# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0557 numbered 1 through 145 Created new target T0557 from T0557.a2m # command:CPU_time= 5.708 sec, elapsed time= 5.775 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lmmA/T0557-3lmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lmmA expands to /projects/compbio/data/pdb/3lmm.pdb.gz 3lmmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0557 read from 3lmmA/T0557-3lmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmmA read from 3lmmA/T0557-3lmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lmmA to template set # found chain 3lmmA in template set T0557 6 :DL 3lmmA 14 :QL # choosing archetypes in rotamer library T0557 8 :LDELNAV 3lmmA 19 :VESILAS T0557 15 :D 3lmmA 34 :T T0557 16 :ESARIEAKRA 3lmmA 36 :ETQSVDFKEE T0557 26 :SDMGKSVMETVIAFANEP 3lmmA 62 :PEAADKLADEVACMANTP T0557 46 :DGGYLLLGVDW 3lmmA 80 :GGGALIVGIED T0557 60 :DKGDTV 3lmmA 91 :KTGRII T0557 68 :PVGLP 3lmmA 97 :GTELD T0557 78 :QRDLASQCASMLN 3lmmA 102 :IDWLRQGIFTRID T0557 93 :LRPEMQLEQVGGKTLLVVYVPEAD 3lmmA 115 :VAPDVVAKRVLGQRVLAIYVAAAA T0557 119 :HKPIYKK 3lmmA 139 :EPIEDTS T0557 131 :GGAYRRIGSSDQRC 3lmmA 146 :DRLRWRVGDSCRPV Number of specific fragments extracted= 12 number of extra gaps= 0 total=12 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 3lmmA/T0557-3lmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3lmmA/T0557-3lmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmmA read from 3lmmA/T0557-3lmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lmmA in template set T0557 5 :TDLLDELNA 3lmmA 16 :IAQVESILA T0557 14 :VDESARIEAKRA 3lmmA 34 :TKETQSVDFKEE T0557 26 :SDMGKSVMETVIAFANEP 3lmmA 62 :PEAADKLADEVACMANTP T0557 46 :DGGYLLLGVD 3lmmA 80 :GGGALIVGIE T0557 60 :DKGD 3lmmA 90 :DKTG T0557 65 :VYRPVGLP 3lmmA 94 :RIIGTELD T0557 78 :QRDLASQCASMLNV 3lmmA 102 :IDWLRQGIFTRIDV T0557 94 :RPEMQLEQVGGKTLLVVYVPEAD 3lmmA 116 :APDVVAKRVLGQRVLAIYVAAAA T0557 120 :KPIYKKA 3lmmA 139 :EPIEDTS T0557 131 :GGAYRRIGSSDQRC 3lmmA 146 :DRLRWRVGDSCRPV Number of specific fragments extracted= 10 number of extra gaps= 0 total=22 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 3lmmA/T0557-3lmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3lmmA/T0557-3lmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmmA read from 3lmmA/T0557-3lmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lmmA in template set T0557 26 :SDMGKSVMETVIAFANEP 3lmmA 62 :PEAADKLADEVACMANTP T0557 46 :DGGYLLLGVDWAINDKGDTVYR 3lmmA 80 :GGGALIVGIEDKTGRIIGTELD T0557 78 :QRDL 3lmmA 102 :IDWL T0557 84 :QCASMLNVALRPEMQLEQVGGKTLLVVYVPEAD 3lmmA 106 :RQGIFTRIDVAPDVVAKRVLGQRVLAIYVAAAA T0557 119 :HKPIYK 3lmmA 139 :EPIEDT T0557 130 :PGGAYRRIGSSDQRCV 3lmmA 145 :SDRLRWRVGDSCRPVD Number of specific fragments extracted= 6 number of extra gaps= 0 total=28 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 3d9rA/T0557-3d9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3d9rA expands to /projects/compbio/data/pdb/3d9r.pdb.gz 3d9rA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 294, because occupancy 0.5 <= existing 0.500 in 3d9rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 298, because occupancy 0.500 <= existing 0.500 in 3d9rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 3d9rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 302, because occupancy 0.370 <= existing 0.380 in 3d9rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 3d9rA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 959, because occupancy 0.500 <= existing 0.500 in 3d9rA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 3d9rA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 3d9rA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 3d9rA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 3d9rA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 3d9rA # T0557 read from 3d9rA/T0557-3d9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d9rA read from 3d9rA/T0557-3d9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3d9rA to template set # found chain 3d9rA in template set T0557 1 :MRSATDLLDELNAV 3d9rA 5 :FNEELAVIEAAAIA T0557 26 :SDMGKSVMETVI 3d9rA 25 :RADIPAVIATYT T0557 46 :DGGYL 3d9rA 37 :DDGVL T0557 54 :VD 3d9rA 42 :MG T0557 60 :DKGDTVY 3d9rA 44 :PGRPAAV T0557 73 :DPDKVQRDLASQCAS 3d9rA 51 :GKDELAEVYLSVFET T0557 89 :LNVALRPEM 3d9rA 66 :VGFDMAYEI T0557 98 :QLEQVGG 3d9rA 76 :EVVQTSA T0557 105 :KTLLVVYV 3d9rA 84 :WAFVRSAT T0557 113 :PEAD 3d9rA 97 :NKAT T0557 119 :HKPIYKK 3d9rA 101 :GVVTPAA T0557 131 :GGA 3d9rA 108 :YQE T0557 134 :YRRIGSSDQRC 3d9rA 114 :LRKSATGSWQT Number of specific fragments extracted= 13 number of extra gaps= 0 total=41 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 3d9rA/T0557-3d9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3d9rA/T0557-3d9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d9rA read from 3d9rA/T0557-3d9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d9rA in template set T0557 3 :SATDLLDELNAV 3d9rA 7 :EELAVIEAAAIA T0557 22 :AKRASDMGKSVMETVI 3d9rA 21 :TAFNRADIPAVIATYT T0557 46 :DGGYL 3d9rA 37 :DDGVL T0557 54 :VD 3d9rA 42 :MG T0557 60 :DKGD 3d9rA 44 :PGRP T0557 68 :PVG 3d9rA 48 :AAV T0557 73 :DPDKVQRDLASQCAS 3d9rA 51 :GKDELAEVYLSVFET T0557 89 :LNVALRPEM 3d9rA 66 :VGFDMAYEI T0557 98 :QLEQVGG 3d9rA 76 :EVVQTSA T0557 105 :KTLLVVYV 3d9rA 84 :WAFVRSAT T0557 113 :PEAD 3d9rA 97 :NKAT T0557 119 :HKPIYKK 3d9rA 101 :GVVTPAA T0557 131 :GGA 3d9rA 108 :YQE T0557 134 :YRRIGSSD 3d9rA 114 :LRKSATGS Number of specific fragments extracted= 14 number of extra gaps= 0 total=55 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 3d9rA/T0557-3d9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3d9rA/T0557-3d9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d9rA read from 3d9rA/T0557-3d9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d9rA in template set T0557 46 :DG 3d9rA 37 :DD T0557 64 :TVYRPVGLPD 3d9rA 39 :GVLMGPGRPA T0557 74 :PDK 3d9rA 52 :KDE T0557 78 :QRDLASQCASMLNVALRPEM 3d9rA 55 :LAEVYLSVFETVGFDMAYEI T0557 98 :QLEQVGG 3d9rA 76 :EVVQTSA T0557 105 :KTLLVVYVP 3d9rA 84 :WAFVRSATE T0557 122 :IYKKATG 3d9rA 93 :GTETNKA T0557 131 :GG 3d9rA 100 :TG T0557 133 :AYRRIGSS 3d9rA 113 :LLRKSATG Number of specific fragments extracted= 9 number of extra gaps= 0 total=64 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 1wcuA/T0557-1wcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wcuA expands to /projects/compbio/data/pdb/1wcu.pdb.gz 1wcuA:Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 668, because occupancy 0.000 <= existing 0.500 in 1wcuA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1wcuA # T0557 read from 1wcuA/T0557-1wcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wcuA read from 1wcuA/T0557-1wcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wcuA to template set # found chain 1wcuA in template set Warning: unaligning (T0557)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)I48 Warning: unaligning (T0557)I20 because of BadResidue code BAD_PEPTIDE at template residue (1wcuA)I48 T0557 13 :AVDESA 1wcuA 41 :DPDEYG T0557 21 :EAKRAS 1wcuA 49 :SLKNLN T0557 42 :EPGL 1wcuA 55 :SNYY T0557 46 :DGGYLLLGVDWA 1wcuA 60 :KGGCIYLQVKTE T0557 60 :DKGDTVYRPVGLPDPDK 1wcuA 72 :TEGLVKVQGVRGYDETE T0557 89 :L 1wcuA 89 :A T0557 90 :NVALRPEMQLEQVGG 1wcuA 96 :RSSSDFTEYKFEVDD T0557 106 :TLLVVYVPEAD 1wcuA 115 :DRIIVQDGPAS T0557 119 :HKPIYKK 1wcuA 126 :NIPIYMR T0557 132 :GAYRRIGSSDQ 1wcuA 133 :YIIYSTGSCDD Number of specific fragments extracted= 10 number of extra gaps= 1 total=74 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 1wcuA/T0557-1wcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1wcuA/T0557-1wcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wcuA read from 1wcuA/T0557-1wcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wcuA in template set Warning: unaligning (T0557)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)I48 Warning: unaligning (T0557)I20 because of BadResidue code BAD_PEPTIDE at template residue (1wcuA)I48 Warning: unaligning (T0557)T106 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)F114 T0557 14 :VDESA 1wcuA 42 :PDEYG T0557 21 :EAKRASD 1wcuA 49 :SLKNLNS T0557 42 :E 1wcuA 59 :G T0557 46 :DGGYLLLGVD 1wcuA 60 :KGGCIYLQVK T0557 56 :WAINDKGDTVYRPVGL 1wcuA 82 :RGYDETEAFNVGSFRS T0557 92 :ALRPEMQLEQV 1wcuA 98 :SSDFTEYKFEV T0557 103 :GGK 1wcuA 110 :DEY T0557 107 :LLVVYVPEAD 1wcuA 116 :RIIVQDGPAS T0557 119 :HKPIYKK 1wcuA 126 :NIPIYMR T0557 132 :GAYRRIGSSDQ 1wcuA 133 :YIIYSTGSCDD Number of specific fragments extracted= 10 number of extra gaps= 2 total=84 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 1wcuA/T0557-1wcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1wcuA/T0557-1wcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wcuA read from 1wcuA/T0557-1wcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wcuA in template set Warning: unaligning (T0557)T106 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)F114 Warning: unaligning (T0557)L107 because of BadResidue code BAD_PEPTIDE at template residue (1wcuA)F114 T0557 46 :DGGYLLLGVDWAINDK 1wcuA 60 :KGGCIYLQVKTETEGL T0557 62 :GDTVYRPVGLPDP 1wcuA 77 :KVQGVRGYDETEA T0557 90 :NVALRPEMQLEQV 1wcuA 94 :SFRSSSDFTEYKF T0557 103 :GGK 1wcuA 110 :DEY T0557 108 :LVVYVP 1wcuA 117 :IIVQDG T0557 116 :DVTHKPIYKK 1wcuA 123 :PASNIPIYMR T0557 132 :GAYRRIGSSDQ 1wcuA 133 :YIIYSTGSCDD Number of specific fragments extracted= 7 number of extra gaps= 1 total=91 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 1dmmA/T0557-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dmmA expands to /projects/compbio/data/pdb/1dmm.pdb.gz 1dmmA:# T0557 read from 1dmmA/T0557-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0557-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dmmA to template set # found chain 1dmmA in template set Warning: unaligning (T0557)L89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1dmmA)K65 Warning: unaligning (T0557)A92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1dmmA)K65 T0557 1 :MRSATDLLDELNAV 1dmmA 3 :LPTAQEVQGLMARY T0557 23 :KRA 1dmmA 17 :IEL T0557 26 :SDMGKSVMETVI 1dmmA 22 :VGDIEAIVQMYA T0557 46 :DGGYL 1dmmA 34 :DDATV T0557 55 :DWA 1dmmA 39 :EDP T0557 60 :DKGDTVY 1dmmA 42 :FGQPPIH T0557 73 :D 1dmmA 49 :G T0557 78 :QRDLASQCASM 1dmmA 50 :REQIAAFFRQG T0557 93 :LRPEMQ 1dmmA 66 :VRACLT T0557 99 :LEQVGGKTL 1dmmA 74 :VRASHNGCG T0557 108 :LVVYVP 1dmmA 84 :MPFRVE T0557 115 :ADVTHKPIYKK 1dmmA 90 :MVWNGQPCALD T0557 131 :GGAYRRIGSSDQ 1dmmA 101 :VIDVMRFDEHGR Number of specific fragments extracted= 13 number of extra gaps= 0 total=104 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 1dmmA/T0557-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1dmmA/T0557-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0557-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dmmA in template set Warning: unaligning (T0557)N90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1dmmA)K65 T0557 1 :MRSATDLLDELNAV 1dmmA 2 :NLPTAQEVQGLMAR T0557 26 :SDMGKSVMETVI 1dmmA 22 :VGDIEAIVQMYA T0557 46 :DGGYL 1dmmA 34 :DDATV T0557 55 :DWA 1dmmA 39 :EDP T0557 60 :DKGD 1dmmA 42 :FGQP T0557 66 :YRP 1dmmA 46 :PIH T0557 73 :D 1dmmA 49 :G T0557 78 :QRDLASQCAS 1dmmA 50 :REQIAAFFRQ T0557 91 :VALRPEMQLEQVGGKTL 1dmmA 66 :VRACLTGPVRASHNGCG T0557 108 :LVVY 1dmmA 86 :FRVE T0557 115 :ADVTHKPIYKK 1dmmA 90 :MVWNGQPCALD T0557 131 :GGAYRRIGSSDQ 1dmmA 101 :VIDVMRFDEHGR Number of specific fragments extracted= 12 number of extra gaps= 0 total=116 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 1dmmA/T0557-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1dmmA/T0557-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0557-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dmmA in template set Warning: unaligning (T0557)A86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1dmmA)K65 Warning: unaligning (T0557)N90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1dmmA)K65 T0557 5 :TDLLDELNAVDESARIE 1dmmA 14 :ARYIELVDVGDIEAIVQ T0557 33 :M 1dmmA 32 :Y T0557 45 :LDGGYL 1dmmA 33 :ADDATV T0557 55 :DWAINDKGDTV 1dmmA 39 :EDPFGQPPIHG T0557 74 :PDKVQRDLAS 1dmmA 50 :REQIAAFFRQ T0557 85 :C 1dmmA 60 :G T0557 91 :VALRPEMQLEQVGGKTL 1dmmA 66 :VRACLTGPVRASHNGCG T0557 108 :LVVYVP 1dmmA 84 :MPFRVE T0557 115 :ADVTHKPIYKKAT 1dmmA 90 :MVWNGQPCALDVI T0557 132 :GAYRRIGSS 1dmmA 103 :DVMRFDEHG Number of specific fragments extracted= 10 number of extra gaps= 0 total=126 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 2cxcA/T0557-2cxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cxcA expands to /projects/compbio/data/pdb/2cxc.pdb.gz 2cxcA:# T0557 read from 2cxcA/T0557-2cxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cxcA read from 2cxcA/T0557-2cxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cxcA to template set # found chain 2cxcA in template set T0557 3 :SATDLLDELNAV 2cxcA 10 :EELRYISVFHSI T0557 16 :ESARIEAKRA 2cxcA 22 :TGVTAYRCIV T0557 26 :SD 2cxcA 33 :EE T0557 47 :GGYLLLGVD 2cxcA 35 :NNRLIFLVS T0557 71 :LPDPDKVQ 2cxcA 44 :EGEAGRAI T0557 80 :DLASQCASMLNVALRP 2cxcA 56 :RLIKLLREALGKNIEV T0557 96 :EMQLEQVGGKTLLVVYVPEA 2cxcA 93 :SINVRERNGVKQVVIKVSED Number of specific fragments extracted= 7 number of extra gaps= 0 total=133 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 2cxcA/T0557-2cxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 2cxcA/T0557-2cxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cxcA read from 2cxcA/T0557-2cxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cxcA in template set T0557 8 :LDELNAV 2cxcA 11 :ELRYISV T0557 15 :DESARIEAKRASD 2cxcA 21 :ITGVTAYRCIVDE T0557 46 :DGGYLLLGVD 2cxcA 34 :ENNRLIFLVS T0557 60 :DK 2cxcA 44 :EG T0557 78 :QRDLA 2cxcA 58 :IKLLR T0557 87 :SMLNVALRP 2cxcA 63 :EALGKNIEV T0557 96 :EMQLEQVGGKTLLVVYVPE 2cxcA 93 :SINVRERNGVKQVVIKVSE Number of specific fragments extracted= 7 number of extra gaps= 0 total=140 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 2cxcA/T0557-2cxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 2cxcA/T0557-2cxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cxcA read from 2cxcA/T0557-2cxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cxcA in template set T0557 14 :VDESARIEAKRASDMGKSVMETVIA 2cxcA 8 :TLEELRYISVFHSITGVTAYRCIVD T0557 43 :P 2cxcA 33 :E T0557 46 :DGGYLLLGVDWA 2cxcA 34 :ENNRLIFLVSEG T0557 62 :GDTVYRP 2cxcA 68 :NIEVVEY T0557 71 :LPDPDKVQRDL 2cxcA 75 :SSDLERIVKNL T0557 89 :LNVALRPEMQLEQVGGKTLLVVYVPE 2cxcA 86 :FPGVKIESINVRERNGVKQVVIKVSE Number of specific fragments extracted= 6 number of extra gaps= 0 total=146 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 1tuhA/T0557-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tuhA expands to /projects/compbio/data/pdb/1tuh.pdb.gz 1tuhA:Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 982, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 984, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1tuhA # T0557 read from 1tuhA/T0557-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0557-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tuhA to template set # found chain 1tuhA in template set Warning: unaligning (T0557)G131 because of BadResidue code BAD_PEPTIDE in next template residue (1tuhA)C121 Warning: unaligning (T0557)G132 because of BadResidue code BAD_PEPTIDE at template residue (1tuhA)C121 T0557 5 :TDLLDELNA 1tuhA 29 :RRGYAAFNS T0557 27 :DMGKSVMETVI 1tuhA 38 :GDMKTLTELFD T0557 46 :DGGYL 1tuhA 49 :ENASW T0557 55 :DWAINDKGDTV 1tuhA 54 :HTPGRSRIAGD T0557 71 :LPDPDKVQRDL 1tuhA 65 :HKGREAIFAQF T0557 83 :SQCASMLNVALRPEM 1tuhA 76 :GRYGGETGGTFKAVL T0557 98 :QLEQVGG 1tuhA 92 :HVLKSDD T0557 105 :KTLLVVYV 1tuhA 100 :RVIGIHRN T0557 116 :DVTHKPIYKK 1tuhA 110 :ERGGKRLDVG T0557 133 :AYRRIGSSD 1tuhA 122 :IVFEFKNGR Number of specific fragments extracted= 10 number of extra gaps= 1 total=156 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 1tuhA/T0557-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1tuhA/T0557-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0557-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tuhA in template set Warning: unaligning (T0557)G131 because of BadResidue code BAD_PEPTIDE in next template residue (1tuhA)C121 Warning: unaligning (T0557)G132 because of BadResidue code BAD_PEPTIDE at template residue (1tuhA)C121 T0557 5 :TDLLDELNAV 1tuhA 25 :AETVRRGYAA T0557 24 :RASDMGKSVMETVI 1tuhA 35 :FNSGDMKTLTELFD T0557 46 :DGGYLL 1tuhA 49 :ENASWH T0557 56 :WAINDKG 1tuhA 55 :TPGRSRI T0557 68 :PVGLPDPDKVQRDL 1tuhA 62 :AGDHKGREAIFAQF T0557 83 :SQCASMLNVALRPEMQ 1tuhA 76 :GRYGGETGGTFKAVLL T0557 99 :LEQVGGKTLLV 1tuhA 93 :VLKSDDGRVIG T0557 110 :VY 1tuhA 105 :HR T0557 113 :PEAD 1tuhA 109 :AERG T0557 119 :HKPIYKK 1tuhA 113 :GKRLDVG T0557 133 :AYRRIGSS 1tuhA 122 :IVFEFKNG Number of specific fragments extracted= 11 number of extra gaps= 1 total=167 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 1tuhA/T0557-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1tuhA/T0557-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0557-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tuhA in template set T0557 5 :TDLLDELNAVDESARIEA 1tuhA 29 :RRGYAAFNSGDMKTLTEL T0557 46 :DGGY 1tuhA 49 :ENAS T0557 52 :LGVDWAINDKGDT 1tuhA 53 :WHTPGRSRIAGDH T0557 72 :PDPDKVQRDLA 1tuhA 66 :KGREAIFAQFG T0557 84 :QCASMLNVALRPEM 1tuhA 77 :RYGGETGGTFKAVL T0557 98 :QLEQVGGKTLLVVYV 1tuhA 92 :HVLKSDDGRVIGIHR T0557 122 :IYKKATGLP 1tuhA 107 :NTAERGGKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=174 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 3ebtA/T0557-3ebtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ebtA expands to /projects/compbio/data/pdb/3ebt.pdb.gz 3ebtA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 19, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 3ebtA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 48, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3ebtA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 343, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 347, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 349, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 407, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 411, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 413, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 415, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 417, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 419, because occupancy 0.300 <= existing 0.700 in 3ebtA Skipped atom 421, because occupancy 0.300 <= existing 0.700 in 3ebtA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 573, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 3ebtA Skipped atom 901, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 902, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 906, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 907, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 909, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 910, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 912, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 913, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 915, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 916, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 918, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 919, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 921, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 922, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 924, because occupancy 0.250 <= existing 0.500 in 3ebtA Skipped atom 925, because occupancy 0.250 <= existing 0.500 in 3ebtA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0557 read from 3ebtA/T0557-3ebtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebtA read from 3ebtA/T0557-3ebtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ebtA to template set # found chain 3ebtA in template set T0557 4 :ATDLLDELNA 3ebtA 8 :VRESYEAFHR T0557 27 :DMGKSVMETVI 3ebtA 18 :RDLPGVLAALA T0557 46 :DGGYLL 3ebtA 29 :PDVRWT T0557 55 :DWAINDKGDTVY 3ebtA 38 :GMSPYGLGGTKH T0557 77 :VQRDLASQCASML 3ebtA 50 :GHDEVIAFIRHVP T0557 90 :NVALRPEMQ 3ebtA 65 :IAEMRLAPD T0557 99 :LEQVGGKTLLVVYV 3ebtA 75 :FIESGERIVVLGTR T0557 117 :VTHKPIYKK 3ebtA 93 :VNGRSATLK T0557 131 :GGAYRRIGSSD 3ebtA 102 :FVHVWRFENGR Number of specific fragments extracted= 9 number of extra gaps= 0 total=183 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 3ebtA/T0557-3ebtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3ebtA/T0557-3ebtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebtA read from 3ebtA/T0557-3ebtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ebtA in template set T0557 1 :MRSATDLLDELNAV 3ebtA 1 :MSNNMQTVRESYEA T0557 24 :RASDMGKSVMETVI 3ebtA 15 :FHRRDLPGVLAALA T0557 46 :DGGYLL 3ebtA 29 :PDVRWT T0557 55 :DWAINDKGD 3ebtA 37 :DGMSPYGLG T0557 65 :V 3ebtA 46 :G T0557 68 :PVG 3ebtA 47 :TKH T0557 77 :VQRDLASQCAS 3ebtA 50 :GHDEVIAFIRH T0557 88 :MLNVALRPEMQ 3ebtA 63 :THIAEMRLAPD T0557 99 :LEQVGGKTLLVVYV 3ebtA 75 :FIESGERIVVLGTR T0557 116 :DVTHKPIYKK 3ebtA 92 :AVNGRSATLK T0557 131 :GGAYRRIGSS 3ebtA 102 :FVHVWRFENG Number of specific fragments extracted= 11 number of extra gaps= 0 total=194 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 3ebtA/T0557-3ebtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3ebtA/T0557-3ebtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebtA read from 3ebtA/T0557-3ebtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ebtA in template set T0557 3 :SATDLLDELNAV 3ebtA 3 :NNMQTVRESYEA T0557 24 :RASDMGKSVMETV 3ebtA 15 :FHRRDLPGVLAAL T0557 46 :DGGYLLLGVDWAINDKGDTVYR 3ebtA 28 :APDVRWTHPDGMSPYGLGGTKH T0557 74 :PDKVQRDLASQCASMLN 3ebtA 50 :GHDEVIAFIRHVPTHIA T0557 92 :ALRPEM 3ebtA 67 :EMRLAP T0557 98 :QLEQVGGKTLLVVY 3ebtA 74 :EFIESGERIVVLGT Number of specific fragments extracted= 6 number of extra gaps= 0 total=200 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 3m05A/T0557-3m05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3m05A expands to /projects/compbio/data/pdb/3m05.pdb.gz 3m05A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0557 read from 3m05A/T0557-3m05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m05A read from 3m05A/T0557-3m05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3m05A to template set # found chain 3m05A in template set Warning: unaligning (T0557)G104 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3m05A)Y89 Warning: unaligning (T0557)K120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3m05A)Y89 T0557 4 :ATDLLDELNAVDESARIEAKRASDMGK 3m05A 15 :ANYLSDQFIDQNVRATKLSTTGGFLQS T0557 46 :DGGYLLLGVDWAI 3m05A 42 :GNTTFMIGIEEER T0557 74 :PDKVQRDLASQCAS 3m05A 55 :VPEVLEIIKKASHT T0557 98 :QLEQVG 3m05A 69 :REEFMT T0557 121 :PIYKKAT 3m05A 90 :PIKVQVG T0557 131 :GGAYRRIGSS 3m05A 97 :GATVLVLPVD Number of specific fragments extracted= 6 number of extra gaps= 0 total=206 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3m05A/T0557-3m05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3m05A/T0557-3m05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m05A read from 3m05A/T0557-3m05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3m05A in template set Warning: unaligning (T0557)D116 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3m05A)Y89 T0557 5 :TDLLDELNAVDESARIEAKRAS 3m05A 16 :NYLSDQFIDQNVRATKLSTTGG T0557 43 :PGLDG 3m05A 38 :FLQSG T0557 48 :GYLLLGVD 3m05A 44 :TTFMIGIE T0557 60 :DKG 3m05A 52 :EER T0557 74 :PDKVQRDLASQCAS 3m05A 55 :VPEVLEIIKKASHT T0557 98 :QLEQV 3m05A 69 :REEFM T0557 119 :HKPIYKK 3m05A 90 :PIKVQVG T0557 131 :GGAYRRIGSSDQR 3m05A 97 :GATVLVLPVDQFE Number of specific fragments extracted= 8 number of extra gaps= 0 total=214 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 3m05A/T0557-3m05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 3m05A/T0557-3m05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m05A read from 3m05A/T0557-3m05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3m05A in template set Warning: unaligning (T0557)E96 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3m05A)Y89 T0557 43 :PGLDGG 3m05A 38 :FLQSGN T0557 49 :YLLLGVDWAI 3m05A 45 :TFMIGIEEER T0557 74 :PDKVQRDLASQC 3m05A 55 :VPEVLEIIKKAS T0557 97 :MQLEQVGGKTLLVVYVP 3m05A 90 :PIKVQVGGATVLVLPVD Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 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 1oh0A/T0557-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oh0A expands to /projects/compbio/data/pdb/1oh0.pdb.gz 1oh0A:# T0557 read from 1oh0A/T0557-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0557-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oh0A to template set # found chain 1oh0A in template set T0557 1 :MRSATDLLDELNA 1oh0A 3 :LPTAQEVQGLMAR T0557 24 :RA 1oh0A 18 :EL T0557 26 :SDMGKSVMETVI 1oh0A 22 :VGDIEAIVQMYA T0557 46 :DGGYL 1oh0A 34 :DDATV T0557 55 :DWA 1oh0A 39 :EDP T0557 60 :DKGDTV 1oh0A 42 :FGQPPI T0557 72 :PDPDKVQRDLASQCA 1oh0A 48 :HGREQIAAFYRQGLG T0557 90 :NVALRPEM 1oh0A 63 :GGKVRACL T0557 98 :QLEQVGGKTL 1oh0A 73 :PVRASHNGCG T0557 108 :LVVYVP 1oh0A 84 :MPFRVE T0557 115 :ADVTHKPIYKK 1oh0A 90 :MVWNGQPCALD T0557 131 :GGAYRRIGSSDQ 1oh0A 101 :VIDVMRFDEHGR Number of specific fragments extracted= 12 number of extra gaps= 0 total=230 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 1oh0A/T0557-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1oh0A/T0557-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0557-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oh0A in template set Warning: unaligning (T0557)R2 because first residue in template chain is (1oh0A)L3 T0557 3 :SATDLLDELNAV 1oh0A 4 :PTAQEVQGLMAR T0557 24 :RA 1oh0A 18 :EL T0557 26 :SDMGKSVMETVI 1oh0A 22 :VGDIEAIVQMYA T0557 46 :DGGYL 1oh0A 34 :DDATV T0557 55 :DWA 1oh0A 39 :EDP T0557 60 :DKGD 1oh0A 42 :FGQP T0557 68 :PV 1oh0A 46 :PI T0557 72 :PDPDKVQRDLASQCA 1oh0A 48 :HGREQIAAFYRQGLG T0557 90 :NVALRPEMQ 1oh0A 63 :GGKVRACLT T0557 99 :LEQVGGKTL 1oh0A 74 :VRASHNGCG T0557 108 :LVVYVP 1oh0A 86 :FRVEMV T0557 117 :VTHKPIYKK 1oh0A 92 :WNGQPCALD T0557 131 :GGAYRRIGSSD 1oh0A 101 :VIDVMRFDEHG Number of specific fragments extracted= 13 number of extra gaps= 0 total=243 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 1oh0A/T0557-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1oh0A/T0557-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0557-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oh0A in template set T0557 5 :TDLLDELNAVDESARIEA 1oh0A 14 :ARYIELVDVGDIEAIVQM T0557 46 :DGGYL 1oh0A 34 :DDATV T0557 55 :DWAINDKGDTV 1oh0A 39 :EDPFGQPPIHG T0557 74 :PDKVQRDLASQC 1oh0A 50 :REQIAAFYRQGL T0557 90 :N 1oh0A 62 :G T0557 92 :ALRPEMQL 1oh0A 63 :GGKVRACL T0557 100 :EQVGGKTL 1oh0A 75 :RASHNGCG T0557 108 :LVVYVP 1oh0A 86 :FRVEMV T0557 117 :VTHKPIYKKAT 1oh0A 92 :WNGQPCALDVI T0557 132 :GAYRRIGSS 1oh0A 103 :DVMRFDEHG Number of specific fragments extracted= 10 number of extra gaps= 0 total=253 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 1nwwA/T0557-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1nwwA/T0557-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0557-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0557)V65 because of BadResidue code BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0557)P68 because of BadResidue code BAD_PEPTIDE at template residue (1nwwA)N55 T0557 6 :DLLDELNAVD 1nwwA 30 :EFMDALTSND T0557 29 :GKSVMET 1nwwA 40 :AAKLIEY T0557 41 :NE 1nwwA 47 :FA T0557 60 :DKGDT 1nwwA 49 :EDTMY T0557 69 :VGLP 1nwwA 56 :MPLP T0557 73 :DPDKVQRDLASQCAS 1nwwA 63 :GRDAVEQTLAGLFTV T0557 91 :VALR 1nwwA 78 :MSID T0557 95 :PEMQLEQVGG 1nwwA 83 :VETFHIGSSN T0557 105 :KTLLVVYVPEA 1nwwA 98 :ERVDVLRALPT T0557 119 :HKPIYKK 1nwwA 109 :GKSYNLS T0557 131 :GGAYRRIGSSD 1nwwA 116 :ILGVFQLTEGK Number of specific fragments extracted= 11 number of extra gaps= 1 total=264 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 1nwwA/T0557-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1nwwA/T0557-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0557-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0557)R67 because of BadResidue code BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0557)P68 because of BadResidue code BAD_PEPTIDE at template residue (1nwwA)N55 T0557 62 :GDTVY 1nwwA 49 :EDTMY T0557 69 :VGLP 1nwwA 56 :MPLP T0557 73 :DPDKVQRDLASQCAS 1nwwA 63 :GRDAVEQTLAGLFTV T0557 91 :VALR 1nwwA 78 :MSID T0557 95 :PEM 1nwwA 83 :VET T0557 98 :QLEQVGGKTLLVVYV 1nwwA 87 :HIGSSNGLVYTERVD T0557 113 :PEAD 1nwwA 106 :LPTG T0557 120 :KPIYKK 1nwwA 110 :KSYNLS T0557 131 :GGAYRRIGSS 1nwwA 116 :ILGVFQLTEG Number of specific fragments extracted= 9 number of extra gaps= 1 total=273 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 1nwwA/T0557-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0557 read from 1nwwA/T0557-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0557-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0557)R67 because of BadResidue code BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0557)P68 because of BadResidue code BAD_PEPTIDE at template residue (1nwwA)N55 T0557 64 :TVY 1nwwA 51 :TMY T0557 69 :VGLPD 1nwwA 56 :MPLPP T0557 74 :PDKVQRDLA 1nwwA 64 :RDAVEQTLA T0557 84 :QCASMLNVALRPEMQLEQVGGKTLLVVYVP 1nwwA 73 :GLFTVMSIDAVETFHIGSSNGLVYTERVDV T0557 122 :IYKKATG 1nwwA 103 :LRALPTG T0557 131 :GGAYRR 1nwwA 110 :KSYNLS Number of specific fragments extracted= 6 number of extra gaps= 1 total=279 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.844 sec, elapsed time= 16.055 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 1481 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.870 sec, elapsed time= 16.082 sec. # command:Reading probabilities from T0557.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 11.388 Optimizing... Probability sum: -254.177, CN propb: -254.177 weights: 0.232 constraints: 408 # command:CPU_time= 41.011 sec, elapsed time= 46.330 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 408 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 408 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1073 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1073 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 41.036 sec, elapsed time= 46.995 sec. # command: