# 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 T0300 numbered 1 through 102 Created new target T0300 from T0300.a2m # command:CPU_time= 6.355 sec, elapsed time= 6.403 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1debA/T0300-1debA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1debA expands to /projects/compbio/data/pdb/1deb.pdb.gz 1debA:# T0300 read from 1debA/T0300-1debA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1debA read from 1debA/T0300-1debA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1debA to template set # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELED # choosing archetypes in rotamer library T0300 56 :SSRALGAVAMRKIEAK 1debA 30 :NSNHLTKLETEASNMK T0300 72 :VRSRA 1debA 47 :VLKQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 1debA/T0300-1debA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1debA/T0300-1debA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1debA read from 1debA/T0300-1debA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELED T0300 56 :SSRALGAVAMRKIEAKVRSRA 1debA 30 :NSNHLTKLETEASNMKEVLKQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=5 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 1debA/T0300-1debA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1debA/T0300-1debA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1debA read from 1debA/T0300-1debA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1debA in template set Warning: unaligning (T0300)P6 because first residue in template chain is (1debA)A2 T0300 7 :DKTYEEMVKEVERLKLENKTLKQKVKSS 1debA 3 :AASYDQLLKQVEALKMENSNLRQELEDN T0300 57 :SRALGAVAMRKIEAKV 1debA 31 :SNHLTKLETEASNMKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=7 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 1pb6A/T0300-1pb6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pb6A expands to /projects/compbio/data/pdb/1pb6.pdb.gz 1pb6A:# T0300 read from 1pb6A/T0300-1pb6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pb6A read from 1pb6A/T0300-1pb6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pb6A to template set # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRSRA 1pb6A 190 :EVFFNQTVENVQRII Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 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 1pb6A/T0300-1pb6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1pb6A/T0300-1pb6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pb6A read from 1pb6A/T0300-1pb6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRSRA 1pb6A 190 :EVFFNQTVENVQRII Number of specific fragments extracted= 3 number of extra gaps= 0 total=13 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 1pb6A/T0300-1pb6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1pb6A/T0300-1pb6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pb6A read from 1pb6A/T0300-1pb6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pb6A in template set T0300 17 :VERLKLENKTLKQKVKSSGAVSS 1pb6A 133 :LKALIDEKSALIAGWVKSGKLAP T0300 44 :LTAAKRESIIVSSSRALG 1pb6A 156 :IDPQHLIFMIWASTQHYA T0300 62 :AVAMRKIEAKVRS 1pb6A 194 :NQTVENVQRIIIE Number of specific fragments extracted= 3 number of extra gaps= 0 total=16 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 1kxu/T0300-1kxu-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kxu expands to /projects/compbio/data/pdb/1kxu.pdb.gz 1kxu:Warning: there is no chain 1kxu will retry with 1kxuA # T0300 read from 1kxu/T0300-1kxu-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kxu read from 1kxu/T0300-1kxu-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kxu to template set # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1kxu 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAM 1kxu 48 :LEPHEEMTLCKYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=19 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 1kxu/T0300-1kxu-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1kxu/T0300-1kxu-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kxu read from 1kxu/T0300-1kxu-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSI 1kxu 26 :ANRKFRCKAVANGKVLPNDPV T0300 44 :LTAAKRESIIVSSSRALGAVAM 1kxu 48 :LEPHEEMTLCKYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=22 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 1kxu/T0300-1kxu-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1kxu/T0300-1kxu-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kxu read from 1kxu/T0300-1kxu-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kxu in template set Warning: unaligning (T0300)K5 because first residue in template chain is (1kxu)W11 T0300 6 :PDKTYEEMVKEVER 1kxu 12 :TFSSEEQLARLRAD T0300 23 :ENKTLKQKVKSSGAVSSDDSILTAAKRESII 1kxu 26 :ANRKFRCKAVANGKVLPNDPVFLEPHEEMTL T0300 54 :VSSSRALGAVAM 1kxu 58 :KYYEKRLLEFCS Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 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 1fmhA/T0300-1fmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fmhA expands to /projects/compbio/data/pdb/1fmh.pdb.gz 1fmhA:# T0300 read from 1fmhA/T0300-1fmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmhA read from 1fmhA/T0300-1fmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fmhA to template set # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=26 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 1fmhA/T0300-1fmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1fmhA/T0300-1fmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmhA read from 1fmhA/T0300-1fmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=27 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 1fmhA/T0300-1fmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1fmhA/T0300-1fmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmhA read from 1fmhA/T0300-1fmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmhA in template set Warning: unaligning (T0300)T9 because first residue in template chain is (1fmhA)E1 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1fmhA 2 :VAQLEKEVAQAEAENYQLEQEVAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 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 1l8dA/T0300-1l8dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l8dA expands to /projects/compbio/data/pdb/1l8d.pdb.gz 1l8dA:# T0300 read from 1l8dA/T0300-1l8dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l8dA read from 1l8dA/T0300-1l8dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l8dA to template set # found chain 1l8dA in template set Warning: unaligning (T0300)L92 because last residue in template chain is (1l8dA)L498 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEE T0300 34 :S 1l8dA 440 :A T0300 35 :GAVSSDDSILTAAKRESIIVSSSRALGAV 1l8dA 442 :GKCPVCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1l8dA 471 :KNTLAKLIDRKSELERELRRIDMEIKR 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=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l8dA/T0300-1l8dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1l8dA/T0300-1l8dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l8dA read from 1l8dA/T0300-1l8dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l8dA in template set Warning: unaligning (T0300)L92 because last residue in template chain is (1l8dA)L498 T0300 10 :YEEMVKEVERLKLENKTLKQKVKS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEE T0300 34 :S 1l8dA 440 :A T0300 35 :GAVSSDDSILTAAKRESIIVSSSRALGAV 1l8dA 442 :GKCPVCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRSRAAKAVTEQELTSLLQS 1l8dA 471 :KNTLAKLIDRKSELERELRRIDMEIKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 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 1l8dA/T0300-1l8dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1l8dA/T0300-1l8dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l8dA read from 1l8dA/T0300-1l8dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l8dA in template set T0300 10 :YEEMVKEVERLKLENKTLKQKVKSSGAVS 1l8dA 413 :RNEITQRIGELKNKIGDLKTAIEELKKAK T0300 39 :SDDSILTAAKRESIIVSSSRALGAV 1l8dA 446 :VCGRELTDEHREELLSKYHLDLNNS T0300 65 :MRKIEAKVRS 1l8dA 471 :KNTLAKLIDR T0300 76 :AAKA 1l8dA 481 :KSEL T0300 82 :EQELTSL 1l8dA 485 :ERELRRI Number of specific fragments extracted= 5 number of extra gaps= 0 total=41 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 1p9iA/T0300-1p9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p9iA expands to /projects/compbio/data/pdb/1p9i.pdb.gz 1p9iA:Skipped atom 44, because occupancy 0.5 <= existing 0.500 in 1p9iA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1p9iA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 1p9iA # T0300 read from 1p9iA/T0300-1p9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p9iA read from 1p9iA/T0300-1p9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p9iA to template set # found chain 1p9iA in template set T0300 59 :ALGAVAMRKIEAKVRSRAAKA 1p9iA 9 :ASLEAENKQLKAKVEELLAKV 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=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p9iA/T0300-1p9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1p9iA/T0300-1p9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p9iA read from 1p9iA/T0300-1p9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p9iA in template set T0300 59 :ALGAVAMRKIEAKVRSRAAKA 1p9iA 9 :ASLEAENKQLKAKVEELLAKV Number of specific fragments extracted= 1 number of extra gaps= 0 total=43 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 1p9iA/T0300-1p9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1p9iA/T0300-1p9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p9iA read from 1p9iA/T0300-1p9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p9iA in template set T0300 18 :ERLKLENKTLKQKVKS 1p9iA 9 :ASLEAENKQLKAKVEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=44 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 1nh1A/T0300-1nh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nh1A expands to /projects/compbio/data/pdb/1nh1.pdb.gz 1nh1A:# T0300 read from 1nh1A/T0300-1nh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nh1A read from 1nh1A/T0300-1nh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nh1A to template set # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 38 :SSDDSIL 1nh1A 217 :HTNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLL 1nh1A 238 :ISSDLSQAELISLI Number of specific fragments extracted= 5 number of extra gaps= 0 total=49 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 1nh1A/T0300-1nh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1nh1A/T0300-1nh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nh1A read from 1nh1A/T0300-1nh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 38 :SSDDSIL 1nh1A 217 :HTNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLL 1nh1A 238 :ISSDLSQAELISLI Number of specific fragments extracted= 5 number of extra gaps= 0 total=54 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 1nh1A/T0300-1nh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1nh1A/T0300-1nh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nh1A read from 1nh1A/T0300-1nh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nh1A in template set T0300 9 :TYEEMVKEVERLKLEN 1nh1A 183 :DTEYLRDRVAHLRTEL T0300 25 :KTLKQKVKSSGAV 1nh1A 201 :KALKQHLQRYNPD T0300 39 :SDDSIL 1nh1A 218 :TNASYL T0300 51 :SIIVSSSRALGAVA 1nh1A 224 :PIIKDHLNDLYRQA T0300 76 :AAKAVTEQELTSLLQ 1nh1A 238 :ISSDLSQAELISLIA Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 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 1j8bA/T0300-1j8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j8bA expands to /projects/compbio/data/pdb/1j8b.pdb.gz 1j8bA: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 Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1j8bA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 1j8bA 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 Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 1j8bA 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 Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1j8bA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1j8bA 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 # T0300 read from 1j8bA/T0300-1j8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8bA read from 1j8bA/T0300-1j8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j8bA to template set # found chain 1j8bA in template set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 34 :SGA 1j8bA 48 :GAH T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 58 :DPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 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 1j8bA/T0300-1j8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1j8bA/T0300-1j8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8bA read from 1j8bA/T0300-1j8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8bA in template set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 34 :SGA 1j8bA 48 :GAH T0300 38 :SSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 58 :DPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 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 1j8bA/T0300-1j8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1j8bA/T0300-1j8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8bA read from 1j8bA/T0300-1j8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8bA in template set Warning: unaligning (T0300)K78 because last residue in template chain is (1j8bA)G98 T0300 18 :ERLKLENKTLKQKVKS 1j8bA 15 :QQMQEKMQKMQEEIAQ T0300 37 :VSSDDSILTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAA 1j8bA 57 :IDPSLMEDDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTA Number of specific fragments extracted= 2 number of extra gaps= 0 total=67 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 1ad1A/T0300-1ad1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ad1A expands to /projects/compbio/data/pdb/1ad1.pdb.gz 1ad1A:# T0300 read from 1ad1A/T0300-1ad1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad1A read from 1ad1A/T0300-1ad1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ad1A to template set # found chain 1ad1A in template set T0300 2 :ASKKPDKTYEEMVKEVERLKLE 1ad1A 18 :SDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRVD 1ad1A 98 :GVDIIND Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 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 1ad1A/T0300-1ad1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1ad1A/T0300-1ad1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad1A read from 1ad1A/T0300-1ad1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ad1A in template set T0300 2 :ASKKPDKTYEEMVKEVERLKLE 1ad1A 18 :SDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRVD 1ad1A 98 :GVDIIND Number of specific fragments extracted= 4 number of extra gaps= 0 total=75 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 1ad1A/T0300-1ad1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 1ad1A/T0300-1ad1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ad1A read from 1ad1A/T0300-1ad1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ad1A in template set T0300 1 :MASKKPDKTYEEMVKEVERLKLE 1ad1A 17 :FSDGGKFNNVESAVTRVKAMMDE T0300 34 :SGAVSSDDSILTAAKRESIIVSSSRAL 1ad1A 48 :GVSTRPGHEMITVEEELNRVLPVVEAI T0300 79 :AVTEQELTSLLQ 1ad1A 85 :TFRSEVAEACLK T0300 91 :SLTLRV 1ad1A 98 :GVDIIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=79 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 2aucA/T0300-2aucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aucA expands to /projects/compbio/data/pdb/2auc.pdb.gz 2aucA:Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2aucA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2aucA 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 # T0300 read from 2aucA/T0300-2aucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aucA read from 2aucA/T0300-2aucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aucA to template set # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :SGA 2aucA 120 :GDS T0300 44 :LTAA 2aucA 123 :LTYE T0300 49 :RESIIVSSSRALGAV 2aucA 127 :QYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=86 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 2aucA/T0300-2aucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 2aucA/T0300-2aucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aucA read from 2aucA/T0300-2aucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :SGA 2aucA 120 :GDS T0300 44 :LTAA 2aucA 123 :LTYE T0300 49 :RESIIVSSSRALGAV 2aucA 127 :QYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=93 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 2aucA/T0300-2aucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0300 read from 2aucA/T0300-2aucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aucA read from 2aucA/T0300-2aucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aucA in template set Warning: unaligning (T0300)K5 because first residue in template chain is (2aucA)N88 T0300 6 :PDKTYEEMVKEVER 2aucA 89 :GKLRIEDASHNARK T0300 25 :KTLKQKVKS 2aucA 109 :STDEKKIRD T0300 34 :S 2aucA 120 :G T0300 42 :SILTA 2aucA 121 :DSLTY T0300 48 :KRESIIVSSSRALGAV 2aucA 126 :EQYLEYLTMCVHDRDN T0300 65 :MRKIEAKVRSRA 2aucA 142 :MEELIKMFSHFD T0300 77 :AKAVTEQELTSLLQS 2aucA 157 :SGFLTKNQMKNILTT Number of specific fragments extracted= 7 number of extra gaps= 0 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.648 sec, elapsed time= 11.288 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 5151 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.661 sec, elapsed time= 11.303 sec. # command:Reading probabilities from T0300.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 3.519 Optimizing... Probability sum: -186.849, CN propb: -186.849 weights: 0.182 constraints: 92 # command:CPU_time= 10.798 sec, elapsed time= 11.455 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 92 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 92 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 134 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 134 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 4145 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 4145 # command:CPU_time= 10.878 sec, elapsed time= 11.638 sec. # command: