# 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 T0360 numbered 1 through 141 Created new target T0360 from T0360.a2m # command:CPU_time= 6.366 sec, elapsed time= 6.404 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dvoA/T0360-1dvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dvoA expands to /projects/compbio/data/pdb/1dvo.pdb.gz 1dvoA:# T0360 read from 1dvoA/T0360-1dvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dvoA read from 1dvoA/T0360-1dvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dvoA to template set # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYD 1dvoA 56 :KKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFD # choosing archetypes in rotamer library T0360 38 :FKRFKPLALGIDQDLIAALP 1dvoA 90 :GDTPRLLACGIRDVLLEDVA T0360 58 :QYDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQAAA 1dvoA 114 :PLSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAELQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 1dvoA/T0360-1dvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1dvoA/T0360-1dvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dvoA read from 1dvoA/T0360-1dvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYD 1dvoA 56 :KKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFD T0360 38 :FKRFKPLALGIDQDLIAAL 1dvoA 90 :GDTPRLLACGIRDVLLEDV T0360 57 :PQYDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQAAA 1dvoA 113 :IPLSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAELQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 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 1dvoA/T0360-1dvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1dvoA/T0360-1dvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dvoA read from 1dvoA/T0360-1dvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dvoA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRFKPLALGIDQDLIAALPQ 1dvoA 55 :AKKAQARQALSIYLNLPTLDEAVNTLKPWWPGLFDGDTPRLLACGIRDVLLEDVAQ T0360 59 :YDAALIARVLANHCRRPRYLKALARGGKRFDLNNRFKGEVTPEEQAIAQNHPFVQQALQQQSAQ 1dvoA 115 :LSHKKLRRAMKAITRSESYLCAMKAGACRYDTEGYVTEHISQEEEVYAAERLDKIRRQNRIKAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=8 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 1w33A/T0360-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w33A expands to /projects/compbio/data/pdb/1w33.pdb.gz 1w33A:Skipped atom 676, because occupancy 0.35 <= existing 0.650 in 1w33A Skipped atom 678, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 680, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 682, because occupancy 0.350 <= existing 0.650 in 1w33A # T0360 read from 1w33A/T0360-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0360-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w33A to template set # found chain 1w33A in template set T0360 1 :MTQETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKR 1w33A 116 :IDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEH T0360 45 :ALGIDQDLIAAL 1w33A 167 :SWGIQFQIEQNL T0360 57 :PQYDAALIARVLANH 1w33A 186 :ENLSQEESKSLLMQI T0360 100 :PEEQAIAQNHPFVQQALQQQSAQAAAETLSVEAEAAESS 1w33A 201 :KSNLEIKQRLKKTLNETLKVYNQNTQDNEKILAEHFNKY T0360 139 :AA 1w33A 247 :KP Number of specific fragments extracted= 5 number of extra gaps= 0 total=13 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 1w33A/T0360-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1w33A/T0360-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0360-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w33A in template set T0360 1 :MTQETALGAALKSAVQTMSKKKQTEMIADHIYGKYDVFKRF 1w33A 116 :IDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEHY T0360 45 :ALGIDQDLIAAL 1w33A 167 :SWGIQFQIEQNL T0360 57 :PQYDAALIARVLANHCRRPRYLKAL 1w33A 186 :ENLSQEESKSLLMQIKSNLEIKQRL T0360 103 :QAIAQNHPFVQQALQQQSAQAAAETLSVEAEAAESSAAE 1w33A 211 :KKTLNETLKVYNQNTQDNEKILAEHFNKYYKDFDTLKPA Number of specific fragments extracted= 4 number of extra gaps= 0 total=17 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 1w33A/T0360-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1w33A/T0360-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0360-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w33A in template set T0360 10 :ALKSAVQTMSKKKQTEMIADHI 1w33A 145 :ILEILKKNSEHYNIIGRLIYHI T0360 45 :ALGIDQDLIAA 1w33A 167 :SWGIQFQIEQN T0360 56 :LPQYDAALIARVLANHCRRPRYLKAL 1w33A 185 :VENLSQEESKSLLMQIKSNLEIKQRL T0360 103 :QAIAQNHPFVQQALQQQSAQAAAETLSV 1w33A 211 :KKTLNETLKVYNQNTQDNEKILAEHFNK Number of specific fragments extracted= 4 number of extra gaps= 0 total=21 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/T0360-1z1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z1dA expands to /projects/compbio/data/pdb/1z1d.pdb.gz 1z1dA:# T0360 read from 1z1dA/T0360-1z1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z1dA read from 1z1dA/T0360-1z1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z1dA to template set # found chain 1z1dA in template set T0360 17 :TMSKKKQTEMIAD 1z1dA 206 :TVAQNQVLNLIKA T0360 35 :YDVFKRF 1z1dA 219 :CPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHC 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/T0360-1z1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1z1dA/T0360-1z1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z1dA read from 1z1dA/T0360-1z1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z1dA in template set Warning: unaligning (T0360)T17 because first residue in template chain is (1z1dA)A202 T0360 18 :MSKKKQTEMIADHIYGKYDVF 1z1dA 203 :NGLTVAQNQVLNLIKACPRPE T0360 47 :GI 1z1dA 224 :GL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/T0360-1z1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1z1dA/T0360-1z1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z1dA read from 1z1dA/T0360-1z1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z1dA in template set Warning: unaligning (T0360)S13 because first residue in template chain is (1z1dA)A202 T0360 14 :AVQTMSKKKQTEMIADHIYGKYD 1z1dA 203 :NGLTVAQNQVLNLIKACPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z1dA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN 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=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mzbA/T0360-1mzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mzbA expands to /projects/compbio/data/pdb/1mzb.pdb.gz 1mzbA:# T0360 read from 1mzbA/T0360-1mzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mzbA read from 1mzbA/T0360-1mzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mzbA to template set # found chain 1mzbA in template set Warning: unaligning (T0360)K39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)F41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 5 :TALGAALKSAVQTMSKKKQTEMIA 1mzbA 3 :ENSELRKAGLKVTLPRVKILQMLD T0360 38 :F 1mzbA 27 :S T0360 42 :KPL 1mzbA 31 :RHM T0360 49 :DQDLIAAL 1mzbA 35 :AEDVYKAL T0360 57 :PQ 1mzbA 45 :AG T0360 59 :YDAALIARVLANH 1mzbA 49 :VGLATVYRVLTQF T0360 81 :LARG 1mzbA 62 :EAAG T0360 85 :GKRFDLNN 1mzbA 67 :VVRHNFDG T0360 93 :RFKGEVTPEEQ 1mzbA 97 :EVIEFMDAEIE T0360 118 :QQSAQAAAETLS 1mzbA 108 :KRQKEIVRERGF Number of specific fragments extracted= 10 number of extra gaps= 0 total=39 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 1mzbA/T0360-1mzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1mzbA/T0360-1mzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mzbA read from 1mzbA/T0360-1mzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mzbA in template set Warning: unaligning (T0360)V37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)K39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 5 :TALGAALKSA 1mzbA 4 :NSELRKAGLK T0360 16 :QTMSKKKQTEMIA 1mzbA 14 :VTLPRVKILQMLD T0360 36 :D 1mzbA 27 :S T0360 40 :RFK 1mzbA 31 :RHM T0360 49 :DQDLIAAL 1mzbA 35 :AEDVYKAL T0360 57 :PQYDAALIARVLANH 1mzbA 47 :EDVGLATVYRVLTQF T0360 81 :LARGG 1mzbA 62 :EAAGL T0360 86 :KRFDLNN 1mzbA 68 :VRHNFDG T0360 93 :RFKGEVTPEEQAIAQNHP 1mzbA 97 :EVIEFMDAEIEKRQKEIV T0360 126 :ET 1mzbA 115 :RE Number of specific fragments extracted= 10 number of extra gaps= 0 total=49 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 1mzbA/T0360-1mzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1mzbA/T0360-1mzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mzbA read from 1mzbA/T0360-1mzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mzbA in template set Warning: unaligning (T0360)H30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mzbA)Q30 Warning: unaligning (T0360)Y32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mzbA)Q30 T0360 4 :ETALGAALKSAVQTMSKKKQTEMIAD 1mzbA 2 :VENSELRKAGLKVTLPRVKILQMLDS T0360 33 :GKYD 1mzbA 31 :RHMS T0360 49 :DQDLIAALPQ 1mzbA 35 :AEDVYKALME T0360 59 :YDAALIARVLANHCR 1mzbA 49 :VGLATVYRVLTQFEA T0360 82 :ARGGKRFDLNNRFK 1mzbA 64 :AGLVVRHNFDGGHA T0360 96 :GEV 1mzbA 96 :GEV T0360 99 :TPEEQAIAQNHPFV 1mzbA 103 :DAEIEKRQKEIVRE Number of specific fragments extracted= 7 number of extra gaps= 0 total=56 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 2c8mA/T0360-2c8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c8mA expands to /projects/compbio/data/pdb/2c8m.pdb.gz 2c8mA:# T0360 read from 2c8mA/T0360-2c8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c8mA read from 2c8mA/T0360-2c8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c8mA to template set # found chain 2c8mA in template set T0360 55 :ALPQYDAALIARVLANHC 2c8mA 201 :DFVDVSIDEVRNALIRGF T0360 78 :LKAL 2c8mA 219 :SETL T0360 87 :R 2c8mA 226 :F T0360 94 :FKGEVTPEEQAIAQNHPFV 2c8mA 227 :REDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=60 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 2c8mA/T0360-2c8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 2c8mA/T0360-2c8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c8mA read from 2c8mA/T0360-2c8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c8mA in template set T0360 57 :PQYDAALIARVLANH 2c8mA 203 :VDVSIDEVRNALIRG T0360 77 :YLKAL 2c8mA 218 :FSETL T0360 86 :KRF 2c8mA 225 :DFR T0360 95 :KGEVTPEEQAIAQNHPFV 2c8mA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=64 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 2c8mA/T0360-2c8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 2c8mA/T0360-2c8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c8mA read from 2c8mA/T0360-2c8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c8mA in template set T0360 56 :LPQYDAALIARVLANHCR 2c8mA 202 :FVDVSIDEVRNALIRGFS T0360 79 :KAL 2c8mA 220 :ETL T0360 84 :GGKRF 2c8mA 223 :HIDFR T0360 95 :KGEVTPEEQAIAQNHPFV 2c8mA 228 :EDTITEKEESLARELFDK Number of specific fragments extracted= 4 number of extra gaps= 0 total=68 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 2fswA/T0360-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0360 read from 2fswA/T0360-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0360-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fswA to template set # found chain 2fswA in template set T0360 7 :LGAALKSAVQTMSKKKQTEMI 2fswA 11 :PVRKSMQIFAGKWTLLIIFQI T0360 38 :FKRFK 2fswA 32 :NRRII T0360 49 :DQDLIAALPQYDAALIARVLANHC 2fswA 38 :YGELKRAIPGISEKMLIDELKFLC T0360 82 :ARGG 2fswA 62 :GKGL T0360 86 :KRFDL 2fswA 76 :PRVEY T0360 97 :EVTP 2fswA 81 :SLTP T0360 105 :IAQNHPFVQQALQQQSAQ 2fswA 85 :LGEKVLPIIDEIAKFGME Number of specific fragments extracted= 7 number of extra gaps= 0 total=75 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 2fswA/T0360-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 2fswA/T0360-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0360-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fswA in template set T0360 6 :ALGAALKSAVQTMSKKKQTEMI 2fswA 10 :CPVRKSMQIFAGKWTLLIIFQI T0360 38 :FKRFK 2fswA 32 :NRRII T0360 49 :DQDLIAALPQYDAALIARVLANHCR 2fswA 38 :YGELKRAIPGISEKMLIDELKFLCG T0360 83 :RGG 2fswA 63 :KGL T0360 86 :K 2fswA 76 :P T0360 93 :RFKGEVTP 2fswA 77 :RVEYSLTP T0360 105 :IAQNHPFVQQALQQQSAQ 2fswA 85 :LGEKVLPIIDEIAKFGME Number of specific fragments extracted= 7 number of extra gaps= 0 total=82 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 2fswA/T0360-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 2fswA/T0360-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0360-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fswA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIAD 2fswA 7 :DEECPVRKSMQIFAGKWTLLIIFQINR T0360 40 :RFK 2fswA 34 :RII T0360 49 :DQDLIAALPQYDAALIARVLANHCR 2fswA 38 :YGELKRAIPGISEKMLIDELKFLCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 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 1dpuA/T0360-1dpuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dpuA expands to /projects/compbio/data/pdb/1dpu.pdb.gz 1dpuA:# T0360 read from 1dpuA/T0360-1dpuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dpuA read from 1dpuA/T0360-1dpuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dpuA to template set # found chain 1dpuA in template set T0360 17 :TMSKKKQTEMIAD 1dpuA 206 :TVAQNQVLNLIKA T0360 35 :YDVFKRFK 1dpuA 219 :CPRPEGLN T0360 49 :DQDLIAALPQYDAALIARVLANHC 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=88 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 1dpuA/T0360-1dpuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1dpuA/T0360-1dpuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dpuA read from 1dpuA/T0360-1dpuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dpuA in template set T0360 18 :MSKKKQTEMIAD 1dpuA 207 :VAQNQVLNLIKA T0360 35 :YDVFKR 1dpuA 219 :CPRPEG T0360 48 :I 1dpuA 225 :L T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 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 1dpuA/T0360-1dpuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1dpuA/T0360-1dpuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dpuA read from 1dpuA/T0360-1dpuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dpuA in template set Warning: unaligning (T0360)S13 because first residue in template chain is (1dpuA)A202 T0360 14 :AVQTMSKKKQTEMIADHIYGKYD 1dpuA 203 :NGLTVAQNQVLNLIKACPRPEGL T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1dpuA 227 :FQDLKNQLKHMSVSSIKQAVDFLSN Number of specific fragments extracted= 2 number of extra gaps= 0 total=94 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 1sfxA/T0360-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sfxA expands to /projects/compbio/data/pdb/1sfx.pdb.gz 1sfxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 76, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 78, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 80, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 82, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 84, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 103, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 105, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 107, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 109, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 111, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 117, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 119, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 121, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 123, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 125, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 156, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 158, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 160, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 162, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 164, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 177, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 231, because occupancy 0.490 <= existing 0.510 in 1sfxA Skipped atom 233, because occupancy 0.490 <= existing 0.510 in 1sfxA Skipped atom 263, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 265, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 267, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 269, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 271, because occupancy 0.370 <= existing 0.630 in 1sfxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 405, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 407, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 409, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 411, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 413, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 415, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 417, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 441, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 443, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 445, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 447, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 449, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 451, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 453, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 486, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 488, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 490, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 492, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 494, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 523, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 525, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 527, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 529, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 531, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 625, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 627, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 629, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 631, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 633, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 657, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 659, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 661, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 703, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 705, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 750, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 752, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 754, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 756, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 758, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 779, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 781, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 783, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 785, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 787, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 793, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 795, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 797, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 799, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 801, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 833, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 835, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 878, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 880, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 882, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 884, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 886, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 892, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 894, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 896, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 898, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 900, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 902, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 904, because occupancy 0.340 <= existing 0.660 in 1sfxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 962, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 964, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 966, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 968, because occupancy 0.310 <= existing 0.690 in 1sfxA # T0360 read from 1sfxA/T0360-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0360-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sfxA to template set # found chain 1sfxA in template set T0360 1 :MTQETALGAALKSAVQTMS 1sfxA 1 :MSNPLGELVKALEKLSFKP T0360 20 :KKKQTEMIADH 1sfxA 21 :DVRIYSLLLER T0360 39 :KRFK 1sfxA 32 :GGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLANH 1sfxA 44 :DLSARFVRDRLKVL T0360 81 :LARGG 1sfxA 58 :LKRGF T0360 86 :KRFDLNNRFKGEV 1sfxA 64 :RREIVEKGWVGYI T0360 99 :T 1sfxA 81 :K T0360 110 :PFVQQALQQQSAQAAAETLS 1sfxA 82 :PEKVLKEFKSSILGEIERIE T0360 135 :A 1sfxA 102 :K Number of specific fragments extracted= 10 number of extra gaps= 0 total=104 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 1sfxA/T0360-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1sfxA/T0360-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0360-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sfxA in template set T0360 1 :MTQETALGAALKSAVQTMSKK 1sfxA 1 :MSNPLGELVKALEKLSFKPSD T0360 22 :KQTEMIADH 1sfxA 23 :RIYSLLLER T0360 39 :KRFK 1sfxA 32 :GGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLANH 1sfxA 44 :DLSARFVRDRLKVL T0360 81 :LARGGKRFD 1sfxA 58 :LKRGFVRRE T0360 90 :L 1sfxA 68 :V T0360 91 :NNRF 1sfxA 70 :KGWV T0360 96 :GEV 1sfxA 74 :GYI T0360 99 :TPEE 1sfxA 81 :KPEK T0360 109 :HPFVQQALQQQSAQAAAET 1sfxA 85 :VLKEFKSSILGEIERIEKM Number of specific fragments extracted= 11 number of extra gaps= 0 total=115 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 1sfxA/T0360-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1sfxA/T0360-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0360-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sfxA in template set T0360 2 :TQETALGAALKSAVQTMSKKKQTEMIADHIYGK 1sfxA 3 :NPLGELVKALEKLSFKPSDVRIYSLLLERGGMR T0360 49 :DQDLIAAL 1sfxA 36 :VSEIAREL T0360 58 :QYDAALIARVLAN 1sfxA 44 :DLSARFVRDRLKV T0360 80 :ALARGGKRFD 1sfxA 57 :LLKRGFVRRE T0360 91 :NNRFK 1sfxA 70 :KGWVG T0360 97 :E 1sfxA 75 :Y T0360 99 :TPE 1sfxA 81 :KPE T0360 105 :IAQNHPFVQQALQQQSAQA 1sfxA 84 :KVLKEFKSSILGEIERIEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=123 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 1x8bA/T0360-1x8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x8bA expands to /projects/compbio/data/pdb/1x8b.pdb.gz 1x8bA:# T0360 read from 1x8bA/T0360-1x8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8bA read from 1x8bA/T0360-1x8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x8bA to template set # found chain 1x8bA in template set T0360 48 :IDQDLIAAL 1x8bA 384 :LADAISENY T0360 58 :Q 1x8bA 395 :M T0360 59 :YDAALIARVLANHCRRPRYLK 1x8bA 398 :FKEAELKDLLLQVGRGLRYIH Number of specific fragments extracted= 3 number of extra gaps= 0 total=126 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 1x8bA/T0360-1x8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1x8bA/T0360-1x8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8bA read from 1x8bA/T0360-1x8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x8bA in template set T0360 48 :IDQDLIAAL 1x8bA 384 :LADAISENY T0360 57 :PQ 1x8bA 395 :MS T0360 59 :YDAALIARVLANHCRRPRYLKA 1x8bA 398 :FKEAELKDLLLQVGRGLRYIHS Number of specific fragments extracted= 3 number of extra gaps= 0 total=129 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 1x8bA/T0360-1x8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1x8bA/T0360-1x8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8bA read from 1x8bA/T0360-1x8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x8bA in template set T0360 48 :IDQDLIAALPQ 1x8bA 384 :LADAISENYRI T0360 59 :YDAALIARVLANHCRRPRYLKA 1x8bA 398 :FKEAELKDLLLQVGRGLRYIHS Number of specific fragments extracted= 2 number of extra gaps= 0 total=131 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 1iscA/T0360-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iscA expands to /projects/compbio/data/pdb/1isc.pdb.gz 1iscA:# T0360 read from 1iscA/T0360-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0360-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iscA to template set # found chain 1iscA in template set T0360 18 :MSKKKQTEMIADHIYGKYDVFKR 1iscA 29 :KHHQTYVTNLNNLIKGTAFEGKS T0360 49 :DQDLIAALP 1iscA 52 :LEEIIRSSE T0360 61 :AALIARVLANHC 1iscA 61 :GGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNHPFVQQALQQQSAQA 1iscA 85 :GGEPTGKVAEAIAASFGSFADFKAQFTDA 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=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iscA/T0360-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1iscA/T0360-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0360-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iscA in template set T0360 19 :SKKKQTEMIADHIYGKYDVFKR 1iscA 30 :HHQTYVTNLNNLIKGTAFEGKS T0360 49 :DQDLIAAL 1iscA 52 :LEEIIRSS T0360 60 :DAALIARVLANHC 1iscA 60 :EGGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNHPFVQ 1iscA 85 :GGEPTGKVAEAIAASFGSF Number of specific fragments extracted= 5 number of extra gaps= 0 total=141 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 1iscA/T0360-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1iscA/T0360-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0360-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iscA in template set T0360 19 :SKKKQTEMIADHIYGKYDVFKR 1iscA 30 :HHQTYVTNLNNLIKGTAFEGKS T0360 49 :DQDLIAA 1iscA 52 :LEEIIRS T0360 59 :YDAALIARVLANHC 1iscA 59 :SEGGVFNNAAQVWN T0360 74 :RPRYLKALARGG 1iscA 73 :HTFYWNCLAPNA T0360 95 :KGEVTPEEQAIAQNH 1iscA 85 :GGEPTGKVAEAIAAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=146 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyvA/T0360-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yyvA expands to /projects/compbio/data/pdb/1yyv.pdb.gz 1yyvA:Skipped atom 310, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 312, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 314, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 316, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 318, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 320, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 322, because occupancy 0.490 <= existing 0.510 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 637, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 639, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 641, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 643, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 645, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 647, because occupancy 0.460 <= existing 0.540 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms # T0360 read from 1yyvA/T0360-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0360-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yyvA to template set # found chain 1yyvA in template set Warning: unaligning (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0360)S129 because last residue in template chain is (1yyvA)E122 T0360 9 :AALKSAVQTMSKKKQTEMIAD 1yyvA 20 :CPSREVLKHVTSRWGVLILVA T0360 37 :VFKRFK 1yyvA 41 :LRDGTH T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHC 1yyvA 63 :LAQSLQALE T0360 82 :ARGG 1yyvA 72 :QDGF T0360 87 :RFDLNNRFKGE 1yyvA 78 :RVSYPVVPPHV T0360 98 :VTPEEQAIA 1yyvA 92 :LTPLGEQVS T0360 110 :PFVQQA 1yyvA 104 :AALADW T0360 117 :QQQSAQAAAETL 1yyvA 110 :IELNLPQVLAQR Number of specific fragments extracted= 10 number of extra gaps= 1 total=156 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 1yyvA/T0360-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1yyvA/T0360-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0360-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yyvA in template set Warning: unaligning (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0360)S129 because last residue in template chain is (1yyvA)E122 T0360 11 :LKSAVQTMSKKKQTEMIA 1yyvA 13 :GNLFAEQCPSREVLKHVT T0360 29 :DHIYG 1yyvA 36 :LILVA T0360 37 :VFKRFK 1yyvA 41 :LRDGTH T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHCR 1yyvA 63 :LAQSLQALEQ T0360 83 :RGG 1yyvA 73 :DGF T0360 87 :RFD 1yyvA 78 :RVS T0360 93 :RFKGEVTPEEQAIA 1yyvA 87 :HVEYSLTPLGEQVS T0360 110 :PFVQQALQQQSAQ 1yyvA 104 :AALADWIELNLPQ T0360 124 :AAETL 1yyvA 117 :VLAQR Number of specific fragments extracted= 11 number of extra gaps= 1 total=167 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 1yyvA/T0360-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1yyvA/T0360-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0360-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yyvA in template set Warning: unaligning (T0360)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0360)L56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0360)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0360)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0360)Q107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0360)H109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0360 13 :SAVQTMSKKKQTEMIADHIYGKY 1yyvA 23 :REVLKHVTSRWGVLILVALRDGT T0360 49 :DQDLI 1yyvA 48 :FSDLR T0360 57 :PQYD 1yyvA 56 :GGVS T0360 64 :IARVLANHCRRP 1yyvA 63 :LAQSLQALEQDG T0360 93 :RFKGE 1yyvA 82 :PVVPP T0360 98 :VTPEEQAIA 1yyvA 92 :LTPLGEQVS T0360 110 :PFVQQAL 1yyvA 104 :AALADWI T0360 129 :SVEAEAAESS 1yyvA 111 :ELNLPQVLAQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=175 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 1v3wA/T0360-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v3wA expands to /projects/compbio/data/pdb/1v3w.pdb.gz 1v3wA:Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 1v3wA # T0360 read from 1v3wA/T0360-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0360-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v3wA to template set # found chain 1v3wA in template set T0360 87 :RFDLNNRFKGEVTPEEQAIAQNHP 1v3wA 133 :VLGVPGKVVRQLTEEEIEWTKKNA T0360 122 :QAAAETLSVEAEA 1v3wA 157 :EIYVELAEKHIKG Number of specific fragments extracted= 2 number of extra gaps= 0 total=177 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 1v3wA/T0360-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1v3wA/T0360-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0360-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v3wA in template set T0360 88 :FDLNNRFKGEVTPEEQAIAQNHPFVQQALQ 1v3wA 134 :LGVPGKVVRQLTEEEIEWTKKNAEIYVELA Number of specific fragments extracted= 1 number of extra gaps= 0 total=178 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 1v3wA/T0360-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1v3wA/T0360-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0360-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v3wA in template set T0360 91 :NNRFKGEVTPEEQAIAQNHPFVQQAL 1v3wA 137 :PGKVVRQLTEEEIEWTKKNAEIYVEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=179 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 1z7uA/T0360-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z7uA expands to /projects/compbio/data/pdb/1z7u.pdb.gz 1z7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 60, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 259, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 299, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 313, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 596, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1z7uA # T0360 read from 1z7uA/T0360-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0360-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z7uA to template set # found chain 1z7uA in template set Warning: unaligning (T0360)T127 because last residue in template chain is (1z7uA)N108 T0360 2 :TQETALG 1z7uA 4 :DKQTSIN T0360 10 :ALKSAVQTMSKKKQTEMIA 1z7uA 11 :LALSTINGKWKLSLMDELF T0360 38 :FKRFK 1z7uA 30 :QGTKR T0360 49 :DQDLIAALPQYDAALIARVLANH 1z7uA 35 :NGELMRALDGITQRVLTDRLREM T0360 81 :LARGG 1z7uA 58 :EKDGL T0360 86 :KRFDLNNRFKGE 1z7uA 64 :HRESFNELPPRV T0360 98 :VTPEEQAIAQNHPFVQQALQQQSAQAAAE 1z7uA 79 :LTPEGYALYDALSSLCHWGETFAQKKARL Number of specific fragments extracted= 7 number of extra gaps= 0 total=186 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 1z7uA/T0360-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1z7uA/T0360-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0360-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7uA in template set Warning: unaligning (T0360)E131 because last residue in template chain is (1z7uA)N108 T0360 2 :T 1z7uA 4 :D T0360 4 :ETALGAALKSAVQTMSKKKQTEMIA 1z7uA 5 :KQTSINLALSTINGKWKLSLMDELF T0360 38 :FKRFK 1z7uA 30 :QGTKR T0360 49 :DQDLIAALPQYDAALIARVLANH 1z7uA 35 :NGELMRALDGITQRVLTDRLREM T0360 81 :LARGG 1z7uA 58 :EKDGL T0360 93 :RFKGEVTPEEQAIA 1z7uA 74 :RVEYTLTPEGYALY T0360 111 :FVQQALQQQSAQAAAETLSV 1z7uA 88 :DALSSLCHWGETFAQKKARL Number of specific fragments extracted= 7 number of extra gaps= 0 total=193 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 1z7uA/T0360-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0360 read from 1z7uA/T0360-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0360-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7uA in template set T0360 3 :QETALGAALKSAVQTMSKKKQTEMIAD 1z7uA 4 :DKQTSINLALSTINGKWKLSLMDELFQ T0360 39 :KRFK 1z7uA 31 :GTKR T0360 49 :DQDLIAALPQYDAALIARVLANHCR 1z7uA 35 :NGELMRALDGITQRVLTDRLREMEK T0360 83 :RGG 1z7uA 60 :DGL T0360 93 :RFKGE 1z7uA 69 :NELPP T0360 98 :VTPEEQAIAQNHPFVQQALQQQSAQAAA 1z7uA 79 :LTPEGYALYDALSSLCHWGETFAQKKAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=199 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 1pmzA/T0360-1pmzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pmzA expands to Error: no filename for 1pmzA # T0360 read from 1pmzA/T0360-1pmzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmzA read from 1pmzA/T0360-1pmzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmzA/T0360-1pmzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pmzA expands to Error: no filename for 1pmzA # T0360 read from 1pmzA/T0360-1pmzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmzA read from 1pmzA/T0360-1pmzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pmzA/T0360-1pmzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pmzA expands to Error: no filename for 1pmzA # T0360 read from 1pmzA/T0360-1pmzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pmzA read from 1pmzA/T0360-1pmzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pmzA to template set Error: can't find template for 1pmzA or 1pmzA, so skipping it. # command:CPU_time= 12.052 sec, elapsed time= 50.206 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 39 Adding 9870 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.081 sec, elapsed time= 50.238 sec. # command:Reading probabilities from T0360.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.790 Optimizing... Probability sum: -211.534, CN propb: -211.534 weights: 0.308 constraints: 172 # command:CPU_time= 17.597 sec, elapsed time= 55.806 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 172 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 172 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 595 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 595 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 8011 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 8011 # command:CPU_time= 17.757 sec, elapsed time= 56.105 sec. # command: