# 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 T0297 numbered 1 through 211 Created new target T0297 from T0297.a2m # command:CPU_time= 6.449 sec, elapsed time= 6.568 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es9A/T0297-1es9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1es9A expands to /projects/compbio/data/pdb/1es9.pdb.gz 1es9A:# T0297 read from 1es9A/T0297-1es9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1es9A read from 1es9A/T0297-1es9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1es9A to template set # found chain 1es9A in template set Warning: unaligning (T0297)P46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)W58 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 6 :LENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1es9A 13 :PVQDVQGDGKWMSLHHRFVADSKDKEPEVVFIGDSLVQLM # choosing archetypes in rotamer library T0297 48 :Q 1es9A 59 :R T0297 52 :G 1es9A 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLD 1es9A 64 :PLHALNFGIGGDSTQHVLWRLE T0297 77 :HLYGGAVDKIFLLIGTND 1es9A 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEY 1es9A 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNP T0297 146 :SNEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 148 :LREKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 8 number of extra gaps= 4 total=8 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 1es9A/T0297-1es9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1es9A/T0297-1es9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1es9A read from 1es9A/T0297-1es9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1es9A in template set Warning: unaligning (T0297)P46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 6 :LENWLLKEQEKIQTK 1es9A 6 :NPASKPTPVQDVQGD T0297 31 :EPNILFIGDSIVEYY 1es9A 38 :EPEVVFIGDSLVQLM T0297 48 :Q 1es9A 59 :R T0297 52 :G 1es9A 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLD 1es9A 64 :PLHALNFGIGGDSTQHVLWRLE T0297 77 :HLYGGAVDKIFLLIGTND 1es9A 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEYQ 1es9A 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPL T0297 147 :NEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 149 :REKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 9 number of extra gaps= 5 total=17 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es9A/T0297-1es9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1es9A/T0297-1es9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1es9A read from 1es9A/T0297-1es9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1es9A in template set Warning: unaligning (T0297)P46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)W58 Warning: unaligning (T0297)Q48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)G52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)D75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 3 :VQLLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1es9A 10 :KPTPVQDVQGDGKWMSLHHRFVADSKDKEPEVVFIGDSLVQLM T0297 49 :E 1es9A 59 :R T0297 53 :TSKTIVNRGIRGYQTGLLLENL 1es9A 63 :SPLHALNFGIGGDSTQHVLWRL T0297 77 :HLYGGAVDKIFLLIGTNDI 1es9A 88 :ELEHIRPKIVVVWVGTNNH T0297 98 :DVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1es9A 107 :GHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQH T0297 143 :YIRSNEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLL Number of specific fragments extracted= 7 number of extra gaps= 5 total=24 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 1ivnA/T0297-1ivnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ivnA expands to /projects/compbio/data/pdb/1ivn.pdb.gz 1ivnA:# T0297 read from 1ivnA/T0297-1ivnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ivnA read from 1ivnA/T0297-1ivnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ivnA to template set # found chain 1ivnA in template set Warning: unaligning (T0297)E31 because first residue in template chain is (1ivnA)A1 T0297 32 :PNILFIGDSIVEYYPLQELFGT 1ivnA 2 :DTLLILGDSLSAGYRMSASAAW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAA T0297 121 :LTEIKLLSI 1ivnA 99 :NAEPLLMQI T0297 130 :LPVNEREEYQ 1ivnA 109 :LPANYGRRYN T0297 151 :QNWNQAYQELASAY 1ivnA 119 :EAFSAIYPKLAKEF T0297 166 :QVEFVPV 1ivnA 133 :DVPLLPF T0297 176 :LTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 140 :FMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 7 number of extra gaps= 0 total=31 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 1ivnA/T0297-1ivnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1ivnA/T0297-1ivnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ivnA read from 1ivnA/T0297-1ivnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ivnA in template set T0297 32 :PNILFIGDSIVEYYP 1ivnA 2 :DTLLILGDSLSAGYR T0297 47 :LQELFGT 1ivnA 23 :WPALLND T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAA T0297 121 :LTEIKLLSI 1ivnA 99 :NAEPLLMQI T0297 130 :LPVNEREEYQ 1ivnA 109 :LPANYGRRYN T0297 151 :QNWNQAYQELASAY 1ivnA 119 :EAFSAIYPKLAKEF T0297 166 :QVEFVPV 1ivnA 133 :DVPLLPF T0297 176 :LTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 140 :FMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 8 number of extra gaps= 0 total=39 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 1ivnA/T0297-1ivnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1ivnA/T0297-1ivnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ivnA read from 1ivnA/T0297-1ivnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ivnA in template set Warning: unaligning (T0297)E31 because first residue in template chain is (1ivnA)A1 T0297 32 :PNILFIGDSIVEYYPLQELFGT 1ivnA 2 :DTLLILGDSLSAGYRMSASAAW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRLPANYGR T0297 148 :EKIQNWNQAYQELASAY 1ivnA 116 :RYNEAFSAIYPKLAKEF T0297 166 :QVEFV 1ivnA 133 :DVPLL T0297 174 :DCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 138 :PFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=44 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 1wab/T0297-1wab-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wab expands to /projects/compbio/data/pdb/1wab.pdb.gz 1wab:Warning: there is no chain 1wab will retry with 1wabA # T0297 read from 1wab/T0297-1wab-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wab read from 1wab/T0297-1wab-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wab to template set # found chain 1wab in template set Warning: unaligning (T0297)P46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)W58 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)L50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 5 :LLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1wab 12 :TPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLM T0297 48 :QE 1wab 59 :RE T0297 52 :G 1wab 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLDA 1wab 64 :PLHALNFGIGGDSTQHVLWRLEN T0297 77 :HLYGGAVDKIFLLIGTND 1wab 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEY 1wab 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNP T0297 146 :SNEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1wab 148 :LREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 7 number of extra gaps= 2 total=51 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 1wab/T0297-1wab-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1wab/T0297-1wab-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wab read from 1wab/T0297-1wab-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wab in template set Warning: unaligning (T0297)L6 because of BadResidue code BAD_PEPTIDE at template residue (1wab)N6 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)L50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 7 :ENWLLKEQEKIQTK 1wab 7 :PASKPTPVQDVQGD T0297 31 :EPNILFIGDSIVEYYP 1wab 38 :EPEVVFIGDSLVQLMH T0297 48 :QE 1wab 59 :RE T0297 52 :G 1wab 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLDA 1wab 64 :PLHALNFGIGGDSTQHVLWRLEN T0297 77 :HLYGGAVDKIFLLIGTND 1wab 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEYQ 1wab 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPL T0297 147 :NEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1wab 149 :REKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 8 number of extra gaps= 3 total=59 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 1wab/T0297-1wab-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1wab/T0297-1wab-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wab read from 1wab/T0297-1wab-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wab in template set Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)W58 Warning: unaligning (T0297)Q48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)G52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 3 :VQLLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYYP 1wab 10 :KPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMH T0297 49 :EL 1wab 59 :RE T0297 53 :TSKTIVNRGIRGYQTGLLLENL 1wab 63 :SPLHALNFGIGGDSTQHVLWRL T0297 75 :DAHLYGGAVDKIFLLIGTNDI 1wab 86 :NGELEHIRPKIVVVWVGTNNH T0297 98 :DVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1wab 107 :GHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQH T0297 143 :YIRSNEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1wab 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLL Number of specific fragments extracted= 6 number of extra gaps= 2 total=65 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 1yzfA/T0297-1yzfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yzfA expands to /projects/compbio/data/pdb/1yzf.pdb.gz 1yzfA:# T0297 read from 1yzfA/T0297-1yzfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzfA read from 1yzfA/T0297-1yzfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yzfA to template set # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYPLQELFGT 1yzfA 2 :RKIVLFGDSITAGYLDEAVSPV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKD 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLD T0297 99 :VPVNEALNNLEAIIQSV 1yzfA 86 :ITVATFRENLETMIHEI T0297 121 :LTE 1yzfA 103 :GSE T0297 124 :IKLLSI 1yzfA 107 :VILITP T0297 130 :LPVNEREEY 1yzfA 115 :ADSGRRPER T0297 146 :SNEKIQNWNQAYQELASAY 1yzfA 124 :PQTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYLY 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=74 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 1yzfA/T0297-1yzfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1yzfA/T0297-1yzfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzfA read from 1yzfA/T0297-1yzfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYP 1yzfA 2 :RKIVLFGDSITAGYL T0297 47 :LQELFGT 1yzfA 24 :LVDLVKR T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKD 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLD T0297 99 :VPVNEALNNLEAIIQSV 1yzfA 86 :ITVATFRENLETMIHEI T0297 121 :LTE 1yzfA 103 :GSE T0297 124 :IKLLSIL 1yzfA 107 :VILITPP T0297 131 :PVNEREEYQ 1yzfA 116 :DSGRRPERP T0297 147 :NEKIQNWNQAYQELASAY 1yzfA 125 :QTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYLY 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREIK Number of specific fragments extracted= 10 number of extra gaps= 0 total=84 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 1yzfA/T0297-1yzfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1yzfA/T0297-1yzfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzfA read from 1yzfA/T0297-1yzfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYPLQELFGT 1yzfA 2 :RKIVLFGDSITAGYLDEAVSPV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIG 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDAS T0297 97 :KDVPVNEALNNLEAIIQSV 1yzfA 84 :RNITVATFRENLETMIHEI T0297 119 :YPLTEIKLLSILPVNERE 1yzfA 104 :SEKVILITPPYADSGRRP T0297 144 :IRSNEKIQNWNQAYQELASAY 1yzfA 122 :ERPQTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYL 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREI 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=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k7cA/T0297-1k7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1k7cA/T0297-1k7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k7cA read from 1k7cA/T0297-1k7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVE 1k7cA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1k7cA 20 :TNGWGEYLAS T0297 54 :SKTIVNRGIRGYQTGLL 1k7cA 32 :SATVVNDAVAGRSARSY T0297 71 :LENLDAHLYGGAV 1k7cA 51 :EGRFENIADVVTA T0297 84 :DKIFLLIGTNDIGKD 1k7cA 65 :DYVIVEFGHNDGGSL T0297 99 :VPVNEA 1k7cA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1k7cA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 133 :NEREEY 1k7cA 137 :NPWETG T0297 139 :Q 1k7cA 148 :P T0297 151 :QNWNQAYQELASAY 1k7cA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQLKK 1k7cA 163 :GVEYVDHWSYVDSIYETLGN T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 1k7cA 188 :YFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 13 number of extra gaps= 1 total=104 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 1k7cA/T0297-1k7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1k7cA/T0297-1k7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k7cA read from 1k7cA/T0297-1k7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVEYYP 1k7cA 2 :TVYLAGDSTMAKNG T0297 47 :LQELFGT 1k7cA 23 :WGEYLAS T0297 54 :SKTIVNRGIRGYQTGLLLE 1k7cA 32 :SATVVNDAVAGRSARSYTR T0297 73 :NLDAHLYGGA 1k7cA 53 :RFENIADVVT T0297 83 :VDKIFLLIGTNDIGKD 1k7cA 64 :GDYVIVEFGHNDGGSL T0297 104 :ALNNLEAIIQSVARD 1k7cA 110 :FPAYLENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 135 :REEYQQAVYIRS 1k7cA 137 :NPWETGTFVNSP T0297 151 :QNWNQAYQELASAY 1k7cA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1k7cA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 11 number of extra gaps= 1 total=115 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 1k7cA/T0297-1k7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1k7cA/T0297-1k7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k7cA read from 1k7cA/T0297-1k7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVEYYPLQELFGT 1k7cA 2 :TVYLAGDSTMAKNGGGSGTNG T0297 54 :SKTIVNRGIRGYQT 1k7cA 32 :SATVVNDAVAGRSA T0297 68 :GLLLENLDAHLYGG 1k7cA 51 :EGRFENIADVVTAG T0297 84 :DKIFLLIGTNDIG 1k7cA 65 :DYVIVEFGHNDGG T0297 103 :EALNNLEAIIQSVARD 1k7cA 109 :TFPAYLENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 133 :NER 1k7cA 137 :NPW T0297 139 :QQAVYIRSNEKIQNWNQAYQELA 1k7cA 140 :ETGTFVNSPTRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1k7cA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLK 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFL Number of specific fragments extracted= 10 number of extra gaps= 1 total=125 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 1vjgA/T0297-1vjgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjgA expands to /projects/compbio/data/pdb/1vjg.pdb.gz 1vjgA:Skipped atom 37, because occupancy 0.35 <= existing 0.650 in 1vjgA Skipped atom 39, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 41, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 43, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 418, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 422, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vjgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0297 read from 1vjgA/T0297-1vjgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjgA read from 1vjgA/T0297-1vjgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjgA to template set # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYPLQELFGT 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLY 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVS T0297 80 :GGAVDKIFLLIGTNDIGKD 1vjgA 74 :KEYNSLVVFSFGLNDTTLE T0297 99 :VPVNEALNNLEAIIQSVARD 1vjgA 98 :VSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVNEREEY 1vjgA 120 :VLMISPAPYIEQQDP T0297 140 :Q 1vjgA 135 :G T0297 146 :SNEKIQNWNQAYQELASAY 1vjgA 136 :RRRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKD 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVEN Number of specific fragments extracted= 8 number of extra gaps= 1 total=133 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 1vjgA/T0297-1vjgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1vjgA/T0297-1vjgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjgA read from 1vjgA/T0297-1vjgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYP 1vjgA 7 :TQIRICFVGDSFVNGTG T0297 47 :LQELFGT 1vjgA 30 :WTGRVCV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGG 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVSLR T0297 82 :A 1vjgA 75 :E T0297 83 :VDKIFLLIGTNDIGKD 1vjgA 77 :NSLVVFSFGLNDTTLE T0297 99 :VPVNEALNNLEAIIQSVARD 1vjgA 98 :VSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVN 1vjgA 120 :VLMISPAPYI T0297 136 :EEYQQAV 1vjgA 130 :EQQDPGR T0297 147 :NEKIQNWNQAYQELASAY 1vjgA 137 :RRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKD 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVEN Number of specific fragments extracted= 10 number of extra gaps= 1 total=143 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 1vjgA/T0297-1vjgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1vjgA/T0297-1vjgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjgA read from 1vjgA/T0297-1vjgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYPLQELFGT 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYG 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVSL T0297 81 :GAVDKIFLLIGTNDIG 1vjgA 75 :EYNSLVVFSFGLNDTT T0297 97 :KDVPVNEALNNLEAIIQSVARD 1vjgA 96 :PRVSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVNERE 1vjgA 120 :VLMISPAPYIEQQ T0297 143 :YIRSNEKIQNWNQAYQELASAY 1vjgA 133 :DPGRRRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLK 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVE Number of specific fragments extracted= 7 number of extra gaps= 1 total=150 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 1esc/T0297-1esc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1esc expands to /projects/compbio/data/pdb/1esc.pdb.gz 1esc:Warning: there is no chain 1esc will retry with 1escA # T0297 read from 1esc/T0297-1esc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1esc read from 1esc/T0297-1esc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1esc to template set # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)T53 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D28 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)Q214 Warning: unaligning (T0297)Q140 because of BadResidue code BAD_PEPTIDE at template residue (1esc)Q214 Warning: unaligning (T0297)A141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D215 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYPLQELFG 1esc 14 :SYTANFGIAPVTN T0297 54 :SKTIVNR 1esc 53 :GITLDVQ T0297 61 :GIRGYQTGLL 1esc 63 :SCGGALIHHF T0297 75 :DAHL 1esc 89 :QDAL T0297 80 :GGAVDKIFLLIGTNDIGKD 1esc 93 :KQDTQLTVGSLGGNTLGFN T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1esc 156 :DQFERVGAELEELLDRIGYFAPDAKRVLVGYPRLV T0297 135 :REEY 1esc 192 :EDTT T0297 142 :VYIRSNEKI 1esc 216 :ALPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQLKK 1esc 239 :GADFVDLYAGTGANTACDGA T0297 186 :EYT 1esc 279 :PWY T0297 192 :LHLSIAGYQALSKSLKDYL 1esc 282 :AHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 13 number of extra gaps= 4 total=163 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 1esc/T0297-1esc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1esc/T0297-1esc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1esc read from 1esc/T0297-1esc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)Q140 because of BadResidue code BAD_PEPTIDE at template residue (1esc)Q214 Warning: unaligning (T0297)A141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D215 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYP 1esc 14 :SYTANFG T0297 47 :LQELFGT 1esc 45 :ATRSLAD T0297 54 :SKTIVNRG 1esc 53 :GITLDVQA T0297 62 :IRGYQTGL 1esc 64 :CGGALIHH T0297 70 :LLENL 1esc 88 :QQDAL T0297 79 :YG 1esc 93 :KQ T0297 82 :AVDKIFLLIGTNDIGKD 1esc 95 :DTQLTVGSLGGNTLGFN T0297 101 :VNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1esc 158 :FERVGAELEELLDRIGYFAPDAKRVLVGYPRLV T0297 142 :VYIRSNEKI 1esc 216 :ALPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQ 1esc 239 :GADFVDLYAGTGANTAC T0297 183 :LKKEYT 1esc 275 :GTKIPW T0297 191 :GLHLSIAGYQALSKSLKDYL 1esc 281 :YAHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 14 number of extra gaps= 3 total=177 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 1esc/T0297-1esc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1esc/T0297-1esc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1esc read from 1esc/T0297-1esc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYP 1esc 14 :SYTANFG T0297 49 :ELFGT 1esc 29 :SERGW T0297 54 :SKTIVNRG 1esc 53 :GITLDVQA T0297 62 :IRGYQT 1esc 64 :CGGALI T0297 75 :DAHLYG 1esc 89 :QDALKQ T0297 82 :AVDKIFLLIGTNDIG 1esc 95 :DTQLTVGSLGGNTLG T0297 102 :NEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREE 1esc 159 :ERVGAELEELLDRIGYFAPDAKRVLVGYPRLVPEDT T0297 143 :YIRSNEKI 1esc 217 :LPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQ 1esc 239 :GADFVDLYAGTGANTAC T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1esc 273 :LLGTKIPWYAHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 12 number of extra gaps= 2 total=189 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 1deoA/T0297-1deoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1deoA expands to /projects/compbio/data/pdb/1deo.pdb.gz 1deoA:# T0297 read from 1deoA/T0297-1deoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1deoA read from 1deoA/T0297-1deoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1deoA to template set # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVE 1deoA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1deoA 20 :TNGWGEYLAS T0297 54 :SKTIVNRGIRGYQTGLL 1deoA 32 :SATVVNDAVAGRSARSY T0297 71 :LENLDAHLYGGAV 1deoA 51 :EGRFENIADVVTA T0297 84 :DKIFLLIGTNDIGKD 1deoA 65 :DYVIVEFGHNDGGSL T0297 99 :VPVNEA 1deoA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1deoA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSILPVNEREEY 1deoA 125 :GAKVILSSQTPNNPWETG T0297 139 :Q 1deoA 148 :P T0297 151 :QNWNQAYQELASAY 1deoA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQLKK 1deoA 163 :GVEYVDHWSYVDSIYETLGN T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 1deoA 188 :YFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=201 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 1deoA/T0297-1deoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1deoA/T0297-1deoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1deoA read from 1deoA/T0297-1deoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVEYYP 1deoA 2 :TVYLAGDSTMAKNG T0297 47 :LQELFGT 1deoA 23 :WGEYLAS T0297 54 :SKTIVNRGIRGYQTGLLLE 1deoA 32 :SATVVNDAVAGRSARSYTR T0297 73 :NLDAHLYGGA 1deoA 53 :RFENIADVVT T0297 83 :VDKIFLLIGTNDIGKD 1deoA 64 :GDYVIVEFGHNDGGSL T0297 99 :VPVNEA 1deoA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1deoA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSILPV 1deoA 125 :GAKVILSSQTPN T0297 135 :REEYQQAVYIRS 1deoA 137 :NPWETGTFVNSP T0297 151 :QNWNQAYQELASAY 1deoA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1deoA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1deoA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=213 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 1deoA/T0297-1deoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1deoA/T0297-1deoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1deoA read from 1deoA/T0297-1deoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVE 1deoA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1deoA 19 :GTNGWGEYLA T0297 54 :SKTIVNRGIRGYQT 1deoA 32 :SATVVNDAVAGRSA T0297 68 :GLLLENLDAHLYGG 1deoA 51 :EGRFENIADVVTAG T0297 84 :DKIFLLIGTNDIG 1deoA 65 :DYVIVEFGHNDGG T0297 103 :EALNNLEAIIQSVARD 1deoA 109 :TFPAYLENAAKLFTAK T0297 121 :LTEIKLLSILPVNERE 1deoA 125 :GAKVILSSQTPNNPWE T0297 139 :QQAVYIRSN 1deoA 141 :TGTFVNSPT T0297 152 :NWNQAYQELASAY 1deoA 150 :RFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1deoA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLK 1deoA 185 :VNSYFPIDHTHTSPAGAEVVAEAFL Number of specific fragments extracted= 11 number of extra gaps= 0 total=224 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 1zmbA/T0297-1zmbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zmbA expands to /projects/compbio/data/pdb/1zmb.pdb.gz 1zmbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0297 read from 1zmbA/T0297-1zmbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmbA read from 1zmbA/T0297-1zmbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zmbA to template set # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYPLQELFGT 1zmbA 4 :SFLMLGQSNMAGRGFINEVPM T0297 54 :SK 1zmbA 71 :DI T0297 56 :TIVNRGIRGYQTGLL 1zmbA 74 :GLIPCAEGGSSIDEW T0297 71 :LENLDAHLYGGAVDKIFLLIGTNDIGKD 1zmbA 99 :LTEAKFAMESSELTGILWHQGESDSLNG T0297 102 :NEALNNLEAIIQSVARDY 1zmbA 129 :KVYYKKLLLIIEALRKEL T0297 120 :PLTEIKLLSILPVNEREEYQQAVYIR 1zmbA 149 :PDIPIIIGGLGDFLGKERFGKGCTEY T0297 151 :QNWNQAYQELASAYMQVEFVPVFDCL 1zmbA 175 :NFINKELQKFAFEQDNCYFVTASGLT T0297 187 :YTTDGLHLSIAGYQALSKSLK 1zmbA 201 :CNPDGIHIDAISQRKFGLRYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=232 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmbA/T0297-1zmbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1zmbA/T0297-1zmbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmbA read from 1zmbA/T0297-1zmbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYP 1zmbA 4 :SFLMLGQSNMAGRG T0297 47 :LQELFGTSK 1zmbA 64 :WSQKNQEDI T0297 56 :TIVNRGIRGYQTGL 1zmbA 74 :GLIPCAEGGSSIDE T0297 70 :LLENLDAHLYGGAVDKIFLLIGTNDIGKD 1zmbA 98 :ALTEAKFAMESSELTGILWHQGESDSLNG T0297 102 :NEALNNLEAIIQSVARD 1zmbA 129 :KVYYKKLLLIIEALRKE T0297 119 :YPLTEIKLLSILPVNEREEYQQAVYI 1zmbA 148 :VPDIPIIIGGLGDFLGKERFGKGCTE T0297 150 :IQNWNQAYQELASAYMQVEFVPV 1zmbA 174 :YNFINKELQKFAFEQDNCYFVTA T0297 184 :KKE 1zmbA 197 :SGL T0297 187 :YTTDGLHLSIAGYQALSKSLK 1zmbA 201 :CNPDGIHIDAISQRKFGLRYF Number of specific fragments extracted= 9 number of extra gaps= 0 total=241 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 1zmbA/T0297-1zmbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1zmbA/T0297-1zmbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmbA read from 1zmbA/T0297-1zmbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYPLQELFGT 1zmbA 4 :SFLMLGQSNMAGRGFINEVPM T0297 54 :SKTIVNRGIRGYQT 1zmbA 72 :IIGLIPCAEGGSSI T0297 68 :GLLLENLDAHLYGGAVDKIFLLIGTNDIG 1zmbA 96 :RHALTEAKFAMESSELTGILWHQGESDSL T0297 98 :DVPVNEALNNLEAIIQSVAR 1zmbA 125 :NGNYKVYYKKLLLIIEALRK T0297 118 :DYPLTEIKLLSILPVNEREEYQQAVY 1zmbA 147 :NVPDIPIIIGGLGDFLGKERFGKGCT T0297 149 :KIQNWNQAYQELASAYMQVEFVPVFDCL 1zmbA 173 :EYNFINKELQKFAFEQDNCYFVTASGLT T0297 187 :YTTDGLHLSIAGYQALS 1zmbA 201 :CNPDGIHIDAISQRKFG Number of specific fragments extracted= 7 number of extra gaps= 0 total=248 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 2apjA/T0297-2apjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2apjA expands to /projects/compbio/data/pdb/2apj.pdb.gz 2apjA:Bad short name: CI2 for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: CI1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 275, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 277, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 279, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 547, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 549, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 551, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 734, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 736, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 738, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1623, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1625, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1627, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1825, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1827, because occupancy 0.350 <= existing 0.650 in 2apjA # T0297 read from 2apjA/T0297-2apjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2apjA read from 2apjA/T0297-2apjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2apjA to template set # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEP 2apjA 18 :PIPP T0297 33 :NIL 2apjA 23 :QIF T0297 36 :FIG 2apjA 27 :LSG T0297 43 :EYYP 2apjA 34 :AGRG T0297 47 :LQELFG 2apjA 42 :DHHNNR T0297 54 :SK 2apjA 111 :AV T0297 56 :TIVNRGIRGYQTGLL 2apjA 114 :GLVPCASGGTAIKEW T0297 71 :LENLDAHLY 2apjA 139 :VKRTEESRK T0297 80 :GGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 2apjA 149 :GGEIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRHD T0297 119 :YPLTEIKLLSILP 2apjA 190 :LPSLPIIQVAIAS T0297 135 :REEY 2apjA 203 :GGGY T0297 154 :NQAYQELASAYM 2apjA 207 :IDKVREAQLGLK T0297 166 :QVEFVPVFDC 2apjA 221 :NVVCVDAKGL T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 2apjA 231 :PLKSDNLHLTTEAQVQLGLSLAQAY Number of specific fragments extracted= 14 number of extra gaps= 0 total=262 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 2apjA/T0297-2apjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 2apjA/T0297-2apjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2apjA read from 2apjA/T0297-2apjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEPN 2apjA 18 :PIPPN T0297 34 :ILFIG 2apjA 25 :FILSG T0297 43 :EYYP 2apjA 34 :AGRG T0297 47 :LQELFGT 2apjA 102 :VKNRLET T0297 54 :SK 2apjA 110 :SA T0297 56 :TIVNRGIRGYQTGL 2apjA 114 :GLVPCASGGTAIKE T0297 70 :LLENLDAHLYGG 2apjA 138 :MVKRTEESRKCG T0297 82 :AVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 2apjA 151 :EIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRHD T0297 119 :YPLTEIKLLSILP 2apjA 190 :LPSLPIIQVAIAS T0297 135 :REEYQ 2apjA 203 :GGGYI T0297 151 :QNWNQAYQE 2apjA 208 :DKVREAQLG T0297 164 :YM 2apjA 217 :LK T0297 166 :QVEFVPVFDC 2apjA 221 :NVVCVDAKGL T0297 187 :YTTDGLHLSIAGYQALSKSLKDY 2apjA 232 :LKSDNLHLTTEAQVQLGLSLAQA Number of specific fragments extracted= 14 number of extra gaps= 0 total=276 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 2apjA/T0297-2apjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 2apjA/T0297-2apjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2apjA read from 2apjA/T0297-2apjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEPNILFI 2apjA 18 :PIPPNQIFI T0297 38 :G 2apjA 29 :G T0297 43 :EYYP 2apjA 34 :AGRG T0297 54 :SKTIVNRGIRGYQT 2apjA 111 :AVIGLVPCASGGTA T0297 68 :GLLLENLDAHLYG 2apjA 136 :ERMVKRTEESRKC T0297 81 :GAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVAR 2apjA 150 :GEIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRH T0297 118 :DYPLTEIKLLSILPVNER 2apjA 189 :NLPSLPIIQVAIASGGGY T0297 150 :IQNWNQAYQE 2apjA 207 :IDKVREAQLG T0297 164 :YMQVEFVPVFDCLTD 2apjA 219 :LSNVVCVDAKGLPLK T0297 189 :TDGLHLSIAGYQALSKSLKDY 2apjA 234 :SDNLHLTTEAQVQLGLSLAQA Number of specific fragments extracted= 10 number of extra gaps= 0 total=286 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 1bwr/T0297-1bwr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwr/T0297-1bwr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwr/T0297-1bwr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwq/T0297-1bwq-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwq/T0297-1bwq-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwq/T0297-1bwq-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwp/T0297-1bwp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwp/T0297-1bwp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwp/T0297-1bwp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jrlA/T0297-1jrlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jrlA/T0297-1jrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jrlA/T0297-1jrlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxwF/T0297-1fxwF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxwF/T0297-1fxwF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxwF/T0297-1fxwF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j00A/T0297-1j00A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j00A/T0297-1j00A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j00A/T0297-1j00A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/T0297-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1hdoA/T0297-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0297-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)Y164 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 31 :EPNILFIGD 1hdoA 3 :VKKIAIFGA T0297 52 :GT 1hdoA 12 :TG T0297 54 :SKTIVNRGIRGYQT 1hdoA 27 :GYEVTVLVRDSSRL T0297 71 :LENLDAHLYG 1hdoA 58 :AADVDKTVAG T0297 83 :VDKIFLLIGTNDIGKDVP 1hdoA 68 :QDAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARD 1hdoA 86 :VMSEGARNIVAAMKAH T0297 121 :LTE 1hdoA 102 :GVD T0297 124 :IKLLSILPVNEREE 1hdoA 106 :VVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVF 1hdoA 144 :LKYVAVM Number of specific fragments extracted= 10 number of extra gaps= 2 total=296 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 1hdoA/T0297-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1hdoA/T0297-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0297-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)M165 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 32 :PNILFIG 1hdoA 4 :KKIAIFG T0297 43 :EYYP 1hdoA 11 :ATGQ T0297 47 :LQELFGT 1hdoA 36 :DSSRLPS T0297 70 :LLENLDAHLYGG 1hdoA 57 :QAADVDKTVAGQ T0297 84 :DKIFLLIGTNDIGKDVP 1hdoA 69 :DAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARD 1hdoA 86 :VMSEGARNIVAAMKAH T0297 121 :LTE 1hdoA 102 :GVD T0297 124 :IKLLSILPVNEREE 1hdoA 106 :VVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVF 1hdoA 144 :LKYVAVM T0297 174 :DCLTDQAGQLKKEYTTDG 1hdoA 152 :PHIGDQPLTGAYTVTLDG Number of specific fragments extracted= 11 number of extra gaps= 2 total=307 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 1hdoA/T0297-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1hdoA/T0297-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0297-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)L160 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 32 :PNILFIG 1hdoA 4 :KKIAIFG T0297 51 :FGT 1hdoA 11 :ATG T0297 54 :SKTIVNRGIRGYQT 1hdoA 27 :GYEVTVLVRDSSRL T0297 68 :GLLLENL 1hdoA 59 :ADVDKTV T0297 79 :Y 1hdoA 66 :A T0297 82 :AVDKIFLLIGTNDIGKDVP 1hdoA 67 :GQDAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARDYPL 1hdoA 86 :VMSEGARNIVAAMKAHGVD T0297 123 :EIKLLSILPVNEREE 1hdoA 105 :KVVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVFDC 1hdoA 144 :LKYVAVMPP Number of specific fragments extracted= 10 number of extra gaps= 2 total=317 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 1vbuA/T0297-1vbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vbuA expands to /projects/compbio/data/pdb/1vbu.pdb.gz 1vbuA:# T0297 read from 1vbuA/T0297-1vbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbuA read from 1vbuA/T0297-1vbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vbuA to template set # found chain 1vbuA in template set T0297 31 :EPNILFI 1vbuA 527 :NIYIGFA T0297 43 :EYYPLQELFGT 1vbuA 534 :AINNFWSLSDA T0297 54 :SKTIV 1vbuA 682 :DAILI T0297 71 :LENLDAHLYGGAV 1vbuA 703 :YNMIKELKEKGVP T0297 84 :DKIFLLIGTN 1vbuA 717 :DGIGFQMHID T0297 96 :GKDVPVNEALN 1vbuA 727 :YRGLNYDSFRR T0297 111 :IIQSVARD 1vbuA 738 :NLERFAKL T0297 121 :LTEIKLLSI 1vbuA 746 :GLQIYITEM T0297 130 :LPVNEREEY 1vbuA 758 :IPLSGSEEY T0297 149 :KIQNWNQAYQELAS 1vbuA 767 :YLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFDCLTDQAGQLKK 1vbuA 784 :DNPAVKAIQFWGFTDKYSWVPGF T0297 186 :EYTTDGLHLSI 1vbuA 814 :LLFDENYNPKP T0297 198 :GYQALSKSLKDYL 1vbuA 825 :CYYAIKEVLEKKI Number of specific fragments extracted= 13 number of extra gaps= 0 total=330 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 1vbuA/T0297-1vbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1vbuA/T0297-1vbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbuA read from 1vbuA/T0297-1vbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vbuA in template set Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0297)S40 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 T0297 35 :LFIG 1vbuA 594 :IVHG T0297 41 :IVEYYP 1vbuA 600 :LVWHNQ T0297 47 :LQELFGT 1vbuA 660 :WYKTIGP T0297 54 :SKTIVNRG 1vbuA 682 :DAILIYND T0297 62 :IRGYQTGLLLENLDAHLYGG 1vbuA 694 :EINAKSNFVYNMIKELKEKG T0297 82 :AVDKIFLLIGTN 1vbuA 715 :PVDGIGFQMHID T0297 96 :GKDVPVNEALNN 1vbuA 727 :YRGLNYDSFRRN T0297 112 :IQSVARD 1vbuA 739 :LERFAKL T0297 121 :LTEIKLLSI 1vbuA 746 :GLQIYITEM T0297 130 :LPVNERE 1vbuA 758 :IPLSGSE T0297 147 :NEKIQNWNQAYQELAS 1vbuA 765 :EYYLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFD 1vbuA 784 :DNPAVKAIQFWG T0297 176 :LTDQAGQ 1vbuA 796 :FTDKYSW T0297 183 :LKKEYTTDGLHLSI 1vbuA 811 :GKALLFDENYNPKP T0297 198 :GYQALSKSLKDYL 1vbuA 825 :CYYAIKEVLEKKI Number of specific fragments extracted= 15 number of extra gaps= 1 total=345 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 1vbuA/T0297-1vbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1vbuA/T0297-1vbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbuA read from 1vbuA/T0297-1vbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vbuA in template set Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0297)S40 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 T0297 36 :FIG 1vbuA 595 :VHG T0297 41 :IVEYYPLQELFGT 1vbuA 600 :LVWHNQLPGWITG T0297 54 :SKTIVNRGIRGYQT 1vbuA 682 :DAILIYNDYSIEEI T0297 68 :GLLLENLDAHLYG 1vbuA 700 :NFVYNMIKELKEK T0297 81 :GAVDKIFLLIGTN 1vbuA 714 :VPVDGIGFQMHID T0297 96 :GKDVPVNEALNNLEAI 1vbuA 727 :YRGLNYDSFRRNLERF T0297 116 :ARD 1vbuA 743 :AKL T0297 121 :LTEIKL 1vbuA 746 :GLQIYI T0297 127 :LSILPVNERE 1vbuA 755 :DVRIPLSGSE T0297 147 :NEKIQNWNQAYQELAS 1vbuA 765 :EYYLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFDC 1vbuA 784 :DNPAVKAIQFWGF T0297 183 :LKKEYTTDGLHLS 1vbuA 811 :GKALLFDENYNPK T0297 197 :AGYQALSKSLKDYL 1vbuA 824 :PCYYAIKEVLEKKI Number of specific fragments extracted= 13 number of extra gaps= 1 total=358 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 1bn7A/T0297-1bn7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bn7A expands to /projects/compbio/data/pdb/1bn7.pdb.gz 1bn7A:Skipped atom 520, because occupancy 0.120 <= existing 1.000 in 1bn7A Skipped atom 608, because occupancy 0.300 <= existing 0.560 in 1bn7A Skipped atom 610, because occupancy 0.310 <= existing 0.650 in 1bn7A Skipped atom 612, because occupancy 0.400 <= existing 0.460 in 1bn7A Skipped atom 614, because occupancy 0.420 <= existing 0.550 in 1bn7A Skipped atom 616, because occupancy 0.260 <= existing 0.270 in 1bn7A Skipped atom 983, because occupancy 0.280 <= existing 0.360 in 1bn7A Skipped atom 985, because occupancy 0.150 <= existing 0.180 in 1bn7A Skipped atom 987, because occupancy 0.120 <= existing 0.350 in 1bn7A Skipped atom 989, because occupancy 0.170 <= existing 0.200 in 1bn7A Skipped atom 1049, because occupancy 0.400 <= existing 0.450 in 1bn7A Skipped atom 1199, because occupancy 0.440 <= existing 0.750 in 1bn7A Skipped atom 1201, because occupancy 0.380 <= existing 0.880 in 1bn7A Skipped atom 1203, because occupancy 0.270 <= existing 0.860 in 1bn7A Skipped atom 1205, because occupancy 0.380 <= existing 1.000 in 1bn7A Skipped atom 1207, because occupancy 0.100 <= existing 0.740 in 1bn7A Skipped atom 1209, because occupancy 0.340 <= existing 0.950 in 1bn7A Skipped atom 1211, because occupancy 0.320 <= existing 0.870 in 1bn7A Skipped atom 1323, because occupancy 0.430 <= existing 0.540 in 1bn7A Skipped atom 2103, because occupancy 0.540 <= existing 0.590 in 1bn7A Skipped atom 2105, because occupancy 0.510 <= existing 0.630 in 1bn7A Skipped atom 2107, because occupancy 0.180 <= existing 0.480 in 1bn7A Skipped atom 2109, because occupancy 0.290 <= existing 0.400 in 1bn7A # T0297 read from 1bn7A/T0297-1bn7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bn7A read from 1bn7A/T0297-1bn7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bn7A to template set # found chain 1bn7A in template set T0297 26 :HISVVEPNILFIGD 1bn7A 38 :VGPRDGTPVLFLHG T0297 47 :LQELFGT 1bn7A 55 :SSYLWRN T0297 54 :SKT 1bn7A 87 :DLD T0297 65 :YQTGLLLENLDAHLY 1bn7A 90 :YFFDDHVRYLDAFIE T0297 80 :GGAVDKIFLLIGTN 1bn7A 131 :PERVKGIACMEFIR T0297 99 :VPVNEALNNLEAIIQSVARD 1bn7A 224 :GEPANIVALVEAYMNWLHQS T0297 121 :LTEIKLLSILPVNERE 1bn7A 244 :PVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFD 1bn7A 260 :PAEAARLAESLPNCKTVDIGP T0297 186 :EYTTDG 1bn7A 284 :YLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 10 number of extra gaps= 0 total=368 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 1bn7A/T0297-1bn7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1bn7A/T0297-1bn7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bn7A read from 1bn7A/T0297-1bn7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bn7A in template set T0297 9 :WLLKEQEKIQT 1bn7A 16 :GTGFPFDPHYV T0297 20 :KYRHLN 1bn7A 29 :LGERMH T0297 26 :HISVVEPNILFIGDSIVEYYP 1bn7A 38 :VGPRDGTPVLFLHGNPTSSYL T0297 47 :LQELFGT 1bn7A 63 :IPHVAPS T0297 54 :SKT 1bn7A 87 :DLD T0297 65 :YQTGLLLENLDAHLYGG 1bn7A 90 :YFFDDHVRYLDAFIEAL T0297 82 :AVDKIFLLIGTNDIGKD 1bn7A 133 :RVKGIACMEFIRPIPTW T0297 99 :VPVNEALNNLEAIIQSVARD 1bn7A 224 :GEPANIVALVEAYMNWLHQS T0297 121 :LTEIKLLSILPVNERE 1bn7A 244 :PVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFDC 1bn7A 260 :PAEAARLAESLPNCKTVDIGPG T0297 184 :KKEYTTDG 1bn7A 282 :LHYLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 12 number of extra gaps= 0 total=380 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 1bn7A/T0297-1bn7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1bn7A/T0297-1bn7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bn7A read from 1bn7A/T0297-1bn7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bn7A in template set T0297 28 :SVVEPNILFIGDSIVEYYPLQEL 1bn7A 40 :PRDGTPVLFLHGNPTSSYLWRNI T0297 54 :SKTIVNRGIRGYQT 1bn7A 69 :SHRCIAPDLIGMGK T0297 68 :GLLLENLDAHLYGGAVDKIFLLIGTNDIG 1bn7A 93 :DDHVRYLDAFIEALGLEEVVLVIHDWGSA T0297 97 :KDVP 1bn7A 223 :AGEP T0297 102 :NEALNNLEAIIQSVAR 1bn7A 227 :ANIVALVEAYMNWLHQ T0297 119 :YPLTEIKLLSILPVNER 1bn7A 243 :SPVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFDCL 1bn7A 260 :PAEAARLAESLPNCKTVDIGPGL T0297 185 :KEYTTDG 1bn7A 283 :HYLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 9 number of extra gaps= 0 total=389 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 1mh1/T0297-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mh1 expands to /projects/compbio/data/pdb/1mh1.pdb.gz 1mh1:Warning: there is no chain 1mh1 will retry with 1mh1A WARNING: atom 11 has residue number 1 < previous residue 2A in 1mh1 Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1mh1 Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1mh1 # T0297 read from 1mh1/T0297-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0297-1mh1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mh1 to template set # found chain 1mh1 in template set T0297 28 :SVVEPNILFIGD 1mh1 2A:SPQAIKCVVVGD T0297 54 :SKTIVNRGIRGYQTGLL 1mh1 47 :DGKPVNLGLWDTAGQED T0297 71 :LENLDAH 1mh1 65 :DRLRPLS T0297 80 :GGAVDKIFLLIGTN 1mh1 72 :YPQTDVSLICFSLV T0297 100 :PVNEA 1mh1 86 :SPASF T0297 106 :NNLEA 1mh1 91 :ENVRA T0297 111 :IIQSVARDYPLTEIKLLSIL 1mh1 97 :WYPEVRHHCPNTPIILVGTK T0297 135 :REEY 1mh1 117 :LDLR T0297 139 :QQAVYIRSNE 1mh1 122 :DKDTIEKLKE T0297 155 :QAYQELASAYMQVEFVPV 1mh1 140 :PQGLAMAKEIGAVKYLEC T0297 174 :DCLTDQA 1mh1 158 :SALTQRG T0297 199 :YQALSKSLKDYL 1mh1 165 :LKTVFDEAIRAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=401 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 1mh1/T0297-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1mh1/T0297-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0297-1mh1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh1 in template set T0297 28 :SVVEPNILFIGDS 1mh1 2A:SPQAIKCVVVGDG T0297 44 :YYP 1mh1 13 :AVG T0297 47 :LQEL 1mh1 24 :TTNA T0297 54 :SKTIVNRGIRGYQT 1mh1 47 :DGKPVNLGLWDTAG T0297 75 :DAHLYGG 1mh1 61 :QEDYDRL T0297 82 :AVDKIFLLIGTN 1mh1 74 :QTDVSLICFSLV T0297 100 :PVNE 1mh1 86 :SPAS T0297 105 :LNNLEA 1mh1 90 :FENVRA T0297 111 :IIQSVARDYPLTEIKLLSI 1mh1 97 :WYPEVRHHCPNTPIILVGT T0297 135 :REEYQQA 1mh1 116 :KLDLRDD T0297 147 :NEKIQNWNQ 1mh1 123 :KDTIEKLKE T0297 156 :AYQELASAY 1mh1 141 :QGLAMAKEI T0297 166 :QVEFVPVFDCLTDQ 1mh1 150 :GAVKYLECSALTQR T0297 198 :GYQALSKSLKDYLY 1mh1 164 :GLKTVFDEAIRAVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=415 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 1mh1/T0297-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1mh1/T0297-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh1 read from 1mh1/T0297-1mh1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh1 in template set T0297 28 :SVVEPNILFIGD 1mh1 2A:SPQAIKCVVVGD T0297 52 :GT 1mh1 12 :GA T0297 54 :SKTIVNRGIRGY 1mh1 50 :PVNLGLWDTAGQ T0297 76 :AHLYG 1mh1 62 :EDYDR T0297 81 :GAVDKIFLLIG 1mh1 73 :PQTDVSLICFS T0297 98 :DVPVNEA 1mh1 84 :LVSPASF T0297 106 :NNLEA 1mh1 91 :ENVRA T0297 111 :IIQSVARDYPLTEIKLLSIL 1mh1 97 :WYPEVRHHCPNTPIILVGTK T0297 143 :YIRSNEKIQNWNQ 1mh1 119 :LRDDKDTIEKLKE T0297 156 :AYQELASAY 1mh1 141 :QGLAMAKEI T0297 166 :QVEFVPVFDCLTDQ 1mh1 150 :GAVKYLECSALTQR T0297 198 :GYQALSKSLKD 1mh1 164 :GLKTVFDEAIR Number of specific fragments extracted= 12 number of extra gaps= 0 total=427 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 1qw9A/T0297-1qw9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1qw9A/T0297-1qw9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qw9A read from 1qw9A/T0297-1qw9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 Warning: unaligning (T0297)P171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qw9A)V297 Warning: unaligning (T0297)V172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qw9A)V297 T0297 31 :EPNILFI 1qw9A 64 :QVPIIRY T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRGIRGYQTGLL 1qw9A 120 :GAEVNMAVNLGTRGIDA T0297 74 :LDAHLY 1qw9A 137 :ARNLVE T0297 80 :GGAVDKIFL 1qw9A 164 :PHKIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :GKD 1qw9A 177 :DGP T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1qw9A 185 :KTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRN T0297 134 :EREEYQQAV 1qw9A 249 :NRDNDTANY T0297 143 :YIRSNEKIQNWNQAYQELASAYM 1qw9A 261 :SLEMDDFIRSVVAIADYVKAKKR T0297 166 :QVEFV 1qw9A 287 :TIHLS T0297 173 :FDCLTDQAGQLKK 1qw9A 298 :WYHSNEADKLIEP Number of specific fragments extracted= 12 number of extra gaps= 3 total=439 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 1qw9A/T0297-1qw9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1qw9A/T0297-1qw9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qw9A read from 1qw9A/T0297-1qw9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 Warning: unaligning (T0297)P171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qw9A)V297 Warning: unaligning (T0297)V172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qw9A)V297 T0297 23 :HLNHISVV 1qw9A 15 :KIAEIDKR T0297 31 :EPNILFI 1qw9A 64 :QVPIIRY T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRG 1qw9A 120 :GAEVNMAV T0297 62 :IRGYQTGLLLENLDAHLYGG 1qw9A 129 :LGTRGIDAARNLVEYCNHPS T0297 82 :AVDKIFL 1qw9A 166 :KIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :GKD 1qw9A 177 :DGP T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1qw9A 185 :KTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRN T0297 135 :REEYQQA 1qw9A 250 :RDNDTAN T0297 142 :VYIRSNEKIQNWNQAYQELASAYM 1qw9A 260 :LSLEMDDFIRSVVAIADYVKAKKR T0297 166 :QVEFV 1qw9A 287 :TIHLS T0297 173 :FDCLTDQAGQ 1qw9A 298 :WYHSNEADKL Number of specific fragments extracted= 13 number of extra gaps= 3 total=452 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 1qw9A/T0297-1qw9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0297 read from 1qw9A/T0297-1qw9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qw9A read from 1qw9A/T0297-1qw9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 T0297 18 :QTKYRHLNH 1qw9A 57 :IELVKELQV T0297 32 :PNILFI 1qw9A 66 :PIIRYP T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRGIRGYQ 1qw9A 120 :GAEVNMAVNLGTR T0297 67 :TGLLLENL 1qw9A 137 :ARNLVEYC T0297 81 :GAVDKIFL 1qw9A 165 :HKIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :G 1qw9A 177 :D T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNERE 1qw9A 183 :GHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPT T0297 139 :QQAV 1qw9A 223 :FAEW T0297 143 :YIRSNEKIQNWNQAYQEL 1qw9A 261 :SLEMDDFIRSVVAIADYV Number of specific fragments extracted= 11 number of extra gaps= 2 total=463 Will force an alignment to be made, even if fragment is small Number of alignments=45 # command:CPU_time= 17.527 sec, elapsed time= 31.348 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 45 Adding 22155 constraints to all_contacts Done adding distance constraints # command:CPU_time= 17.602 sec, elapsed time= 31.428 sec. # command:Reading probabilities from T0297.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 19.510 Optimizing... Probability sum: -367.252, CN propb: -367.252 weights: 0.401 constraints: 548 # command:CPU_time= 59.344 sec, elapsed time= 73.247 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 548 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 548 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1416 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1416 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 18539 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 18539 # command:CPU_time= 59.717 sec, elapsed time= 73.900 sec. # command: