# 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 T0367 numbered 1 through 125 Created new target T0367 from T0367.a2m # command:CPU_time= 6.341 sec, elapsed time= 6.401 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wolA/T0367-1wolA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wolA expands to /projects/compbio/data/pdb/1wol.pdb.gz 1wolA:# T0367 read from 1wolA/T0367-1wolA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wolA read from 1wolA/T0367-1wolA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wolA to template set # found chain 1wolA in template set Warning: unaligning (T0367)R87 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)E88 because of BadResidue code BAD_PEPTIDE at template residue (1wolA)T81 Warning: unaligning (T0367)E89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 Warning: unaligning (T0367)V121 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (1wolA)K122 T0367 1 :MDELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1wolA 1 :MKRVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHS # choosing archetypes in rotamer library T0367 59 :TIYLI 1wolA 58 :ISHLL T0367 71 :GLSDDDCSKLSRAFDL 1wolA 64 :NPPADILQCATFLDKQ T0367 90 :SDYGIYKE 1wolA 83 :SRYPDVYY T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1wolA 98 :YTERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 5 number of extra gaps= 2 total=5 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 1wolA/T0367-1wolA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1wolA/T0367-1wolA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wolA read from 1wolA/T0367-1wolA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wolA in template set Warning: unaligning (T0367)F84 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 Warning: unaligning (T0367)V121 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (1wolA)K122 T0367 1 :MDELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1wolA 1 :MKRVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHS T0367 59 :TIYLI 1wolA 58 :ISHLL T0367 71 :GLSDD 1wolA 64 :NPPAD T0367 76 :DCSKLSRA 1wolA 72 :CATFLDKQ T0367 86 :LREESDYGIYKE 1wolA 83 :SRYPDVYYEGAP T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1wolA 98 :YTERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 6 number of extra gaps= 3 total=11 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 1wolA/T0367-1wolA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1wolA/T0367-1wolA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wolA read from 1wolA/T0367-1wolA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wolA in template set Warning: unaligning (T0367)C77 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)S78 because of BadResidue code BAD_PEPTIDE at template residue (1wolA)T81 Warning: unaligning (T0367)K79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRGTIYL 1wolA 3 :RVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHSISHLL T0367 65 :ECREELGLSDDD 1wolA 68 :DILQCATFLDKQ T0367 80 :LSRAFDLREESDYGIY 1wolA 83 :SRYPDVYYEGAPYEYY T0367 99 :SKDLAIKILKDAEIFVQKAKNA 1wolA 99 :TERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=15 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 1ufbA/T0367-1ufbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ufbA expands to /projects/compbio/data/pdb/1ufb.pdb.gz 1ufbA:# T0367 read from 1ufbA/T0367-1ufbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufbA read from 1ufbA/T0367-1ufbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ufbA to template set # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHS T0367 59 :TIYLIWECREELGLSDDD 1ufbA 58 :ILDLLADLPEDVDVPEDL T0367 77 :CSKLSRAF 1ufbA 79 :AKVLDKYY T0367 85 :DLREESDYGIYKE 1ufbA 88 :PTRYPDAHPAGPA T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1ufbA 104 :YTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 5 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 1ufbA/T0367-1ufbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1ufbA/T0367-1ufbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufbA read from 1ufbA/T0367-1ufbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHS T0367 59 :TIYLIWECREELGLSDDDC 1ufbA 58 :ILDLLADLPEDVDVPEDLV T0367 78 :SKLSRAF 1ufbA 80 :KVLDKYY T0367 85 :DLREESDYGIYKE 1ufbA 88 :PTRYPDAHPAGPA T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1ufbA 104 :YTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=25 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 1ufbA/T0367-1ufbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1ufbA/T0367-1ufbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufbA read from 1ufbA/T0367-1ufbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRGTIYLIW 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHSILDLLAD T0367 65 :ECREELGLSDDDCSKLSRAFDLREE 1ufbA 74 :DLVEAAKVLDKYYIPTRYPDAHPAG T0367 91 :DYG 1ufbA 99 :PAA T0367 96 :KEVSKDLAIKILKDAEIFVQKAKNA 1ufbA 102 :RHYTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 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 1o3uA/T0367-1o3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o3uA expands to /projects/compbio/data/pdb/1o3u.pdb.gz 1o3uA:Skipped atom 37, because occupancy 0.4 <= existing 0.600 in 1o3uA Skipped atom 39, because occupancy 0.400 <= existing 0.600 in 1o3uA Skipped atom 41, because occupancy 0.400 <= existing 0.600 in 1o3uA Skipped atom 228, because occupancy 0.200 <= existing 0.800 in 1o3uA Skipped atom 230, because occupancy 0.200 <= existing 0.800 in 1o3uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1o3uA/T0367-1o3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3uA read from 1o3uA/T0367-1o3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o3uA to template set # found chain 1o3uA in template set Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o3uA)D86 Warning: unaligning (T0367)I94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYS T0367 59 :TIYLIWECREELGLSDDDCSKLSRAFDL 1o3uA 51 :VPDFLGELSSRFEIPEELMDHALELDKA T0367 95 :YKE 1o3uA 87 :ALP T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 97 :YSRIEAERLVNYAEKIIRFCEDLLSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 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 1o3uA/T0367-1o3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1o3uA/T0367-1o3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3uA read from 1o3uA/T0367-1o3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o3uA in template set Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o3uA)D86 Warning: unaligning (T0367)I94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 Warning: unaligning (T0367)N124 because last residue in template chain is (1o3uA)I123 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYS T0367 59 :TIYLIWECREELGLSDDDCSKLSRAFDL 1o3uA 51 :VPDFLGELSSRFEIPEELMDHALELDKA T0367 95 :YKE 1o3uA 87 :ALP T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 97 :YSRIEAERLVNYAEKIIRFCEDLLSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 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 1o3uA/T0367-1o3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1o3uA/T0367-1o3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o3uA read from 1o3uA/T0367-1o3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o3uA in template set Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 Warning: unaligning (T0367)N124 because last residue in template chain is (1o3uA)I123 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRG 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYSV T0367 60 :IYLIWECREELGLSDDDCSKLS 1o3uA 52 :PDFLGELSSRFEIPEELMDHAL T0367 89 :ESDYGI 1o3uA 87 :ALPSGS T0367 95 :YKEVSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 94 :RNRYSRIEAERLVNYAEKIIRFCEDLLSR 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=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwpA/T0367-1wwpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wwpA expands to /projects/compbio/data/pdb/1wwp.pdb.gz 1wwpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1wwpA/T0367-1wwpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwpA read from 1wwpA/T0367-1wwpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wwpA to template set # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEFEMG 1wwpA 2 :AEKALATLKELAFLE T0367 26 :LYERCCSTAY 1wwpA 22 :ERDAAIQRFE T0367 36 :YAMFHAAKAMLLGY 1wwpA 35 :EAFWKALQAYLREK T0367 50 :GRDSKTHRGTIYLIWE 1wwpA 50 :GLEGASPKGVIRLARE T0367 70 :LG 1wwpA 66 :VG T0367 72 :LSDDDCSKLSRAFDLREESDYGI 1wwpA 69 :LRDEEARLALGMVDDRSLTVHTY T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNKNR 1wwpA 92 :NEPLARAIFRRLPDYARLMEQVLGRLR Number of specific fragments extracted= 7 number of extra gaps= 0 total=48 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 1wwpA/T0367-1wwpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1wwpA/T0367-1wwpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwpA read from 1wwpA/T0367-1wwpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEF 1wwpA 2 :AEKALATLKELA T0367 23 :EMGLYERCCSTAYYAMFHAAKAMLLGY 1wwpA 19 :SPVERDAAIQRFEYTFEAFWKALQAYL T0367 50 :GRDSKTHRGTIYLIWEC 1wwpA 50 :GLEGASPKGVIRLAREV T0367 71 :G 1wwpA 67 :G T0367 72 :LSDDDCSKLSRAFDLREESDYGI 1wwpA 69 :LRDEEARLALGMVDDRSLTVHTY T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNKN 1wwpA 92 :NEPLARAIFRRLPDYARLMEQVLGRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=54 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 1wwpA/T0367-1wwpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1wwpA/T0367-1wwpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwpA read from 1wwpA/T0367-1wwpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEF 1wwpA 2 :AEKALATLKELA T0367 23 :EMGLYERCCSTAYYAMFHAAKAM 1wwpA 19 :SPVERDAAIQRFEYTFEAFWKAL T0367 46 :LL 1wwpA 45 :LR T0367 48 :GYGRDSKTHRGTIYLIWE 1wwpA 48 :KEGLEGASPKGVIRLARE T0367 70 :LGLSDDDCSKLS 1wwpA 66 :VGLLRDEEARLA T0367 82 :RAFDLREE 1wwpA 79 :GMVDDRSL T0367 94 :IYKEVSKDLAIKILKDAEIFVQKAKNAVNK 1wwpA 87 :TVHTYNEPLARAIFRRLPDYARLMEQVLGR Number of specific fragments extracted= 7 number of extra gaps= 0 total=61 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 1na3A/T0367-1na3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1na3A expands to /projects/compbio/data/pdb/1na3.pdb.gz 1na3A:# T0367 read from 1na3A/T0367-1na3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1na3A read from 1na3A/T0367-1na3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1na3A to template set # found chain 1na3A in template set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 53 :SKTHRGTIYLIWECREELGLSDDDCSKLSRAFDLREES 1na3A 34 :DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNN T0367 101 :DLAIK 1na3A 72 :AEAKQ T0367 107 :LKDAEI 1na3A 78 :LGNAKQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=65 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 1na3A/T0367-1na3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1na3A/T0367-1na3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1na3A read from 1na3A/T0367-1na3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1na3A in template set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 54 :KTHRGTIYLIWECREELG 1na3A 35 :PNNAEAWYNLGNAYYKQG T0367 99 :SKDLAIKILKDAEIF 1na3A 53 :DYDEAIEYYQKALEL T0367 117 :AKN 1na3A 74 :AKQ T0367 121 :VNK 1na3A 78 :LGN Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 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 1na3A/T0367-1na3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1na3A/T0367-1na3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1na3A read from 1na3A/T0367-1na3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1na3A in template set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 53 :SKTHRGTIYLIWECREELG 1na3A 34 :DPNNAEAWYNLGNAYYKQG T0367 99 :SKDLAIKILKDAEIF 1na3A 53 :DYDEAIEYYQKALEL T0367 117 :AKN 1na3A 74 :AKQ T0367 121 :VNK 1na3A 78 :LGN Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 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 1v3wA/T0367-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v3wA expands to /projects/compbio/data/pdb/1v3w.pdb.gz 1v3wA:Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 1v3wA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 1v3wA # T0367 read from 1v3wA/T0367-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0367-1v3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v3wA to template set # found chain 1v3wA in template set T0367 95 :YKEVSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 141 :VRQLTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=76 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 1v3wA/T0367-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1v3wA/T0367-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0367-1v3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v3wA in template set T0367 96 :KEVSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 142 :RQLTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=77 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 1v3wA/T0367-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1v3wA/T0367-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v3wA read from 1v3wA/T0367-1v3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v3wA in template set T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 144 :LTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=78 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 1qhdA/T0367-1qhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qhdA expands to /projects/compbio/data/pdb/1qhd.pdb.gz 1qhdA:Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 1771, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2271, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2273, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3111, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3113, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3138, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3140, because occupancy 0.500 <= existing 0.500 in 1qhdA # T0367 read from 1qhdA/T0367-1qhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qhdA read from 1qhdA/T0367-1qhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qhdA to template set # found chain 1qhdA in template set T0367 37 :AMFHAAKAM 1qhdA 3 :VLYSLSKTL T0367 46 :LLGY 1qhdA 14 :ARDK T0367 50 :GRDSKTHRGTIYLIWECREEL 1qhdA 21 :GTLYSNVSDLIQQFNQMIITM T0367 71 :G 1qhdA 43 :G T0367 86 :LREESDYGIYKE 1qhdA 57 :RNWNFDFGLLGT T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1qhdA 73 :LDANYVETARNTIDYFVDFVDNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=84 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 1qhdA/T0367-1qhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1qhdA/T0367-1qhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qhdA read from 1qhdA/T0367-1qhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qhdA in template set T0367 34 :AYYAMFHAAKAMLLG 1qhdA 3 :VLYSLSKTLKDARDK T0367 49 :YGRDSKTHRGTIYLIWECREELG 1qhdA 20 :EGTLYSNVSDLIQQFNQMIITMN T0367 72 :LS 1qhdA 54 :LP T0367 86 :LR 1qhdA 56 :IR T0367 88 :EESDYGIYKE 1qhdA 59 :WNFDFGLLGT T0367 98 :VSKDLAIKILKDAEIFVQKAKNAV 1qhdA 73 :LDANYVETARNTIDYFVDFVDNVC 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=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qhdA/T0367-1qhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1qhdA/T0367-1qhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qhdA read from 1qhdA/T0367-1qhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qhdA in template set T0367 15 :VQDAKKEF 1qhdA 11 :LKDARDKI T0367 48 :GYGRDSKTHRGTIYLIWECREELGLSDDDCSKLSRAFDLREESDYGI 1qhdA 19 :VEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGL T0367 95 :YKEVS 1qhdA 70 :LLNLD T0367 100 :KDLAIKILKDAEIFVQKAK 1qhdA 78 :VETARNTIDYFVDFVDNVC Number of specific fragments extracted= 4 number of extra gaps= 0 total=94 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 1khoA/T0367-1khoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1khoA expands to /projects/compbio/data/pdb/1kho.pdb.gz 1khoA:# T0367 read from 1khoA/T0367-1khoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1khoA read from 1khoA/T0367-1khoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1khoA to template set # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDS 1khoA 134 :PYHAANVTA T0367 54 :KTHRGTIYLIWEC 1khoA 146 :PGHVKFETFAEDR T0367 73 :SDDDCS 1khoA 172 :NDAFYS T0367 79 :KLSRAFDLREES 1khoA 196 :FAKTAKDLYYSH T0367 94 :IYKEVSKDLAIKILKDA 1khoA 208 :ANMSCSWDEWDYAAKVA Number of specific fragments extracted= 6 number of extra gaps= 0 total=100 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 1khoA/T0367-1khoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1khoA/T0367-1khoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1khoA read from 1khoA/T0367-1khoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDS 1khoA 134 :PYHAANVTA T0367 54 :KTHRGTIYLI 1khoA 146 :PGHVKFETFA T0367 78 :SKLSRAFDLREESD 1khoA 195 :SFAKTAKDLYYSHA T0367 95 :YKEVSKDLAIKILKDA 1khoA 209 :NMSCSWDEWDYAAKVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=105 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 1khoA/T0367-1khoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1khoA/T0367-1khoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1khoA read from 1khoA/T0367-1khoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDSKTHRGTIYLIWECREELGLSDDDCSKLS 1khoA 134 :PYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSK T0367 82 :RAFDLREESDYG 1khoA 175 :FYSNILTNEDFN T0367 101 :DLAIKI 1khoA 187 :SWSKEF T0367 110 :AEIFVQKAKNAVN 1khoA 193 :ARSFAKTAKDLYY Number of specific fragments extracted= 5 number of extra gaps= 0 total=110 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 1t0qA/T0367-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0qA expands to /projects/compbio/data/pdb/1t0q.pdb.gz 1t0qA:# T0367 read from 1t0qA/T0367-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0367-1t0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0qA to template set # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 21 :EFEMGLYERCCSTAYYAMFHAAKAMLL 1t0qA 245 :LVENGKKDEAQQMVDVAIWRSWKLFSV T0367 48 :GYGRDSKTHR 1t0qA 278 :DYYTPLESRN T0367 58 :GTIYLIWECREELGLS 1t0qA 297 :WIVAQFERQLLDLGLD T0367 75 :DDCSKLSRAFDL 1t0qA 315 :WYWDQFMQDLDE T0367 89 :ESDYGIYKEVSKDLAIKI 1t0qA 341 :TVWWDPAAGVSPEEREWL T0367 107 :LKDAEIFVQKAKNAVNKNR 1t0qA 366 :NDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 6 number of extra gaps= 2 total=116 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 1t0qA/T0367-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1t0qA/T0367-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0367-1t0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 21 :EFEMGLYERCCSTAYYAMFHAAKAMLLGY 1t0qA 245 :LVENGKKDEAQQMVDVAIWRSWKLFSVLT T0367 50 :GRDSKT 1t0qA 280 :YTPLES T0367 57 :RGTIYLIWECREELGLS 1t0qA 296 :EWIVAQFERQLLDLGLD T0367 75 :DDCSK 1t0qA 318 :DQFMQ T0367 80 :LSRAF 1t0qA 324 :LDETH T0367 89 :ESDYGIYKEVSKDLAIKI 1t0qA 341 :TVWWDPAAGVSPEEREWL T0367 107 :LKDAEIFVQKAKNAVNKNR 1t0qA 366 :NDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 7 number of extra gaps= 2 total=123 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 1t0qA/T0367-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1t0qA/T0367-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0qA read from 1t0qA/T0367-1t0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)D75 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 22 :FEMGLYERCCSTAYYAMFHAAKAMLLGY 1t0qA 246 :VENGKKDEAQQMVDVAIWRSWKLFSVLT T0367 50 :GRDSKTHRGTIYL 1t0qA 282 :PLESRNQSFKEFM T0367 63 :IWECREELGLS 1t0qA 302 :FERQLLDLGLD T0367 76 :DCSKLS 1t0qA 315 :WYWDQF T0367 82 :R 1t0qA 323 :D T0367 83 :AFDL 1t0qA 335 :VWYW T0367 89 :ESDYGIYKEVSKDLAIK 1t0qA 344 :WDPAAGVSPEEREWLEE T0367 106 :ILKDAEIFVQKAKNAVNKNR 1t0qA 365 :WNDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 8 number of extra gaps= 2 total=131 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 1sauA/T0367-1sauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1sauA/T0367-1sauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sauA read from 1sauA/T0367-1sauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sauA in training set T0367 54 :KTHRGTIYLIWECREELGLSD 1sauA 48 :EEHWKIIRYLRDYFIKYGVAP T0367 77 :CSKLSRAF 1sauA 70 :VRMLVKHC T0367 86 :L 1sauA 79 :K T0367 93 :GIYKEVSKDLAIKI 1sauA 80 :EVRPDCNLQYIYKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=135 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 1sauA/T0367-1sauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1sauA/T0367-1sauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sauA read from 1sauA/T0367-1sauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sauA in training set T0367 53 :SKTHRGTIYLIWECREELG 1sauA 47 :TEEHWKIIRYLRDYFIKYG T0367 72 :LSD 1sauA 67 :APP T0367 77 :CSKLSRAF 1sauA 70 :VRMLVKHC T0367 94 :IYKE 1sauA 80 :EVRP T0367 98 :VSKDLAIKI 1sauA 85 :CNLQYIYKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=140 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 1sauA/T0367-1sauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0367 read from 1sauA/T0367-1sauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sauA read from 1sauA/T0367-1sauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sauA in training set T0367 101 :DLAIKILKDAEIFV 1sauA 48 :EEHWKIIRYLRDYF T0367 116 :KAKNAVNK 1sauA 72 :MLVKHCKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=142 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 11.864 sec, elapsed time= 12.471 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 7750 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.886 sec, elapsed time= 12.495 sec. # command:Reading probabilities from T0367.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 9.784 Optimizing... Probability sum: -190.502, CN propb: -190.502 weights: 0.547 constraints: 178 # command:CPU_time= 16.734 sec, elapsed time= 17.370 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 178 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 178 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 694 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 694 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 5914 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 5914 # command:CPU_time= 16.856 sec, elapsed time= 17.601 sec. # command: