# 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 T0342 numbered 1 through 188 Created new target T0342 from T0342.a2m # command:CPU_time= 6.742 sec, elapsed time= 6.782 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g0qA/T0342-2g0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g0qA expands to /projects/compbio/data/pdb/2g0q.pdb.gz 2g0qA:# T0342 read from 2g0qA/T0342-2g0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g0qA read from 2g0qA/T0342-2g0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g0qA to template set # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKL 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQR # choosing archetypes in rotamer library T0342 61 :SQTWHGGIATIFQSPGDEVWG 2g0qA 53 :FRLKGRLYPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQE 2g0qA 75 :VLMGVTSDELENLDAVE T0342 102 :SGMYVVIEVKVATQE 2g0qA 92 :GNEYERVTVGIVRED T0342 117 :GKEITCRSYLMTN 2g0qA 108 :SEKMAVKTYMWIN T0342 130 :YESAPPS 2g0qA 123 :DPDMFGE T0342 155 :EYQEKLK 2g0qA 131 :NFEEWKR T0342 178 :DIIKKG 2g0qA 138 :LHKKKF Number of specific fragments extracted= 8 number of extra gaps= 0 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 2g0qA/T0342-2g0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2g0qA/T0342-2g0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g0qA read from 2g0qA/T0342-2g0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFG 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQRFRL T0342 61 :SQ 2g0qA 56 :KG T0342 66 :GGIATIFQSPGDEVWG 2g0qA 58 :RLYPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQEG 2g0qA 75 :VLMGVTSDELENLDAVEG T0342 103 :GMYVVIEVKVATQE 2g0qA 93 :NEYERVTVGIVRED T0342 117 :GKEITCRSYLMTNYESAPPS 2g0qA 108 :SEKMAVKTYMWINKADPDMF T0342 155 :EYQEKLKAI 2g0qA 131 :NFEEWKRLH T0342 169 :TGKVSEEIEDIIKKGETQ 2g0qA 140 :KKKFIETFKKIMECKKKP Number of specific fragments extracted= 8 number of extra gaps= 0 total=16 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 2g0qA/T0342-2g0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2g0qA/T0342-2g0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g0qA read from 2g0qA/T0342-2g0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 Warning: unaligning (T0342)Q186 because last residue in template chain is (2g0qA)Q158 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKL 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQR T0342 53 :FGNSQGK 2g0qA 53 :FRLKGRL T0342 68 :IATIFQSPGDEVWG 2g0qA 60 :YPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQEG 2g0qA 75 :VLMGVTSDELENLDAVEG T0342 103 :GMYVVIEVKV 2g0qA 93 :NEYERVTVGI T0342 113 :ATQEGKEITCRSYLM 2g0qA 104 :REDNSEKMAVKTYMW T0342 128 :TNYESAPPS 2g0qA 121 :KADPDMFGE T0342 155 :EYQEKLKAIEP 2g0qA 131 :NFEEWKRLHKK T0342 170 :GKVSEEIEDIIKKGET 2g0qA 142 :KFIETFKKIMECKKKP Number of specific fragments extracted= 9 number of extra gaps= 0 total=25 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vkbA/T0342-1vkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vkbA expands to /projects/compbio/data/pdb/1vkb.pdb.gz 1vkbA:Skipped atom 175, because occupancy 0.35 <= existing 0.650 in 1vkbA Skipped atom 177, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 181, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 233, because occupancy 0.200 <= existing 0.800 in 1vkbA Skipped atom 235, because occupancy 0.200 <= existing 0.800 in 1vkbA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 323, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 325, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 686, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 688, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 690, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 692, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 711, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 713, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 719, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 721, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 723, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 725, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 1072, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 1074, because occupancy 0.350 <= existing 0.650 in 1vkbA # T0342 read from 1vkbA/T0342-1vkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkbA read from 1vkbA/T0342-1vkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vkbA to template set # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNLLTERIH 1vkbA 0 :HMAHIFVYGTLKRGQPNH T0342 33 :LR 1vkbA 23 :HS T0342 38 :AAFFCVARLQD 1vkbA 28 :AAFRGRGCTVE T0342 49 :FKLDFGNSQG 1vkbA 40 :FPLVIAGEHN T0342 68 :IATIFQSPG 1vkbA 50 :IPWLLYLPG T0342 77 :DEVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 61 :HCVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQE 1vkbA 86 :SMYQRTALQVQVLE T0342 118 :KEITCRSYLMTN 1vkbA 108 :DSVQCFVYTTAT T0342 130 :YES 1vkbA 129 :YHE Number of specific fragments extracted= 9 number of extra gaps= 0 total=34 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vkbA/T0342-1vkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1vkbA/T0342-1vkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkbA read from 1vkbA/T0342-1vkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNLLTERIHLRN 1vkbA 0 :HMAHIFVYGTLKRGQPNHKVM T0342 36 :PSAAFFCVARLQD 1vkbA 26 :GLAAFRGRGCTVE T0342 49 :FKLDF 1vkbA 40 :FPLVI T0342 59 :KTSQTW 1vkbA 45 :AGEHNI T0342 69 :ATIFQSPG 1vkbA 51 :PWLLYLPG T0342 77 :DEVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 61 :HCVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQE 1vkbA 86 :SMYQRTALQVQVLE T0342 118 :KEITCRSYLMTN 1vkbA 108 :DSVQCFVYTTAT T0342 130 :YESAPPS 1vkbA 124 :WLFLPYH T0342 164 :EPNDYTG 1vkbA 131 :ESYDSEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=44 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 1vkbA/T0342-1vkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1vkbA/T0342-1vkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkbA read from 1vkbA/T0342-1vkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNL 1vkbA 0 :HMAHIFVYGTLK T0342 27 :LTERIH 1vkbA 16 :NHKVML T0342 33 :LRNPSAAFFCVARLQD 1vkbA 23 :HSHGLAAFRGRGCTVE T0342 49 :FKLDFGN 1vkbA 40 :FPLVIAG T0342 65 :HGGIATIFQSPGD 1vkbA 47 :EHNIPWLLYLPGK T0342 78 :EVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 62 :CVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQ 1vkbA 86 :SMYQRTALQVQVL T0342 117 :GKEITCRSYLMTNYESA 1vkbA 107 :GDSVQCFVYTTATYAPE Number of specific fragments extracted= 8 number of extra gaps= 0 total=52 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 1v30A/T0342-1v30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v30A expands to /projects/compbio/data/pdb/1v30.pdb.gz 1v30A:# T0342 read from 1v30A/T0342-1v30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v30A read from 1v30A/T0342-1v30A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v30A to template set # found chain 1v30A in template set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNS 1v30A 8 :VRIAVYGTLRKGKPLHWYLKGAKFLGEDWIEGYQLYFEYL T0342 69 :ATIFQSPG 1v30A 48 :PYAVKGKG T0342 78 :EVWGVVWKMNKSNLNSLDEQEGV 1v30A 56 :KLKVEVYEVDKETFERINEIEIG T0342 102 :SG 1v30A 79 :TG T0342 105 :YVVIEVK 1v30A 81 :YRLVEVS T0342 114 :TQEGK 1v30A 88 :TKFGK T0342 122 :CRSYLMTN 1v30A 93 :AFLWEWGS Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v30A/T0342-1v30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1v30A/T0342-1v30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v30A read from 1v30A/T0342-1v30A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v30A in template set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDF 1v30A 8 :VRIAVYGTLRKGKPLHWYLKGAKFLGEDWIEGYQLYF T0342 62 :QTW 1v30A 45 :EYL T0342 69 :ATIFQSPG 1v30A 48 :PYAVKGKG T0342 78 :EVWGVVWKMNKSNLNSLDEQEG 1v30A 56 :KLKVEVYEVDKETFERINEIEI T0342 102 :SGMYVVIEVK 1v30A 78 :GTGYRLVEVS T0342 114 :TQEGK 1v30A 88 :TKFGK T0342 122 :CRSYLMTN 1v30A 93 :AFLWEWGS Number of specific fragments extracted= 7 number of extra gaps= 0 total=66 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 1v30A/T0342-1v30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1v30A/T0342-1v30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v30A read from 1v30A/T0342-1v30A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v30A in template set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNL 1v30A 8 :VRIAVYGTLR T0342 32 :HLRNPSAAFFCVARLQDFKLDFG 1v30A 23 :HWYLKGAKFLGEDWIEGYQLYFE T0342 58 :GK 1v30A 46 :YL T0342 69 :ATIFQS 1v30A 48 :PYAVKG T0342 76 :GDEVWGVVWKMNKSNLNSLDEQEGV 1v30A 54 :KGKLKVEVYEVDKETFERINEIEIG T0342 103 :GMYV 1v30A 79 :TGYR T0342 109 :EVKVATQEGK 1v30A 83 :LVEVSTKFGK T0342 121 :TCRSYLMTNYES 1v30A 93 :AFLWEWGSKPRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=74 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 1xhsA/T0342-1xhsA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xhsA expands to /projects/compbio/data/pdb/1xhs.pdb.gz 1xhsA:# T0342 read from 1xhsA/T0342-1xhsA-t06-local-adpstyle5.a2m # 1xhsA read from 1xhsA/T0342-1xhsA-t06-local-adpstyle5.a2m # adding 1xhsA to template set # found chain 1xhsA in template set Warning: unaligning (T0342)F17 because first residue in template chain is (1xhsA)M1 T0342 18 :LYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKL 1xhsA 2 :RIFVYGSLRHKQGNSHWMTNAQLLGDFSIDNYQL T0342 63 :TWHGGIATIFQSPG 1xhsA 36 :YSLGHYPGAVPGNG T0342 78 :EVWGVVWKMNKSNLNSLDEQEGVK 1xhsA 50 :TVHGEVYRIDNATLAELDALRTRG T0342 103 :GMYVVIEVK 1xhsA 74 :GEYARQLIQ T0342 114 :TQEG 1xhsA 83 :TPYG T0342 121 :TCRSYLMTNYESAPPSPQYKKIIC 1xhsA 87 :SAWMYVYQRPVDGLKLIESGDWLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=80 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 1eejA/T0342-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eejA expands to /projects/compbio/data/pdb/1eej.pdb.gz 1eejA:# T0342 read from 1eejA/T0342-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0342-1eejA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eejA to template set # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDFG 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVLT T0342 65 :HGGIATI 1eejA 33 :NSGVLYI T0342 74 :SPGDE 1eejA 40 :TDDGK T0342 79 :VWGVVWKM 1eejA 116 :ITVRYLAF T0342 88 :KSNLNSLDEQE 1eejA 130 :SDAEKEMKAIW T0342 99 :GVKSGM 1eejA 178 :GVSGTP T0342 111 :KVATQEGKEIT 1eejA 184 :AVVLSNGTLVP T0342 132 :SAPPSPQYKKIICMGAKE 1eejA 195 :GYQPPKEMKEFLDEHQKM Number of specific fragments extracted= 8 number of extra gaps= 0 total=88 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 1eejA/T0342-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1eejA/T0342-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0342-1eejA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDF 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVL T0342 64 :WHGGIATI 1eejA 32 :TNSGVLYI T0342 73 :QS 1eejA 40 :TD T0342 75 :PGD 1eejA 84 :PQE T0342 120 :ITCRSYLMTN 1eejA 116 :ITVRYLAFPR T0342 130 :YESA 1eejA 127 :GLDS T0342 138 :QYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGK 1eejA 131 :DAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCD T0342 172 :VSEEIEDIIK 1eejA 166 :DIADHYALGV Number of specific fragments extracted= 8 number of extra gaps= 0 total=96 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 1eejA/T0342-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1eejA/T0342-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eejA read from 1eejA/T0342-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDF 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVL T0342 64 :WHGGIATIF 1eejA 32 :TNSGVLYIT T0342 74 :SPGDEV 1eejA 41 :DDGKHI T0342 80 :WGVVWKMN 1eejA 48 :QGPMYDVS T0342 90 :NLNSLDEQEGVKSGMY 1eejA 63 :TNKMLLKQLNALEKEM T0342 110 :VKVATQEGKEI 1eejA 79 :IVYKAPQEKHV T0342 155 :EYQEKLKAIEPN 1eejA 131 :DAEKEMKAIWCA T0342 170 :GKVSEEIEDIIKKGE 1eejA 143 :KDKNKAFDDVMAGKS Number of specific fragments extracted= 8 number of extra gaps= 0 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 1cjxA/T0342-1cjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cjxA expands to /projects/compbio/data/pdb/1cjx.pdb.gz 1cjxA:Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2047, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2049, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2051, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2459, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2461, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2464, because occupancy 0.500 <= existing 0.500 in 1cjxA # T0342 read from 1cjxA/T0342-1cjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjxA read from 1cjxA/T0342-1cjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cjxA to template set # found chain 1cjxA in template set Warning: unaligning (T0342)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1cjxA)E132 Warning: unaligning (T0342)S102 because of BadResidue code BAD_PEPTIDE at template residue (1cjxA)E132 Warning: unaligning (T0342)G103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cjxA)G133 T0342 14 :E 1cjxA 7 :P T0342 15 :ESFLYFAYGS 1cjxA 11 :MGFEFIEFAS T0342 34 :RNPS 1cjxA 21 :PTPG T0342 38 :AAFFCVARLQDFKLD 1cjxA 35 :FTKVATHRSKNVHLY T0342 63 :TWHGGIATIFQSPGDE 1cjxA 50 :RQGEINLILNNEPNSI T0342 79 :VWGVVWKM 1cjxA 77 :VCGMAFRV T0342 87 :N 1cjxA 86 :D T0342 88 :KSNLNSLDEQE 1cjxA 88 :QKAYNRALELG T0342 99 :GV 1cjxA 129 :RF T0342 104 :M 1cjxA 134 :S T0342 112 :VATQEG 1cjxA 141 :FVYLEG T0342 123 :RSYLMTN 1cjxA 241 :VAFLTDD T0342 139 :YKK 1cjxA 248 :LVK T0342 143 :ICMGAKENG 1cjxA 251 :TWDALKKIG T0342 152 :LPLEYQEKL 1cjxA 266 :PPDTYYEML T0342 161 :KAIEPNDYT 1cjxA 276 :GRLPDHGEP T0342 173 :SEEIEDI 1cjxA 285 :VDQLQAR Number of specific fragments extracted= 17 number of extra gaps= 1 total=121 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 1cjxA/T0342-1cjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1cjxA/T0342-1cjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjxA read from 1cjxA/T0342-1cjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjxA in template set Warning: unaligning (T0342)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1cjxA)E132 Warning: unaligning (T0342)S102 because of BadResidue code BAD_PEPTIDE at template residue (1cjxA)E132 Warning: unaligning (T0342)G103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cjxA)G133 T0342 16 :SFLYFAYGSN 1cjxA 12 :GFEFIEFASP T0342 26 :LLTERIHLRN 1cjxA 25 :TLEPIFEIMG T0342 38 :AAFFCVARLQDFKL 1cjxA 35 :FTKVATHRSKNVHL T0342 62 :QTWHGGIATIFQSPGD 1cjxA 49 :YRQGEINLILNNEPNS T0342 79 :VWGVVWKM 1cjxA 77 :VCGMAFRV T0342 87 :N 1cjxA 86 :D T0342 88 :KSNLNSLDEQ 1cjxA 88 :QKAYNRALEL T0342 99 :GV 1cjxA 98 :GA T0342 104 :M 1cjxA 134 :S T0342 112 :VATQEG 1cjxA 141 :FVYLEG T0342 122 :CRSYLMTN 1cjxA 240 :HVAFLTDD T0342 143 :ICMGAKENG 1cjxA 251 :TWDALKKIG T0342 152 :LPLEYQEKL 1cjxA 266 :PPDTYYEML T0342 161 :KAIEPNDYT 1cjxA 276 :GRLPDHGEP T0342 173 :SEEIEDI 1cjxA 285 :VDQLQAR Number of specific fragments extracted= 15 number of extra gaps= 1 total=136 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 1cjxA/T0342-1cjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1cjxA/T0342-1cjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjxA read from 1cjxA/T0342-1cjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjxA in template set T0342 16 :SFLYFAYGSN 1cjxA 12 :GFEFIEFASP T0342 26 :LLTERIHLRN 1cjxA 25 :TLEPIFEIMG T0342 40 :FFCVARLQDF 1cjxA 35 :FTKVATHRSK T0342 50 :KLDF 1cjxA 47 :HLYR T0342 64 :WHGGIATIFQSPGD 1cjxA 51 :QGEINLILNNEPNS T0342 79 :VWGVVWKMN 1cjxA 77 :VCGMAFRVK T0342 88 :KSNLNSLDEQ 1cjxA 88 :QKAYNRALEL T0342 103 :GMYV 1cjxA 98 :GAQP T0342 110 :VKVATQEGKEIT 1cjxA 102 :IHIDTGPMELNL T0342 122 :CRSYLMTN 1cjxA 240 :HVAFLTDD T0342 140 :KKIICMGAKENGL 1cjxA 248 :LVKTWDALKKIGM T0342 153 :PLEYQEKLKAI 1cjxA 267 :PDTYYEMLEGR T0342 165 :PNDYTGKVSEEIE 1cjxA 278 :LPDHGEPVDQLQA Number of specific fragments extracted= 13 number of extra gaps= 0 total=149 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 2bzlA/T0342-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bzlA expands to /projects/compbio/data/pdb/2bzl.pdb.gz 2bzlA:Skipped atom 1123, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1137, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1139, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 2bzlA # T0342 read from 2bzlA/T0342-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0342-2bzlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bzlA to template set # found chain 2bzlA in template set T0342 3 :NSGCKDVTGPDE 2bzlA 946 :EENRVELIPTKE T0342 33 :LRNPSAAFFCVARLQDFKLDF 2bzlA 959 :NTGYINASHIKVVVGGAEWHY T0342 68 :IATIFQSPG 2bzlA 980 :IATQGPLPH T0342 99 :GVK 2bzlA 1047 :DSV T0342 104 :MYVVIEVKVAT 2bzlA 1050 :CYATTGLKVKH T0342 115 :QEGKEITCRSYLMTN 2bzlA 1062 :LSGQERTVWHLQYTD T0342 130 :YESAPP 2bzlA 1078 :PDHGCP T0342 136 :SPQYKKIIC 2bzlA 1086 :VQGFLSYLE T0342 155 :EYQEKLKAIEPN 2bzlA 1095 :EIQSVRRHTNSM T0342 167 :DYTGKV 2bzlA 1109 :GTKNRH Number of specific fragments extracted= 10 number of extra gaps= 0 total=159 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 2bzlA/T0342-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2bzlA/T0342-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0342-2bzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bzlA in template set T0342 2 :ANSGCKDVTGPDEESFLY 2bzlA 946 :EENRVELIPTKENNTGYI T0342 38 :AAFFCVARLQDFKLDF 2bzlA 964 :NASHIKVVVGGAEWHY T0342 68 :IATIFQS 2bzlA 980 :IATQGPL T0342 100 :V 2bzlA 1048 :S T0342 103 :GMYVVIEVKVATQ 2bzlA 1049 :VCYATTGLKVKHL T0342 116 :EGKEITCRSYLMTN 2bzlA 1063 :SGQERTVWHLQYTD T0342 130 :YESAPPS 2bzlA 1078 :PDHGCPE T0342 137 :PQYKKIICMGAKE 2bzlA 1090 :LSYLEEIQSVRRH T0342 163 :IE 2bzlA 1103 :TN T0342 165 :PNDYTG 2bzlA 1107 :LEGTKN Number of specific fragments extracted= 10 number of extra gaps= 0 total=169 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 2bzlA/T0342-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2bzlA/T0342-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bzlA read from 2bzlA/T0342-2bzlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bzlA in template set T0342 42 :CVARLQDFKLDFG 2bzlA 1031 :SSATYGKFKVTTK T0342 60 :TSQTWHGGIAT 2bzlA 1044 :FRTDSVCYATT T0342 81 :G 2bzlA 1055 :G T0342 108 :IEVKVATQEGKEITCRSYLMTNYESAPPSP 2bzlA 1056 :LKVKHLLSGQERTVWHLQYTDWPDHGCPED T0342 138 :QYKKIICMGAKEN 2bzlA 1091 :SYLEEIQSVRRHT T0342 164 :EPNDYTG 2bzlA 1106 :MLEGTKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=175 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 1t5hX/T0342-1t5hX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t5hX expands to /projects/compbio/data/pdb/1t5h.pdb.gz 1t5hX:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 1t5hX/T0342-1t5hX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t5hX read from 1t5hX/T0342-1t5hX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t5hX to template set # found chain 1t5hX in template set T0342 6 :CKDVTGPDEESFLYFAYGSNLLTE 1t5hX 264 :HAGSSLKLDSLRHVTFAGATMPDA T0342 30 :RIHLRNPSAAFFCVAR 1t5hX 291 :TVHQHLPGEKVNIYGT T0342 48 :DFKLDFGNSQGKTSQTWHG 1t5hX 309 :AMNSLYMRQPKTGTEMAPG T0342 67 :GIATIFQSPGDE 1t5hX 330 :SEVRIVRIGGGV T0342 85 :KM 1t5hX 396 :RI T0342 87 :NKSN 1t5hX 400 :RVDD T0342 91 :LNSLDEQEGVKSGMYVVIEVKVATQEGKE 1t5hX 414 :PSEIERVLGTAPGVTEVVVIGLADQRWGQ T0342 121 :TCRSYLMTNYESAPPSPQYKKI 1t5hX 443 :SVTACVVPRLGETLSADALDTF T0342 147 :AKENGLPL 1t5hX 465 :CRSSELAD T0342 163 :IEPNDYTGKVSEEIEDII 1t5hX 485 :LPKNALNKVLRRQLVQQV Number of specific fragments extracted= 10 number of extra gaps= 0 total=185 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 1t5hX/T0342-1t5hX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1t5hX/T0342-1t5hX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t5hX read from 1t5hX/T0342-1t5hX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t5hX in template set T0342 3 :N 1t5hX 266 :G T0342 9 :VTGPDEESFLYFAYGSNLLTERI 1t5hX 267 :SSLKLDSLRHVTFAGATMPDAVL T0342 75 :PGDE 1t5hX 347 :NGEE T0342 81 :G 1t5hX 351 :G T0342 82 :VVWKMN 1t5hX 353 :LIVAAS T0342 88 :KSNLN 1t5hX 369 :PQATA T0342 102 :SGMYVVIEVKVATQEG 1t5hX 378 :DGWYRTSDVAVWTPEG T0342 118 :KE 1t5hX 441 :GQ T0342 121 :TCRSYLMTNYESAPPSPQYKKII 1t5hX 443 :SVTACVVPRLGETLSADALDTFC T0342 148 :KENGLPL 1t5hX 466 :RSSELAD T0342 163 :IEPNDYTGKVSEEIEDII 1t5hX 485 :LPKNALNKVLRRQLVQQV Number of specific fragments extracted= 11 number of extra gaps= 0 total=196 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 1t5hX/T0342-1t5hX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1t5hX/T0342-1t5hX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t5hX read from 1t5hX/T0342-1t5hX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t5hX in template set T0342 18 :LYFAYGSNLLTER 1t5hX 276 :HVTFAGATMPDAV T0342 31 :IHLRN 1t5hX 292 :VHQHL T0342 36 :PSAAFFCVARLQDF 1t5hX 316 :RQPKTGTEMAPGFF T0342 50 :KLDFGNSQGKTSQTW 1t5hX 331 :EVRIVRIGGGVDEIV T0342 66 :GGIATIFQSPGDEVW 1t5hX 382 :RTSDVAVWTPEGTVR T0342 81 :G 1t5hX 399 :G T0342 87 :NKSN 1t5hX 400 :RVDD T0342 91 :LNSLDEQEGVKSGMYVVIEVKVATQEGKEITCRSYLMTNYESAP 1t5hX 414 :PSEIERVLGTAPGVTEVVVIGLADQRWGQSVTACVVPRLGETLS T0342 137 :P 1t5hX 458 :A T0342 154 :LEYQEKLKAIEPND 1t5hX 459 :DALDTFCRSSELAD Number of specific fragments extracted= 10 number of extra gaps= 0 total=206 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 2fh7A/T0342-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fh7A expands to /projects/compbio/data/pdb/2fh7.pdb.gz 2fh7A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1796, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1798, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1800, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1802, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1804, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1806, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1808, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3718, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3720, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3722, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3724, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3726, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3728, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3730, because occupancy 0.500 <= existing 0.500 in 2fh7A # T0342 read from 2fh7A/T0342-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0342-2fh7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fh7A to template set # found chain 2fh7A in template set Warning: unaligning (T0342)E149 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)N150 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)G151 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 34 :RNPSAAFF 2fh7A 1505 :WPNRGTET T0342 42 :CVARLQDFKL 2fh7A 1516 :IQVTLLDTIE T0342 61 :SQTWHGGIATIFQSPGDE 2fh7A 1526 :LATFCVRTFSLHKNGSSE T0342 88 :KSNLNSLDEQE 2fh7A 1758 :AETTEDFWRML T0342 99 :GVK 2fh7A 1814 :NMP T0342 104 :MYVVIEVKVAT 2fh7A 1817 :QYILREFKVTD T0342 115 :QEGKEITCRSYLMTN 2fh7A 1829 :RDGQSRTVRQFQFTD T0342 130 :YESAPP 2fh7A 1845 :PEQGVP T0342 136 :S 2fh7A 1853 :G T0342 137 :PQYKKIICMGAK 2fh7A 1857 :IDFIGQVHKTKE T0342 152 :LP 2fh7A 1872 :QD Number of specific fragments extracted= 11 number of extra gaps= 1 total=217 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 2fh7A/T0342-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2fh7A/T0342-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0342-2fh7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fh7A in template set Warning: unaligning (T0342)A162 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)I163 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)E164 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 38 :AAFFCVARLQDFKL 2fh7A 1444 :SDYINANYVDGYRR T0342 62 :QT 2fh7A 1458 :QN T0342 67 :GIATIFQS 2fh7A 1460 :AYIATQGP T0342 76 :GDEVWG 2fh7A 1797 :ERSARY T0342 82 :VVWKMN 2fh7A 1806 :VVDPMA T0342 100 :VKSGMYVVIEVKVATQ 2fh7A 1813 :YNMPQYILREFKVTDA T0342 116 :EGKEITCRSYLMTN 2fh7A 1830 :DGQSRTVRQFQFTD T0342 130 :YESAP 2fh7A 1846 :EQGVP T0342 135 :PSPQYKKIICM 2fh7A 1852 :SGEGFIDFIGQ T0342 156 :YQEKLK 2fh7A 1863 :VHKTKE T0342 165 :P 2fh7A 1872 :Q Number of specific fragments extracted= 11 number of extra gaps= 1 total=228 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 2fh7A/T0342-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 2fh7A/T0342-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fh7A read from 2fh7A/T0342-2fh7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fh7A in template set Warning: unaligning (T0342)E149 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)N150 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)G151 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 9 :VTGPDEESFLYFAYGSN 2fh7A 1741 :IDGYRQQKAYIATQGPL T0342 26 :LLTERIHLRN 2fh7A 1759 :ETTEDFWRML T0342 41 :FCVARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPG 2fh7A 1779 :LTKLREMGREKCHQYWPAERSARYQYFVVDPMAEYN T0342 102 :SGMYVVIEVKV 2fh7A 1815 :MPQYILREFKV T0342 113 :ATQEGKEITCRSYLMTNYESAPPSP 2fh7A 1827 :DARDGQSRTVRQFQFTDWPEQGVPK T0342 138 :QYKKIICMGAK 2fh7A 1858 :DFIGQVHKTKE T0342 152 :LP 2fh7A 1872 :QD Number of specific fragments extracted= 7 number of extra gaps= 1 total=235 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 1g4wR/T0342-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g4wR expands to /projects/compbio/data/pdb/1g4w.pdb.gz 1g4wR:# T0342 read from 1g4wR/T0342-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0342-1g4wR-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g4wR to template set # found chain 1g4wR in template set T0342 60 :TSQTWHGGIATI 1g4wR 325 :LSDGMPVPVNTL T0342 73 :QSPGDE 1g4wR 337 :TFDGKP T0342 79 :VWGVVWKM 1g4wR 399 :VHTNSQKV T0342 88 :KSN 1g4wR 407 :SSA T0342 102 :SGMYVVIEVKVAT 1g4wR 412 :GEAIDQYNMQLSC T0342 116 :EGKEITCRSYLMTN 1g4wR 425 :GEKRYTIPVLHVKN T0342 130 :YESAPPSPQYKKIICMGAKENGLP 1g4wR 441 :DHQPLPSTDQLEYLADRVKNSNQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=242 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 1g4wR/T0342-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1g4wR/T0342-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0342-1g4wR-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4wR in template set T0342 35 :NPS 1g4wR 325 :LSD T0342 38 :AAFFCVARL 1g4wR 330 :PVPVNTLTF T0342 62 :QTWHGGIATIFQS 1g4wR 339 :DGKPVALAGSYPK T0342 75 :PG 1g4wR 397 :GE T0342 79 :VWGVVWKM 1g4wR 399 :VHTNSQKV T0342 88 :KSN 1g4wR 407 :SSA T0342 101 :KSGMYVVIEVKVAT 1g4wR 411 :QGEAIDQYNMQLSC T0342 116 :EGKEITCRSYLMTN 1g4wR 425 :GEKRYTIPVLHVKN T0342 130 :YESAPPSPQYKKIICMGAKENGLP 1g4wR 441 :DHQPLPSTDQLEYLADRVKNSNQN T0342 164 :EPNDYTG 1g4wR 465 :GAPGRSS Number of specific fragments extracted= 10 number of extra gaps= 0 total=252 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 1g4wR/T0342-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0342 read from 1g4wR/T0342-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g4wR read from 1g4wR/T0342-1g4wR-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g4wR in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDFGNSQGK 1g4wR 378 :EDQMQAKQLPPYFRGSYTFGEVHTNSQKVSSA T0342 100 :VKSGMYVVIEVKVATQEGKEIT 1g4wR 410 :SQGEAIDQYNMQLSCGEKRYTI T0342 122 :CRSYLMTNYESAPPSPQYKKIICMGAKEN 1g4wR 433 :VLHVKNWPDHQPLPSTDQLEYLADRVKNS Number of specific fragments extracted= 3 number of extra gaps= 0 total=255 Will force an alignment to be made, even if fragment is small Number of alignments=28 # command:CPU_time= 13.125 sec, elapsed time= 13.916 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 28 Adding 17578 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.173 sec, elapsed time= 13.971 sec. # command:Reading probabilities from T0342.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 8.813 Optimizing... Probability sum: -332.758, CN propb: -332.758 weights: 0.345 constraints: 488 # command:CPU_time= 50.742 sec, elapsed time= 51.579 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 488 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 488 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1036 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1036 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 14586 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 14586 # command:CPU_time= 51.033 sec, elapsed time= 52.090 sec. # command: