# 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 T0569 numbered 1 through 79 Created new target T0569 from T0569.a2m # command:CPU_time= 6.001 sec, elapsed time= 6.420 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i57A/T0569-3i57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i57A expands to /projects/compbio/data/pdb/3i57.pdb.gz 3i57A:# T0569 read from 3i57A/T0569-3i57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i57A read from 3i57A/T0569-3i57A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i57A to template set # found chain 3i57A in template set T0569 3 :EDATITYVDDD 3i57A 2 :QKVHVQYIDGE # choosing archetypes in rotamer library T0569 15 :GGAQVGDIV 3i57A 13 :TDQMLRQDD T0569 25 :VTGKTDDSTTYTV 3i57A 22 :LDGYTDETIPYST T0569 41 :DGYEYVGTDGG 3i57A 44 :DGYELFKDNFP T0569 56 :DGKT 3i57A 55 :AGEK T0569 64 :FAADDSDN 3i57A 59 :FDNDDTND T0569 72 :VVIHLKHG 3i57A 69 :YTVIFKHH Number of specific fragments extracted= 7 number of extra gaps= 0 total=7 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 3i57A/T0569-3i57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 3i57A/T0569-3i57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i57A read from 3i57A/T0569-3i57A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i57A in template set Warning: unaligning (T0569)D2 because first residue in template chain is (3i57A)M1 T0569 3 :EDATITYVDDDK 3i57A 2 :QKVHVQYIDGET T0569 16 :GAQVGDIV 3i57A 14 :DQMLRQDD T0569 25 :VTGKTDDSTTYTV 3i57A 22 :LDGYTDETIPYST T0569 41 :DGYEYVGTDGG 3i57A 44 :DGYELFKDNFP T0569 56 :DGKT 3i57A 55 :AGEK T0569 64 :FAADDSDN 3i57A 59 :FDNDDTND T0569 72 :VVIHLKHG 3i57A 69 :YTVIFKHH Number of specific fragments extracted= 7 number of extra gaps= 0 total=14 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 3i57A/T0569-3i57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 3i57A/T0569-3i57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i57A read from 3i57A/T0569-3i57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i57A in template set T0569 3 :EDATITYVDDDKG 3i57A 2 :QKVHVQYIDGETD T0569 18 :QVGDIVTVTGKTDDSTTYTV 3i57A 15 :QMLRQDDLDGYTDETIPYST T0569 41 :DGYEYVGTD 3i57A 44 :DGYELFKDN T0569 50 :GGVVSS 3i57A 56 :GEKFDN T0569 67 :DDSD 3i57A 62 :DDTN T0569 71 :NVVIHLKH 3i57A 68 :FYTVIFKH Number of specific fragments extracted= 6 number of extra gaps= 0 total=20 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 2kt7A/T0569-2kt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2kt7A expands to /projects/compbio/data/pdb/2kt7.pdb.gz 2kt7A:# T0569 read from 2kt7A/T0569-2kt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kt7A read from 2kt7A/T0569-2kt7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kt7A to template set # found chain 2kt7A in template set T0569 3 :EDATITYVD 2kt7A 39 :FTVKVEYVD T0569 14 :KGGAQVGDIVTVTGKTDDSTTYT 2kt7A 48 :ADGAEIAPSDTLTDYHYVSTPKD T0569 40 :PDGYEYVGTDGG 2kt7A 71 :IPGYKLREIPHN T0569 52 :VVSSDGKTVTITFAADDSD 2kt7A 86 :NITDTGIIVRYIYDKIIDV Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 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 2kt7A/T0569-2kt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2kt7A/T0569-2kt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kt7A read from 2kt7A/T0569-2kt7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kt7A in template set T0569 3 :EDATITYVD 2kt7A 39 :FTVKVEYVD T0569 14 :KGGAQVGDIVTVTGKTDDSTTYT 2kt7A 48 :ADGAEIAPSDTLTDYHYVSTPKD T0569 40 :PDGYEYVGTDGG 2kt7A 71 :IPGYKLREIPHN T0569 52 :VVSSDGKTVTITFAADDS 2kt7A 86 :NITDTGIIVRYIYDKIID Number of specific fragments extracted= 4 number of extra gaps= 0 total=28 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 2kt7A/T0569-2kt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2kt7A/T0569-2kt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kt7A read from 2kt7A/T0569-2kt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kt7A in template set T0569 4 :DATITYVDDDK 2kt7A 40 :TVKVEYVDADG T0569 17 :AQVGDIVTVTGK 2kt7A 51 :AEIAPSDTLTDY T0569 32 :STTYTVTIPDGYEYVGTDGGVVSS 2kt7A 63 :HYVSTPKDIPGYKLREIPHNATGN T0569 56 :DGKTVTITF 2kt7A 90 :TGIIVRYIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 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 2go2A/T0569-2go2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2go2A expands to /projects/compbio/data/pdb/2go2.pdb.gz 2go2A:Skipped atom 86, because occupancy 0.5 <= existing 0.500 in 2go2A Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 477, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 479, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 481, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 483, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 485, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 487, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 489, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 491, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 493, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 495, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 497, because occupancy 0.400 <= existing 0.600 in 2go2A Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2go2A Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 2go2A # T0569 read from 2go2A/T0569-2go2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go2A read from 2go2A/T0569-2go2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2go2A to template set # found chain 2go2A in template set Warning: unaligning (T0569)D13 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)D94 Warning: unaligning (T0569)K14 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)D94 Warning: unaligning (T0569)Y35 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)K113 Warning: unaligning (T0569)D56 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)G130 Warning: unaligning (T0569)G57 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)G130 T0569 6 :TITYVDD 2go2A 86 :GVWDVIQ T0569 15 :GGAQV 2go2A 95 :PIGLA T0569 23 :VTVTGKTDDSTT 2go2A 100 :VKVTDTKSLLGP T0569 36 :TVTIPDGYEYV 2go2A 114 :VEKEGEGYKIV T0569 52 :VVSS 2go2A 125 :YYPE T0569 58 :KT 2go2A 131 :QT T0569 60 :VTITFAADDSDNVV 2go2A 134 :LDIGLVHRNDKYYL T0569 75 :HL 2go2A 148 :AV Number of specific fragments extracted= 8 number of extra gaps= 3 total=40 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 2go2A/T0569-2go2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2go2A/T0569-2go2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go2A read from 2go2A/T0569-2go2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go2A in template set Warning: unaligning (T0569)D13 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)D94 Warning: unaligning (T0569)K14 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)D94 Warning: unaligning (T0569)Y35 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)K113 Warning: unaligning (T0569)G51 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)G130 Warning: unaligning (T0569)D56 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)G130 T0569 6 :TITYVDD 2go2A 86 :GVWDVIQ T0569 15 :GGAQV 2go2A 95 :PIGLA T0569 23 :VTVTGKTDDSTT 2go2A 100 :VKVTDTKSLLGP T0569 36 :TVTIPDGYEYVGTDG 2go2A 114 :VEKEGEGYKIVYYPE T0569 57 :GKTVTITFAADDS 2go2A 131 :QTGLDIGLVHRND T0569 71 :NVVIHLKH 2go2A 144 :KYYLAVKD Number of specific fragments extracted= 6 number of extra gaps= 3 total=46 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 2go2A/T0569-2go2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2go2A/T0569-2go2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go2A read from 2go2A/T0569-2go2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go2A in template set Warning: unaligning (T0569)D12 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)D94 Warning: unaligning (T0569)D13 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)D94 Warning: unaligning (T0569)T34 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)K113 Warning: unaligning (T0569)Y35 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)K113 Warning: unaligning (T0569)S55 because of BadResidue code BAD_PEPTIDE in next template residue (2go2A)G130 Warning: unaligning (T0569)D56 because of BadResidue code BAD_PEPTIDE at template residue (2go2A)G130 T0569 3 :EDATITYVD 2go2A 84 :DSGVWDVIQ T0569 14 :KGGAQVGD 2go2A 95 :PIGLAVKV T0569 25 :VTGKTDDST 2go2A 103 :TDTKSLLGP T0569 36 :TVTIPDGYEYVGTD 2go2A 114 :VEKEGEGYKIVYYP T0569 54 :S 2go2A 128 :E T0569 57 :GKTVTITFAADDSDNVVIHLKH 2go2A 131 :QTGLDIGLVHRNDKYYLAVKDG Number of specific fragments extracted= 6 number of extra gaps= 3 total=52 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 1a8pA/T0569-1a8pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a8pA expands to /projects/compbio/data/pdb/1a8p.pdb.gz 1a8pA:# T0569 read from 1a8pA/T0569-1a8pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a8pA read from 1a8pA/T0569-1a8pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a8pA to template set # found chain 1a8pA in template set T0569 4 :DATI 1a8pA 4 :LNVE T0569 18 :QVGDIVTV 1a8pA 8 :RVLSVHHW T0569 29 :TDDSTTYTVTIPDGYEYV 1a8pA 16 :NDTLFSFKTTRNPSLRFE T0569 49 :DGGVV 1a8pA 34 :NGQFV T0569 54 :SSDGKTVTITFA 1a8pA 43 :EVDGRPLMRAYS T0569 66 :ADDSDNVVIHLKH 1a8pA 58 :PNYEEHLEFFSIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=58 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 1a8pA/T0569-1a8pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 1a8pA/T0569-1a8pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a8pA read from 1a8pA/T0569-1a8pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a8pA in template set T0569 5 :ATI 1a8pA 5 :NVE T0569 18 :QVGDIVT 1a8pA 8 :RVLSVHH T0569 28 :KTDDSTTYTVTIPDGYEYV 1a8pA 15 :WNDTLFSFKTTRNPSLRFE T0569 49 :DGG 1a8pA 34 :NGQ T0569 52 :VVSSDGKTVTITFA 1a8pA 41 :GLEVDGRPLMRAYS T0569 66 :ADDSDNVVIHLKH 1a8pA 58 :PNYEEHLEFFSIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=64 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a8pA/T0569-1a8pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 1a8pA/T0569-1a8pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a8pA read from 1a8pA/T0569-1a8pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a8pA in template set T0569 17 :AQVGDIVTV 1a8pA 7 :ERVLSVHHW T0569 29 :TDDSTTYTVTIPDGYEY 1a8pA 16 :NDTLFSFKTTRNPSLRF T0569 48 :TDGGVV 1a8pA 33 :ENGQFV T0569 54 :SSDGKTVTITFA 1a8pA 43 :EVDGRPLMRAYS T0569 66 :ADDSDNVVIHLKH 1a8pA 58 :PNYEEHLEFFSIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=69 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3g5wA/T0569-3g5wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3g5wA expands to /projects/compbio/data/pdb/3g5w.pdb.gz 3g5wA:# T0569 read from 3g5wA/T0569-3g5wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3g5wA read from 3g5wA/T0569-3g5wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3g5wA to template set # found chain 3g5wA in template set Warning: unaligning (T0569)V73 because of BadResidue code BAD_PEPTIDE in next template residue (3g5wA)I293 Warning: unaligning (T0569)I74 because of BadResidue code BAD_PEPTIDE at template residue (3g5wA)I293 T0569 4 :DATITYV 3g5wA 251 :ISQIAFK T0569 15 :GGAQVGDIVT 3g5wA 258 :DGFPLDKPIK T0569 34 :TYTVTIP 3g5wA 268 :GDTVLIG T0569 56 :DGKTVTITFAADDSDNV 3g5wA 275 :PGERYDVILNMDNPGLW T0569 75 :HLK 3g5wA 294 :HDH Number of specific fragments extracted= 5 number of extra gaps= 1 total=74 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 3g5wA/T0569-3g5wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 3g5wA/T0569-3g5wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3g5wA read from 3g5wA/T0569-3g5wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3g5wA in template set Warning: unaligning (T0569)V73 because of BadResidue code BAD_PEPTIDE in next template residue (3g5wA)I293 Warning: unaligning (T0569)I74 because of BadResidue code BAD_PEPTIDE at template residue (3g5wA)I293 T0569 6 :TITYVDD 3g5wA 251 :ISQIAFK T0569 15 :GGAQVGDIVT 3g5wA 258 :DGFPLDKPIK T0569 34 :TYTVTIPD 3g5wA 268 :GDTVLIGP T0569 57 :GKTVTITFAADDSDNV 3g5wA 276 :GERYDVILNMDNPGLW T0569 75 :HLK 3g5wA 294 :HDH Number of specific fragments extracted= 5 number of extra gaps= 1 total=79 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 3g5wA/T0569-3g5wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 3g5wA/T0569-3g5wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3g5wA read from 3g5wA/T0569-3g5wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3g5wA in template set Warning: unaligning (T0569)V73 because of BadResidue code BAD_PEPTIDE in next template residue (3g5wA)I293 Warning: unaligning (T0569)I74 because of BadResidue code BAD_PEPTIDE at template residue (3g5wA)I293 T0569 5 :ATITYVDD 3g5wA 250 :HISQIAFK T0569 15 :GGAQVGDIVT 3g5wA 258 :DGFPLDKPIK T0569 34 :TYTVTIPD 3g5wA 268 :GDTVLIGP T0569 57 :GKTVTITFAADDSDNV 3g5wA 276 :GERYDVILNMDNPGLW T0569 75 :HLKHG 3g5wA 294 :HDHVD Number of specific fragments extracted= 5 number of extra gaps= 1 total=84 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 2gzbA/T0569-2gzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gzbA expands to /projects/compbio/data/pdb/2gzb.pdb.gz 2gzbA:# T0569 read from 2gzbA/T0569-2gzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzbA read from 2gzbA/T0569-2gzbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gzbA to template set # found chain 2gzbA in template set T0569 6 :TITYVDDDKGGAQ 2gzbA 85 :EVWDVSKQYPIGL T0569 22 :IVTVTGKTDDSTT 2gzbA 98 :AVKVTDTKSFVGP T0569 35 :YTVTIPDGYEYVGTDG 2gzbA 112 :RVEKEGEGYKIVYYPD T0569 51 :GVVSSDGKT 2gzbA 136 :GLVHRNDKY T0569 73 :VIHLKHG 2gzbA 145 :YLAATEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=89 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 2gzbA/T0569-2gzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2gzbA/T0569-2gzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzbA read from 2gzbA/T0569-2gzbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gzbA in template set T0569 7 :ITYVDDDKGGAQ 2gzbA 86 :VWDVSKQYPIGL T0569 22 :IVTVTGKTDDSTT 2gzbA 98 :AVKVTDTKSFVGP T0569 35 :YTVTIPDGYEYVGTDGG 2gzbA 112 :RVEKEGEGYKIVYYPDR T0569 52 :VVSSDG 2gzbA 137 :LVHRND T0569 60 :VTITFAADDSDNVVIHLKH 2gzbA 143 :KYYLAATEGEPFVFKIRKA Number of specific fragments extracted= 5 number of extra gaps= 0 total=94 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 2gzbA/T0569-2gzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2gzbA/T0569-2gzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzbA read from 2gzbA/T0569-2gzbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gzbA in template set T0569 9 :YVDDDKGGAQVGDI 2gzbA 88 :DVSKQYPIGLAVKV T0569 26 :TGKTDDSTTYT 2gzbA 102 :TDTKSFVGPFR T0569 37 :VTIPDGYEYVGTD 2gzbA 114 :EKEGEGYKIVYYP T0569 54 :SSDGKTVTITFAADDSDNVVIHLKH 2gzbA 127 :DRGQTGLDIGLVHRNDKYYLAATEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=98 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 2f05A/T0569-2f05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f05A expands to /projects/compbio/data/pdb/2f05.pdb.gz 2f05A:# T0569 read from 2f05A/T0569-2f05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f05A read from 2f05A/T0569-2f05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f05A to template set # found chain 2f05A in template set Warning: unaligning (T0569)E44 because last residue in template chain is (2f05A)R85 T0569 39 :IPDGY 2f05A 80 :LPEAK Number of specific fragments extracted= 1 number of extra gaps= 0 total=99 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 2f05A/T0569-2f05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2f05A/T0569-2f05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f05A read from 2f05A/T0569-2f05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f05A in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=99 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f05A/T0569-2f05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2f05A/T0569-2f05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f05A read from 2f05A/T0569-2f05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f05A in template set Warning: unaligning (T0569)E44 because last residue in template chain is (2f05A)R85 T0569 40 :PDGY 2f05A 81 :PEAK Number of specific fragments extracted= 1 number of extra gaps= 0 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cjcA/T0569-1cjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cjcA expands to /projects/compbio/data/pdb/1cjc.pdb.gz 1cjcA:# T0569 read from 1cjcA/T0569-1cjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjcA read from 1cjcA/T0569-1cjcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cjcA to template set # found chain 1cjcA in template set T0569 5 :ATITYVDDDKGGAQVGDIVTVTGKTDDSTTYTVTIPDG 1cjcA 278 :RSPQQVLPSPDGRRAAGIRLAVTRLEGIGEATRAVPTG T0569 49 :DGGVVSSD 1cjcA 316 :DVEDLPCG Number of specific fragments extracted= 2 number of extra gaps= 0 total=102 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 1cjcA/T0569-1cjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 1cjcA/T0569-1cjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjcA read from 1cjcA/T0569-1cjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjcA in template set T0569 8 :TYVDD 1cjcA 282 :QVLPS T0569 14 :KGGAQVG 1cjcA 287 :PDGRRAA T0569 21 :DIVTVTGK 1cjcA 298 :AVTRLEGI T0569 31 :DSTTYTVTIP 1cjcA 306 :GEATRAVPTG T0569 49 :DGGVVSSD 1cjcA 316 :DVEDLPCG Number of specific fragments extracted= 5 number of extra gaps= 0 total=107 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 1cjcA/T0569-1cjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 1cjcA/T0569-1cjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjcA read from 1cjcA/T0569-1cjcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjcA in template set T0569 5 :ATITYVDDDKGGAQVGDIVTVTGKTDDSTT 1cjcA 278 :RSPQQVLPSPDGRRAAGIRLAVTRLEGIGE T0569 35 :YTVTIPDGYEYVGT 1cjcA 309 :TRAVPTGDVEDLPC Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 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 2gpjA/T0569-2gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gpjA expands to /projects/compbio/data/pdb/2gpj.pdb.gz 2gpjA: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 330, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2gpjA Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2gpjA 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 # T0569 read from 2gpjA/T0569-2gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gpjA read from 2gpjA/T0569-2gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gpjA to template set # found chain 2gpjA in template set Warning: unaligning (T0569)D2 because first residue in template chain is (2gpjA)P5 T0569 3 :EDATITYV 2gpjA 6 :APRELEVI T0569 18 :QVGDIV 2gpjA 14 :RSTYIT T0569 30 :DDSTTYTVTIPDGYEYVG 2gpjA 20 :PHMLRITLGGAGLAGFPA T0569 48 :TDGG 2gpjA 39 :QESA T0569 52 :VVSSDGK 2gpjA 47 :LFPQAGE T0569 59 :TVTITFAADDSDNVVIHLK 2gpjA 57 :MRTYTIRQQRDDEIDVDFV Number of specific fragments extracted= 6 number of extra gaps= 0 total=115 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 2gpjA/T0569-2gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2gpjA/T0569-2gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gpjA read from 2gpjA/T0569-2gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gpjA in template set Warning: unaligning (T0569)D2 because first residue in template chain is (2gpjA)P5 T0569 3 :EDATITYV 2gpjA 6 :APRELEVI T0569 18 :QVGDIV 2gpjA 14 :RSTYIT T0569 30 :DDSTTYTVTIPDGYEY 2gpjA 20 :PHMLRITLGGAGLAGF T0569 49 :DGGV 2gpjA 36 :PADQ T0569 56 :DGKTVTITFAADDSDNVVIHL 2gpjA 40 :ESAYIKLLFPQAGERPLMRTY Number of specific fragments extracted= 5 number of extra gaps= 0 total=120 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 2gpjA/T0569-2gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2gpjA/T0569-2gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gpjA read from 2gpjA/T0569-2gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gpjA in template set T0569 1 :MDEDATITYVDDDKGGAQVGDIVTV 2gpjA 38 :DQESAYIKLLFPQAGERPLMRTYTI T0569 37 :VTIPDGYEYVG 2gpjA 63 :RQQRDDEIDVD T0569 51 :GVVS 2gpjA 74 :FVLH T0569 55 :SDGKTVTITFAAD 2gpjA 91 :QVGELIQIGGPGL T0569 68 :DSDNVVI 2gpjA 110 :EADWFLL Number of specific fragments extracted= 5 number of extra gaps= 0 total=125 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 2v05A/T0569-2v05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2v05A expands to /projects/compbio/data/pdb/2v05.pdb.gz 2v05A:# T0569 read from 2v05A/T0569-2v05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v05A read from 2v05A/T0569-2v05A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2v05A to template set # found chain 2v05A in template set T0569 5 :ATI 2v05A 215 :KYV T0569 8 :TYVDDDKGGAQVG 2v05A 221 :WYYLDNKNGDMKT T0569 35 :YTVTIPDGYEYVGTDGG 2v05A 234 :GWQYLGNKWYYLRSSGA T0569 52 :VVSSDGKTVT 2v05A 255 :WYQDGLTWYY T0569 64 :FAADD 2v05A 265 :LNAGN Number of specific fragments extracted= 5 number of extra gaps= 0 total=130 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 2v05A/T0569-2v05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2v05A/T0569-2v05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v05A read from 2v05A/T0569-2v05A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v05A in template set T0569 2 :DEDATI 2v05A 192 :TDWQKV T0569 8 :TYVDDDKGGAQVGDIVTVTGKT 2v05A 200 :KWYYFGSSGSMATGWKYVRGKW T0569 30 :DDSTTYTVTIPDGYEYVGTDGG 2v05A 229 :GDMKTGWQYLGNKWYYLRSSGA T0569 52 :VVSSDGKTVTI 2v05A 255 :WYQDGLTWYYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=134 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 2v05A/T0569-2v05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0569 read from 2v05A/T0569-2v05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v05A read from 2v05A/T0569-2v05A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v05A in template set T0569 8 :TYVDDDKGGAQVGDIVTVTGKT 2v05A 200 :KWYYFGSSGSMATGWKYVRGKW T0569 30 :DDSTT 2v05A 226 :NKNGD T0569 35 :YTVTIPDGYEYVGTDG 2v05A 234 :GWQYLGNKWYYLRSSG T0569 51 :GVVSSDGKTVTI 2v05A 254 :GWYQDGLTWYYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 Will force an alignment to be made, even if fragment is small Number of alignments=29 # command:CPU_time= 10.010 sec, elapsed time= 11.742 sec. # command:DEBUG: alignment library has 29 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 29 # Adding 829 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.021 sec, elapsed time= 11.753 sec. # command:Reading probabilities from T0569.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 8.967 Optimizing... Probability sum: -153.040, CN propb: -153.040 weights: 0.296 constraints: 228 # command:CPU_time= 18.147 sec, elapsed time= 19.926 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 228 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 228 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 601 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 601 # 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= 18.160 sec, elapsed time= 20.936 sec. # command: