0317-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0317-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wrmA to template set # found chain 1wrmA in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGP 1wrmA 3 :NGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPM # choosing archetypes in rotamer library T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQT 1wrmA 45 :LEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 1wrmA/T0317-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1wrmA/T0317-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0317-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrmA in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVS 1wrmA 3 :NGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVH T0317 46 :QQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1wrmA 39 :DSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEK T0317 148 :TLQA 1wrmA 145 :QYRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=5 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 1wrmA/T0317-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1wrmA/T0317-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0317-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrmA in template set T0317 6 :AAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQP 1wrmA -1 :PMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSAR T0317 50 :PRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQT 1wrmA 43 :PMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=7 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 1yz4A/T0317-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yz4A expands to /projects/compbio/data/pdb/1yz4.pdb.gz 1yz4A:# T0317 read from 1yz4A/T0317-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0317-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yz4A to template set # found chain 1yz4A in template set T0317 7 :APPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGP 1yz4A 1 :MGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIHESPQPL T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 45 :LQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW T0317 148 :TLQ 1yz4A 145 :KLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 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 1yz4A/T0317-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yz4A/T0317-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0317-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yz4A in template set T0317 7 :APPPFARVAPALFIGNARAAGATELLVRAGITLCVNVS 1yz4A 1 :MGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIH T0317 46 :QQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 39 :ESPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW T0317 148 :TLQA 1yz4A 145 :KLRR Number of specific fragments extracted= 3 number of extra gaps= 0 total=13 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 1yz4A/T0317-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yz4A/T0317-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0317-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yz4A in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSR 1yz4A -1 :SHMGNGMTKVLPGLYLGNFIDAKDLDQLGRNKITHIISIHE T0317 47 :QPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1yz4A 40 :SPQPLLQDITYLRIPVADTPEVPIKKHFKECINFIHCCRLNGGNCLVHSFAGISRSTTIVTAYVMTVTGLGWRDVLEAIKATRPIANPNPGFRQQLEEFGW Number of specific fragments extracted= 2 number of extra gaps= 0 total=15 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 1vhrA/T0317-1vhrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vhrA expands to /projects/compbio/data/pdb/1vhr.pdb.gz 1vhrA:# T0317 read from 1vhrA/T0317-1vhrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhrA read from 1vhrA/T0317-1vhrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vhrA to template set # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 2 :GTSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1vhrA 21 :GCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMH T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 80 :DSGITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSAR 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNR T0317 131 :VAEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 159 :EIGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=19 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 1vhrA/T0317-1vhrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1vhrA/T0317-1vhrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhrA read from 1vhrA/T0317-1vhrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 2 :GTSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1vhrA 21 :GCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 82 :GITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSAR 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNR T0317 131 :VAEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 159 :EIGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=23 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 1vhrA/T0317-1vhrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1vhrA/T0317-1vhrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhrA read from 1vhrA/T0317-1vhrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhrA in template set Warning: unaligning (T0317)R157 because last residue in template chain is (1vhrA)P185 T0317 3 :TSEAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1vhrA 22 :CYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1vhrA 82 :GITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARP 1vhrA 116 :KNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNRE T0317 132 :AEPNLGFWAQLQKYEQTLQAQAILP 1vhrA 160 :IGPNDGFLAQLCQLNDRLAKEGKLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=27 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 1mkp/T0317-1mkp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mkp expands to /projects/compbio/data/pdb/1mkp.pdb.gz 1mkp:Warning: there is no chain 1mkp will retry with 1mkpA # T0317 read from 1mkp/T0317-1mkp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkp read from 1mkp/T0317-1mkp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mkp to template set # found chain 1mkp in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLF T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 250 :AGEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 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 1mkp/T0317-1mkp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1mkp/T0317-1mkp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkp read from 1mkp/T0317-1mkp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkp in template set Warning: unaligning (T0317)P8 because first residue in template chain is (1mkp)A204 T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRA 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFE T0317 53 :PGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 251 :GEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 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 1mkp/T0317-1mkp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1mkp/T0317-1mkp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkp read from 1mkp/T0317-1mkp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkp in template set T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 1mkp 205 :SFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFEN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQ 1mkp 252 :EFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFER Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 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 1d5rA/T0317-1d5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d5rA expands to /projects/compbio/data/pdb/1d5r.pdb.gz 1d5rA:# T0317 read from 1d5rA/T0317-1d5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5rA read from 1d5rA/T0317-1d5rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d5rA to template set # found chain 1d5rA in template set T0317 9 :PPFARVAPALFIGNARA 1d5rA 36 :GFPAERLEGVYRNNIDD T0317 29 :TELLVRA 1d5rA 54 :VRFLDSK T0317 36 :GITLCVNVS 1d5rA 63 :NHYKIYNLC T0317 45 :RQQPGPRAPGVAELRVPVFDDPAEDL 1d5rA 73 :ERHYDTAKFNCRVAQYPFEDHNPPQL T0317 72 :THLEPTCAAMEAAVRDG 1d5rA 99 :ELIKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSARPV 1d5rA 146 :LKAQEALDFYGEVRTR T0317 132 :AEPNLGFWAQLQKYEQTLQAQAILPRE 1d5rA 165 :GVTIPSQRRYVYYYSYLLKNHLDYRPV Number of specific fragments extracted= 8 number of extra gaps= 0 total=41 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 1d5rA/T0317-1d5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1d5rA/T0317-1d5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5rA read from 1d5rA/T0317-1d5rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d5rA in template set T0317 9 :PPFARVAPALFIGNA 1d5rA 36 :GFPAERLEGVYRNNI T0317 26 :AGATELLVR 1d5rA 51 :DDVVRFLDS T0317 35 :AGITLCVNVS 1d5rA 62 :KNHYKIYNLC T0317 45 :RQQPGPRAPGVAELRVPVFDDPAEDLLT 1d5rA 73 :ERHYDTAKFNCRVAQYPFEDHNPPQLEL T0317 74 :LEPTCAAMEAAVRDG 1d5rA 101 :IKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSAR 1d5rA 146 :LKAQEALDFYGEVR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQAILPR 1d5rA 163 :KKGVTIPSQRRYVYYYSYLLKNHLDYRP Number of specific fragments extracted= 8 number of extra gaps= 0 total=49 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 1d5rA/T0317-1d5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1d5rA/T0317-1d5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d5rA read from 1d5rA/T0317-1d5rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d5rA in template set T0317 3 :TSEAAPPPFARVAPALFIGNARAAGA 1d5rA 17 :QEDGFDLDLTYIYPNIIAMGFPAERL T0317 29 :TELLVRA 1d5rA 50 :IDDVVRF T0317 36 :GITLCVNVSRQQPGPRAP 1d5rA 63 :NHYKIYNLCAERHYDTAK T0317 54 :GVAELRVPVFD 1d5rA 82 :NCRVAQYPFED T0317 66 :PAEDLLTHLEPTCAAMEAAVRDG 1d5rA 93 :HNPPQLELIKPFCEDLDQWLSED T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRG 1d5rA 118 :HVAAIHCKAGKGRTGVMICAYLLHRGK T0317 116 :HSLDRAFQMVKSAR 1d5rA 146 :LKAQEALDFYGEVR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQAILPRE 1d5rA 163 :KKGVTIPSQRRYVYYYSYLLKNHLDYRPV Number of specific fragments extracted= 8 number of extra gaps= 0 total=57 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 1oheA/T0317-1oheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oheA expands to /projects/compbio/data/pdb/1ohe.pdb.gz 1oheA:# T0317 read from 1oheA/T0317-1oheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oheA read from 1oheA/T0317-1oheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oheA to template set # found chain 1oheA in template set Warning: unaligning (T0317)L155 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1oheA)G380 Warning: unaligning (T0317)P156 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1oheA)G380 T0317 6 :AAPPPFARVAPALFIGNA 1oheA 228 :CGPHSRARLESGYHQHSP T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1oheA 246 :ETYIQYFKNHNVTTIIRLNKRMYDAK T0317 52 :APGVAELRVPVFDDPAEDL 1oheA 275 :DAGFDHHDLFFADGSTPTD T0317 72 :THLEPTCAAME 1oheA 294 :AIVKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNL 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGP T0317 138 :FWAQLQKYEQTLQ 1oheA 356 :QQQFLVMKQTNLW T0317 151 :AQAI 1oheA 375 :RQKL Number of specific fragments extracted= 7 number of extra gaps= 1 total=64 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 1oheA/T0317-1oheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1oheA/T0317-1oheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oheA read from 1oheA/T0317-1oheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oheA in template set T0317 6 :AAPPPFARVAPA 1oheA 228 :CGPHSRARLESG T0317 20 :IGNARAAGATELLVRAGITLCVNVSRQQPGPR 1oheA 240 :YHQHSPETYIQYFKNHNVTTIIRLNKRMYDAK T0317 52 :APGVAELRVPVFDDPAEDLLT 1oheA 275 :DAGFDHHDLFFADGSTPTDAI T0317 74 :LEPTCAAME 1oheA 296 :VKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAE 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSV T0317 135 :NLGFWAQLQKYEQTLQAQA 1oheA 353 :IGPQQQFLVMKQTNLWLEG Number of specific fragments extracted= 6 number of extra gaps= 0 total=70 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 1oheA/T0317-1oheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1oheA/T0317-1oheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oheA read from 1oheA/T0317-1oheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oheA in template set T0317 29 :TELLVRAGITLCVNVSRQQPGP 1oheA 249 :IQYFKNHNVTTIIRLNKRMYDA T0317 54 :GVAELRVPVFD 1oheA 277 :GFDHHDLFFAD T0317 66 :PAEDLLTHLEPTCAAME 1oheA 288 :GSTPTDAIVKEFLDICE T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNL 1oheA 307 :EGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGP T0317 138 :FWAQLQKYEQTLQAQA 1oheA 356 :QQQFLVMKQTNLWLEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 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 1rxdA/T0317-1rxdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rxdA expands to /projects/compbio/data/pdb/1rxd.pdb.gz 1rxdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1rxdA/T0317-1rxdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxdA read from 1rxdA/T0317-1rxdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rxdA to template set # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 18 :LFIGNARAAG 1rxdA 19 :LITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1rxdA 33 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVP 1rxdA 59 :KEGIHVLDWP T0317 66 :PAEDL 1rxdA 73 :APPSN T0317 72 :THLEPTCAAMEAAVR 1rxdA 78 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1rxdA 117 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1rxdA 141 :NSKQLLYLEK T0317 154 :ILPRE 1rxdA 151 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=84 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 1rxdA/T0317-1rxdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1rxdA/T0317-1rxdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxdA read from 1rxdA/T0317-1rxdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 20 :IGNARA 1rxdA 21 :THNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1rxdA 30 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 54 :GVAELRVP 1rxdA 61 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1rxdA 120 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1rxdA 141 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=91 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 1rxdA/T0317-1rxdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1rxdA/T0317-1rxdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxdA read from 1rxdA/T0317-1rxdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxdA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rxdA)G72 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rxdA)G72 T0317 16 :PALFIGNARAAGA 1rxdA 17 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1rxdA 33 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVP 1rxdA 61 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1rxdA 73 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1rxdA 95 :PGCCIAVHCVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1rxdA 121 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQ 1rxdA 140 :FNSKQLLYLE T0317 152 :QAILPREP 1rxdA 150 :KYRPKMRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=99 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 2c46A/T0317-2c46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c46A expands to /projects/compbio/data/pdb/2c46.pdb.gz 2c46A:Skipped atom 119, because occupancy 0.5 <= existing 0.500 in 2c46A Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2c46A Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2c46A # T0317 read from 2c46A/T0317-2c46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c46A read from 2c46A/T0317-2c46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c46A to template set # found chain 2c46A in template set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c46A)P119 T0317 4 :SEAAPPPFARVAPA 2c46A 29 :TMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGITL 2c46A 43 :NRFHPSMLSNYLKSLKVKM T0317 40 :CVNVSRQQPGPR 2c46A 64 :LVDLTNTSRFYD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2c46A 81 :KEGIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :Q 2c46A 178 :G T0317 151 :AQAILPREPIDP 2c46A 182 :EAPPPPLLPDWC Number of specific fragments extracted= 7 number of extra gaps= 0 total=106 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 2c46A/T0317-2c46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2c46A/T0317-2c46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c46A read from 2c46A/T0317-2c46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c46A in template set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c46A)P119 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c46A)P119 T0317 3 :TSEAAPPPFARVAPA 2c46A 28 :KTMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGIT 2c46A 43 :NRFHPSMLSNYLKSLKVK T0317 39 :LCVNVSRQQPGPRAP 2c46A 63 :LLVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2c46A 83 :GIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 151 :AQAILPREPID 2c46A 180 :IEEAPPPPLLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 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 2c46A/T0317-2c46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2c46A/T0317-2c46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c46A read from 2c46A/T0317-2c46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c46A in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c46A)P119 T0317 2 :GTSEAAPPPFARVAPALFIGNA 2c46A 8 :PRWLNCPRRGQPVAGRFLPLKT T0317 29 :TELLVRAGITL 2c46A 51 :SNYLKSLKVKM T0317 40 :CVNVSRQQPGPRAP 2c46A 64 :LVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAME 2c46A 83 :GIKYIKLQCKGHGECPTTENTETFIRLCE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 2c46A 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :Q 2c46A 178 :G T0317 151 :AQAILPREPI 2c46A 180 :IEEAPPPPLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=119 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 1yn9A/T0317-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yn9A expands to /projects/compbio/data/pdb/1yn9.pdb.gz 1yn9A:Skipped atom 2, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 4, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 6, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 8, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 10, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 12, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 14, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 16, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 175, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 177, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 596, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 598, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 600, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 635, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 637, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 639, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 641, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 643, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 645, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 647, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 941, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 943, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 945, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 947, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1yn9A # T0317 read from 1yn9A/T0317-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0317-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yn9A to template set # found chain 1yn9A in template set T0317 14 :VAPALF 1yn9A 28 :LRPELF T0317 20 :IGNARAAGATELLVR 1yn9A 36 :VTSEEDVWTAEQIVK T0317 35 :AGITLCVNVSRQQPGPR 1yn9A 53 :PSIGAIIDLTNTSKYYD T0317 52 :APGVAELRVPVFDDPAEDL 1yn9A 75 :RAGLLYKKIQVPGQTLPPE T0317 72 :THLEPTCAAMEAAVR 1yn9A 94 :SIVQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=125 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 1yn9A/T0317-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yn9A/T0317-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0317-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yn9A in template set T0317 4 :SEAAPPPFARVA 1yn9A 26 :TPLRPELFAYVT T0317 22 :NARAAGATELLVR 1yn9A 38 :SEEDVWTAEQIVK T0317 35 :AGITLCVNVSRQQPGPRAP 1yn9A 53 :PSIGAIIDLTNTSKYYDGV T0317 54 :GVAELRVPVFDDPAEDLLT 1yn9A 77 :GLLYKKIQVPGQTLPPESI T0317 74 :LEPTCAAMEAAVR 1yn9A 96 :VQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 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 1yn9A/T0317-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yn9A/T0317-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0317-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yn9A in template set T0317 22 :NARAAGATELLVRA 1yn9A 38 :SEEDVWTAEQIVKQ T0317 36 :GITLCVNVSRQQPGPRAP 1yn9A 54 :SIGAIIDLTNTSKYYDGV T0317 54 :GVAELRVPVFDDPAED 1yn9A 77 :GLLYKKIQVPGQTLPP T0317 71 :LTHLEPTCAAMEAAVR 1yn9A 93 :ESIVQEFIDTVKEFTE T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQ 1yn9A 111 :PGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLL Number of specific fragments extracted= 5 number of extra gaps= 0 total=136 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 2b49A/T0317-2b49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b49A expands to /projects/compbio/data/pdb/2b49.pdb.gz 2b49A:Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1568, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1614, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1618, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2b49A # T0317 read from 2b49A/T0317-2b49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b49A read from 2b49A/T0317-2b49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b49A to template set # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARAAGA 2b49A 716 :ATQGPLPHTCA T0317 29 :TELLVRAGITLCVNVS 2b49A 729 :WQVVWDQKLSLIVMLT T0317 45 :RQQPGPR 2b49A 756 :QYWPDPP T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRH 2b49A 799 :HTVTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMC T0317 114 :RG 2b49A 864 :RN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 868 :IYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 6 number of extra gaps= 0 total=142 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 2b49A/T0317-2b49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2b49A/T0317-2b49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b49A read from 2b49A/T0317-2b49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARA 2b49A 716 :ATQGPLPH T0317 26 :AGATELLVRAGITLCVNVS 2b49A 726 :AQFWQVVWDQKLSLIVMLT T0317 49 :GPR 2b49A 758 :WPD T0317 54 :GVAELRVP 2b49A 803 :HLQYVAWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAY 2b49A 811 :DHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTME T0317 110 :LMRHRGHS 2b49A 860 :CLTERNLP T0317 118 :LDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 870 :PLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 7 number of extra gaps= 0 total=149 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 2b49A/T0317-2b49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2b49A/T0317-2b49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b49A read from 2b49A/T0317-2b49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b49A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2b49A)E904 T0317 18 :LFIGNARAAGA 2b49A 716 :ATQGPLPHTCA T0317 29 :TELLVRAGITLCVNVSR 2b49A 729 :WQVVWDQKLSLIVMLTT T0317 46 :QQPGPRAP 2b49A 755 :HQYWPDPP T0317 54 :GVAEL 2b49A 800 :TVTHL T0317 59 :RVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCT 2b49A 806 :YVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVT T0317 108 :AYLMRHRG 2b49A 858 :AMCLTERN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2b49A 868 :IYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYE Number of specific fragments extracted= 7 number of extra gaps= 0 total=156 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 1fpzA/T0317-1fpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fpzA expands to /projects/compbio/data/pdb/1fpz.pdb.gz 1fpzA:# T0317 read from 1fpzA/T0317-1fpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fpzA read from 1fpzA/T0317-1fpzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fpzA to template set # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 15 :APAL 1fpzA 53 :FKDV T0317 22 :NARAAGATELLVRAGITLCVNVS 1fpzA 57 :RRNVQKDTEELKSCGIQDIFVFC T0317 45 :RQQPG 1fpzA 87 :YRVPN T0317 52 :APGVAELRVPVFDDPAEDL 1fpzA 98 :QCGIITHHHPIADGGTPDI T0317 72 :THLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRG 1fpzA 117 :ASCCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSD T0317 116 :HSLDRAFQMVKSARPV 1fpzA 162 :ISPEQAIDSLRDLRGS T0317 132 :AEPNLGFWAQLQKYEQTLQAQ 1fpzA 179 :AIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=163 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 1fpzA/T0317-1fpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1fpzA/T0317-1fpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fpzA read from 1fpzA/T0317-1fpzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 22 :NARAAGATELLVRAGITLCVNVS 1fpzA 57 :RRNVQKDTEELKSCGIQDIFVFC T0317 45 :RQQP 1fpzA 87 :YRVP T0317 54 :GVAELRVPVFDDPAEDLLT 1fpzA 100 :GIITHHHPIADGGTPDIAS T0317 74 :LEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGH 1fpzA 119 :CCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSDT T0317 117 :SLDRAFQMVKSAR 1fpzA 163 :SPEQAIDSLRDLR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQ 1fpzA 177 :SGAIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 6 number of extra gaps= 0 total=169 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 1fpzA/T0317-1fpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1fpzA/T0317-1fpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fpzA read from 1fpzA/T0317-1fpzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fpzA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1fpzA)L200 T0317 23 :ARAAGATELLVRAGITLCVNVSR 1fpzA 58 :RNVQKDTEELKSCGIQDIFVFCT T0317 54 :GVAELRVPVFDDPAED 1fpzA 100 :GIITHHHPIADGGTPD T0317 71 :LTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRG 1fpzA 116 :IASCCEIMEELTTCLKNYRKTLIHSYGGLGRSCLVAACLLLYLSD T0317 116 :HSLDRAFQMVKSAR 1fpzA 162 :ISPEQAIDSLRDLR T0317 130 :PVAEPNLGFWAQLQKYEQTLQAQ 1fpzA 177 :SGAIQTIKQYNYLHEFRDKLAAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=174 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 2fh7A/T0317-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fh7A expands to /projects/compbio/data/pdb/2fh7.pdb.gz 2fh7A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1796, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1798, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1800, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1802, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1804, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1806, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1808, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3718, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3720, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3722, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3724, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3726, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3728, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3730, because occupancy 0.500 <= existing 0.500 in 2fh7A # T0317 read from 2fh7A/T0317-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0317-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fh7A to template set # found chain 2fh7A in template set Warning: unaligning (T0317)D87 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 18 :LFIGNARAAGA 2fh7A 1752 :ATQGPLAETTE T0317 29 :TELLVRAGITLCVNVS 2fh7A 1765 :WRMLWENNSTIVVMLT T0317 47 :QPGPR 2fh7A 1794 :WPAER T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1834 :RTVRQFQFTDWPEQGVPKSGEGFIDFIGQVHKTKE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2fh7A 1874 :GPISVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 2fh7A 1899 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 7 number of extra gaps= 1 total=181 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 2fh7A/T0317-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2fh7A/T0317-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0317-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fh7A in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 18 :LFIGNARA 2fh7A 1752 :ATQGPLAE T0317 26 :AGA 2fh7A 1761 :TED T0317 29 :TELLVRAGITLCVNVS 2fh7A 1765 :WRMLWENNSTIVVMLT T0317 47 :QPGP 2fh7A 1795 :PAER T0317 54 :GVAELRVP 2fh7A 1838 :QFQFTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1846 :EQGVPKSGEGFIDFIGQVHKTKE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2fh7A 1874 :GPISVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 2fh7A 1899 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 9 number of extra gaps= 0 total=190 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 2fh7A/T0317-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2fh7A/T0317-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0317-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fh7A in template set Warning: unaligning (T0317)D87 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0317)Q152 because last residue in template chain is (2fh7A)S1942 T0317 4 :SEAAPPPFARVAPA 2fh7A 1731 :EGSDYINASFIDGY T0317 18 :LFIGNARAAGA 2fh7A 1751 :IATQGPLAETT T0317 29 :TELLVRAGITLCVNVSR 2fh7A 1765 :WRMLWENNSTIVVMLTK T0317 46 :QQPGPRAP 2fh7A 1791 :HQYWPAER T0317 54 :GVAELRV 2fh7A 1830 :DGQSRTV T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVR 2fh7A 1843 :DWPEQGVPKSGEGFIDFIGQVHKTKE T0317 88 :GGSCLVYCKNGRSRSAAVCTA 2fh7A 1873 :DGPISVHCSAGVGRTGVFITL T0317 109 :YLMRHRG 2fh7A 1898 :ERMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2fh7A 1906 :VDIFQTVKMLRTQRPAMVQTEDEYQFCYQAALEYLG Number of specific fragments extracted= 9 number of extra gaps= 1 total=199 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 2bzlA/T0317-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bzlA expands to /projects/compbio/data/pdb/2bzl.pdb.gz 2bzlA:Skipped atom 1123, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1137, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1139, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 2bzlA # T0317 read from 2bzlA/T0317-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0317-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bzlA to template set # found chain 2bzlA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVS 2bzlA 994 :WQMVWEQGVNVIAMVT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 2bzlA 1067 :RTVWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=206 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 2bzlA/T0317-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bzlA/T0317-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0317-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bzlA in template set Warning: unaligning (T0317)R51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bzlA)K1029 Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVS 2bzlA 994 :WQMVWEQGVNVIAMVT T0317 49 :GP 2bzlA 1023 :WP T0317 54 :GVAELRVP 2bzlA 1071 :HLQYTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2bzlA 1079 :DHGCPEDVQGFLSYLEEIQSVRR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 9 number of extra gaps= 0 total=215 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 2bzlA/T0317-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bzlA/T0317-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0317-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bzlA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (2bzlA)S1184 T0317 18 :LFIGNARAAGA 2bzlA 981 :ATQGPLPHTCH T0317 29 :TELLVRAGITLCVNVSRQ 2bzlA 994 :WQMVWEQGVNVIAMVTAE T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2bzlA 1069 :VWHLQYTDWPDHGCPEDVQGFLSYLEEIQSVRR T0317 87 :DG 2bzlA 1108 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bzlA 1115 :PPIVVHCSAGVGRTGVLILSELMIY T0317 114 :RG 2bzlA 1143 :HN T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2bzlA 1147 :VEVPMMLRLLREQRMFMIQTIAQYKFVYQVLIQFLQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=222 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 2f71A/T0317-2f71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f71A expands to /projects/compbio/data/pdb/2f71.pdb.gz 2f71A:Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 166, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 170, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 172, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 174, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 176, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 178, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1977, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1981, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1983, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2352, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2481, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2493, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2503, because occupancy 0.500 <= existing 0.500 in 2f71A # T0317 read from 2f71A/T0317-2f71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f71A read from 2f71A/T0317-2f71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f71A to template set # found chain 2f71A in template set T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2f71A 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 2f71A 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 2f71A 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 2f71A 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2f71A 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHRG 2f71A 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=230 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 2f71A/T0317-2f71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2f71A/T0317-2f71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f71A read from 2f71A/T0317-2f71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f71A in template set Warning: unaligning (T0317)I154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f71A)G283 Warning: unaligning (T0317)L155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f71A)G283 T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2f71A 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRA 2f71A 126 :PQKEEKEM T0317 54 :GVAELRVP 2f71A 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 2f71A 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 2f71A 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2f71A 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHRG 2f71A 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI T0317 156 :P 2f71A 284 :D Number of specific fragments extracted= 10 number of extra gaps= 1 total=240 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 2f71A/T0317-2f71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2f71A/T0317-2f71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f71A read from 2f71A/T0317-2f71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f71A in template set T0317 18 :LFIGNARAAGA 2f71A 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 2f71A 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVPVFDDPAEDLL 2f71A 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 2f71A 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 2f71A 209 :GPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHRG 2f71A 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 2f71A 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 7 number of extra gaps= 0 total=247 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 1pa1A/T0317-1pa1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pa1A expands to /projects/compbio/data/pdb/1pa1.pdb.gz 1pa1A:Skipped atom 52, because occupancy 0.460 <= existing 0.490 in 1pa1A Skipped atom 56, because occupancy 0.570 <= existing 0.570 in 1pa1A Skipped atom 58, because occupancy 0.500 <= existing 0.550 in 1pa1A Skipped atom 60, because occupancy 0.510 <= existing 0.540 in 1pa1A Skipped atom 62, because occupancy 0.410 <= existing 0.430 in 1pa1A Skipped atom 64, because occupancy 0.450 <= existing 0.470 in 1pa1A Skipped atom 66, because occupancy 0.470 <= existing 0.470 in 1pa1A Skipped atom 443, because occupancy 0.540 <= existing 0.540 in 1pa1A Skipped atom 447, because occupancy 0.460 <= existing 0.500 in 1pa1A Skipped atom 451, because occupancy 0.440 <= existing 0.520 in 1pa1A Skipped atom 455, because occupancy 0.260 <= existing 0.420 in 1pa1A Skipped atom 548, because occupancy 0.500 <= existing 0.580 in 1pa1A Skipped atom 550, because occupancy 0.380 <= existing 0.720 in 1pa1A Skipped atom 554, because occupancy 0.190 <= existing 0.370 in 1pa1A Skipped atom 558, because occupancy 0.340 <= existing 0.630 in 1pa1A Skipped atom 560, because occupancy 0.350 <= existing 0.570 in 1pa1A Skipped atom 562, because occupancy 0.280 <= existing 0.590 in 1pa1A Skipped atom 564, because occupancy 0.380 <= existing 0.630 in 1pa1A Skipped atom 566, because occupancy 0.380 <= existing 0.470 in 1pa1A Skipped atom 570, because occupancy 0.420 <= existing 0.890 in 1pa1A Skipped atom 572, because occupancy 0.270 <= existing 0.420 in 1pa1A Skipped atom 574, because occupancy 0.190 <= existing 0.620 in 1pa1A Skipped atom 578, because occupancy 0.560 <= existing 0.670 in 1pa1A Skipped atom 580, because occupancy 0.610 <= existing 0.990 in 1pa1A Skipped atom 590, because occupancy 0.430 <= existing 0.580 in 1pa1A Skipped atom 592, because occupancy 0.320 <= existing 0.500 in 1pa1A Skipped atom 594, because occupancy 0.330 <= existing 0.490 in 1pa1A Skipped atom 596, because occupancy 0.210 <= existing 0.510 in 1pa1A Skipped atom 598, because occupancy 0.160 <= existing 0.270 in 1pa1A Skipped atom 606, because occupancy 0.300 <= existing 0.480 in 1pa1A Skipped atom 608, because occupancy 0.090 <= existing 0.300 in 1pa1A Skipped atom 610, because occupancy 0.090 <= existing 0.470 in 1pa1A Skipped atom 618, because occupancy 0.300 <= existing 0.310 in 1pa1A Skipped atom 805, because occupancy 0.440 <= existing 0.570 in 1pa1A Skipped atom 971, because occupancy 0.480 <= existing 0.540 in 1pa1A Skipped atom 975, because occupancy 0.480 <= existing 0.480 in 1pa1A Skipped atom 977, because occupancy 0.440 <= existing 0.670 in 1pa1A Skipped atom 1079, because occupancy 0.440 <= existing 0.460 in 1pa1A Skipped atom 1081, because occupancy 0.470 <= existing 0.590 in 1pa1A Skipped atom 1085, because occupancy 0.530 <= existing 0.530 in 1pa1A Skipped atom 1091, because occupancy 0.560 <= existing 0.610 in 1pa1A Skipped atom 1093, because occupancy 0.510 <= existing 0.540 in 1pa1A Skipped atom 1097, because occupancy 0.490 <= existing 0.560 in 1pa1A Skipped atom 1101, because occupancy 0.430 <= existing 0.470 in 1pa1A Skipped atom 1103, because occupancy 0.590 <= existing 0.660 in 1pa1A Skipped atom 1423, because occupancy 0.510 <= existing 0.550 in 1pa1A Skipped atom 1427, because occupancy 0.420 <= existing 0.550 in 1pa1A Skipped atom 1431, because occupancy 0.550 <= existing 0.620 in 1pa1A Skipped atom 1433, because occupancy 0.630 <= existing 0.750 in 1pa1A Skipped atom 1455, because occupancy 0.400 <= existing 0.620 in 1pa1A Skipped atom 1457, because occupancy 0.470 <= existing 0.540 in 1pa1A Skipped atom 1459, because occupancy 0.520 <= existing 0.630 in 1pa1A Skipped atom 1618, because occupancy 0.280 <= existing 0.760 in 1pa1A Skipped atom 1620, because occupancy 0.300 <= existing 0.730 in 1pa1A Skipped atom 1622, because occupancy 0.290 <= existing 0.630 in 1pa1A Skipped atom 1624, because occupancy 0.100 <= existing 0.670 in 1pa1A Skipped atom 1626, because occupancy 0.270 <= existing 0.590 in 1pa1A Skipped atom 1628, because occupancy 0.380 <= existing 0.670 in 1pa1A Skipped atom 1630, because occupancy 0.220 <= existing 0.830 in 1pa1A Skipped atom 1632, because occupancy 0.160 <= existing 0.870 in 1pa1A Skipped atom 1634, because occupancy 0.110 <= existing 0.710 in 1pa1A Skipped atom 1636, because occupancy 0.150 <= existing 0.760 in 1pa1A Skipped atom 1638, because occupancy 0.160 <= existing 0.760 in 1pa1A Skipped atom 1640, because occupancy 0.210 <= existing 0.740 in 1pa1A Skipped atom 1642, because occupancy 0.190 <= existing 0.830 in 1pa1A Skipped atom 1644, because occupancy 0.250 <= existing 0.670 in 1pa1A Skipped atom 1646, because occupancy 0.180 <= existing 0.890 in 1pa1A Skipped atom 1648, because occupancy 0.390 <= existing 0.910 in 1pa1A Skipped atom 1650, because occupancy 0.080 <= existing 0.800 in 1pa1A Skipped atom 1652, because occupancy 0.140 <= existing 0.790 in 1pa1A Skipped atom 1654, because occupancy 0.210 <= existing 0.810 in 1pa1A Skipped atom 1656, because occupancy 0.300 <= existing 0.730 in 1pa1A Skipped atom 1658, because occupancy 0.080 <= existing 0.890 in 1pa1A Skipped atom 1660, because occupancy 0.110 <= existing 0.940 in 1pa1A Skipped atom 1662, because occupancy 0.050 <= existing 0.910 in 1pa1A Skipped atom 1664, because occupancy 0.050 <= existing 0.870 in 1pa1A Skipped atom 1666, because occupancy 0.360 <= existing 0.820 in 1pa1A Skipped atom 1668, because occupancy 0.340 <= existing 0.880 in 1pa1A Skipped atom 1670, because occupancy 0.050 <= existing 0.860 in 1pa1A Skipped atom 1672, because occupancy 0.050 <= existing 0.830 in 1pa1A Skipped atom 1674, because occupancy 0.350 <= existing 0.810 in 1pa1A Skipped atom 1676, because occupancy 0.050 <= existing 0.830 in 1pa1A Skipped atom 1678, because occupancy 0.210 <= existing 0.650 in 1pa1A Skipped atom 1680, because occupancy 0.150 <= existing 0.800 in 1pa1A Skipped atom 1682, because occupancy 0.390 <= existing 0.840 in 1pa1A Skipped atom 1684, because occupancy 0.140 <= existing 0.760 in 1pa1A Skipped atom 1686, because occupancy 0.280 <= existing 0.700 in 1pa1A Skipped atom 1688, because occupancy 0.210 <= existing 0.760 in 1pa1A Skipped atom 1690, because occupancy 0.060 <= existing 0.660 in 1pa1A Skipped atom 1692, because occupancy 0.480 <= existing 0.620 in 1pa1A Skipped atom 1694, because occupancy 0.390 <= existing 0.710 in 1pa1A Skipped atom 1696, because occupancy 0.360 <= existing 0.810 in 1pa1A Skipped atom 1698, because occupancy 0.300 <= existing 0.680 in 1pa1A Skipped atom 1700, because occupancy 0.370 <= existing 0.510 in 1pa1A Skipped atom 1702, because occupancy 0.050 <= existing 0.470 in 1pa1A Skipped atom 1704, because occupancy 0.450 <= existing 0.840 in 1pa1A Skipped atom 1706, because occupancy 0.320 <= existing 0.960 in 1pa1A Skipped atom 1710, because occupancy 0.340 <= existing 0.650 in 1pa1A Skipped atom 1712, because occupancy 0.230 <= existing 0.870 in 1pa1A Skipped atom 1714, because occupancy 0.330 <= existing 0.610 in 1pa1A Skipped atom 1716, because occupancy 0.110 <= existing 0.420 in 1pa1A Skipped atom 1718, because occupancy 0.420 <= existing 0.500 in 1pa1A Skipped atom 1720, because occupancy 0.460 <= existing 0.580 in 1pa1A Skipped atom 1722, because occupancy 0.370 <= existing 0.500 in 1pa1A Skipped atom 1726, because occupancy 0.240 <= existing 0.750 in 1pa1A Skipped atom 1728, because occupancy 0.130 <= existing 0.810 in 1pa1A Skipped atom 1730, because occupancy 0.610 <= existing 0.750 in 1pa1A Skipped atom 1732, because occupancy 0.440 <= existing 0.800 in 1pa1A Skipped atom 1734, because occupancy 0.320 <= existing 0.760 in 1pa1A Skipped atom 1736, because occupancy 0.280 <= existing 0.830 in 1pa1A Skipped atom 1738, because occupancy 0.430 <= existing 0.760 in 1pa1A Skipped atom 1740, because occupancy 0.220 <= existing 0.720 in 1pa1A Skipped atom 1742, because occupancy 0.340 <= existing 0.840 in 1pa1A Skipped atom 1744, because occupancy 0.410 <= existing 0.930 in 1pa1A Skipped atom 1746, because occupancy 0.050 <= existing 0.670 in 1pa1A Skipped atom 1748, because occupancy 0.200 <= existing 0.900 in 1pa1A Skipped atom 1750, because occupancy 0.270 <= existing 0.870 in 1pa1A Skipped atom 1752, because occupancy 0.340 <= existing 0.730 in 1pa1A Skipped atom 1754, because occupancy 0.530 <= existing 0.660 in 1pa1A Skipped atom 1756, because occupancy 0.280 <= existing 0.780 in 1pa1A Skipped atom 1758, because occupancy 0.330 <= existing 0.790 in 1pa1A Skipped atom 1760, because occupancy 0.050 <= existing 0.780 in 1pa1A Skipped atom 1762, because occupancy 0.190 <= existing 0.690 in 1pa1A Skipped atom 1764, because occupancy 0.350 <= existing 0.740 in 1pa1A Skipped atom 1766, because occupancy 0.480 <= existing 0.540 in 1pa1A Skipped atom 1768, because occupancy 0.330 <= existing 0.740 in 1pa1A Skipped atom 1770, because occupancy 0.310 <= existing 0.850 in 1pa1A Skipped atom 1774, because occupancy 0.160 <= existing 0.260 in 1pa1A Skipped atom 1776, because occupancy 0.280 <= existing 0.750 in 1pa1A Skipped atom 1778, because occupancy 0.210 <= existing 0.780 in 1pa1A Skipped atom 1780, because occupancy 0.290 <= existing 0.700 in 1pa1A Skipped atom 1782, because occupancy 0.090 <= existing 0.630 in 1pa1A Skipped atom 1784, because occupancy 0.320 <= existing 0.660 in 1pa1A Skipped atom 1786, because occupancy 0.300 <= existing 0.710 in 1pa1A Skipped atom 1788, because occupancy 0.190 <= existing 0.620 in 1pa1A Skipped atom 1790, because occupancy 0.200 <= existing 0.730 in 1pa1A Skipped atom 1792, because occupancy 0.230 <= existing 0.710 in 1pa1A Skipped atom 1794, because occupancy 0.220 <= existing 0.550 in 1pa1A Skipped atom 1796, because occupancy 0.170 <= existing 0.690 in 1pa1A Skipped atom 1798, because occupancy 0.350 <= existing 0.710 in 1pa1A Skipped atom 1800, because occupancy 0.080 <= existing 0.680 in 1pa1A Skipped atom 1802, because occupancy 0.340 <= existing 0.750 in 1pa1A Skipped atom 1804, because occupancy 0.280 <= existing 0.800 in 1pa1A Skipped atom 1819, because occupancy 0.420 <= existing 0.470 in 1pa1A Skipped atom 1821, because occupancy 0.440 <= existing 0.450 in 1pa1A Skipped atom 2055, because occupancy 0.490 <= existing 0.540 in 1pa1A Skipped atom 2059, because occupancy 0.450 <= existing 0.480 in 1pa1A Skipped atom 2063, because occupancy 0.520 <= existing 0.530 in 1pa1A Skipped atom 2067, because occupancy 0.250 <= existing 0.750 in 1pa1A Skipped atom 2069, because occupancy 0.330 <= existing 0.710 in 1pa1A Skipped atom 2071, because occupancy 0.300 <= existing 0.680 in 1pa1A Skipped atom 2073, because occupancy 0.400 <= existing 0.710 in 1pa1A Skipped atom 2075, because occupancy 0.160 <= existing 0.700 in 1pa1A Skipped atom 2107, because occupancy 0.440 <= existing 0.640 in 1pa1A Skipped atom 2109, because occupancy 0.470 <= existing 0.560 in 1pa1A Skipped atom 2111, because occupancy 0.510 <= existing 0.510 in 1pa1A Skipped atom 2113, because occupancy 0.500 <= existing 0.530 in 1pa1A Skipped atom 2115, because occupancy 0.430 <= existing 0.530 in 1pa1A Skipped atom 2262, because occupancy 0.460 <= existing 0.510 in 1pa1A Skipped atom 2266, because occupancy 0.470 <= existing 0.520 in 1pa1A Skipped atom 2268, because occupancy 0.510 <= existing 0.520 in 1pa1A Skipped atom 2272, because occupancy 0.500 <= existing 0.660 in 1pa1A Skipped atom 2274, because occupancy 0.380 <= existing 0.570 in 1pa1A Skipped atom 2276, because occupancy 0.450 <= existing 0.590 in 1pa1A Skipped atom 2328, because occupancy 0.310 <= existing 0.320 in 1pa1A Skipped atom 2331, because occupancy 0.240 <= existing 0.400 in 1pa1A Skipped atom 2334, because occupancy 0.320 <= existing 0.340 in 1pa1A Skipped atom 2335, because occupancy 0.290 <= existing 0.340 in 1pa1A Skipped atom 2338, because occupancy 0.310 <= existing 0.350 in 1pa1A Skipped atom 2340, because occupancy 0.320 <= existing 0.320 in 1pa1A Skipped atom 2343, because occupancy 0.250 <= existing 0.410 in 1pa1A Skipped atom 2344, because occupancy 0.330 <= existing 0.410 in 1pa1A Skipped atom 2347, because occupancy 0.330 <= existing 0.350 in 1pa1A Skipped atom 2349, because occupancy 0.360 <= existing 0.460 in 1pa1A Skipped atom 2350, because occupancy 0.200 <= existing 0.460 in 1pa1A Skipped atom 2602, because occupancy 0.390 <= existing 0.400 in 1pa1A Skipped atom 2604, because occupancy 0.370 <= existing 0.370 in 1pa1A Skipped atom 2606, because occupancy 0.320 <= existing 0.330 in 1pa1A Skipped atom 2610, because occupancy 0.360 <= existing 0.410 in 1pa1A # T0317 read from 1pa1A/T0317-1pa1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pa1A read from 1pa1A/T0317-1pa1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pa1A to template set # found chain 1pa1A in template set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1pa1A 596 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1pa1A 626 :PQKEEKE T0317 52 :APGVAELRVPVFD 1pa1A 669 :REILHFHYTTWPD T0317 67 :AEDLLTHLEPTCAAMEA 1pa1A 684 :VPESPASFLNFLFKVRE T0317 84 :AVRDG 1pa1A 703 :SLSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1pa1A 709 :GPVVVHDSAGIGRSGTFCLAD T0317 110 :LMRHRG 1pa1A 734 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=256 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 1pa1A/T0317-1pa1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1pa1A/T0317-1pa1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pa1A read from 1pa1A/T0317-1pa1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pa1A in template set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1pa1A 596 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRAP 1pa1A 626 :PQKEEKEMI T0317 54 :GVAELRVP 1pa1A 673 :HFHYTTWP T0317 64 :D 1pa1A 681 :D T0317 67 :AEDLLTHLEPTCAAMEAA 1pa1A 684 :VPESPASFLNFLFKVRES T0317 85 :VRDG 1pa1A 704 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1pa1A 709 :GPVVVHDSAGIGRSGTFCLAD T0317 110 :LMRHRG 1pa1A 734 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDS Number of specific fragments extracted= 10 number of extra gaps= 1 total=266 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 1pa1A/T0317-1pa1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1pa1A/T0317-1pa1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pa1A read from 1pa1A/T0317-1pa1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pa1A in template set Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pa1A)G683 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pa1A)G683 T0317 18 :LFIGNARAAGA 1pa1A 583 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1pa1A 596 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVPVFD 1pa1A 671 :ILHFHYTTWPD T0317 67 :AEDLL 1pa1A 684 :VPESP T0317 75 :EPTCAAMEAAVRDG 1pa1A 689 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1pa1A 709 :GPVVVHDSAGIGRSGTFCLA T0317 109 :YLMRHRG 1pa1A 733 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQ 1pa1A 744 :VDIKKVLLEMRKFRMGLIQTADQLRFSY Number of specific fragments extracted= 8 number of extra gaps= 1 total=274 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 1wchA/T0317-1wchA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wchA expands to /projects/compbio/data/pdb/1wch.pdb.gz 1wchA:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1921, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2200, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2202, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2204, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2206, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2371, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2373, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2375, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2377, because occupancy 0.500 <= existing 0.500 in 1wchA Skipped atom 2379, because occupancy 0.500 <= existing 0.500 in 1wchA # T0317 read from 1wchA/T0317-1wchA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wchA read from 1wchA/T0317-1wchA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wchA to template set # found chain 1wchA in template set T0317 18 :LFIGNARAAGA 1wchA 2281 :ACQGPLPTTVG T0317 29 :TELLVRAGITLCVNVS 1wchA 2294 :WQMIWEQKSTVIAMMT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 1wchA 2366 :RHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIH T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLG T0317 114 :RG 1wchA 2430 :QD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=280 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 1wchA/T0317-1wchA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1wchA/T0317-1wchA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wchA read from 1wchA/T0317-1wchA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wchA in template set T0317 18 :LFIGNARA 1wchA 2281 :ACQGPLPT T0317 26 :AGATEL 1wchA 2290 :VGDFWQ T0317 32 :LVRAGITLCVNVS 1wchA 2297 :IWEQKSTVIAMMT T0317 46 :QQPGPRAP 1wchA 2320 :QRYWPNIL T0317 54 :GVAELRVP 1wchA 2367 :HISHLNFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAA 1wchA 2376 :WPDHDTPSQPDDLLTFISYMRHI T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLM 1wchA 2399 :HRSGPIITHCSAGIGRSGTLICIDVV T0317 112 :RHRG 1wchA 2428 :ISQD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTR Number of specific fragments extracted= 9 number of extra gaps= 0 total=289 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 1wchA/T0317-1wchA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1wchA/T0317-1wchA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wchA read from 1wchA/T0317-1wchA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wchA in template set T0317 17 :ALFIGNARAAGA 1wchA 2280 :IACQGPLPTTVG T0317 29 :TELLVRAGITLCVNVSRQ 1wchA 2294 :WQMIWEQKSTVIAMMTQE T0317 47 :QPGPR 1wchA 2322 :YWPNI T0317 54 :GVAELRVP 1wchA 2367 :HISHLNFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAA 1wchA 2376 :WPDHDTPSQPDDLLTFISYMRHI T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRHR 1wchA 2400 :RSGPIITHCSAGIGRSGTLICIDVVLGL T0317 115 :G 1wchA 2431 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1wchA 2434 :FDISDLVRCMRLQRHGMVQTEDQYIFCYQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=297 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 1zckA/T0317-1zckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zckA expands to /projects/compbio/data/pdb/1zck.pdb.gz 1zckA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1zckA/T0317-1zckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zckA read from 1zckA/T0317-1zckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zckA to template set # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 18 :LFIGNARAAG 1zckA 20 :LITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1zckA 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVP 1zckA 60 :KEGIHVLDWP T0317 66 :PAEDL 1zckA 74 :APPSN T0317 72 :THLEPTCAAMEAAVR 1zckA 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1zckA 96 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1zckA 118 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zckA 142 :NSKQLLYLEK T0317 154 :ILPRE 1zckA 152 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=306 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 1zckA/T0317-1zckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1zckA/T0317-1zckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zckA read from 1zckA/T0317-1zckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)P66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 19 :FIGNARA 1zckA 21 :ITHNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1zckA 31 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 54 :GVAELRVP 1zckA 62 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zckA 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zckA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zckA 142 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=313 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 1zckA/T0317-1zckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1zckA/T0317-1zckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zckA read from 1zckA/T0317-1zckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zckA in template set Warning: unaligning (T0317)V62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zckA)G73 Warning: unaligning (T0317)D65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zckA)G73 T0317 16 :PALFIGNARAAGA 1zckA 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1zckA 34 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVP 1zckA 62 :GIHVLDWP T0317 67 :AEDLLTHLEPTCAAMEAAVR 1zckA 74 :APPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1zckA 96 :PGCCIAVHCVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1zckA 122 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQ 1zckA 141 :FNSKQLLYLE T0317 152 :QAILPREP 1zckA 151 :KYRPKMRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=321 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 2bv5A/T0317-2bv5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bv5A expands to /projects/compbio/data/pdb/2bv5.pdb.gz 2bv5A:Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 602, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 604, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 2bv5A Bad short name: OCD for alphabet: pdb_atoms Bad short name: OCD for alphabet: pdb_atoms Skipped atom 1796, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1798, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1804, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2039, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2047, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2049, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2051, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2141, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2145, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2147, because occupancy 0.500 <= existing 0.500 in 2bv5A # T0317 read from 2bv5A/T0317-2bv5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bv5A read from 2bv5A/T0317-2bv5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bv5A to template set # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0317)I20 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 11 :FARVAPAL 2bv5A 337 :GYGGEEKV T0317 21 :GNARAAGA 2bv5A 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVS 2bv5A 360 :WRMVWQEHTPIIVMIT T0317 45 :RQQPGPR 2bv5A 385 :TEYWPEE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 2bv5A 425 :RGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLV 2bv5A 466 :APIIV T0317 97 :NGRSRSAAVCTAYLMRH 2bv5A 474 :AGIGRTGCFIATSICCQ T0317 114 :RG 2bv5A 495 :EG T0317 116 :HSLDRAFQMVKSARPV 2bv5A 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQ 2bv5A 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 10 number of extra gaps= 2 total=331 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 2bv5A/T0317-2bv5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bv5A/T0317-2bv5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bv5A read from 2bv5A/T0317-2bv5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0317)I20 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 11 :FARVAPAL 2bv5A 337 :GYGGEEKV T0317 21 :GNARA 2bv5A 350 :GPIVS T0317 26 :AGATEL 2bv5A 356 :VADFWR T0317 32 :LVRAGITLCVNVS 2bv5A 363 :VWQEHTPIIVMIT T0317 49 :GPR 2bv5A 386 :EYW T0317 54 :GVAELRVP 2bv5A 426 :GLKHYWFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVRDG 2bv5A 435 :WPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLV 2bv5A 466 :APIIV T0317 97 :NGRSRSAAVCTAY 2bv5A 474 :AGIGRTGCFIATS T0317 110 :LMRHRGH 2bv5A 491 :QLRQEGV T0317 117 :SLDRAFQMVKSARPV 2bv5A 499 :DILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQ 2bv5A 516 :QTCEQYQFVHHVMSLYEKQ Number of specific fragments extracted= 12 number of extra gaps= 2 total=343 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 2bv5A/T0317-2bv5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bv5A/T0317-2bv5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bv5A read from 2bv5A/T0317-2bv5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bv5A in template set Warning: unaligning (T0317)F19 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 Warning: unaligning (T0317)R51 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv5A)K383 Warning: unaligning (T0317)A52 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv5A)K383 Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bv5A)S473 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bv5A)S473 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I515 T0317 20 :I 2bv5A 347 :A T0317 21 :GNARAAGA 2bv5A 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVSRQQPGP 2bv5A 360 :WRMVWQEHTPIIVMITNIEEMN T0317 53 :P 2bv5A 384 :C T0317 54 :GVAELRVP 2bv5A 426 :GLKHYWFT T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVRDGGS 2bv5A 435 :WPDQKTPDRAPPLLHLVREVEEAAQQEGP T0317 91 :CLV 2bv5A 468 :IIV T0317 97 :NGRSRSAAVCTAYL 2bv5A 474 :AGIGRTGCFIATSI T0317 111 :MRHRG 2bv5A 492 :LRQEG T0317 116 :HSLDRAFQMVKSARPV 2bv5A 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQK 2bv5A 516 :QTCEQYQFVHH Number of specific fragments extracted= 11 number of extra gaps= 3 total=354 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 1x24A/T0317-1x24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x24A expands to /projects/compbio/data/pdb/1x24.pdb.gz 1x24A:# T0317 read from 1x24A/T0317-1x24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x24A read from 1x24A/T0317-1x24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x24A to template set # found chain 1x24A in template set T0317 18 :LFIGNARAAG 1x24A 20 :LITHNPTNAT T0317 28 :A 1x24A 31 :N T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1x24A 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFDDPAEDL 1x24A 60 :KEGIHVLDWPFDDGAPPSN T0317 72 :THLEPTCAAMEAAVR 1x24A 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1x24A 96 :PGCCIAVHCVAGLGRAPVLVAL T0317 110 :LMRHRGHSLDRAFQMVKSARPVAE 1x24A 118 :ALIEGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1x24A 142 :NSKQLLYLEK T0317 154 :ILPRE 1x24A 152 :YRPKM Number of specific fragments extracted= 9 number of extra gaps= 0 total=363 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 1x24A/T0317-1x24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1x24A/T0317-1x24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x24A read from 1x24A/T0317-1x24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x24A in template set T0317 22 :NARAAGATELLVRAGITLCVNVSRQQPGPR 1x24A 27 :NATLNKFIEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFD 1x24A 60 :KEGIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1x24A 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1x24A 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1x24A 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1x24A 142 :NSKQLLYLEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=369 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 1x24A/T0317-1x24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1x24A/T0317-1x24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x24A read from 1x24A/T0317-1x24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x24A in template set Warning: unaligning (T0317)F11 because first residue in template chain is (1x24A)P9 T0317 12 :ARVA 1x24A 10 :VEVT T0317 16 :PALFIGNARAAGA 1x24A 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPG 1x24A 34 :IEELKKYGVTTIVRVCEATYD T0317 54 :GVAELRVPVFD 1x24A 62 :GIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1x24A 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1x24A 96 :PGCCIAVHCVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARP 1x24A 121 :EGGMKYEDAVQFIRQKRR T0317 132 :AEPNLGFWAQLQ 1x24A 139 :GAFNSKQLLYLE T0317 152 :QAILPREP 1x24A 151 :KYRPKMRL Number of specific fragments extracted= 9 number of extra gaps= 0 total=378 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 1zclA/T0317-1zclA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zclA expands to /projects/compbio/data/pdb/1zcl.pdb.gz 1zclA:# T0317 read from 1zclA/T0317-1zclA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zclA read from 1zclA/T0317-1zclA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zclA to template set # found chain 1zclA in template set T0317 15 :APALFIGNARAAG 1zclA 17 :MRFLITHNPTNAT T0317 29 :TELLVRAGITLCVNVSRQQPGPR 1zclA 34 :IEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFDDPAEDL 1zclA 60 :KEGIHVLDWPFDDGAPPSN T0317 72 :THLEPTCAAMEAAVR 1zclA 79 :QIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQKY 1zclA 142 :NSKQLLYLEKY T0317 155 :LPREP 1zclA 153 :RPKMR Number of specific fragments extracted= 8 number of extra gaps= 0 total=386 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 1zclA/T0317-1zclA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1zclA/T0317-1zclA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zclA read from 1zclA/T0317-1zclA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zclA in template set T0317 16 :PALFIGNARA 1zclA 18 :RFLITHNPTN T0317 26 :AGATELLVRAGITLCVNVSRQQPGPR 1zclA 31 :NKFIEELKKYGVTTIVRVCEATYDTT T0317 52 :APGVAELRVPVFD 1zclA 60 :KEGIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1zclA 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLM 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALI T0317 113 :HRGHSLDRAFQMVKSARPVAE 1zclA 121 :EGGMKYEDAVQFIRQKRRGAF T0317 135 :NLGFWAQLQK 1zclA 142 :NSKQLLYLEK Number of specific fragments extracted= 7 number of extra gaps= 0 total=393 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 1zclA/T0317-1zclA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1zclA/T0317-1zclA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zclA read from 1zclA/T0317-1zclA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zclA in template set Warning: unaligning (T0317)F11 because first residue in template chain is (1zclA)P9 T0317 12 :ARVA 1zclA 10 :VEVT T0317 16 :PALFIGNARAAGA 1zclA 18 :RFLITHNPTNATL T0317 29 :TELLVRAGITLCVNVSRQQPGP 1zclA 34 :IEELKKYGVTTIVRVCEATYDT T0317 54 :GVAELRVPVFD 1zclA 62 :GIHVLDWPFDD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1zclA 73 :GAPPSNQIVDDWLSLVKIKFR T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMR 1zclA 96 :PGCCIAVHSVAGLGRAPVLVALALIE T0317 114 :RGHSLDRAFQMVKSARPVA 1zclA 122 :GGMKYEDAVQFIRQKRRGA T0317 134 :PNLGFWAQLQK 1zclA 141 :FNSKQLLYLEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=401 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 1i9sA/T0317-1i9sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i9sA expands to /projects/compbio/data/pdb/1i9s.pdb.gz 1i9sA:Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 86, because occupancy 0.400 <= existing 0.600 in 1i9sA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 1i9sA Skipped atom 1121, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1123, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1125, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 1i9sA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 1i9sA # T0317 read from 1i9sA/T0317-1i9sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9sA read from 1i9sA/T0317-1i9sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i9sA to template set # found chain 1i9sA in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 4 :SEAAPPPFARVAPA 1i9sA 29 :TMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAG 1i9sA 43 :NRFHPSMLSNYLKSLK T0317 37 :ITLCVNVSRQQPGPR 1i9sA 61 :MSLLVDLTNTSRFYD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1i9sA 81 :KEGIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :QAQAILPREPIDPE 1i9sA 178 :GDIEEAPPPPVLPD Number of specific fragments extracted= 6 number of extra gaps= 0 total=407 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 1i9sA/T0317-1i9sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1i9sA/T0317-1i9sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9sA read from 1i9sA/T0317-1i9sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i9sA in template set Warning: unaligning (T0317)A84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i9sA)P119 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 3 :TSEAAPPPFARVAPA 1i9sA 28 :KTMLGPRYDSQVAEE T0317 21 :GNARAAGATELLVRAGIT 1i9sA 43 :NRFHPSMLSNYLKSLKVK T0317 39 :LCVNVSRQQPGPRAP 1i9sA 63 :LLVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1i9sA 83 :GIKYIKLQCKGHGECPTTENTETFIRLCER T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 151 :AQAILPREPID 1i9sA 180 :IEEAPPPPVLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=413 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 1i9sA/T0317-1i9sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1i9sA/T0317-1i9sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9sA read from 1i9sA/T0317-1i9sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i9sA in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i9sA)P119 T0317 2 :GTSEAAPPPFARVAPALFIGNARA 1i9sA 8 :PRWLNCPRRGQPVAGRFLPLKTML T0317 26 :AGA 1i9sA 33 :PRY T0317 29 :TELLVRAGITL 1i9sA 51 :SNYLKSLKVKM T0317 40 :CVNVSRQQPGPRAP 1i9sA 64 :LVDLTNTSRFYDRN T0317 54 :GVAELRVPVFDDPAEDLLTHLEPTCAAME 1i9sA 83 :GIKYIKLQCKGHGECPTTENTETFIRLCE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYE 1i9sA 120 :ELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRY T0317 150 :QAQAILPREPIDPE 1i9sA 178 :GDIEEAPPPPVLPD Number of specific fragments extracted= 7 number of extra gaps= 0 total=420 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 1xriA/T0317-1xriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xriA expands to /projects/compbio/data/pdb/1xri.pdb.gz 1xriA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1xriA/T0317-1xriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xriA read from 1xriA/T0317-1xriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xriA to template set # found chain 1xriA in template set Warning: unaligning (T0317)S4 because first residue in template chain is (1xriA)H52 T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPES T0317 53 :PGVAELRVPVFDDPAE 1xriA 107 :NGIRLFQFGIEGNKEP T0317 69 :DL 1xriA 127 :PD T0317 72 :THLEPTCAAM 1xriA 129 :HKIRMALKVL T0317 85 :VRDG 1xriA 139 :LDEK T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSAR 1xriA 164 :LRKLQKWCLTSIFDEYQRFA T0317 131 :VAEPNLGFWAQLQ 1xriA 184 :AAKARVSDQRFME Number of specific fragments extracted= 8 number of extra gaps= 0 total=428 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 1xriA/T0317-1xriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1xriA/T0317-1xriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xriA read from 1xriA/T0317-1xriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xriA in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPG 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYP T0317 54 :GVAELRVPVFDDPAEDL 1xriA 108 :GIRLFQFGIEGNKEPFV T0317 71 :LTHLEPTCAAM 1xriA 128 :DHKIRMALKVL T0317 85 :VRDG 1xriA 139 :LDEK T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSAR 1xriA 164 :LRKLQKWCLTSIFDEYQRFA T0317 131 :VAEPNLGFWAQLQ 1xriA 184 :AAKARVSDQRFME Number of specific fragments extracted= 7 number of extra gaps= 0 total=435 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 1xriA/T0317-1xriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1xriA/T0317-1xriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xriA read from 1xriA/T0317-1xriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xriA in template set T0317 5 :EAAPPPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPG 1xriA 53 :LIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYP T0317 54 :GVAELRVPVFDDPAEDL 1xriA 108 :GIRLFQFGIEGNKEPFV T0317 71 :LTHLEPTCAAME 1xriA 128 :DHKIRMALKVLL T0317 89 :GSCLVYCKNGRSRSAAVCTA 1xriA 144 :HPVLIHCKRGKHRTGCLVGC T0317 110 :LMRHRGHSLDRAFQMVKSARP 1xriA 164 :LRKLQKWCLTSIFDEYQRFAA T0317 132 :AEPNLGFWAQLQ 1xriA 185 :AKARVSDQRFME Number of specific fragments extracted= 6 number of extra gaps= 0 total=441 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 1ywfA/T0317-1ywfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ywfA expands to /projects/compbio/data/pdb/1ywf.pdb.gz 1ywfA:# T0317 read from 1ywfA/T0317-1ywfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywfA read from 1ywfA/T0317-1ywfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ywfA to template set # found chain 1ywfA in template set T0317 14 :VAPA 1ywfA 22 :LRPG T0317 18 :LFIGNARA 1ywfA 27 :LFRSSELS T0317 26 :AGATELLVRAGITLCVNVS 1ywfA 38 :DAGRATLRRLGITDVADLR T0317 47 :QPGPRAPGVAELRVPVFD 1ywfA 65 :GPGRVPDGIDVHLLPFPD T0317 69 :DLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTA 1ywfA 134 :PTRNGAQRALHRVVTLLAAGRPVLTHCFAGKDRTGFVVAL T0317 110 :LMRHRGHSLDRAFQMVKS 1ywfA 174 :VLEAVGLDRDVIVADYLR T0317 132 :AEP 1ywfA 192 :SND T0317 138 :FWAQLQKYEQTLQAQAILPRE 1ywfA 195 :SVPQLRARISEMIQQRFDTEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=449 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 1ywfA/T0317-1ywfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ywfA/T0317-1ywfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywfA read from 1ywfA/T0317-1ywfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ywfA in template set Warning: unaligning (T0317)A67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywfA)S117 T0317 15 :APA 1ywfA 23 :RPG T0317 18 :LFIGNARA 1ywfA 27 :LFRSSELS T0317 26 :AGATELLVRAGITLCVNVS 1ywfA 38 :DAGRATLRRLGITDVADLR T0317 47 :QPGPRAPGVAELRVPVFDDP 1ywfA 65 :GPGRVPDGIDVHLLPFPDLA T0317 85 :VRDGGSCLVYCKNGRSRSAAVCTAY 1ywfA 150 :LAAGRPVLTHCFAGKDRTGFVVALV T0317 111 :MRHRGHSLDRAFQMVK 1ywfA 175 :LEAVGLDRDVIVADYL T0317 131 :VAEPN 1ywfA 191 :RSNDS T0317 139 :WAQLQKYEQTLQAQAILP 1ywfA 196 :VPQLRARISEMIQQRFDT Number of specific fragments extracted= 8 number of extra gaps= 0 total=457 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 1ywfA/T0317-1ywfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ywfA/T0317-1ywfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ywfA read from 1ywfA/T0317-1ywfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ywfA in template set Warning: unaligning (T0317)A67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ywfA)S117 T0317 16 :PALFIGNARAAGA 1ywfA 25 :GRLFRSSELSRLD T0317 29 :TELLVRAGITLCVNVSR 1ywfA 41 :RATLRRLGITDVADLRS T0317 47 :QPGPRAPGVAELRVPVFDDP 1ywfA 65 :GPGRVPDGIDVHLLPFPDLA T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1ywfA 152 :AGRPVLTHCFAGKDRTGFVVAL T0317 110 :LMRHRGHSLDRAFQMVKSARP 1ywfA 174 :VLEAVGLDRDVIVADYLRSND T0317 138 :FWAQLQKYEQTLQAQAI 1ywfA 195 :SVPQLRARISEMIQQRF Number of specific fragments extracted= 6 number of extra gaps= 0 total=463 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 1larA/T0317-1larA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1larA expands to /projects/compbio/data/pdb/1lar.pdb.gz 1larA:# T0317 read from 1larA/T0317-1larA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1larA read from 1larA/T0317-1larA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1larA to template set # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 18 :LFIGNARAAGATE 1larA 1683 :YIATQGPLAESTE T0317 31 :LLVRAGITLCVNVS 1larA 1700 :MLWEHNSTIIVMLT T0317 47 :QPGPR 1larA 1727 :WPAER T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1larA 1767 :RTIRQFQFTDWPEQGVPKTGEGFIDFIGQVHKTKE T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1larA 1807 :GPITVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 1larA 1832 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 8 number of extra gaps= 0 total=471 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 1larA/T0317-1larA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1larA/T0317-1larA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1larA read from 1larA/T0317-1larA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 18 :LFIGNARA 1larA 1685 :ATQGPLAE T0317 26 :AGATEL 1larA 1694 :TEDFWR T0317 32 :LVRAGITLCVNVS 1larA 1701 :LWEHNSTIIVMLT T0317 46 :QQP 1larA 1727 :WPA T0317 54 :GVAELRVP 1larA 1771 :QFQFTDWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1larA 1779 :EQGVPKTGEGFIDFIGQVHKTKE T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1larA 1807 :GPITVHCSAGVGRTGVFITLS T0317 110 :LMRHRG 1larA 1832 :RMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 10 number of extra gaps= 0 total=481 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 1larA/T0317-1larA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1larA/T0317-1larA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1larA read from 1larA/T0317-1larA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1larA in template set Warning: unaligning (T0317)A153 because last residue in template chain is (1larA)F1876 T0317 2 :GTSEAAPPPFARVAPA 1larA 1662 :GVEGSDYINASFLDGY T0317 18 :LFIGNARAAGA 1larA 1685 :ATQGPLAESTE T0317 29 :TELLVRAGITLCVNVSR 1larA 1698 :WRMLWEHNSTIIVMLTK T0317 46 :QQPGPRAP 1larA 1724 :HQYWPAER T0317 54 :GVAELRVP 1larA 1763 :DGQSRTIR T0317 62 :VFDDPAEDLLTHLEPTCAAMEAAVR 1larA 1774 :FTDWPEQGVPKTGEGFIDFIGQVHK T0317 87 :DG 1larA 1803 :FG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1larA 1807 :GPITVHCSAGVGRTGVFITL T0317 109 :YLMRHRG 1larA 1831 :ERMRYEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1larA 1839 :VDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGS Number of specific fragments extracted= 10 number of extra gaps= 0 total=491 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 2b3oA/T0317-2b3oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b3oA expands to /projects/compbio/data/pdb/2b3o.pdb.gz 2b3oA:# T0317 read from 2b3oA/T0317-2b3oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3oA read from 2b3oA/T0317-2b3oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b3oA to template set # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPA 2b3oA 308 :KNQLLGPDENAKT T0317 18 :LFIGNARA 2b3oA 322 :IASQGCLE T0317 26 :AGA 2b3oA 331 :TVN T0317 29 :TELLVRAGITLCVNVS 2b3oA 336 :WQMAWQENSRVIVMTT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2b3oA 407 :REIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 114 :RG 2b3oA 478 :LD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 482 :IDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 9 number of extra gaps= 0 total=500 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 2b3oA/T0317-2b3oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2b3oA/T0317-2b3oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3oA read from 2b3oA/T0317-2b3oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPA 2b3oA 308 :KNQLLGPDENAKT T0317 18 :LFIGNARA 2b3oA 322 :IASQGCLE T0317 26 :AGATELL 2b3oA 332 :VNDFWQM T0317 33 :VRAGITLCVNVS 2b3oA 340 :WQENSRVIVMTT T0317 45 :RQQPGPRA 2b3oA 361 :CVPYWPEV T0317 54 :GVAELRVP 2b3oA 411 :HYQYLSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2b3oA 419 :DHGVPSEPGGVLSFLDQINQRQE T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 114 :RGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 480 :CDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=510 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 2b3oA/T0317-2b3oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2b3oA/T0317-2b3oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3oA read from 2b3oA/T0317-2b3oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3oA in template set Warning: unaligning (T0317)I160 because last residue in template chain is (2b3oA)L526 T0317 5 :EAAPPPFARVAPALFI 2b3oA 309 :NQLLGPDENAKTYIAS T0317 21 :GNARAAGA 2b3oA 326 :GCLEATVN T0317 29 :TELLVRAGITLCVNVSRQ 2b3oA 336 :WQMAWQENSRVIVMTTRE T0317 47 :QPGPRAP 2b3oA 361 :CVPYWPE T0317 54 :GVAELRVPVFD 2b3oA 409 :IWHYQYLSWPD T0317 65 :DPAEDLLTHLEPTCAAMEA 2b3oA 424 :SEPGGVLSFLDQINQRQES T0317 87 :DG 2b3oA 444 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2b3oA 447 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 115 :G 2b3oA 479 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPREP 2b3oA 482 :IDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=520 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 1g4wR/T0317-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g4wR expands to /projects/compbio/data/pdb/1g4w.pdb.gz 1g4wR:# T0317 read from 1g4wR/T0317-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0317-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g4wR to template set # found chain 1g4wR in template set T0317 19 :FIGNARAAGA 1g4wR 349 :YPKNTPDALE T0317 29 :TELLVRAGITLCVNVS 1g4wR 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPG 1g4wR 384 :KQLPP T0317 52 :APGVAELRV 1g4wR 428 :RYTIPVLHV T0317 61 :PVFDDPAEDLLTHLEPTCAAME 1g4wR 438 :NWPDHQPLPSTDQLEYLADRVK T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1g4wR 472 :SDKHLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSARPV 1g4wR 501 :PHSNLEQVRADFRDSRNN T0317 132 :AEPNLGFWAQLQKYEQTLQ 1g4wR 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=528 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 1g4wR/T0317-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g4wR/T0317-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0317-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4wR in template set T0317 19 :FIGNARAAGA 1g4wR 349 :YPKNTPDALE T0317 29 :TELLVRAGITLCVNVS 1g4wR 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPGPRAP 1g4wR 384 :KQLPPYFRG T0317 54 :GVAELRV 1g4wR 430 :TIPVLHV T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4wR 439 :WPDHQPLPSTDQLEYLADRVK T0317 87 :DG 1g4wR 467 :PG T0317 91 :CLVYCKNGRSRSAAVCTAYLMRH 1g4wR 477 :PMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4wR 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4wR 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 9 number of extra gaps= 0 total=537 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 1g4wR/T0317-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g4wR/T0317-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0317-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4wR in template set T0317 18 :LFIGNARAAGA 1g4wR 345 :LAGSYPKNTPD T0317 29 :TELLVRAGITLCVNVSR 1g4wR 361 :MKMLLEKECSCLVVLTS T0317 46 :QQPGPRAP 1g4wR 385 :QLPPYFRG T0317 54 :GVAELRVP 1g4wR 425 :GEKRYTIP T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4wR 439 :WPDHQPLPSTDQLEYLADRVK T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1g4wR 473 :DKHLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4wR 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4wR 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=545 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p15A/T0317-1p15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p15A expands to /projects/compbio/data/pdb/1p15.pdb.gz 1p15A:# T0317 read from 1p15A/T0317-1p15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p15A read from 1p15A/T0317-1p15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p15A to template set # found chain 1p15A in template set Warning: unaligning (T0317)Q46 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)Q152 because last residue in template chain is (1p15A)A786 T0317 13 :RVAPALFIGNARAAGATELL 1p15A 590 :RQKDSYIASQGPLLHTIEDF T0317 33 :VRAGITLCVNVS 1p15A 614 :WEWKSCSIVMLT T0317 45 :R 1p15A 627 :L T0317 50 :PR 1p15A 632 :QE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1p15A 679 :RQIRQFHFHGWPEVGIPSDGKGMINIIAAVQKQQQ T0317 87 :D 1p15A 716 :G T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1p15A 718 :HPITVHCSAGAGRTGTFCALSTVLE T0317 114 :RG 1p15A 747 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 750 :LDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 9 number of extra gaps= 1 total=554 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p15A/T0317-1p15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1p15A/T0317-1p15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p15A read from 1p15A/T0317-1p15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p15A in template set Warning: unaligning (T0317)Q46 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)P53 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)A636 T0317 13 :RVAPALFIGNARAAGATELL 1p15A 590 :RQKDSYIASQGPLLHTIEDF T0317 33 :VRAGITLCVNVS 1p15A 614 :WEWKSCSIVMLT T0317 50 :PRA 1p15A 632 :QEK T0317 54 :GVAELRVP 1p15A 683 :QFHFHGWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1p15A 691 :EVGIPSDGKGMINIIAAVQKQQQ T0317 87 :DGGSCLVYCKNGRSRSAAVCTAY 1p15A 716 :GNHPITVHCSAGAGRTGTFCALS T0317 110 :LMRHRGH 1p15A 743 :RVKAEGI T0317 117 :SLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 751 :DVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 8 number of extra gaps= 2 total=562 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p15A/T0317-1p15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1p15A/T0317-1p15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p15A read from 1p15A/T0317-1p15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p15A in template set Warning: unaligning (T0317)Q47 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)E629 Warning: unaligning (T0317)P48 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)E629 Warning: unaligning (T0317)G49 because of BadResidue code BAD_PEPTIDE in next template residue (1p15A)G631 Warning: unaligning (T0317)P50 because of BadResidue code BAD_PEPTIDE at template residue (1p15A)G631 Warning: unaligning (T0317)Q152 because last residue in template chain is (1p15A)A786 T0317 13 :RVAPALFIGNARAAGATE 1p15A 590 :RQKDSYIASQGPLLHTIE T0317 31 :LLVRAGITLCVNVSRQ 1p15A 612 :MIWEWKSCSIVMLTEL T0317 51 :RAP 1p15A 632 :QEK T0317 54 :GVAELRVPVFDDPAED 1p15A 680 :QIRQFHFHGWPEVGIP T0317 70 :LLTHLEPTCAAMEAAVRD 1p15A 697 :DGKGMINIIAAVQKQQQQ T0317 88 :GGSCLVYCKNGRSRSAAVCTA 1p15A 717 :NHPITVHCSAGAGRTGTFCAL T0317 109 :YLMRHRG 1p15A 742 :ERVKAEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1p15A 750 :LDVFQTVKSLRLQRPHMVQTLEQYEFCYKVVQEYID Number of specific fragments extracted= 8 number of extra gaps= 1 total=570 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f46A/T0317-2f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f46A expands to /projects/compbio/data/pdb/2f46.pdb.gz 2f46A:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 6, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 10, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 784, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 786, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 788, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 790, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 792, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 794, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 847, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 849, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 851, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 853, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 855, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 857, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 859, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 861, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 863, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 865, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 867, because occupancy 0.200 <= existing 0.800 in 2f46A Skipped atom 869, because occupancy 0.200 <= existing 0.800 in 2f46A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 991, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 993, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 995, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 997, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 999, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1001, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1003, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1005, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1007, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1025, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1027, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1029, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1031, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1033, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1035, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1037, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1039, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1041, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1043, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1045, because occupancy 0.300 <= existing 0.700 in 2f46A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2f46A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2f46A # T0317 read from 2f46A/T0317-2f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f46A read from 2f46A/T0317-2f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f46A to template set # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEES T0317 52 :APGVAELRVP 2f46A 70 :AGVTGFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAM 2f46A 88 :HDVETFRQLI T0317 86 :R 2f46A 98 :G T0317 88 :G 2f46A 99 :Q T0317 89 :GSCLVYCKNGR 2f46A 102 :YPVLAYCRTGT T0317 101 :RSAA 2f46A 113 :RCSL T0317 106 :CTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWA 2f46A 117 :LWGFRRAAEGMPVDEIIRRAQAAGVNLENFRERLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=579 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f46A/T0317-2f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2f46A/T0317-2f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f46A read from 2f46A/T0317-2f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEESQP T0317 54 :GV 2f46A 71 :GV T0317 56 :AELRVP 2f46A 74 :GFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAME 2f46A 88 :HDVETFRQLIG T0317 88 :G 2f46A 99 :Q T0317 89 :GSCLVYCKNGR 2f46A 102 :YPVLAYCRTGT T0317 102 :SAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWA 2f46A 113 :RCSLLWGFRRAAEGMPVDEIIRRAQAAGVNLENFRERLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=587 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f46A/T0317-2f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2f46A/T0317-2f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f46A read from 2f46A/T0317-2f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f46A in template set Warning: unaligning (T0317)P8 because first residue in template chain is (2f46A)K13 Warning: unaligning (T0317)P9 because of BadResidue code BAD_PEPTIDE at template residue (2f46A)M14 Warning: unaligning (T0317)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2f46A)T81 Warning: unaligning (T0317)F63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2f46A)T81 T0317 10 :PFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAP 2f46A 15 :AILKLDEHLYISPQLTKADAEQIAQLGIKTIICNRPDREEESQP T0317 54 :GVAELRVP 2f46A 72 :VTGFHHQP T0317 64 :DDPAED 2f46A 82 :ARDIQK T0317 72 :THLEPTCAAME 2f46A 88 :HDVETFRQLIG T0317 87 :D 2f46A 99 :Q T0317 88 :GGSCLVYCKNGRS 2f46A 101 :EYPVLAYCRTGTR T0317 103 :AAVCTAYLMRHRGHSLDRAFQMVKSARPVA 2f46A 114 :CSLLWGFRRAAEGMPVDEIIRRAQAAGVNL T0317 136 :LGFWAQLQK 2f46A 144 :ENFRERLDN Number of specific fragments extracted= 8 number of extra gaps= 1 total=595 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2shpA/T0317-2shpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2shpA expands to /projects/compbio/data/pdb/2shp.pdb.gz 2shpA:# T0317 read from 2shpA/T0317-2shpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2shpA read from 2shpA/T0317-2shpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2shpA to template set # found chain 2shpA in template set Warning: unaligning (T0317)V14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2shpA)K324 Warning: unaligning (T0317)A17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0317)L18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)R24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 15 :AP 2shpA 325 :KS T0317 19 :FIGN 2shpA 329 :ATQG T0317 25 :A 2shpA 335 :Q T0317 26 :AGA 2shpA 337 :TVN T0317 29 :TELLVRAGITLCVNVS 2shpA 342 :WRMVFQENSRVIVMTT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 2shpA 413 :RTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQE T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 114 :RG 2shpA 484 :VD T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 10 number of extra gaps= 2 total=605 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2shpA/T0317-2shpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2shpA/T0317-2shpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2shpA read from 2shpA/T0317-2shpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2shpA in template set Warning: unaligning (T0317)N22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 18 :LFIG 2shpA 329 :ATQG T0317 24 :RA 2shpA 335 :QN T0317 26 :AGATEL 2shpA 338 :VNDFWR T0317 32 :LVRAGITLCVNVS 2shpA 345 :VFQENSRVIVMTT T0317 54 :GVAELRVP 2shpA 417 :QYHFRTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 2shpA 425 :DHGVPSDPGGVLDFLEEVHHKQE T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 114 :RGHS 2shpA 484 :VDCD T0317 118 :LDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 2shpA 490 :VPKTIQMVRSQRSGMVQTEAQYRSIYMAVQHYIET Number of specific fragments extracted= 10 number of extra gaps= 1 total=615 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2shpA/T0317-2shpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2shpA/T0317-2shpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2shpA read from 2shpA/T0317-2shpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2shpA in template set Warning: unaligning (T0317)A17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)I328 Warning: unaligning (T0317)L18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)I328 Warning: unaligning (T0317)A23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2shpA)L334 Warning: unaligning (T0317)R24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2shpA)L334 T0317 15 :AP 2shpA 325 :KS T0317 19 :FIGN 2shpA 329 :ATQG T0317 25 :A 2shpA 335 :Q T0317 26 :AGA 2shpA 338 :VND T0317 29 :TELLVRAGITLCVNVSRQ 2shpA 342 :WRMVFQENSRVIVMTTKE T0317 54 :GVAELRVPVFDDPAEDLL 2shpA 415 :VWQYHFRTWPDHGVPSDP T0317 75 :EPTCAAMEAAVR 2shpA 433 :GGVLDFLEEVHH T0317 87 :DG 2shpA 450 :MD T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2shpA 453 :GPVVVHCSAGIGRTGTFIVIDILID T0317 115 :G 2shpA 485 :D T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 2shpA 488 :IDVPKTIQMVRSQRSGMVQTEAQYRSIYMA Number of specific fragments extracted= 11 number of extra gaps= 2 total=626 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jlnA/T0317-1jlnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jlnA expands to /projects/compbio/data/pdb/1jln.pdb.gz 1jlnA:# T0317 read from 1jlnA/T0317-1jlnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jlnA read from 1jlnA/T0317-1jlnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jlnA to template set # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 10 :PFARVAPA 1jlnA 346 :GYSGKEKA T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVS 1jlnA 369 :WQMVWQEDSPVIVMIT T0317 45 :RQQPGPR 1jlnA 386 :LKEKNEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1jlnA 434 :QHVKHYWYTSWPDHKTPDSAQPLLQLMLDVEEDRL T0317 87 :DG 1jlnA 471 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1jlnA 474 :GPVVVHCSAGIGRTGCFIATS T0317 110 :LMRHRG 1jlnA 499 :QLKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 9 number of extra gaps= 0 total=635 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jlnA/T0317-1jlnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1jlnA/T0317-1jlnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jlnA read from 1jlnA/T0317-1jlnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 11 :FARVAPA 1jlnA 346 :GYSGKEK T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVS 1jlnA 369 :WQMVWQEDSPVIVMIT T0317 45 :RQQPGPRAP 1jlnA 387 :KEKNEKCVL T0317 54 :GVAELRVP 1jlnA 438 :HYWYTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVR 1jlnA 446 :DHKTPDSAQPLLQLMLDVEEDRL T0317 87 :DG 1jlnA 471 :EG T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1jlnA 474 :GPVVVHCSAGIGRTGCFIATS T0317 110 :LMRHRG 1jlnA 499 :QLKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 10 number of extra gaps= 0 total=645 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jlnA/T0317-1jlnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1jlnA/T0317-1jlnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jlnA read from 1jlnA/T0317-1jlnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jlnA in template set Warning: unaligning (T0317)E158 because last residue in template chain is (1jlnA)V548 T0317 18 :LFIGNARAAGA 1jlnA 356 :ATQGPMINTVN T0317 29 :TELLVRAGITLCVNVSRQQPGPRAP 1jlnA 369 :WQMVWQEDSPVIVMITKLKEKNEKC T0317 54 :GVAELRV 1jlnA 435 :HVKHYWY T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVRD 1jlnA 443 :SWPDHKTPDSAQPLLQLMLDVEEDRLA T0317 88 :G 1jlnA 472 :G T0317 89 :GSCLVYCKNGRSRSAAVCTAYL 1jlnA 474 :GPVVVHCSAGIGRTGCFIATSI T0317 111 :MRHRG 1jlnA 500 :LKEEG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1jlnA 506 :VDALSIVCQLRVDRGGMVQTSEQYEFVHHALCLFESRLSPET Number of specific fragments extracted= 8 number of extra gaps= 0 total=653 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptvA/T0317-1ptvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ptvA expands to /projects/compbio/data/pdb/1ptv.pdb.gz 1ptvA:# T0317 read from 1ptvA/T0317-1ptvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptvA read from 1ptvA/T0317-1ptvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ptvA to template set # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1ptvA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1ptvA 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1ptvA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 84 :AVRDG 1ptvA 203 :SLSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1ptvA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1ptvA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGA Number of specific fragments extracted= 8 number of extra gaps= 0 total=661 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptvA/T0317-1ptvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ptvA/T0317-1ptvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptvA read from 1ptvA/T0317-1ptvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1ptvA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPRAP 1ptvA 126 :PQKEEKEMI T0317 54 :GVAELRVP 1ptvA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1ptvA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1ptvA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1ptvA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1ptvA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQ 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYLAVIEGAKF Number of specific fragments extracted= 9 number of extra gaps= 0 total=670 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptvA/T0317-1ptvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ptvA/T0317-1ptvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptvA read from 1ptvA/T0317-1ptvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ptvA in template set T0317 18 :LFIGNARAAGA 1ptvA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1ptvA 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVP 1ptvA 170 :EILHFHYT T0317 62 :VFDDPAED 1ptvA 179 :WPDFGVPE T0317 73 :HLEPTCAAMEAAVRDG 1ptvA 187 :SPASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1ptvA 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1ptvA 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1ptvA 244 :VDIKKVLLDMRKFRMGLIQTADQLRFSYL Number of specific fragments extracted= 8 number of extra gaps= 0 total=678 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bijA/T0317-2bijA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bijA expands to /projects/compbio/data/pdb/2bij.pdb.gz 2bijA:Skipped atom 616, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 618, because occupancy 0.350 <= existing 0.650 in 2bijA Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bijA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 2bijA # T0317 read from 2bijA/T0317-2bijA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bijA read from 2bijA/T0317-2bijA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bijA to template set # found chain 2bijA in template set Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0317 12 :ARVAPALFI 2bijA 338 :YGGEEKVYI T0317 21 :GNARAAGA 2bijA 350 :GPIVSTVA T0317 29 :TELLVRAGITLCVNVS 2bijA 360 :WRMVWQEHTPIIVMIT T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 2bijA 425 :RGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2bijA 466 :APIIVHCSAGIGRTGCFIATSICCQ T0317 114 :RG 2bijA 495 :EG T0317 116 :HSLDRAFQMVKSARPV 2bijA 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQAI 2bijA 516 :QTCEQYQFVHHVMSLYEKQLS Number of specific fragments extracted= 8 number of extra gaps= 1 total=686 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bijA/T0317-2bijA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bijA/T0317-2bijA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bijA read from 2bijA/T0317-2bijA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bijA in template set Warning: unaligning (T0317)Q46 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 Warning: unaligning (T0317)L155 because last residue in template chain is (2bijA)H537 T0317 11 :FARVAPALFI 2bijA 337 :GYGGEEKVYI T0317 21 :GNARA 2bijA 350 :GPIVS T0317 26 :AGATEL 2bijA 356 :VADFWR T0317 32 :LVRAGITLCVNVS 2bijA 363 :VWQEHTPIIVMIT T0317 47 :QPGPRAP 2bijA 384 :CTEYWPE T0317 54 :GVAELRVP 2bijA 429 :HYWFTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 2bijA 437 :DQKTPDRAPPLLHLVREVEEAAQQE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2bijA 466 :APIIVHCSAGIGRTGCFIATS T0317 110 :LMRHRGH 2bijA 491 :QLRQEGV T0317 117 :SLDRAFQMVKSARPV 2bijA 499 :DILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKYEQTLQAQAI 2bijA 516 :QTCEQYQFVHHVMSLYEKQLS Number of specific fragments extracted= 11 number of extra gaps= 1 total=697 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bijA/T0317-2bijA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2bijA/T0317-2bijA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bijA read from 2bijA/T0317-2bijA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bijA in template set Warning: unaligning (T0317)P48 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bijA)K383 Warning: unaligning (T0317)A52 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bijA)K383 Warning: unaligning (T0317)A132 because of BadResidue code BAD_PEPTIDE in next template residue (2bijA)I515 Warning: unaligning (T0317)E133 because of BadResidue code BAD_PEPTIDE at template residue (2bijA)I515 T0317 18 :LFIGNARAAGA 2bijA 347 :ATQGPIVSTVA T0317 29 :TELLVRAGITLCVNVSRQQ 2bijA 360 :WRMVWQEHTPIIVMITNIE T0317 53 :P 2bijA 384 :C T0317 54 :GVAELRV 2bijA 426 :GLKHYWF T0317 61 :PVFDDPAEDLLTHLEPTCAAMEAAVRDGGS 2bijA 434 :SWPDQKTPDRAPPLLHLVREVEEAAQQEGP T0317 91 :CLVYCKNGRSRSAAVCTAYL 2bijA 468 :IIVHCSAGIGRTGCFIATSI T0317 111 :MRHRG 2bijA 492 :LRQEG T0317 116 :HSLDRAFQMVKSARPV 2bijA 498 :VDILKTTCQLRQDRGG T0317 134 :PNLGFWAQLQKY 2bijA 516 :QTCEQYQFVHHV Number of specific fragments extracted= 9 number of extra gaps= 1 total=706 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7fA/T0317-1g7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g7fA expands to /projects/compbio/data/pdb/1g7f.pdb.gz 1g7fA:# T0317 read from 1g7fA/T0317-1g7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g7fA read from 1g7fA/T0317-1g7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g7fA to template set # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1g7fA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1g7fA 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAA 1g7fA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1g7fA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1g7fA 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHR 1g7fA 234 :LMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQKYEQTLQA 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 9 number of extra gaps= 1 total=715 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7fA/T0317-1g7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g7fA/T0317-1g7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g7fA read from 1g7fA/T0317-1g7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1g7fA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1g7fA 126 :PQKEEKE T0317 54 :GVAELRVP 1g7fA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1g7fA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1g7fA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1g7fA 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LMRHR 1g7fA 234 :LMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQKYEQTLQAQAILPRE 1g7fA 253 :MRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSS Number of specific fragments extracted= 10 number of extra gaps= 1 total=725 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7fA/T0317-1g7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g7fA/T0317-1g7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g7fA read from 1g7fA/T0317-1g7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g7fA in template set Warning: unaligning (T0317)G115 because of BadResidue code BAD_PEPTIDE in next template residue (1g7fA)D240 T0317 18 :LFIGNARAAGA 1g7fA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1g7fA 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGPR 1g7fA 123 :QYWPQK T0317 54 :GVAELRVPVFDDPAEDLL 1g7fA 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVR 1g7fA 189 :ASFLNFLFKVRE T0317 87 :DGGSCLVYCKNGRSRSAAVCTA 1g7fA 207 :EHGPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHR 1g7fA 233 :LLMDKR T0317 116 :HSLDRAFQ 1g7fA 244 :VDIKKVLL T0317 125 :VKSARPVAEPNLGFWAQLQ 1g7fA 253 :MRKFRMGLIQTADQLRFSY Number of specific fragments extracted= 9 number of extra gaps= 1 total=734 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lyvA/T0317-1lyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lyvA expands to /projects/compbio/data/pdb/1lyv.pdb.gz 1lyvA:Skipped atom 97, because occupancy 0.380 <= existing 0.620 in 1lyvA Skipped atom 208, because occupancy 0.360 <= existing 0.640 in 1lyvA Skipped atom 210, because occupancy 0.360 <= existing 0.640 in 1lyvA Skipped atom 212, because occupancy 0.360 <= existing 0.640 in 1lyvA Skipped atom 214, because occupancy 0.360 <= existing 0.640 in 1lyvA Skipped atom 281, because occupancy 0.360 <= existing 0.640 in 1lyvA Skipped atom 406, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 408, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 410, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 412, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 414, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 671, because occupancy 0.470 <= existing 0.530 in 1lyvA Skipped atom 995, because occupancy 0.340 <= existing 0.670 in 1lyvA Skipped atom 1144, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1146, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1148, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1150, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1175, because occupancy 0.170 <= existing 0.820 in 1lyvA Skipped atom 1177, because occupancy 0.170 <= existing 0.820 in 1lyvA Skipped atom 1179, because occupancy 0.170 <= existing 0.820 in 1lyvA Skipped atom 1181, because occupancy 0.170 <= existing 0.820 in 1lyvA Skipped atom 1396, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 1398, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 1400, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 1402, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 1404, because occupancy 0.490 <= existing 0.510 in 1lyvA Skipped atom 1480, because occupancy 0.290 <= existing 0.710 in 1lyvA Skipped atom 1482, because occupancy 0.290 <= existing 0.710 in 1lyvA Skipped atom 1484, because occupancy 0.290 <= existing 0.710 in 1lyvA Skipped atom 1486, because occupancy 0.290 <= existing 0.710 in 1lyvA Skipped atom 1488, because occupancy 0.290 <= existing 0.710 in 1lyvA Skipped atom 1580, because occupancy 0.430 <= existing 0.570 in 1lyvA Skipped atom 1812, because occupancy 0.380 <= existing 0.620 in 1lyvA Skipped atom 1814, because occupancy 0.380 <= existing 0.620 in 1lyvA Skipped atom 1922, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1924, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1926, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1928, because occupancy 0.440 <= existing 0.560 in 1lyvA Skipped atom 1942, because occupancy 0.330 <= existing 0.670 in 1lyvA Skipped atom 1948, because occupancy 0.300 <= existing 1.000 in 1lyvA Skipped atom 1950, because occupancy 0.300 <= existing 1.000 in 1lyvA Skipped atom 1952, because occupancy 0.300 <= existing 1.000 in 1lyvA Skipped atom 1954, because occupancy 0.300 <= existing 1.000 in 1lyvA Skipped atom 1956, because occupancy 0.300 <= existing 1.000 in 1lyvA # T0317 read from 1lyvA/T0317-1lyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lyvA read from 1lyvA/T0317-1lyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lyvA to template set # found chain 1lyvA in template set T0317 21 :GNARAAG 1lyvA 261 :YPLQSQL T0317 28 :ATELLVRAGITLCVNVS 1lyvA 270 :HFRMLAENRTPVLAVLA T0317 45 :RQQPGP 1lyvA 299 :PDYFRQ T0317 52 :APGV 1lyvA 342 :KTIS T0317 56 :AELRVPVFDDPAEDL 1lyvA 348 :VVHVGNWPDQTAVSS T0317 72 :THLEPTCAAMEAAV 1lyvA 363 :EVTKALASLVDQTA T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCMND T0317 114 :RGHSLDRAFQMVKSARPV 1lyvA 425 :SQLSVEDMVSQMRVQRNG T0317 132 :AEPNLGFWAQLQKYEQTL 1lyvA 444 :MVQKDEQLDVLIKLAEGQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=743 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lyvA/T0317-1lyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1lyvA/T0317-1lyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lyvA read from 1lyvA/T0317-1lyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lyvA in template set T0317 26 :AGATELLVRAGITLCVNVS 1lyvA 268 :ESHFRMLAENRTPVLAVLA T0317 45 :RQQPGPRAP 1lyvA 296 :FGMPDYFRQ T0317 54 :GVAELRV 1lyvA 345 :SVPVVHV T0317 62 :VFDDPAEDL 1lyvA 354 :WPDQTAVSS T0317 72 :THLEPTCAAMEAA 1lyvA 363 :EVTKALASLVDQT T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLM 1lyvA 394 :DSKLRPVIHSRAGVGRTAQLIGAMCM T0317 114 :RGHSLDRAFQMVKSAR 1lyvA 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1lyvA 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=751 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lyvA/T0317-1lyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1lyvA/T0317-1lyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lyvA read from 1lyvA/T0317-1lyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lyvA in template set T0317 21 :GNARAAGA 1lyvA 261 :YPLQSQLE T0317 29 :TELLVRAGITLCVNVSR 1lyvA 271 :FRMLAENRTPVLAVLAS T0317 46 :QQPGPRAP 1lyvA 297 :GMPDYFRQ T0317 54 :GVAELRVP 1lyvA 340 :GQKTISVP T0317 62 :VFD 1lyvA 354 :WPD T0317 66 :PAEDLLTHLEPTCAAMEAAVR 1lyvA 357 :QTAVSSEVTKALASLVDQTAE T0317 87 :DG 1lyvA 386 :KG T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMR 1lyvA 397 :LRPVIHSRAGVGRTAQLIGAMCMN T0317 114 :RGHSLDRAFQMVKSAR 1lyvA 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1lyvA 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=761 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u24A/T0317-1u24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u24A expands to /projects/compbio/data/pdb/1u24.pdb.gz 1u24A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0317 read from 1u24A/T0317-1u24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u24A read from 1u24A/T0317-1u24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u24A to template set # found chain 1u24A in template set T0317 3 :TSEAAPPPFARVAPALFIGNARAAGATELL 1u24A 168 :TVYIAPLGKHKLPEGGEVRRVQKVQTEQEV T0317 33 :VRAGITL 1u24A 199 :EAAGMRY T0317 58 :LRVPVFDDPAEDL 1u24A 206 :FRIAATDHVWPTP T0317 72 :THLEPTCAAMEAA 1u24A 219 :ENIDRFLAFYRTL T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 232 :PQDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSARPV 1u24A 261 :PSVSLKDILYRQHEIGGF T0317 136 :LGFWAQLQKYEQTLQAQAILP 1u24A 302 :IVMIEQFYRYVQENRADGYQT Number of specific fragments extracted= 7 number of extra gaps= 0 total=768 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u24A/T0317-1u24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1u24A/T0317-1u24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u24A read from 1u24A/T0317-1u24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u24A in template set T0317 4 :SEAAPPPFARVAPALFIGNARAAGATELL 1u24A 169 :VYIAPLGKHKLPEGGEVRRVQKVQTEQEV T0317 33 :VRAGITL 1u24A 199 :EAAGMRY T0317 58 :LRVPVFDDPAE 1u24A 206 :FRIAATDHVWP T0317 70 :LLTHLEPTCAAMEA 1u24A 217 :TPENIDRFLAFYRT T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 233 :QDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSAR 1u24A 261 :PSVSLKDILYRQHEIG T0317 132 :AE 1u24A 285 :IK T0317 136 :LGFWAQLQKYEQTLQAQAILP 1u24A 302 :IVMIEQFYRYVQENRADGYQT Number of specific fragments extracted= 8 number of extra gaps= 0 total=776 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u24A/T0317-1u24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1u24A/T0317-1u24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u24A read from 1u24A/T0317-1u24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u24A in template set T0317 17 :ALFIGNARAAGA 1u24A 90 :HISGSSAFTPAQ T0317 29 :TELLVRA 1u24A 106 :AAKLREK T0317 36 :GITLCVNVSRQQ 1u24A 115 :GPIYDVDLRQES T0317 54 :GVAELRVPVFD 1u24A 202 :GMRYFRIAATD T0317 66 :PAEDLLTHLEPTCAAMEA 1u24A 213 :HVWPTPENIDRFLAFYRT T0317 87 :DGGSCLVYCKNGRSRSAAVCTAYLMRH 1u24A 233 :QDAWLHFHCEAGVGRTTAFMVMTDMLK T0317 114 :RGHSLDRAFQMVKSARPVA 1u24A 261 :PSVSLKDILYRQHEIGGFY Number of specific fragments extracted= 7 number of extra gaps= 0 total=783 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a5y/T0317-1a5y-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a5y expands to /projects/compbio/data/pdb/1a5y.pdb.gz 1a5y:Warning: there is no chain 1a5y will retry with 1a5yA Bad short name: P for alphabet: pdb_atoms Bad short name: O1P for alphabet: pdb_atoms Bad short name: O2P for alphabet: pdb_atoms Bad short name: O3P for alphabet: pdb_atoms # T0317 read from 1a5y/T0317-1a5y-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5y read from 1a5y/T0317-1a5y-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a5y to template set # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)R157 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1a5y 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1a5y 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1a5y 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 1a5y 204 :LSPE T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTAY 1a5y 217 :AGIGRSGTFCLAD T0317 110 :LMRHRG 1a5y 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILP 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAKFIMGD Number of specific fragments extracted= 9 number of extra gaps= 0 total=792 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a5y/T0317-1a5y-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1a5y/T0317-1a5y-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5y read from 1a5y/T0317-1a5y-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)R157 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1a5y 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 1a5y 126 :PQKEEK T0317 54 :GVAELRVP 1a5y 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEA 1a5y 181 :DFGVPESPASFLNFLFKVRE T0317 87 :DG 1a5y 206 :PE T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTAY 1a5y 217 :AGIGRSGTFCLAD T0317 110 :LMRHRG 1a5y 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILP 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRFSYLAVIEGAKFIMGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=802 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a5y/T0317-1a5y-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1a5y/T0317-1a5y-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5y read from 1a5y/T0317-1a5y-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a5y in template set Warning: unaligning (T0317)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a5y)S216 Warning: unaligning (T0317)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a5y)S216 Warning: unaligning (T0317)A153 because last residue in template chain is (1a5y)S285 T0317 18 :LFIGNARAAGA 1a5y 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1a5y 96 :WEMVWEQKSRGVVMLNR T0317 47 :QPGPR 1a5y 123 :QYWPQ T0317 54 :GVAELRVPVFDDPAEDLL 1a5y 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1a5y 189 :ASFLNFLFKVRESG T0317 89 :GSCLV 1a5y 209 :GPVVV T0317 97 :NGRSRSAAVCTA 1a5y 217 :AGIGRSGTFCLA T0317 109 :YLMRHRG 1a5y 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQ 1a5y 244 :VDIKKVLLDMRKFRMGLIATAEQLRF T0317 142 :LQKYEQTLQAQ 1a5y 274 :VIEGAKFIMGD Number of specific fragments extracted= 10 number of extra gaps= 0 total=812 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpmA/T0317-1rpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rpmA expands to /projects/compbio/data/pdb/1rpm.pdb.gz 1rpmA:# T0317 read from 1rpmA/T0317-1rpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpmA read from 1rpmA/T0317-1rpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rpmA to template set # found chain 1rpmA in template set T0317 15 :APALFIGNARAAGATELL 1rpmA 965 :PNHYIATQGPMQETIYDF T0317 33 :VRAGITLCVNVS 1rpmA 987 :WHENTASIIMVT T0317 45 :RQ 1rpmA 1009 :CK T0317 47 :QPGP 1rpmA 1012 :WPDD T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 1rpmA 1051 :REIRQFHFTGWPDHGVPYHATGLLGFVRQVKSKSPPS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIMLD T0317 114 :RG 1rpmA 1118 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEA Number of specific fragments extracted= 8 number of extra gaps= 0 total=820 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpmA/T0317-1rpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1rpmA/T0317-1rpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpmA read from 1rpmA/T0317-1rpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rpmA in template set T0317 18 :LFIGNARA 1rpmA 970 :ATQGPMQE T0317 26 :AGA 1rpmA 979 :IYD T0317 29 :TELLVRAGITLCVNVS 1rpmA 983 :WRMVWHENTASIIMVT T0317 46 :QQP 1rpmA 1012 :WPD T0317 54 :GVAELRVP 1rpmA 1055 :QFHFTGWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 1rpmA 1063 :DHGVPYHATGLLGFVRQVKSKSPPS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIM T0317 112 :RHRG 1rpmA 1116 :EREG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHDAILEA Number of specific fragments extracted= 9 number of extra gaps= 0 total=829 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpmA/T0317-1rpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1rpmA/T0317-1rpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpmA read from 1rpmA/T0317-1rpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rpmA in template set T0317 16 :PALFIGNARAAGA 1rpmA 966 :NHYIATQGPMQET T0317 29 :TELLVRAGITLCVNVSRQ 1rpmA 983 :WRMVWHENTASIIMVTNL T0317 47 :QPGPRAP 1rpmA 1008 :CCKYWPD T0317 54 :GVAELRVPVFDDPAE 1rpmA 1052 :EIRQFHFTGWPDHGV T0317 71 :LTHLEPTCAAMEAAVR 1rpmA 1067 :PYHATGLLGFVRQVKS T0317 87 :D 1rpmA 1087 :S T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1rpmA 1089 :GPLVVHCSAGAGRTGCFIVIDIMLD T0317 114 :RG 1rpmA 1118 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1rpmA 1121 :VDIYNCVRELRSRRVNMVQTEEQYVFIHD Number of specific fragments extracted= 9 number of extra gaps= 0 total=838 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eeoA/T0317-1eeoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eeoA expands to /projects/compbio/data/pdb/1eeo.pdb.gz 1eeoA:# T0317 read from 1eeoA/T0317-1eeoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eeoA read from 1eeoA/T0317-1eeoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eeoA to template set # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1eeoA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 1eeoA 126 :PQKEEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEA 1eeoA 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRE T0317 85 :VRDG 1eeoA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1eeoA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1eeoA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 8 number of extra gaps= 0 total=846 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eeoA/T0317-1eeoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1eeoA/T0317-1eeoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eeoA read from 1eeoA/T0317-1eeoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1eeoA 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPG 1eeoA 126 :PQKEE T0317 54 :GVAELRVP 1eeoA 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1eeoA 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1eeoA 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1eeoA 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1eeoA 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAILPR 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDS Number of specific fragments extracted= 9 number of extra gaps= 0 total=855 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eeoA/T0317-1eeoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1eeoA/T0317-1eeoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eeoA read from 1eeoA/T0317-1eeoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eeoA in template set T0317 18 :LFIGNARAAGA 1eeoA 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1eeoA 96 :WEMVWEQKSRGVVMLNR T0317 54 :GVAELRVP 1eeoA 170 :EILHFHYT T0317 62 :VFDDPAEDLL 1eeoA 179 :WPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1eeoA 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1eeoA 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1eeoA 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1eeoA 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=863 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytw/T0317-1ytw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ytw expands to /projects/compbio/data/pdb/1ytw.pdb.gz 1ytw:Warning: there is no chain 1ytw will retry with 1ytwA Skipped atom 1776, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1778, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1780, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1782, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1784, because occupancy 0.450 <= existing 0.550 in 1ytw Skipped atom 1786, because occupancy 0.450 <= existing 0.550 in 1ytw # T0317 read from 1ytw/T0317-1ytw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ytw read from 1ytw/T0317-1ytw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ytw to template set # found chain 1ytw in template set T0317 25 :AAGATELLVRAGITLCVNVS 1ytw 267 :LESHFRMLAENRTPVLAVLA T0317 45 :RQQPGP 1ytw 299 :PDYFRQ T0317 52 :APGVAELRV 1ytw 343 :TISVPVVHV T0317 61 :PVFDDPAEDL 1ytw 353 :NWPDQTAVSS T0317 72 :THLEPTCAAMEAAV 1ytw 363 :EVTKALASLVDQTA T0317 86 :RDGGSCLVYCKNGRSRSAAVCTAYLMRH 1ytw 394 :DSKLRPVIHCRAGVGRTAQLIGAMCMND T0317 114 :RGHSLDRAFQMVKSARPV 1ytw 425 :SQLSVEDMVSQMRVQRNG T0317 132 :AEPNLGFWAQLQKYEQTL 1ytw 444 :MVQKDEQLDVLIKLAEGQ T0317 154 :ILP 1ytw 462 :GRP Number of specific fragments extracted= 9 number of extra gaps= 0 total=872 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytw/T0317-1ytw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ytw/T0317-1ytw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ytw read from 1ytw/T0317-1ytw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ytw in template set T0317 25 :AAGATELLVRAGITLCVNVS 1ytw 267 :LESHFRMLAENRTPVLAVLA T0317 45 :RQQPGPRAP 1ytw 296 :FGMPDYFRQ T0317 54 :GVAELRVP 1ytw 340 :GQKTISVP T0317 62 :VFDDPAEDL 1ytw 354 :WPDQTAVSS T0317 72 :THLEPTCAAMEAA 1ytw 363 :EVTKALASLVDQT T0317 86 :RD 1ytw 394 :DS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1ytw 397 :LRPVIHCRAGVGRTAQLIGAMCM T0317 114 :RGHSLDRAFQMVKSAR 1ytw 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1ytw 442 :GIMVQKDEQLDVLIKLAEG T0317 152 :Q 1ytw 461 :Q Number of specific fragments extracted= 10 number of extra gaps= 0 total=882 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ytw/T0317-1ytw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1ytw/T0317-1ytw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ytw read from 1ytw/T0317-1ytw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ytw in template set T0317 29 :TELLVRAGITLCVNVSR 1ytw 271 :FRMLAENRTPVLAVLAS T0317 46 :QQPGPRAP 1ytw 297 :GMPDYFRQ T0317 54 :GVAELRVP 1ytw 340 :GQKTISVP T0317 62 :VFDDP 1ytw 354 :WPDQT T0317 68 :EDLLTHLEPTCAAMEAAVR 1ytw 359 :AVSSEVTKALASLVDQTAE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMR 1ytw 397 :LRPVIHCRAGVGRTAQLIGAMCMN T0317 114 :RGHSLDRAFQMVKSAR 1ytw 425 :SQLSVEDMVSQMRVQR T0317 130 :PVAEPNLGFWAQLQKYEQT 1ytw 442 :GIMVQKDEQLDVLIKLAEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=890 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aax/T0317-1aax-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aax expands to /projects/compbio/data/pdb/1aax.pdb.gz 1aax:Warning: there is no chain 1aax will retry with 1aaxA # T0317 read from 1aax/T0317-1aax-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aax read from 1aax/T0317-1aax-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aax to template set # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1aax 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1aax 126 :PQKEEKE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAA 1aax 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1aax 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1aax 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1aax 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=898 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aax/T0317-1aax-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1aax/T0317-1aax-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aax read from 1aax/T0317-1aax-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 1aax 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGPR 1aax 126 :PQKEEKE T0317 54 :GVAELRVP 1aax 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEAA 1aax 181 :DFGVPESPASFLNFLFKVRES T0317 85 :VRDG 1aax 204 :LSPE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 1aax 209 :GPVVVHSSAGIGRSGTFCLAD T0317 110 :LMRHRG 1aax 234 :LMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAI 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIM Number of specific fragments extracted= 9 number of extra gaps= 0 total=907 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aax/T0317-1aax-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1aax/T0317-1aax-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aax read from 1aax/T0317-1aax-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aax in template set T0317 18 :LFIGNARAAGA 1aax 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 1aax 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGP 1aax 123 :QYWPQ T0317 54 :GVAELRVPVFDDPAEDLL 1aax 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 1aax 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 1aax 209 :GPVVVHSSAGIGRSGTFCLA T0317 109 :YLMRHRG 1aax 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKY 1aax 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=915 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfoA/T0317-1yfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yfoA expands to /projects/compbio/data/pdb/1yfo.pdb.gz 1yfoA:# T0317 read from 1yfoA/T0317-1yfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfoA read from 1yfoA/T0317-1yfoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yfoA to template set # found chain 1yfoA in template set T0317 14 :VAPA 1yfoA 297 :EKNK T0317 18 :LFIGNARAAGA 1yfoA 303 :AAQGPKEETVN T0317 29 :TELLVRAGITLCVNVS 1yfoA 316 :WRMIWEQNTATIVMVT T0317 45 :RQQPGPR 1yfoA 343 :QYWPDQG T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 1yfoA 389 :RLITQFHFTSWPDFGVPFTPIGMLKFLKKVKACNPQY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAMLD T0317 114 :RG 1yfoA 456 :ER T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQ 1yfoA 459 :VDVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHY Number of specific fragments extracted= 8 number of extra gaps= 0 total=923 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfoA/T0317-1yfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yfoA/T0317-1yfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfoA read from 1yfoA/T0317-1yfoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yfoA in template set Warning: unaligning (T0317)Q152 because last residue in template chain is (1yfoA)Y495 T0317 18 :LFIGNARA 1yfoA 303 :AAQGPKEE T0317 26 :AGA 1yfoA 312 :VND T0317 29 :TELLVRAGITLCVNVS 1yfoA 316 :WRMIWEQNTATIVMVT T0317 45 :RQQPGPR 1yfoA 346 :PDQGCWT T0317 54 :GVAELRVP 1yfoA 393 :QFHFTSWP T0317 64 :DDPAEDLLTHLEPTCAAMEAAVRDG 1yfoA 401 :DFGVPFTPIGMLKFLKKVKACNPQY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLM 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAM T0317 112 :RHRGH 1yfoA 453 :MHSER T0317 117 :SLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQA 1yfoA 460 :DVYGFVSRIRAQRCQMVQTDMQYVFIYQALLEHYL Number of specific fragments extracted= 9 number of extra gaps= 0 total=932 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfoA/T0317-1yfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1yfoA/T0317-1yfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfoA read from 1yfoA/T0317-1yfoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yfoA in template set T0317 16 :PALFI 1yfoA 299 :NKFIA T0317 21 :GNARAAGA 1yfoA 306 :GPKEETVN T0317 29 :TELLVRAGITLCVNVSR 1yfoA 316 :WRMIWEQNTATIVMVTN T0317 46 :QQPGPRAP 1yfoA 342 :AQYWPDQG T0317 54 :GVAELRVPVFDDPAEDL 1yfoA 391 :ITQFHFTSWPDFGVPFT T0317 74 :LEPTCAAMEAAVR 1yfoA 408 :PIGMLKFLKKVKA T0317 87 :DG 1yfoA 424 :QY T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHR 1yfoA 427 :GAIVVHCSAGVGRTGTFVVIDAMLDM T0317 115 :G 1yfoA 457 :R T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQK 1yfoA 459 :VDVYGFVSRIRAQRCQMVQTDMQYVFIYQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=942 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m3gA/T0317-1m3gA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m3gA expands to /projects/compbio/data/pdb/1m3g.pdb.gz 1m3gA:# T0317 read from 1m3gA/T0317-1m3gA-t06-local-adpstyle5.a2m # 1m3gA read from 1m3gA/T0317-1m3gA-t06-local-adpstyle5.a2m # adding 1m3gA to template set # found chain 1m3gA in template set Warning: unaligning (T0317)P8 because first residue in template chain is (1m3gA)Q170 T0317 9 :PPFARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDGGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 1m3gA 171 :GGPVEILPYLFLGSCSHSSDLQGLQACGITAVLNVSASCPNHFEGLFRYKSIPVEDNQMVEISAWFQEAIGFIDWVKNSGGRVLVHSQAGISRSATICLAYLMQSRRVRLDEAFDFVKQRRGVISPNFSFMGQLLQFETQV Number of specific fragments extracted= 1 number of extra gaps= 0 total=943 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j4xA/T0317-1j4xA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j4xA expands to /projects/compbio/data/pdb/1j4x.pdb.gz 1j4xA:# T0317 read from 1j4xA/T0317-1j4xA-t06-local-adpstyle5.a2m # 1j4xA read from 1j4xA/T0317-1j4xA-t06-local-adpstyle5.a2m # adding 1j4xA to template set # found chain 1j4xA in template set Warning: unaligning (T0317)A52 because of BadResidue code BAD_PEPTIDE at template residue (1j4xA)D80 Warning: unaligning (T0317)D87 because of BadResidue code BAD_PEPTIDE in next template residue (1j4xA)K116 Warning: unaligning (T0317)G88 because of BadResidue code BAD_PEPTIDE at template residue (1j4xA)K116 Warning: unaligning (T0317)I154 because of BadResidue code BAD_PEPTIDE in next template residue (1j4xA)L183 T0317 11 :FARVAPALFIGNARAAGATELLVRAGITLCVNVSRQQPGPR 1j4xA 30 :CNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMH T0317 53 :PGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1j4xA 81 :SGITYLGIKANDTQEFNLSAYFERAADFIDQALA T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSAR 1j4xA 118 :GRVLVHSREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNR T0317 131 :VAEPNLGFWAQLQKYEQTLQAQA 1j4xA 159 :EIGPNDGFLAQLCQLNDRLAKEG Number of specific fragments extracted= 4 number of extra gaps= 3 total=947 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnp/T0317-2hnp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hnp expands to /projects/compbio/data/pdb/2hnp.pdb.gz 2hnp:Warning: there is no chain 2hnp will retry with 2hnpA # T0317 read from 2hnp/T0317-2hnp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnp read from 2hnp/T0317-2hnp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hnp to template set # found chain 2hnp in template set Warning: unaligning (T0317)I154 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2hnp 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 2hnp 126 :PQKEEK T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAV 2hnp 169 :REILHFHYTTWPDFGVPESPASFLNFLFKVRESG T0317 87 :DG 2hnp 206 :PE T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2hnp 209 :GPVVVHCSAGIGRSGTFCLADTCLL T0317 114 :RG 2hnp 241 :PS T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 8 number of extra gaps= 0 total=955 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnp/T0317-2hnp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2hnp/T0317-2hnp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnp read from 2hnp/T0317-2hnp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hnp in template set Warning: unaligning (T0317)I154 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVS 2hnp 96 :WEMVWEQKSRGVVMLN T0317 45 :RQQPGP 2hnp 126 :PQKEEK T0317 54 :GVAELRVP 2hnp 173 :HFHYTTWP T0317 64 :DDPAEDLLTHLEPTCAAMEA 2hnp 181 :DFGVPESPASFLNFLFKVRE T0317 87 :DG 2hnp 206 :PE T0317 89 :GSCLVYCKNGRSRSAAVCTAY 2hnp 209 :GPVVVHCSAGIGRSGTFCLAD T0317 110 :LM 2hnp 234 :LM T0317 114 :RGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQA 2hnp 242 :SSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFI Number of specific fragments extracted= 9 number of extra gaps= 0 total=964 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnp/T0317-2hnp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 2hnp/T0317-2hnp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnp read from 2hnp/T0317-2hnp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hnp in template set Warning: unaligning (T0317)Q150 because last residue in template chain is (2hnp)M282 T0317 18 :LFIGNARAAGA 2hnp 83 :LTQGPLPNTCG T0317 29 :TELLVRAGITLCVNVSR 2hnp 96 :WEMVWEQKSRGVVMLNR T0317 46 :QQPGPR 2hnp 123 :QYWPQK T0317 54 :GVAELRVPVFDDPAEDLL 2hnp 171 :ILHFHYTTWPDFGVPESP T0317 75 :EPTCAAMEAAVRDG 2hnp 189 :ASFLNFLFKVRESG T0317 89 :GSCLVYCKNGRSRSAAVCTA 2hnp 209 :GPVVVHCSAGIGRSGTFCLA T0317 109 :YLMRHRG 2hnp 233 :LLMDKRK T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQ 2hnp 244 :VDIKKVLLEMRKFRMGLIQTADQLRF T0317 142 :LQKYEQTL 2hnp 274 :VIEGAKFI Number of specific fragments extracted= 9 number of extra gaps= 0 total=973 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4uS/T0317-1g4uS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g4uS expands to /projects/compbio/data/pdb/1g4u.pdb.gz 1g4uS:# T0317 read from 1g4uS/T0317-1g4uS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4uS read from 1g4uS/T0317-1g4uS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g4uS to template set # found chain 1g4uS in template set Warning: unaligning (T0317)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 18 :LFIGNARAAGA 1g4uS 344 :ALAGSYPKNTP T0317 29 :TELLVRAGITLCVNVS 1g4uS 361 :MKMLLEKECSCLVVLT T0317 45 :RQQPGP 1g4uS 408 :SASQGE T0317 52 :APGVAELRVPVFDDPAEDLLTHLEPTCAAME 1g4uS 429 :YTIPVLHVKNWPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSARPV 1g4uS 501 :PHSNLEQVRADFRDSRNN T0317 132 :AEPNLGFWAQLQKYEQTLQ 1g4uS 520 :MLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 7 number of extra gaps= 0 total=980 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4uS/T0317-1g4uS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g4uS/T0317-1g4uS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4uS read from 1g4uS/T0317-1g4uS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4uS in template set Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 21 :GNARA 1g4uS 347 :GSYPK T0317 26 :AGATEL 1g4uS 353 :TPDALE T0317 32 :LVRAGITLCVNVS 1g4uS 364 :LLEKECSCLVVLT T0317 45 :RQQPGPRAP 1g4uS 384 :KQLPPYFRG T0317 54 :GVAELRV 1g4uS 430 :TIPVLHV T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4uS 439 :WPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4uS 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4uS 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 9 number of extra gaps= 0 total=989 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4uS/T0317-1g4uS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0317 read from 1g4uS/T0317-1g4uS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4uS read from 1g4uS/T0317-1g4uS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4uS in template set Warning: unaligning (T0317)A83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1g4uS)K474 Warning: unaligning (T0317)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1g4uS)K474 T0317 19 :FIGNARAAGA 1g4uS 345 :LAGSYPKNTP T0317 29 :TELLVRAGITLCVNVSR 1g4uS 361 :MKMLLEKECSCLVVLTS T0317 46 :QQPGPRAP 1g4uS 385 :QLPPYFRG T0317 54 :GVAELRVP 1g4uS 425 :GEKRYTIP T0317 62 :VFDDPAEDLLTHLEPTCAAME 1g4uS 439 :WPDHQPLPSTDQLEYLADRVK T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1g4uS 475 :HLPMIHCLGGVGRTGTMAAALVLKD T0317 114 :RGHSLDRAFQMVKSAR 1g4uS 501 :PHSNLEQVRADFRDSR T0317 130 :PVAEPNLGFWAQLQKYEQTLQ 1g4uS 518 :NRMLEDASQFVQLKAMQAQLL Number of specific fragments extracted= 8 number of extra gaps= 0 total=997 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ohcA/T0317-1ohcA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ohcA expands to /projects/compbio/data/pdb/1ohc.pdb.gz 1ohcA:# T0317 read from 1ohcA/T0317-1ohcA-t06-local-adpstyle5.a2m # 1ohcA read from 1ohcA/T0317-1ohcA-t06-local-adpstyle5.a2m # adding 1ohcA to template set # found chain 1ohcA in template set T0317 28 :ATELLVRAGITLCVNVS 1ohcA 248 :YIQYFKNHNVTTIIRLN T0317 45 :RQQPGPRAPGVAELRVPVFDDPAEDL 1ohcA 268 :YDAKRFTDAGFDHHDLFFADGSTPTD T0317 72 :THLEPTCAAMEAA 1ohcA 294 :AIVKEFLDICENA T0317 88 :GGSCLVYCKNGRSRSAAVCTAYLMRHRGHSLDRAFQMVKSARPVAEPNL 1ohcA 307 :EGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGP T0317 138 :FWAQLQKYEQTLQ 1ohcA 356 :QQQFLVMKQTNLW T0317 153 :A 1ohcA 371 :G Number of specific fragments extracted= 6 number of extra gaps= 0 total=1003 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gwz/T0317-1gwz-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gwz expands to /projects/compbio/data/pdb/1gwz.pdb.gz 1gwz:Warning: there is no chain 1gwz will retry with 1gwzA # T0317 read from 1gwz/T0317-1gwz-t06-local-adpstyle5.a2m # 1gwz read from 1gwz/T0317-1gwz-t06-local-adpstyle5.a2m # adding 1gwz to template set # found chain 1gwz in template set Warning: unaligning (T0317)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gwz)G405 T0317 2 :GTSEAAPPPFARVAPALF 1gwz 359 :GRNKCVPYWPEVGMQRAY T0317 21 :GNARAAG 1gwz 377 :GPYSVTN T0317 28 :ATELLVRAGITL 1gwz 385 :GEHDTTEYKLRT T0317 41 :VNVS 1gwz 397 :LQVS T0317 49 :GPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVR 1gwz 406 :DLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQE T0317 87 :DG 1gwz 446 :PH T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 1gwz 449 :GPIIVHCSAGIGRTGTIIVIDMLME T0317 114 :RGHSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTLQAQAI 1gwz 482 :CDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTK Number of specific fragments extracted= 8 number of extra gaps= 0 total=1011 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c7sA/T0317-2c7sA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c7sA expands to /projects/compbio/data/pdb/2c7s.pdb.gz 2c7sA:Skipped atom 1213, because occupancy 0.400 <= existing 0.600 in 2c7sA Skipped atom 1217, because occupancy 0.400 <= existing 0.600 in 2c7sA Skipped atom 1219, because occupancy 0.400 <= existing 0.600 in 2c7sA Skipped atom 1221, because occupancy 0.400 <= existing 0.600 in 2c7sA Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 2c7sA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2c7sA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2c7sA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2c7sA # T0317 read from 2c7sA/T0317-2c7sA-t06-local-adpstyle5.a2m # 2c7sA read from 2c7sA/T0317-2c7sA-t06-local-adpstyle5.a2m # adding 2c7sA to template set # found chain 2c7sA in template set Warning: unaligning (T0317)V41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c7sA)T1029 Warning: unaligning (T0317)N42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c7sA)T1029 T0317 2 :GTSEAAPPPFA 2c7sA 992 :GRVKCYKYWPD T0317 16 :PALFIGNARAAG 2c7sA 1003 :DTEVYGDFKVTC T0317 28 :ATELLVRAGITL 2c7sA 1016 :EMEPLAEYVVRT T0317 43 :VSRQQPGPRAPGVAELRVPVFDDPAEDLLTHLEPTCAAMEAAVRDG 2c7sA 1030 :LERRGYNEIREVKQFHFTGWPDHGVPYHATGLLSFIRRVKLSNPPS T0317 89 :GSCLVYCKNGRSRSAAVCTAYLMRH 2c7sA 1077 :GPIVVHCSAGAGRTGCYIVIDIMLD T0317 114 :RG 2c7sA 1106 :EG T0317 116 :HSLDRAFQMVKSARPVAEPNLGFWAQLQKYEQTL 2c7sA 1109 :VDIYNCVKALRSRRINMVQTEEQYIFIHDAILEA Number of specific fragments extracted= 7 number of extra gaps= 1 total=1018 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfvA/T0317-2cfvA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cfvA expands to /projects/compbio/data/pdb/2cfv.pdb.gz 2cfvA:# T0317 read from 2cfvA/T0317-2cfvA-t06-local-adpstyle5.a2m # 2cfvA read from 2cfvA/T0317-2cfvA-t06-local-adpstyle5.a2m # adding 2cfvA to template set # found chain 2cfvA in template set Warning: unaligning (T0317)P8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)E1151 Warning: unaligning (T0317)A12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cfvA)A1158 Warning: unaligning (T0317)A15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)A1158 Warning: unaligning (T0317)L32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cfvA)W1177 Warning: unaligning (T0317)A35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)W1177 Warning: unaligning (T0317)Q47 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cfvA)E1191 Warning: unaligning (T0317)P50 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)E1191 Warning: unaligning (T0317)V60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cfvA)T1211 Warning: unaligning (T0317)L70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)T1211 Warning: unaligning (T0317)A83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfvA)Y1225 Warning: unaligning (T0317)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfvA)Y1225 Warning: unaligning (T0317)S90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cfvA)P1234 Warning: unaligning (T0317)E133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfvA)Q1283 Warning: unaligning (T0317)P134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfvA)Q1283 Warning: unaligning (T0317)A151 because last residue in template chain is (2cfvA)R1300 T0317 9 :PPF 2cfvA 1152 :YWP T0317 16 :PA 2cfvA 1159 :QD T0317 20 :IGNARAAG 2cfvA 1161 :YGDITVAM T0317 28 :ATEL 2cfvA 1170 :SEIV T0317 36 :GITL 2cfvA 1178 :TIRD T0317 41 :VNVSRQ 2cfvA 1182 :FTVKNI T0317 51 :RAPGVAELR 2cfvA 1192 :SHPLRQFHF T0317 71 :LTHLEPTCAAME 2cfvA 1212 :TDLLINFRYLVR T0317 91 :CLVYCKNGRSRSAAVCTAYLMRH 2cfvA 1235 :ILVHCSAGVGRTGTFIAIDRLIY T0317 114 :RG 2cfvA 1262 :EN T0317 116 :HSLDRAFQMVKSARPVA 2cfvA 1265 :VDVYGIVYDLRMHRPLM T0317 135 :NLGFWAQLQKYEQTLQ 2cfvA 1284 :TEDQYVFLNQCVLDIV Number of specific fragments extracted= 12 number of extra gaps= 2 total=1030 Will force an alignment to be made, even if fragment is small Number of alignments=135 # command:CPU_time= 29.133 sec, elapsed time= 31.936 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 135 Adding 13203 constraints to all_contacts Done adding distance constraints # command:CPU_time= 29.239 sec, elapsed time= 32.055 sec. # command:Reading probabilities from T0317.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 58.869 Optimizing... Probability sum: -273.626, CN propb: -273.626 weights: 0.419 constraints: 348 # command:CPU_time= 51.326 sec, elapsed time= 54.202 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 348 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 348 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1120 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1120 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 10467 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 10467 # command:CPU_time= 51.546 sec, elapsed time= 54.601 sec. # command: