# 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 T0357 numbered 1 through 141 Created new target T0357 from T0357.a2m # command:CPU_time= 6.746 sec, elapsed time= 6.783 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v7lA/T0357-1v7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v7lA expands to /projects/compbio/data/pdb/1v7l.pdb.gz 1v7lA:# T0357 read from 1v7lA/T0357-1v7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v7lA read from 1v7lA/T0357-1v7lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v7lA to template set # found chain 1v7lA in template set T0357 50 :AGRILVFPG 1v7lA 51 :PGDVVVAGK # choosing archetypes in rotamer library T0357 59 :GKGST 1v7lA 62 :GIGSS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 76 :GVA 1v7lA 78 :GIA T0357 95 :AAMAE 1v7lA 81 :GVIAE T0357 100 :IPLVEVRDE 1v7lA 100 :IPLLLGKTE T0357 113 :AVKTGDRVVVNADEGYVE 1v7lA 109 :GLKDGDLVTVNWETGEVR T0357 131 :LIELEHHH 1v7lA 131 :ILMFEPLE 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 1v7lA/T0357-1v7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1v7lA/T0357-1v7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v7lA read from 1v7lA/T0357-1v7lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v7lA in template set T0357 13 :RAEGEALVTKEYISFLGGIDKETG 1v7lA 2 :ITTGKVWKFGDDISTDEITPGRYN T0357 39 :KEDC 1v7lA 27 :TKDP T0357 50 :AGRILVFPGGKG 1v7lA 51 :PGDVVVAGKNFG T0357 62 :ST 1v7lA 65 :SS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 76 :GV 1v7lA 78 :GI T0357 94 :GAAMAE 1v7lA 80 :AGVIAE T0357 100 :IPLVEVRDEK 1v7lA 100 :IPLLLGKTEG T0357 114 :VKTGDRVVVNADEGYV 1v7lA 110 :LKDGDLVTVNWETGEV T0357 130 :ELIELEHHH 1v7lA 130 :EILMFEPLE Number of specific fragments extracted= 10 number of extra gaps= 0 total=18 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 1v7lA/T0357-1v7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1v7lA/T0357-1v7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v7lA read from 1v7lA/T0357-1v7lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v7lA in template set T0357 50 :AGRILVFPG 1v7lA 51 :PGDVVVAGK T0357 59 :GKGST 1v7lA 62 :GIGSS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 79 :PKAIINKKTETIIAVGAAMAEIPLVEVR 1v7lA 79 :IAGVIAESFGRIFYRNAINIGIPLLLGK T0357 111 :FEAVKTGDRVVVNADEGYVEL 1v7lA 107 :TEGLKDGDLVTVNWETGEVRK Number of specific fragments extracted= 5 number of extra gaps= 0 total=23 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 2d13A/T0357-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0357 read from 2d13A/T0357-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0357-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0357)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0357 52 :RILVF 2d13A 6 :DVAVL T0357 59 :GKGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 11 :YSGGKDSNYALYWALKSGLRVRYLVSMVSE T0357 100 :IPLVEVR 2d13A 64 :IPIIKGF T0357 108 :EKFFEAVKT 2d13A 80 :EDLKNVLEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=27 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 2d13A/T0357-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 2d13A/T0357-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0357-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0357)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0357 53 :ILVF 2d13A 7 :VAVL T0357 59 :GKGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 11 :YSGGKDSNYALYWALKSGLRVRYLVSMVSE T0357 100 :IPLVEVR 2d13A 64 :IPIIKGF T0357 108 :EKFFEAVKT 2d13A 80 :EDLKNVLEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=31 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 2d13A/T0357-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 2d13A/T0357-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0357-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 T0357 52 :RILVFP 2d13A 6 :DVAVLY T0357 60 :KGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 12 :SGGKDSNYALYWALKSGLRVRYLVSMVSE Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 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 2etlA/T0357-2etlA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2etlA expands to /projects/compbio/data/pdb/2etl.pdb.gz 2etlA:# T0357 read from 2etlA/T0357-2etlA-t06-local-adpstyle5.a2m # 2etlA read from 2etlA/T0357-2etlA-t06-local-adpstyle5.a2m # adding 2etlA to template set # found chain 2etlA in template set T0357 42 :CEIKGESVAGRILVFPGGKGSTVGSYVLLNLRKNGVA 2etlA 68 :EELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQD Number of specific fragments extracted= 1 number of extra gaps= 0 total=34 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 1qdlB/T0357-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qdlB expands to /projects/compbio/data/pdb/1qdl.pdb.gz 1qdlB:# T0357 read from 1qdlB/T0357-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0357-1qdlB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qdlB to template set # found chain 1qdlB in template set T0357 4 :FACRAITRGR 1qdlB 99 :RRARKVFHGK T0357 15 :EGEALVT 1qdlB 109 :ISNIILV T0357 22 :KEYISFLGGI 1qdlB 117 :NSPLSLYYGI T0357 36 :G 1qdlB 137 :S T0357 37 :IVKE 1qdlB 139 :VVDE T0357 49 :VA 1qdlB 143 :VH T0357 76 :GVAPKAIINKKTETIIA 1qdlB 145 :RPLIVDAISAEDNEIMA T0357 96 :AMAE 1qdlB 162 :IHHE T0357 100 :IPLVEV 1qdlB 167 :YPIYGV Number of specific fragments extracted= 9 number of extra gaps= 0 total=43 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 1qdlB/T0357-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1qdlB/T0357-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0357-1qdlB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qdlB in template set T0357 3 :KFACRAITRGR 1qdlB 98 :IRRARKVFHGK T0357 15 :EGEALV 1qdlB 109 :ISNIIL T0357 21 :TKEYISFLGGI 1qdlB 116 :NNSPLSLYYGI T0357 37 :IVKE 1qdlB 139 :VVDE T0357 59 :GK 1qdlB 143 :VH T0357 76 :GVAPKAIINKKTETIIAV 1qdlB 145 :RPLIVDAISAEDNEIMAI T0357 97 :MAE 1qdlB 163 :HHE T0357 100 :IPLVE 1qdlB 167 :YPIYG Number of specific fragments extracted= 8 number of extra gaps= 0 total=51 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 1qdlB/T0357-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1qdlB/T0357-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qdlB read from 1qdlB/T0357-1qdlB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qdlB in template set T0357 51 :GRILVFPGGKGS 1qdlB 47 :DRLIISPGPGTP T0357 63 :TVGSYVLLNLR 1qdlB 65 :GVSLDVIKYLG T0357 76 :GVAPKAIIN 1qdlB 76 :KRTPILGVC T0357 91 :IAVGAAMAEIP 1qdlB 85 :LGHQAIGYAFG T0357 106 :RD 1qdlB 96 :AK T0357 111 :FEAVKT 1qdlB 98 :IRRARK T0357 121 :VVNADEGY 1qdlB 104 :VFHGKISN T0357 132 :IELEHHHH 1qdlB 112 :IILVNNSP Number of specific fragments extracted= 8 number of extra gaps= 0 total=59 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 2g74A/T0357-2g74A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g74A expands to /projects/compbio/data/pdb/2g74.pdb.gz 2g74A:Skipped atom 252, because occupancy 0.35 <= existing 0.650 in 2g74A Skipped atom 254, because occupancy 0.350 <= existing 0.650 in 2g74A Skipped atom 502, because occupancy 0.350 <= existing 0.650 in 2g74A Skipped atom 504, because occupancy 0.350 <= existing 0.650 in 2g74A # T0357 read from 2g74A/T0357-2g74A-t06-local-adpstyle5.a2m # 2g74A read from 2g74A/T0357-2g74A-t06-local-adpstyle5.a2m # adding 2g74A to template set # found chain 2g74A in template set Warning: unaligning (T0357)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g74A)V117 Warning: unaligning (T0357)T87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g74A)V117 T0357 13 :RAEGEALVTKEYISFLGGIDKETG 2g74A 41 :NAKGQLLVTRRALSKKAWPGVWTN T0357 37 :I 2g74A 66 :V T0357 40 :EDCEIKGESVAGRILV 2g74A 67 :CGHPQLGESNEDAVIR T0357 56 :FPGGKGSTVGSYVLLNLRKNGVAPKAIINK 2g74A 86 :YELGVEITPPESIYPDFRFRATDPSGIVEN T0357 88 :ETIIA 2g74A 118 :CPVFA Number of specific fragments extracted= 5 number of extra gaps= 1 total=64 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 1x83A/T0357-1x83A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x83A expands to /projects/compbio/data/pdb/1x83.pdb.gz 1x83A:# T0357 read from 1x83A/T0357-1x83A-t06-local-adpstyle5.a2m # 1x83A read from 1x83A/T0357-1x83A-t06-local-adpstyle5.a2m # adding 1x83A to template set # found chain 1x83A in template set Warning: unaligning (T0357)G36 because of BadResidue code BAD_PEPTIDE in next template residue (1x83A)S65 Warning: unaligning (T0357)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1x83A)V117 Warning: unaligning (T0357)T87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1x83A)V117 T0357 13 :RAEGEALVTKEYISFLGGIDKET 1x83A 41 :NAKGQLLVTRRALSKKAWPGVWT T0357 37 :I 1x83A 66 :V T0357 40 :EDCEIKGESVAGRILV 1x83A 67 :CGHPQLGESNEDAVIR T0357 56 :FPGGKGSTVGSYVLLNLRKNGVAPKAIINK 1x83A 86 :YELGVEITPPESIYPDFRFRATDPSGIVEN T0357 88 :ETIIA 1x83A 118 :CPVFA Number of specific fragments extracted= 5 number of extra gaps= 2 total=69 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 1vi4A/T0357-1vi4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vi4A expands to /projects/compbio/data/pdb/1vi4.pdb.gz 1vi4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 187, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1vi4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0357 read from 1vi4A/T0357-1vi4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi4A read from 1vi4A/T0357-1vi4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vi4A to template set # found chain 1vi4A in template set T0357 47 :ESVAGRILVFP 1vi4A 55 :QNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 64 :VGSYVLLNLRKNGV 1vi4A 75 :MGDQLAILAIKNDW T0357 88 :ETIIAVGAA 1vi4A 89 :EGVIIYGAV T0357 101 :PLVEVRD 1vi4A 130 :VTLTMQN T0357 112 :EAVKTGDRVVVNADEGYVE 1vi4A 137 :QIVEPGDYLYADWNGILMS T0357 133 :E 1vi4A 156 :E Number of specific fragments extracted= 7 number of extra gaps= 0 total=76 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 1vi4A/T0357-1vi4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1vi4A/T0357-1vi4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi4A read from 1vi4A/T0357-1vi4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi4A in template set T0357 46 :GESVAGRILVFP 1vi4A 54 :SQNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 64 :VGSYVLLNLRKNGVA 1vi4A 75 :MGDQLAILAIKNDWE T0357 89 :TIIAVGAA 1vi4A 90 :GVIIYGAV T0357 100 :IPLVEVRD 1vi4A 110 :IKALGTSP T0357 113 :AVKTGDRVVVNADEGYV 1vi4A 138 :IVEPGDYLYADWNGILM Number of specific fragments extracted= 6 number of extra gaps= 0 total=82 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 1vi4A/T0357-1vi4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1vi4A/T0357-1vi4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi4A read from 1vi4A/T0357-1vi4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi4A in template set T0357 47 :ESVAGRILVFP 1vi4A 55 :QNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 65 :GSYVLLNLRKNGVA 1vi4A 76 :GDQLAILAIKNDWE T0357 80 :KAIINKKTETIIAV 1vi4A 90 :GVIIYGAVRDVVAM T0357 94 :GAAMAEIPLVEVRDEKFF 1vi4A 109 :GIKALGTSPFKTEKRGAG T0357 112 :EAVKTGDRVVVNADEGYV 1vi4A 137 :QIVEPGDYLYADWNGILM Number of specific fragments extracted= 6 number of extra gaps= 0 total=88 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 1ppvA/T0357-1ppvA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ppvA expands to /projects/compbio/data/pdb/1ppv.pdb.gz 1ppvA:# T0357 read from 1ppvA/T0357-1ppvA-t06-local-adpstyle5.a2m # 1ppvA read from 1ppvA/T0357-1ppvA-t06-local-adpstyle5.a2m # adding 1ppvA to template set # found chain 1ppvA in template set Warning: unaligning (T0357)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ppvA)V117 Warning: unaligning (T0357)T87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ppvA)V117 T0357 13 :RAEGEALVTKEYISFLGGIDKETG 1ppvA 41 :NAKGQLLVTRRALSKKAWPGVWTN T0357 37 :I 1ppvA 66 :V T0357 40 :EDCEIKGESVAGRILV 1ppvA 67 :CGHPQLGESNEDAVIR T0357 56 :FPGGKGSTVGSYVLLNLRKNGVAPKAIINK 1ppvA 86 :YELGVEITPPESIYPDFRYRATDPSGIVEN T0357 88 :ETIIA 1ppvA 118 :CPVFA Number of specific fragments extracted= 5 number of extra gaps= 1 total=93 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 1vbkA/T0357-1vbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vbkA expands to /projects/compbio/data/pdb/1vbk.pdb.gz 1vbkA:# T0357 read from 1vbkA/T0357-1vbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbkA read from 1vbkA/T0357-1vbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vbkA to template set # found chain 1vbkA in template set T0357 8 :AITRG 1vbkA 155 :EIMQG T0357 17 :EALVTKEYISFLGGIDKETG 1vbkA 160 :KAYIYTEKIKGWGGLPIGTE T0357 51 :GRILVFPGG 1vbkA 180 :GRMIGILHD T0357 63 :TVGSYVLLNLRKNGVA 1vbkA 189 :ELSALAIFLMMKRGVE T0357 92 :AVGAAMAE 1vbkA 205 :VIPVYIGK T0357 100 :IPLVEVRD 1vbkA 236 :GFLVVAES T0357 108 :EKFFEAVKT 1vbkA 245 :DRVLKLIRD Number of specific fragments extracted= 7 number of extra gaps= 0 total=100 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 1vbkA/T0357-1vbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1vbkA/T0357-1vbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbkA read from 1vbkA/T0357-1vbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vbkA in template set T0357 8 :AITRG 1vbkA 155 :EIMQG T0357 17 :EALVTKEYISFLGGIDKET 1vbkA 160 :KAYIYTEKIKGWGGLPIGT T0357 50 :AGRILVFPGG 1vbkA 179 :EGRMIGILHD T0357 63 :TVGSYVLLNLRKNGVAPKAIINKKTE 1vbkA 189 :ELSALAIFLMMKRGVEVIPVYIGKDD T0357 100 :IPLVEVRDEK 1vbkA 236 :GFLVVAESFD T0357 110 :FFEAVKT 1vbkA 247 :VLKLIRD Number of specific fragments extracted= 6 number of extra gaps= 0 total=106 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 1vbkA/T0357-1vbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0357 read from 1vbkA/T0357-1vbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vbkA read from 1vbkA/T0357-1vbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vbkA in template set T0357 2 :VKFACR 1vbkA 150 :IEIGIE T0357 9 :ITRG 1vbkA 156 :IMQG T0357 17 :EALVTKEYISFLGGIDKET 1vbkA 160 :KAYIYTEKIKGWGGLPIGT T0357 50 :AGRILVFPGG 1vbkA 179 :EGRMIGILHD T0357 63 :TVGSYVLLNLRKNGVAPKAIINKKTET 1vbkA 189 :ELSALAIFLMMKRGVEVIPVYIGKDDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=111 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 1q54A/T0357-1q54A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q54A expands to /projects/compbio/data/pdb/1q54.pdb.gz 1q54A:# T0357 read from 1q54A/T0357-1q54A-t06-local-adpstyle5.a2m # 1q54A read from 1q54A/T0357-1q54A-t06-local-adpstyle5.a2m # adding 1q54A to template set # found chain 1q54A in template set Warning: unaligning (T0357)K86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q54A)V117 Warning: unaligning (T0357)T87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q54A)V117 T0357 13 :RAEGEALVTKEYISFLGGIDKETG 1q54A 41 :NAKGQLLVTRRALSKKAWPGVWTN T0357 37 :I 1q54A 66 :V T0357 40 :EDCEIKGESVAGRILV 1q54A 67 :AGHPQLGESNEDAVIR T0357 56 :FPGGKGSTVGSYVLLNLRKNGVAPKAIINK 1q54A 86 :YELGVEITPPESIYPDFRYRATDPSGIVEN T0357 88 :ETIIA 1q54A 118 :CPVFA Number of specific fragments extracted= 5 number of extra gaps= 1 total=116 Will force an alignment to be made, even if fragment is small Number of alignments=20 # command:CPU_time= 10.785 sec, elapsed time= 11.415 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 20 Adding 9870 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.806 sec, elapsed time= 11.441 sec. # command:Reading probabilities from T0357.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 3.368 Optimizing... Probability sum: -277.221, CN propb: -277.221 weights: 0.260 constraints: 433 # command:CPU_time= 16.307 sec, elapsed time= 16.960 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 433 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 433 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 355 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 355 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 7990 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 7990 # command:CPU_time= 16.463 sec, elapsed time= 17.258 sec. # command: