# 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 T0312 numbered 1 through 146 Created new target T0312 from T0312.a2m # command:CPU_time= 6.320 sec, elapsed time= 6.340 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xv2A/T0312-1xv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xv2A expands to /projects/compbio/data/pdb/1xv2.pdb.gz 1xv2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0312 read from 1xv2A/T0312-1xv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xv2A read from 1xv2A/T0312-1xv2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xv2A to template set # found chain 1xv2A in template set T0312 20 :KDLVRQIEEFLEEKGI 1xv2A 93 :DDVFAQIKNEMLSENL # choosing archetypes in rotamer library T0312 37 :AAHISAIGAVRSAVIGYYDQEKKEY 1xv2A 109 :FSAVKIYGTFKHMHVRMMPAQQPPY T0312 62 :VKKELME 1xv2A 144 :PEEKRQD T0312 70 :LE 1xv2A 151 :IR T0312 73 :LSLSGNVSMKD 1xv2A 153 :GAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDGEVYGGHLFSAEVFACEVFVLPLS 1xv2A 166 :GVGSAGFHIHFADDERAYGGHVLDFEVDDVVVEIQNFE 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 1xv2A/T0312-1xv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1xv2A/T0312-1xv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xv2A read from 1xv2A/T0312-1xv2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xv2A in template set T0312 9 :GKGFLLRLDYGKDLVRQIEEFLEEKG 1xv2A 82 :SKTFPLQQLSQDDVFAQIKNEMLSEN T0312 36 :HAAHISAIGAVRSAVIGYYDQEKKEY 1xv2A 108 :LFSAVKIYGTFKHMHVRMMPAQQPPY T0312 67 :MEPLE 1xv2A 142 :RQPEE T0312 72 :ILSLSGNVSMKD 1xv2A 152 :RGAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDGEVYGGHLFSAEVFACEVFVLPLS 1xv2A 166 :GVGSAGFHIHFADDERAYGGHVLDFEVDDVVVEIQNFE T0312 124 :APERAFDEQ 1xv2A 204 :TFQQHFPVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=12 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 1xv2A/T0312-1xv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1xv2A/T0312-1xv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xv2A read from 1xv2A/T0312-1xv2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xv2A in template set T0312 19 :GKDLVRQIEEF 1xv2A 92 :QDDVFAQIKNE T0312 36 :HAAHISAIGAVRSAVIGYYDQEKKE 1xv2A 108 :LFSAVKIYGTFKHMHVRMMPAQQPP T0312 61 :YVKKELME 1xv2A 143 :QPEEKRQD T0312 71 :EILSLSGNVSMKD 1xv2A 151 :IRGAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDG 1xv2A 168 :GSAGFHIHFADDERA T0312 101 :YGGHLFSAEVFACEVFVLPLS 1xv2A 183 :YGGHVLDFEVDDVVVEIQNFE Number of specific fragments extracted= 6 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 2al3A/T0312-2al3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2al3A expands to /projects/compbio/data/pdb/2al3.pdb.gz 2al3A:# T0312 read from 2al3A/T0312-2al3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2al3A read from 2al3A/T0312-2al3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2al3A to template set # found chain 2al3A in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 15 :LAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFN T0312 46 :VRSAVIGY 2al3A 47 :PSEYDLKF Number of specific fragments extracted= 2 number of extra gaps= 0 total=20 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 2al3A/T0312-2al3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 2al3A/T0312-2al3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2al3A read from 2al3A/T0312-2al3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2al3A in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 15 :LAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFN T0312 46 :VRSAVIGYYD 2al3A 47 :PSEYDLKFQR T0312 64 :KELMEPL 2al3A 57 :TVLDLSL Number of specific fragments extracted= 3 number of extra gaps= 0 total=23 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 2al3A/T0312-2al3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 2al3A/T0312-2al3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2al3A read from 2al3A/T0312-2al3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2al3A in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 16 :APNGRRHTVKVTPSTVLLQVLEDTCRRQDFN T0312 46 :VRSAVIGY 2al3A 47 :PSEYDLKF Number of specific fragments extracted= 2 number of extra gaps= 0 total=25 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 1c1yB/T0312-1c1yB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c1yB expands to /projects/compbio/data/pdb/1c1y.pdb.gz 1c1yB:Skipped atom 1478, because occupancy 0.5 <= existing 0.500 in 1c1yB Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 1c1yB # T0312 read from 1c1yB/T0312-1c1yB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c1yB read from 1c1yB/T0312-1c1yB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c1yB to template set # found chain 1c1yB in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 61 :FLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 48 :SAVIGYYDQEKKEY 1c1yB 95 :CCAVFRLLHEHKGK T0312 63 :KKELM 1c1yB 109 :KARLD Number of specific fragments extracted= 3 number of extra gaps= 0 total=28 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 1c1yB/T0312-1c1yB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1c1yB/T0312-1c1yB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c1yB read from 1c1yB/T0312-1c1yB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c1yB in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 62 :LPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 47 :RSA 1c1yB 94 :ECC T0312 50 :VIGYYDQEKKEYVKKELME 1c1yB 98 :VFRLLHEHKGKKARLDWNT Number of specific fragments extracted= 3 number of extra gaps= 0 total=31 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 1c1yB/T0312-1c1yB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1c1yB/T0312-1c1yB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c1yB read from 1c1yB/T0312-1c1yB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c1yB in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 62 :LPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 56 :QEK 1c1yB 93 :PEC T0312 113 :CEVFVLPLSGEAPERAFDEQTGLFLW 1c1yB 96 :CAVFRLLHEHKGKKARLDWNTDAASL Number of specific fragments extracted= 3 number of extra gaps= 0 total=34 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 1ys7A/T0312-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ys7A expands to /projects/compbio/data/pdb/1ys7.pdb.gz 1ys7A:# T0312 read from 1ys7A/T0312-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0312-1ys7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ys7A to template set # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAH 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVAT Number of specific fragments extracted= 1 number of extra gaps= 0 total=35 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 1ys7A/T0312-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1ys7A/T0312-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0312-1ys7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAHI 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVATA Number of specific fragments extracted= 1 number of extra gaps= 0 total=36 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 1ys7A/T0312-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1ys7A/T0312-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys7A read from 1ys7A/T0312-1ys7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAH 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVAT Number of specific fragments extracted= 1 number of extra gaps= 0 total=37 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 1wrvA/T0312-1wrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wrvA expands to /projects/compbio/data/pdb/1wrv.pdb.gz 1wrvA:# T0312 read from 1wrvA/T0312-1wrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrvA read from 1wrvA/T0312-1wrvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wrvA to template set # found chain 1wrvA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAV 1wrvA 76 :EELEEAIKEVVRRNGYRSCYIRPLAWM T0312 48 :SAVIGYY 1wrvA 116 :PAEVMVA T0312 76 :SGNVSMKDSKPFCH 1wrvA 181 :EALLLDEEGYVAEG T0312 90 :IHVLLGKDGEVYG 1wrvA 197 :ENLFFVRDGVIYA Number of specific fragments extracted= 4 number of extra gaps= 0 total=41 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wrvA/T0312-1wrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1wrvA/T0312-1wrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrvA read from 1wrvA/T0312-1wrvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrvA in template set T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 1wrvA 75 :PEELEEAIKEVVRRNGYRSCYI T0312 49 :AVIGYYDQEKKEYV 1wrvA 98 :PLAWMGAKALGVNP T0312 67 :MEPLEILSLS 1wrvA 114 :NNPAEVMVAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=44 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 1wrvA/T0312-1wrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1wrvA/T0312-1wrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrvA read from 1wrvA/T0312-1wrvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrvA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHIS 1wrvA 76 :EELEEAIKEVVRRNGYRSCYIR T0312 51 :IGYYDQEKKE 1wrvA 99 :LAWMGAKALG T0312 68 :EPLEILSLSGN 1wrvA 115 :NPAEVMVAAWE Number of specific fragments extracted= 3 number of extra gaps= 0 total=47 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 1m1hA/T0312-1m1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m1hA expands to /projects/compbio/data/pdb/1m1h.pdb.gz 1m1hA:# T0312 read from 1m1hA/T0312-1m1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1hA read from 1m1hA/T0312-1m1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m1hA to template set # found chain 1m1hA in template set T0312 3 :VFEFE 1m1hA 6 :VQELE T0312 9 :GKGFLLRLDYGK 1m1hA 11 :KKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 43 :IGAVRSAVIGY 1m1hA 48 :VPAEEKVVIRA T0312 57 :EKKEYVKKELMEPLEILSLSG 1m1hA 59 :QGKEKYRLSLKGNARDISVLG T0312 84 :SKPFCHIHV 1m1hA 80 :KKGVTTFRI T0312 96 :KDGEVYG 1m1hA 89 :ENGEVKV T0312 107 :SAEVF 1m1hA 113 :PGQKI T0312 112 :A 1m1hA 119 :C T0312 113 :CEVFVLP 1m1hA 124 :TEAKIVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=57 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 1m1hA/T0312-1m1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1m1hA/T0312-1m1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1hA read from 1m1hA/T0312-1m1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m1hA in template set Warning: unaligning (T0312)K2 because first residue in template chain is (1m1hA)Q5 T0312 3 :VFEFE 1m1hA 6 :VQELE T0312 9 :GKGFLLRLDYGK 1m1hA 11 :KKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 47 :RSAVIGY 1m1hA 52 :EKVVIRA T0312 57 :EKKEYVKKELMEPLEILSLSG 1m1hA 59 :QGKEKYRLSLKGNARDISVLG T0312 84 :SKPFCHIHV 1m1hA 80 :KKGVTTFRI T0312 96 :KDGE 1m1hA 89 :ENGE T0312 115 :VFVLPLSG 1m1hA 93 :VKVVESVE T0312 123 :EAP 1m1hA 108 :PPI T0312 126 :ERAFDEQTGLFLW 1m1hA 115 :QKITCKENKTEAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=67 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 1m1hA/T0312-1m1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1m1hA/T0312-1m1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1hA read from 1m1hA/T0312-1m1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m1hA in template set T0312 7 :EVGKGFLLRLDYGK 1m1hA 9 :LEKKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 46 :VRSAVIGYYD 1m1hA 49 :PAEEKVVIRA T0312 57 :EKKEYVKKELMEPLEILSL 1m1hA 59 :QGKEKYRLSLKGNARDISV T0312 76 :SGNVSMKDSKPFCH 1m1hA 83 :VTTFRIENGEVKVV T0312 94 :LGKDG 1m1hA 110 :ISKPG T0312 109 :EVF 1m1hA 115 :QKI T0312 112 :ACEVFVLPLSG 1m1hA 123 :KTEAKIVLDNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=75 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iyeA/T0312-1iyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iyeA expands to /projects/compbio/data/pdb/1iye.pdb.gz 1iyeA:# T0312 read from 1iyeA/T0312-1iyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iyeA read from 1iyeA/T0312-1iyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iyeA to template set # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1iyeA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKKEL 1iyeA 98 :PLIFVGDVGMGVNPPAGY T0312 69 :PLEILSLS 1iyeA 116 :STDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 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 1iyeA/T0312-1iyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1iyeA/T0312-1iyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iyeA read from 1iyeA/T0312-1iyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1iyeA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKK 1iyeA 98 :PLIFVGDVGMGVNPPA T0312 67 :MEPLEILSLS 1iyeA 114 :GYSTDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=81 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 1iyeA/T0312-1iyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1iyeA/T0312-1iyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iyeA read from 1iyeA/T0312-1iyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHIS 1iyeA 76 :DELMEACRDVIRKNNLTSAYIR T0312 49 :AVIGYYDQEKK 1iyeA 98 :PLIFVGDVGMG T0312 62 :VKKELMEPLEILSLS 1iyeA 109 :VNPPAGYSTDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=84 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 1wn2A/T0312-1wn2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1wn2A/T0312-1wn2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wn2A read from 1wn2A/T0312-1wn2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wn2A in training set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHI 1wn2A 71 :LKAEAEKLGLPNALI T0312 52 :GYYDQEK 1wn2A 86 :RDAGLTE T0312 61 :YV 1wn2A 93 :IP T0312 67 :MEPLEILSL 1wn2A 95 :PGTVTVLAV T0312 77 :G 1wn2A 104 :G Number of specific fragments extracted= 6 number of extra gaps= 0 total=90 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 1wn2A/T0312-1wn2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1wn2A/T0312-1wn2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wn2A read from 1wn2A/T0312-1wn2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wn2A in training set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHI 1wn2A 71 :LKAEAEKLGLPNALI T0312 53 :YYDQEKK 1wn2A 90 :LTEIPPG T0312 69 :PLEILS 1wn2A 97 :TVTVLA T0312 76 :SGN 1wn2A 103 :VGP Number of specific fragments extracted= 5 number of extra gaps= 0 total=95 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 1wn2A/T0312-1wn2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1wn2A/T0312-1wn2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wn2A read from 1wn2A/T0312-1wn2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wn2A in training set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHIS 1wn2A 71 :LKAEAEKLGLPNALIR T0312 54 :YDQEK 1wn2A 88 :AGLTE T0312 81 :MKDSKPFCHIHV 1wn2A 93 :IPPGTVTVLAVG Number of specific fragments extracted= 4 number of extra gaps= 0 total=99 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 1vcoA/T0312-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0312 read from 1vcoA/T0312-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0312-1vcoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vcoA to template set # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=100 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 1vcoA/T0312-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1vcoA/T0312-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0312-1vcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=101 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 1vcoA/T0312-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1vcoA/T0312-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vcoA read from 1vcoA/T0312-1vcoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=102 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 1fukA/T0312-1fukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fukA expands to /projects/compbio/data/pdb/1fuk.pdb.gz 1fukA:# T0312 read from 1fukA/T0312-1fukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fukA read from 1fukA/T0312-1fukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fukA to template set # found chain 1fukA in template set Warning: unaligning (T0312)G9 because first residue in template chain is (1fukA)I233 T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISAI 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCN Number of specific fragments extracted= 1 number of extra gaps= 0 total=103 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 1fukA/T0312-1fukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1fukA/T0312-1fukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fukA read from 1fukA/T0312-1fukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fukA in template set Warning: unaligning (T0312)G9 because first residue in template chain is (1fukA)I233 T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISAI 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCN Number of specific fragments extracted= 1 number of extra gaps= 0 total=104 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 1fukA/T0312-1fukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0312 read from 1fukA/T0312-1fukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fukA read from 1fukA/T0312-1fukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fukA in template set T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISA 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFC Number of specific fragments extracted= 1 number of extra gaps= 0 total=105 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 11.076 sec, elapsed time= 12.029 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 10585 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.103 sec, elapsed time= 12.056 sec. # command:Reading probabilities from T0312.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 4.626 Optimizing... Probability sum: -267.571, CN propb: -267.571 weights: 0.280 constraints: 540 # command:CPU_time= 17.014 sec, elapsed time= 17.991 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 540 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 540 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 358 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 358 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 8555 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 8555 # command:CPU_time= 17.184 sec, elapsed time= 18.308 sec. # command: