# 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 T0309 numbered 1 through 76 Created new target T0309 from T0309.a2m # command:CPU_time= 6.340 sec, elapsed time= 6.371 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d1uA/T0309-2d1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d1uA expands to /projects/compbio/data/pdb/2d1u.pdb.gz 2d1uA:# T0309 read from 2d1uA/T0309-2d1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d1uA read from 2d1uA/T0309-2d1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d1uA to template set # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ # choosing archetypes in rotamer library T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 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 2d1uA/T0309-2d1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2d1uA/T0309-2d1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d1uA read from 2d1uA/T0309-2d1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 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 2d1uA/T0309-2d1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2d1uA/T0309-2d1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d1uA read from 2d1uA/T0309-2d1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d1uA in template set T0309 24 :EQTKEAEYTYDFKEILSE 2d1uA 35 :KQSNGLHGDYDVESGLQQ T0309 42 :FNGKNV 2d1uA 54 :LDGSGL T0309 48 :SITVKEENELPVKGVEMAGD 2d1uA 68 :SWTLEPAPAPKEDALTVVGD T0309 68 :PLEHHHHHH 2d1uA 96 :DLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 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 2fvtA/T0309-2fvtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fvtA expands to /projects/compbio/data/pdb/2fvt.pdb.gz 2fvtA:# T0309 read from 2fvtA/T0309-2fvtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvtA read from 2fvtA/T0309-2fvtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fvtA to template set # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 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 2fvtA/T0309-2fvtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2fvtA/T0309-2fvtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvtA read from 2fvtA/T0309-2fvtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=18 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 2fvtA/T0309-2fvtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2fvtA/T0309-2fvtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fvtA read from 2fvtA/T0309-2fvtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fvtA in template set T0309 34 :DFKEILSE 2fvtA 108 :TYNIMIGE T0309 44 :GKNVSITVKE 2fvtA 116 :RRRVAAALIA T0309 67 :DPLEHHHHHH 2fvtA 126 :VPLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 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 1hyuA/T0309-1hyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hyuA expands to /projects/compbio/data/pdb/1hyu.pdb.gz 1hyuA:# T0309 read from 1hyuA/T0309-1hyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyuA read from 1hyuA/T0309-1hyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hyuA to template set # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE Number of specific fragments extracted= 4 number of extra gaps= 0 total=25 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 1hyuA/T0309-1hyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1hyuA/T0309-1hyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyuA read from 1hyuA/T0309-1hyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE 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=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hyuA/T0309-1hyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1hyuA/T0309-1hyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyuA read from 1hyuA/T0309-1hyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hyuA in template set T0309 5 :KVHQI 1hyuA 20 :PVELI T0309 20 :MEVTEQTKEA 1hyuA 25 :ATLDDSAKSA T0309 34 :DFKEILSEFNGKNVSITVKEENELPV 1hyuA 35 :EIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEHH 1hyuA 74 :QGPRFAGSPLGHE 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=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dyqA/T0309-1dyqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dyqA expands to /projects/compbio/data/pdb/1dyq.pdb.gz 1dyqA:Skipped atom 105, because occupancy 0.5 <= existing 0.500 in 1dyqA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1dyqA Skipped atom 1755, because occupancy 0.500 <= existing 0.500 in 1dyqA # T0309 read from 1dyqA/T0309-1dyqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dyqA read from 1dyqA/T0309-1dyqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dyqA to template set # found chain 1dyqA in template set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=35 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dyqA/T0309-1dyqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1dyqA/T0309-1dyqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dyqA read from 1dyqA/T0309-1dyqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dyqA in template set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=37 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 1dyqA/T0309-1dyqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1dyqA/T0309-1dyqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dyqA read from 1dyqA/T0309-1dyqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dyqA in template set T0309 5 :KVHQINVKGFFDMD 1dyqA 48 :RQHTILFKGFFTDH T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKE 1dyqA 62 :SWYNDLLVRFDSKDIVDKYKGKKVDLYGAY Number of specific fragments extracted= 2 number of extra gaps= 0 total=39 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 1m93A/T0309-1m93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m93A expands to /projects/compbio/data/pdb/1m93.pdb.gz 1m93A:Skipped atom 15, because occupancy 0.440 <= existing 0.560 in 1m93A Skipped atom 17, because occupancy 0.440 <= existing 0.560 in 1m93A Skipped atom 19, because occupancy 0.440 <= existing 0.560 in 1m93A Skipped atom 84, because occupancy 0.470 <= existing 0.530 in 1m93A Skipped atom 92, because occupancy 0.320 <= existing 0.680 in 1m93A Skipped atom 94, because occupancy 0.320 <= existing 0.680 in 1m93A Skipped atom 197, because occupancy 0.410 <= existing 0.590 in 1m93A # T0309 read from 1m93A/T0309-1m93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93A read from 1m93A/T0309-1m93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m93A to template set # found chain 1m93A in template set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=40 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 1m93A/T0309-1m93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1m93A/T0309-1m93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93A read from 1m93A/T0309-1m93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m93A in template set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=41 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 1m93A/T0309-1m93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1m93A/T0309-1m93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93A read from 1m93A/T0309-1m93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m93A in template set T0309 35 :FKEILSEFNGKNVSI 1m93A 4 :FREIASSMKGENVFI Number of specific fragments extracted= 1 number of extra gaps= 0 total=42 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 1zynA/T0309-1zynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zynA expands to /projects/compbio/data/pdb/1zyn.pdb.gz 1zynA:# T0309 read from 1zynA/T0309-1zynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zynA read from 1zynA/T0309-1zynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zynA to template set # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 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 1zynA/T0309-1zynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1zynA/T0309-1zynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zynA read from 1zynA/T0309-1zynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 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 1zynA/T0309-1zynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1zynA/T0309-1zynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zynA read from 1zynA/T0309-1zynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zynA in template set T0309 9 :INVKGFFDM 1zynA 21 :VELIATLDD T0309 25 :QTK 1zynA 30 :SAK T0309 32 :TYDFKEILSEFNGKNVSITVKEENELPV 1zynA 33 :SAEIKELLAEIAELSDKVTFKEDNTLPV T0309 60 :KGVEMAGDPLEH 1zynA 74 :QGPRFAGSPLGH Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 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 1repC/T0309-1repC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1repC expands to /projects/compbio/data/pdb/1rep.pdb.gz 1repC:# T0309 read from 1repC/T0309-1repC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1repC read from 1repC/T0309-1repC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1repC to template set # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=55 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 1repC/T0309-1repC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1repC/T0309-1repC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1repC read from 1repC/T0309-1repC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=56 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 1repC/T0309-1repC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1repC/T0309-1repC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1repC read from 1repC/T0309-1repC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1repC in template set Warning: unaligning (T0309)T50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1repC)E110 Warning: unaligning (T0309)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1repC)E110 T0309 27 :KEAEYTYDFKEILSEFNGKNVSI 1repC 74 :TSAEASKDIRQALKSFAGKEVVF Number of specific fragments extracted= 1 number of extra gaps= 0 total=57 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 1y96B/T0309-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y96B expands to /projects/compbio/data/pdb/1y96.pdb.gz 1y96B:# T0309 read from 1y96B/T0309-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0309-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y96B to template set # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=58 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 1y96B/T0309-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1y96B/T0309-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0309-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=59 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 1y96B/T0309-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1y96B/T0309-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0309-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y96B in template set T0309 24 :EQTKEAEYTYDFKEILSEFNGKNVSITVKEENELPV 1y96B 55 :EQRARAALRERYLRSLLAMVGHQVSFTLHEGVRVAA Number of specific fragments extracted= 1 number of extra gaps= 0 total=60 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 2a2pA/T0309-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a2pA expands to /projects/compbio/data/pdb/2a2p.pdb.gz 2a2pA:# T0309 read from 2a2pA/T0309-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0309-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a2pA to template set # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=64 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 2a2pA/T0309-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2a2pA/T0309-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0309-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=68 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 2a2pA/T0309-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 2a2pA/T0309-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0309-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2pA in template set T0309 15 :FDMDVMEVTEQTKEAEYT 2a2pA 78 :ADPELVLLSRNYQELERI T0309 34 :DFKEILSEFNGKNVS 2a2pA 104 :EINALVQELGFYRKS T0309 52 :KEENELPVKGVEMAG 2a2pA 119 :APEAQVPPEYLWAPA T0309 67 :DPLEHHHHHH 2a2pA 143 :DDLEHHHHHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 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 1q59A/T0309-1q59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q59A expands to /projects/compbio/data/pdb/1q59.pdb.gz 1q59A:# T0309 read from 1q59A/T0309-1q59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q59A read from 1q59A/T0309-1q59A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q59A to template set # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :ENELP 1q59A 155 :EDNIP T0309 64 :MAGDPLEHHHHHH 1q59A 160 :GDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=75 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 1q59A/T0309-1q59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1q59A/T0309-1q59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q59A read from 1q59A/T0309-1q59A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :ENELP 1q59A 155 :EDNIP T0309 64 :MAGDPLEHHHHHH 1q59A 160 :GDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q59A/T0309-1q59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0309 read from 1q59A/T0309-1q59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q59A read from 1q59A/T0309-1q59A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q59A in template set T0309 35 :FKEILSEFNG 1q59A 140 :LDGWIHQQGG T0309 54 :EN 1q59A 155 :ED T0309 61 :GVEMAGDPLEHHHHHH 1q59A 157 :NIPGDDDDLEHHHHHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=81 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.141 sec, elapsed time= 10.880 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 2850 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.151 sec, elapsed time= 10.890 sec. # command:Reading probabilities from T0309.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.864 Optimizing... Probability sum: -161.779, CN propb: -161.779 weights: 0.281 constraints: 103 # command:CPU_time= 10.300 sec, elapsed time= 11.065 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 103 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 103 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 88 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 88 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 2087 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 2087 # command:CPU_time= 10.342 sec, elapsed time= 11.175 sec. # command: