# 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 T0299 numbered 1 through 180 Created new target T0299 from T0299.a2m # command:CPU_time= 6.489 sec, elapsed time= 6.530 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1atg/T0299-1atg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1atg/T0299-1atg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1atg read from 1atg/T0299-1atg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1atg in training set T0299 55 :QLVEKLETFFAVHYPFIQSFSLLSLEDFEAEL 1atg 13 :GTLEQLAGQFAKQTGHAVVISSGSSGPVYAQI # choosing archetypes in rotamer library T0299 87 :ENLPA 1atg 46 :NGAPY T0299 101 :DFLFYTEG 1atg 51 :NVFFSADE T0299 113 :QVIATVESLEL 1atg 59 :KSPEKLDNQGF T0299 124 :KDEVLYFGKLGIFWGKFSEESYSKTAY 1atg 73 :GSRFTYAIGKLVLWSAKPGLVDNQGKV T0299 155 :LKVPFYRHITIRN 1atg 100 :LAGNGWRHIAISN Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 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 1atg/T0299-1atg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1atg/T0299-1atg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1atg read from 1atg/T0299-1atg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1atg in training set T0299 55 :QLVEKLETFFAVHYPFIQSFSLLSLEDFEAELEN 1atg 13 :GTLEQLAGQFAKQTGHAVVISSGSSGPVYAQIVN T0299 89 :L 1atg 48 :A T0299 99 :RKDFLFYTEG 1atg 49 :PYNVFFSADE T0299 113 :QVIATVESLEL 1atg 59 :KSPEKLDNQGF T0299 124 :KDEVLYFGKLGIFWGKFSEESYSKTAYHK 1atg 73 :GSRFTYAIGKLVLWSAKPGLVDNQGKVLA T0299 156 :KVPFYR 1atg 102 :GNGWRH T0299 163 :ITIRN 1atg 108 :IAISN T0299 168 :AKTFDKIGQMLK 1atg 119 :GLAGTQVLTHLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=14 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 1atg/T0299-1atg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1atg/T0299-1atg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1atg read from 1atg/T0299-1atg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1atg in training set T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELEN 1atg 14 :TLEQLAGQFAKQTGHAVVISSGSSGPVYAQIVN T0299 98 :ARKDFLFYTEGLDVDQVIATVESLELKDEVLYFGKLGIFWGKFSEESYSKTA 1atg 47 :GAPYNVFFSADEKSPEKLDNQGFALPGSRFTYAIGKLVLWSAKPGLVDNQGK T0299 154 :LLKVPFYRHITIRN 1atg 99 :VLAGNGWRHIAISN T0299 168 :AKTFDKIGQMLK 1atg 119 :GLAGTQVLTHLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 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 1fp1D/T0299-1fp1D-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fp1D expands to /projects/compbio/data/pdb/1fp1.pdb.gz 1fp1D:# T0299 read from 1fp1D/T0299-1fp1D-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp1D read from 1fp1D/T0299-1fp1D-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fp1D to template set # found chain 1fp1D in template set T0299 21 :MAELRQE 1fp1D 197 :MKRMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLEL 1fp1D 279 :NWSDEKCIEFLSNCHK T0299 129 :YFGKLGIFWGKFSEESYSKTAYHKYLLK 1fp1D 297 :SPNGKVIIVEFILPEEPNTSEESKLVST T0299 157 :VPF 1fp1D 332 :TVG T0299 163 :ITIRNAKTFDKIGQMLK 1fp1D 335 :GRERTEKQYEKLSKLSG Number of specific fragments extracted= 10 number of extra gaps= 0 total=28 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 1fp1D/T0299-1fp1D-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1fp1D/T0299-1fp1D-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp1D read from 1fp1D/T0299-1fp1D-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fp1D in template set T0299 23 :ELRQE 1fp1D 199 :RMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLEL 1fp1D 279 :NWSDEKCIEFLSNCHK T0299 129 :YFGKLGIFWGKFSEESYSKTAYHKYLLK 1fp1D 297 :SPNGKVIIVEFILPEEPNTSEESKLVST T0299 157 :VPF 1fp1D 332 :TVG T0299 163 :ITIRNAKTFDKIGQMLK 1fp1D 335 :GRERTEKQYEKLSKLSG Number of specific fragments extracted= 10 number of extra gaps= 0 total=38 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 1fp1D/T0299-1fp1D-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1fp1D/T0299-1fp1D-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp1D read from 1fp1D/T0299-1fp1D-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fp1D in template set T0299 22 :AELRQE 1fp1D 198 :KRMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLELK 1fp1D 279 :NWSDEKCIEFLSNCHKA T0299 128 :LYFGKLGIFWGK 1fp1D 296 :LSPNGKVIIVEF T0299 140 :FSEESYSKTAY 1fp1D 310 :PEEPNTSEESK T0299 151 :HKYLLKVPFYRH 1fp1D 325 :LDNLMFITVGGR T0299 165 :IRNAKTFDKIGQMLK 1fp1D 337 :ERTEKQYEKLSKLSG Number of specific fragments extracted= 11 number of extra gaps= 0 total=49 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 1vjrA/T0299-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.33 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0299 read from 1vjrA/T0299-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0299-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0299 21 :MAELRQELTNLGL 1vjrA 26 :SLEFLETLKEKNK T0299 37 :ESYINSGN 1vjrA 39 :RFVFFTNN T0299 49 :SIDSKAQLVEKLET 1vjrA 47 :SSLGAQDYVRKLRN T0299 63 :FFAVHYP 1vjrA 80 :HMLKRFG T0299 71 :IQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQ 1vjrA 87 :RCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYER T0299 115 :IATVESLELKDEVL 1vjrA 130 :LKKACILLRKGKFY T0299 138 :GKFSEES 1vjrA 151 :NCPSKEG T0299 146 :SKTAYHKYLLKVPFYRHITIRNAKTFDKIGQMLK 1vjrA 164 :SIMAAIEASTGRKPDLIAGKPNPLVVDVISEKFG Number of specific fragments extracted= 8 number of extra gaps= 0 total=57 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/T0299-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1vjrA/T0299-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0299-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0299 3 :RYALLVRG 1vjrA 39 :RFVFFTNN T0299 17 :NKVVMAELRQELTNLGL 1vjrA 47 :SSLGAQDYVRKLRNMGV T0299 34 :EKVES 1vjrA 68 :DAVVT T0299 63 :FFAVHYP 1vjrA 80 :HMLKRFG T0299 71 :IQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLD 1vjrA 87 :RCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLT T0299 112 :DQVIATVESLELKDEVLYFGK 1vjrA 127 :YERLKKACILLRKGKFYIATH T0299 138 :GKFSEESYSK 1vjrA 151 :NCPSKEGPVP T0299 148 :TAYHKYLLKVPFYRHITIRNAKTFDKIGQMLK 1vjrA 166 :MAAIEASTGRKPDLIAGKPNPLVVDVISEKFG Number of specific fragments extracted= 8 number of extra gaps= 0 total=65 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 1vjrA/T0299-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1vjrA/T0299-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0299-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0299 3 :RYALLVR 1vjrA 39 :RFVFFTN T0299 13 :VGG 1vjrA 46 :NSS T0299 19 :VVMAELRQELTNLGL 1vjrA 49 :LGAQDYVRKLRNMGV T0299 34 :EKVES 1vjrA 68 :DAVVT T0299 63 :FFAVHYPF 1vjrA 80 :HMLKRFGR T0299 72 :QSFSLLSLEDFEAELENLPAWWSRDL 1vjrA 88 :CRIFLLGTPQLKKVFEAYGHVIDEEN T0299 99 :RKDFLFYTEGLDVDQVIATVESLELKDEVLYFGK 1vjrA 114 :PDFVVLGFDKTLTYERLKKACILLRKGKFYIATH T0299 138 :GKFSEESYS 1vjrA 151 :NCPSKEGPV T0299 147 :KTAYHKYLLKVPFYRHITIRNAKTFDKIGQMLKK 1vjrA 165 :IMAAIEASTGRKPDLIAGKPNPLVVDVISEKFGV 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=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xzoA/T0299-1xzoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xzoA expands to /projects/compbio/data/pdb/1xzo.pdb.gz 1xzoA:# T0299 read from 1xzoA/T0299-1xzoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xzoA read from 1xzoA/T0299-1xzoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xzoA to template set # found chain 1xzoA in template set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)D125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0299)E126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0299 3 :RYALLV 1xzoA 35 :VWLADF T0299 11 :INVG 1xzoA 41 :IFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYINSGN 1xzoA 70 :VRIISFSVD T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVESL 1xzoA 101 :WDFLTGYSQSEIEEFALKS T0299 124 :K 1xzoA 135 :H T0299 127 :VLYF 1xzoA 138 :SFYL T0299 131 :GKLGIFWGKFSEESYSKTAYHKYLL 1xzoA 144 :PDGKVLKDYNGVENTPYDDIISDVK Number of specific fragments extracted= 10 number of extra gaps= 3 total=84 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 1xzoA/T0299-1xzoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1xzoA/T0299-1xzoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xzoA read from 1xzoA/T0299-1xzoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xzoA in template set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)E126 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 T0299 6 :LLVRGINVG 1xzoA 36 :WLADFIFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYINSGN 1xzoA 70 :VRIISFSVD T0299 50 :ID 1xzoA 79 :PE T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVES 1xzoA 101 :WDFLTGYSQSEIEEFALK T0299 124 :KD 1xzoA 128 :EG T0299 127 :VLYFGK 1xzoA 139 :FYLVGP T0299 133 :LGIFWGKFSEESYSKTAYHKYL 1xzoA 146 :GKVLKDYNGVENTPYDDIISDV Number of specific fragments extracted= 10 number of extra gaps= 3 total=94 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 1xzoA/T0299-1xzoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1xzoA/T0299-1xzoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xzoA read from 1xzoA/T0299-1xzoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xzoA in template set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)E126 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 Warning: unaligning (T0299)V127 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)D131 Warning: unaligning (T0299)L128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)Q132 Warning: unaligning (T0299)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)V133 Warning: unaligning (T0299)K132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0299)L133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0299 6 :LLVRGINVG 1xzoA 36 :WLADFIFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYI 1xzoA 70 :VRIIS T0299 47 :FTSID 1xzoA 75 :FSVDP T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVESL 1xzoA 101 :WDFLTGYSQSEIEEFALKS T0299 122 :ELKD 1xzoA 126 :KPEG T0299 130 :FG 1xzoA 134 :IH T0299 134 :GIFWGKFSEES 1xzoA 138 :SFYLVGPDGKV Number of specific fragments extracted= 10 number of extra gaps= 4 total=104 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 1zghA/T0299-1zghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zghA expands to /projects/compbio/data/pdb/1zgh.pdb.gz 1zghA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0299 read from 1zghA/T0299-1zghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zghA read from 1zghA/T0299-1zghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zghA to template set # found chain 1zghA in template set T0299 8 :VRGINVGGKN 1zghA 100 :ISAIKVDGGI T0299 41 :NSGNIFF 1zghA 110 :DTGDIFF T0299 49 :SIDSKAQLVEKLETFFAVHY 1zghA 122 :LYGTAEEIFMRASKIIFNDM T0299 82 :FEAELENLPAWWSRDLARKDF 1zghA 142 :IPELLTKRPVPQKQEGEATVF T0299 105 :YTEGLDVDQVIATVESLEL 1zghA 172 :ISPDFDLEKIYDYIRMLDG T0299 124 :KDEVLYFGKL 1zghA 201 :GKYRLEFSRA T0299 139 :KFSEE 1zghA 211 :SMKNG Number of specific fragments extracted= 7 number of extra gaps= 0 total=111 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 1zghA/T0299-1zghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1zghA/T0299-1zghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zghA read from 1zghA/T0299-1zghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zghA in template set Warning: unaligning (T0299)L128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zghA)I198 Warning: unaligning (T0299)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zghA)I198 T0299 8 :VRGINVGGKN 1zghA 100 :ISAIKVDGGI T0299 41 :NSGNIFFT 1zghA 110 :DTGDIFFK T0299 49 :S 1zghA 121 :D T0299 50 :IDSKAQLVEKLETFFAVHY 1zghA 123 :YGTAEEIFMRASKIIFNDM T0299 82 :FEAELENLPAWWSRDLARKDF 1zghA 142 :IPELLTKRPVPQKQEGEATVF T0299 105 :YTEGLDVDQVIATVESLELKD 1zghA 172 :ISPDFDLEKIYDYIRMLDGEG T0299 126 :EV 1zghA 195 :RA T0299 130 :FGK 1zghA 199 :KYG T0299 133 :LGIFWGKF 1zghA 203 :YRLEFSRA Number of specific fragments extracted= 9 number of extra gaps= 1 total=120 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 1zghA/T0299-1zghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1zghA/T0299-1zghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zghA read from 1zghA/T0299-1zghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zghA in template set Warning: unaligning (T0299)L89 because of BadResidue code BAD_PEPTIDE in next template residue (1zghA)S57 Warning: unaligning (T0299)P90 because of BadResidue code BAD_PEPTIDE at template residue (1zghA)S57 T0299 44 :NIFFTSI 1zghA 2 :NIIIATT T0299 53 :KAQLVEKLETFFAVHYPFIQSFSLL 1zghA 9 :KSWNIKNAQKFKKENESKYNTTIIT T0299 78 :SLEDFEAE 1zghA 39 :TFEKVKLI T0299 91 :AWWSRD 1zghA 58 :WIIPKE T0299 97 :LARKDFLFYTEGLDV 1zghA 66 :ENFTCVVFHMTDLPF T0299 114 :V 1zghA 86 :P T0299 117 :TVESLELKDEVL 1zghA 87 :LQNLIERGIKKT T0299 133 :LGIFWGKFSEESYSKTA 1zghA 99 :KISAIKVDGGIDTGDIF T0299 153 :YLLKVPFYRHI 1zghA 116 :FKRDLDLYGTA T0299 168 :AKTFDKIGQML 1zghA 127 :EEIFMRASKII Number of specific fragments extracted= 10 number of extra gaps= 1 total=130 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6nA/T0299-1t6nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t6nA expands to /projects/compbio/data/pdb/1t6n.pdb.gz 1t6nA:# T0299 read from 1t6nA/T0299-1t6nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6nA read from 1t6nA/T0299-1t6nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t6nA to template set # found chain 1t6nA in template set T0299 4 :YALLVR 1t6nA 116 :VLVMCH T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELEN 1t6nA 164 :NCPHIVVGTPGRILALARN T0299 94 :SRDLARKDFLFYTE 1t6nA 184 :SLNLKHIKHFILDE T0299 112 :DQVIATVES 1t6nA 205 :LDMRRDVQE T0299 121 :LELKDEV 1t6nA 217 :MTPHEKQ T0299 134 :GIFWGKFSEESY 1t6nA 224 :VMMFSATLSKEI T0299 148 :TAYHKYLLKVPFYRH 1t6nA 236 :RPVCRKFMQDPMEIF Number of specific fragments extracted= 10 number of extra gaps= 0 total=140 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 1t6nA/T0299-1t6nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1t6nA/T0299-1t6nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6nA read from 1t6nA/T0299-1t6nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6nA in template set T0299 4 :YALLVR 1t6nA 116 :VLVMCH T0299 20 :V 1t6nA 122 :T T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELENL 1t6nA 164 :NCPHIVVGTPGRILALARNK T0299 94 :SRDLARKDFLFYTE 1t6nA 184 :SLNLKHIKHFILDE T0299 111 :VDQVIATVESLEL 1t6nA 204 :QLDMRRDVQEIFR T0299 124 :KDEV 1t6nA 220 :HEKQ T0299 134 :GIFWGKFSEESY 1t6nA 224 :VMMFSATLSKEI T0299 148 :TAYHKYLLKVPFY 1t6nA 236 :RPVCRKFMQDPME Number of specific fragments extracted= 11 number of extra gaps= 0 total=151 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 1t6nA/T0299-1t6nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1t6nA/T0299-1t6nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6nA read from 1t6nA/T0299-1t6nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6nA in template set T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELENLPA 1t6nA 164 :NCPHIVVGTPGRILALARNKSL T0299 96 :DLARKDFLFYTE 1t6nA 186 :NLKHIKHFILDE T0299 110 :DVDQVIATVESLE 1t6nA 203 :EQLDMRRDVQEIF Number of specific fragments extracted= 6 number of extra gaps= 0 total=157 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 1ispA/T0299-1ispA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ispA expands to /projects/compbio/data/pdb/1isp.pdb.gz 1ispA:Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 162, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 165, because occupancy 0.250 <= existing 0.500 in 1ispA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 1ispA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1ispA # T0299 read from 1ispA/T0299-1ispA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ispA read from 1ispA/T0299-1ispA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ispA to template set # found chain 1ispA in template set T0299 5 :ALLVRGINVGGKN 1ispA 6 :VVMVHGIGGASFN T0299 21 :MAELRQELTNLGLEKVESYI 1ispA 19 :FAGIKSYLVSQGWSRDKLYA T0299 45 :IFFTSID 1ispA 39 :VDFWDKT T0299 53 :KAQLVEKLETFFAVHYPFIQSFSLLSL 1ispA 52 :GPVLSRFVQKVLDETGAKKVDIVAHSM T0299 85 :ELENLPAWWS 1ispA 86 :YIKNLDGGNK T0299 95 :RDLARKDFLFYTEG 1ispA 118 :DPNQKILYTSIYSS T0299 109 :LDVDQ 1ispA 136 :VMNYL T0299 121 :LELKDEVL 1ispA 141 :SRLDGARN T0299 140 :FSEESYSKTAYHK 1ispA 149 :VQIHGVGHIGLLY T0299 167 :NAKTFDKIGQMLK 1ispA 162 :SSQVNSLIKEGLN Number of specific fragments extracted= 10 number of extra gaps= 0 total=167 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 1ispA/T0299-1ispA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1ispA/T0299-1ispA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ispA read from 1ispA/T0299-1ispA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ispA in template set T0299 5 :ALLVRGI 1ispA 6 :VVMVHGI T0299 14 :GGKN 1ispA 13 :GGAS T0299 21 :MAELRQELTNLGLEKVESYI 1ispA 19 :FAGIKSYLVSQGWSRDKLYA T0299 45 :IFFTSID 1ispA 39 :VDFWDKT T0299 52 :SK 1ispA 47 :TN T0299 54 :AQLVEKLETFFAVHYPFIQSFSLLSL 1ispA 53 :PVLSRFVQKVLDETGAKKVDIVAHSM T0299 82 :FEAELENLPAWWS 1ispA 83 :TLYYIKNLDGGNK T0299 101 :DFLFY 1ispA 98 :NVVTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=175 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ispA/T0299-1ispA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1ispA/T0299-1ispA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ispA read from 1ispA/T0299-1ispA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ispA in template set T0299 5 :ALLVRGINVGGKN 1ispA 6 :VVMVHGIGGASFN T0299 21 :MAELRQELTNLGLEKVESYIN 1ispA 19 :FAGIKSYLVSQGWSRDKLYAV T0299 46 :FFTSID 1ispA 40 :DFWDKT T0299 52 :SKAQ 1ispA 47 :TNYN T0299 56 :LVEKLETFFAVHYPFIQSFSLLSL 1ispA 55 :LSRFVQKVLDETGAKKVDIVAHSM T0299 82 :FEAELENL 1ispA 83 :TLYYIKNL T0299 96 :DLARKDFLFYTEG 1ispA 91 :DGGNKVANVVTLG Number of specific fragments extracted= 7 number of extra gaps= 0 total=182 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 1ccwA/T0299-1ccwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ccwA expands to /projects/compbio/data/pdb/1ccw.pdb.gz 1ccwA:# T0299 read from 1ccwA/T0299-1ccwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ccwA read from 1ccwA/T0299-1ccwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ccwA to template set # found chain 1ccwA in template set Warning: unaligning (T0299)T2 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)K4 Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)I71 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGLE 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGFN T0299 36 :VESY 1ccwA 34 :VVNI T0299 44 :N 1ccwA 39 :V T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 72 :QSFSLLS 1ccwA 57 :AILVSSL T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFY 1ccwA 82 :GLEGILLYVG T0299 106 :TEGLDVDQVIATVESLEL 1ccwA 96 :VGKQHWPDVEKRFKDMGY T0299 138 :GKFSEESYSKTAYHKYLLKV 1ccwA 114 :DRVYAPGTPPEVGIADLKKD Number of specific fragments extracted= 11 number of extra gaps= 2 total=193 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 1ccwA/T0299-1ccwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1ccwA/T0299-1ccwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ccwA read from 1ccwA/T0299-1ccwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ccwA in template set Warning: unaligning (T0299)T2 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)K4 Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 Warning: unaligning (T0299)E107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ccwA)I94 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGL 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGF T0299 35 :KVESY 1ccwA 33 :NVVNI T0299 40 :IN 1ccwA 39 :VL T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 73 :SFSLLS 1ccwA 57 :AILVSS T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFYT 1ccwA 82 :GLEGILLYVGG T0299 108 :GLDVDQVIATVESLEL 1ccwA 98 :KQHWPDVEKRFKDMGY T0299 138 :GKFSEESYSKTAYHKYLLK 1ccwA 114 :DRVYAPGTPPEVGIADLKK Number of specific fragments extracted= 11 number of extra gaps= 3 total=204 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 1ccwA/T0299-1ccwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1ccwA/T0299-1ccwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ccwA read from 1ccwA/T0299-1ccwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ccwA in template set Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 Warning: unaligning (T0299)E107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ccwA)I94 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGL 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGF T0299 35 :KVESY 1ccwA 33 :NVVNI T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 73 :SFSLLS 1ccwA 57 :AILVSS T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFYT 1ccwA 82 :GLEGILLYVGG T0299 108 :GLDVDQVIATVESLELKD 1ccwA 98 :KQHWPDVEKRFKDMGYDR T0299 140 :FSEESYSKTA 1ccwA 116 :VYAPGTPPEV T0299 170 :TFDKIGQMLKK 1ccwA 126 :GIADLKKDLNI Number of specific fragments extracted= 11 number of extra gaps= 3 total=215 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 1u0sA/T0299-1u0sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u0sA expands to /projects/compbio/data/pdb/1u0s.pdb.gz 1u0sA:Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 1u0sA # T0299 read from 1u0sA/T0299-1u0sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u0sA read from 1u0sA/T0299-1u0sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u0sA to template set # found chain 1u0sA in template set T0299 45 :IFFT 1u0sA 183 :VILK T0299 49 :SIDSKAQL 1u0sA 189 :TQLKSARI T0299 58 :EKLETFFAV 1u0sA 197 :YLVFHKLEE T0299 68 :YPFIQSFSLLSLEDFE 1u0sA 206 :LKCEVVRTIPSVEEIE T0299 94 :SRDLARKDFLFYTEGLDVDQVIATVESLE 1u0sA 222 :EEKFENEVELFVISPVDLEKLSEALSSIA T0299 124 :KDEVLYFGK 1u0sA 251 :DIERVIIKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=221 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 1u0sA/T0299-1u0sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1u0sA/T0299-1u0sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u0sA read from 1u0sA/T0299-1u0sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u0sA in template set T0299 45 :IFFT 1u0sA 183 :VILK T0299 49 :SIDSKAQLVEKLETFFAV 1u0sA 188 :GTQLKSARIYLVFHKLEE T0299 68 :YPFIQSFSLLSLEDFE 1u0sA 206 :LKCEVVRTIPSVEEIE T0299 94 :SRDLARKDFLFYTEGLDVDQVIATVESLE 1u0sA 222 :EEKFENEVELFVISPVDLEKLSEALSSIA T0299 124 :KDEVLYFGK 1u0sA 251 :DIERVIIKE Number of specific fragments extracted= 5 number of extra gaps= 0 total=226 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 1u0sA/T0299-1u0sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1u0sA/T0299-1u0sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u0sA read from 1u0sA/T0299-1u0sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u0sA in template set T0299 22 :AELRQELTNLGLE 1u0sA 197 :YLVFHKLEELKCE T0299 46 :FFTSIDSKAQLV 1u0sA 210 :VVRTIPSVEEIE T0299 65 :AVHYPFIQSFSL 1u0sA 222 :EEKFENEVELFV T0299 78 :SLEDFEAELENLPAW 1u0sA 238 :DLEKLSEALSSIADI T0299 126 :E 1u0sA 253 :E Number of specific fragments extracted= 5 number of extra gaps= 0 total=231 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 1wdjA/T0299-1wdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wdjA expands to /projects/compbio/data/pdb/1wdj.pdb.gz 1wdjA:# T0299 read from 1wdjA/T0299-1wdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdjA read from 1wdjA/T0299-1wdjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wdjA to template set # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFT 1wdjA 34 :GRLWVS T0299 49 :SIDSK 1wdjA 41 :TGGES T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLED 1wdjA 84 :SPDAAFVERGA T0299 86 :LENLPAWWS 1wdjA 95 :WEALSEAER T0299 95 :RDLARKDFLFYTEGLDVDQVIATVESL 1wdjA 108 :PLAPKAVFEVRSASQDPEELRAKMGIY T0299 122 :ELK 1wdjA 136 :RNG T0299 127 :VLYFGKLGIFW 1wdjA 144 :LVDPYARAVEV T0299 140 :FSEESY 1wdjA 155 :FRPGKP Number of specific fragments extracted= 11 number of extra gaps= 0 total=242 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 1wdjA/T0299-1wdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1wdjA/T0299-1wdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdjA read from 1wdjA/T0299-1wdjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFTSIDSK 1wdjA 34 :GRLWVSPTGGE T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLEDFE 1wdjA 84 :SPDAAFVERGAWE T0299 84 :AELENLPAW 1wdjA 101 :AEREGFPPL T0299 97 :LARKDFLFYTEGLDVDQVIATVESLEL 1wdjA 110 :APKAVFEVRSASQDPEELRAKMGIYLR T0299 127 :VLYFGKLGIFW 1wdjA 144 :LVDPYARAVEV T0299 140 :FSEESY 1wdjA 155 :FRPGKP Number of specific fragments extracted= 9 number of extra gaps= 0 total=251 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 1wdjA/T0299-1wdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0299 read from 1wdjA/T0299-1wdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdjA read from 1wdjA/T0299-1wdjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFTSID 1wdjA 34 :GRLWVSPTG T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLE 1wdjA 84 :SPDAAFVERG T0299 85 :ELENLPAWWSRDLARKD 1wdjA 94 :AWEALSEAEREGFPPLA T0299 102 :FLFYTE 1wdjA 113 :AVFEVR T0299 108 :GLDVDQVIATVESLELKD 1wdjA 121 :SQDPEELRAKMGIYLRNG T0299 126 :EVLYFGKLGIFWGKFSEESYS 1wdjA 143 :VLVDPYARAVEVFRPGKPPLR Number of specific fragments extracted= 9 number of extra gaps= 0 total=260 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 13.008 sec, elapsed time= 13.755 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 16110 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.050 sec, elapsed time= 13.801 sec. # command:Reading probabilities from T0299.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.644 Optimizing... Probability sum: -306.124, CN propb: -306.124 weights: 0.256 constraints: 506 # command:CPU_time= 42.786 sec, elapsed time= 43.596 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 506 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 506 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1282 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1282 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 12918 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 12918 # command:CPU_time= 43.050 sec, elapsed time= 44.075 sec. # command: