# 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 T0283 numbered 1 through 112 Created new target T0283 from T0283.a2m # command:CPU_time= 5.178 sec, elapsed time= 5.212 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tffA/T0283-1tffA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tffA expands to /projects/compbio/data/pdb/1tff.pdb.gz 1tffA: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 # T0283 read from 1tffA/T0283-1tffA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tffA read from 1tffA/T0283-1tffA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tffA to template set # found chain 1tffA in template set T0283 6 :KMIGSLNDKREWKAMEARAKALP 1tffA 60 :YLESLLGKSREIFKFKERVLQTP # choosing archetypes in rotamer library T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFEEGAA 1tffA 129 :DHIVQFLRLLTS T0283 82 :DVAAFCDELMKDTKTWMDKYRTKL 1tffA 145 :NRADFFRHFIDEEMDIKDFCTHEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tffA/T0283-1tffA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1tffA/T0283-1tffA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tffA read from 1tffA/T0283-1tffA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tffA in template set T0283 6 :KMIGSLNDKREWKAMEARAKALP 1tffA 60 :YLESLLGKSREIFKFKERVLQTP T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFEEGAA 1tffA 129 :DHIVQFLRLLTS T0283 82 :DVAAFCDELMKDTKTWMDKYRTKL 1tffA 145 :NRADFFRHFIDEEMDIKDFCTHEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=10 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 1tffA/T0283-1tffA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1tffA/T0283-1tffA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tffA read from 1tffA/T0283-1tffA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tffA in template set T0283 8 :IGSLNDKREWKAMEARAKALP 1tffA 62 :ESLLGKSREIFKFKERVLQTP T0283 29 :KEYHHAYKAIQKYMWTSG 1tffA 96 :RNFFNAFYSVVELVEKDG T0283 50 :DWQDTKRIF 1tffA 114 :SVSSLLKVF T0283 59 :GGILDLFE 1tffA 129 :DHIVQFLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=14 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 1b8zA/T0283-1b8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b8zA expands to /projects/compbio/data/pdb/1b8z.pdb.gz 1b8zA:# T0283 read from 1b8zA/T0283-1b8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b8zA read from 1b8zA/T0283-1b8zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b8zA to template set # found chain 1b8zA in template set T0283 14 :KREWKAMEAR 1b8zA 4 :KELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=17 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 1b8zA/T0283-1b8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1b8zA/T0283-1b8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b8zA read from 1b8zA/T0283-1b8zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b8zA in template set T0283 14 :KREWKAMEAR 1b8zA 4 :KELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=20 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 1b8zA/T0283-1b8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1b8zA/T0283-1b8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b8zA read from 1b8zA/T0283-1b8zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b8zA in template set T0283 12 :NDKREWKAMEAR 1b8zA 2 :NKKELIDRVAKK T0283 45 :S 1b8zA 14 :A T0283 48 :PTDWQDTKRIFGGILDLFEEGAAEGKKV 1b8zA 15 :GAKKKDVKLILDTILETITEALAKGEKV Number of specific fragments extracted= 3 number of extra gaps= 0 total=23 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 1sheA/T0283-1sheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sheA expands to /projects/compbio/data/pdb/1she.pdb.gz 1sheA:Skipped atom 145, because occupancy 0.4 <= existing 0.600 in 1sheA Skipped atom 147, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 149, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 151, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 1sheA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 1sheA Skipped atom 178, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 180, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 182, because occupancy 0.300 <= existing 0.500 in 1sheA Skipped atom 284, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 286, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 288, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 290, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 292, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 538, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 540, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 542, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 544, because occupancy 0.350 <= existing 0.650 in 1sheA Skipped atom 546, because occupancy 0.350 <= existing 0.650 in 1sheA # T0283 read from 1sheA/T0283-1sheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sheA read from 1sheA/T0283-1sheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sheA to template set # found chain 1sheA in template set Warning: unaligning (T0283)T49 because first residue in template chain is (1sheA)S2 T0283 50 :DWQDTKRIFGGILDLFEEGAAEGKKVTDLT 1sheA 3 :TRGDLIRILGEIEEKMNELKMDGFNPDIIL T0283 80 :GEDVAAFCDELMKD 1sheA 34 :GREAYNFLSNLLKK Number of specific fragments extracted= 2 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 1sheA/T0283-1sheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1sheA/T0283-1sheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sheA read from 1sheA/T0283-1sheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sheA in template set Warning: unaligning (T0283)T49 because first residue in template chain is (1sheA)S2 T0283 50 :DWQDTKRIFGGILDLFEEGAAEGKKVTDLT 1sheA 3 :TRGDLIRILGEIEEKMNELKMDGFNPDIIL T0283 80 :GEDVAAFCDELMKD 1sheA 34 :GREAYNFLSNLLKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=27 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 1sheA/T0283-1sheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1sheA/T0283-1sheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sheA read from 1sheA/T0283-1sheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sheA in template set Warning: unaligning (T0283)P48 because first residue in template chain is (1sheA)S2 T0283 49 :T 1sheA 3 :T T0283 51 :WQDTKRIFGGILDLFEEGAAEGKKVTDL 1sheA 4 :RGDLIRILGEIEEKMNELKMDGFNPDII T0283 79 :TGEDVAAFCDELMKDTKT 1sheA 33 :FGREAYNFLSNLLKKEME Number of specific fragments extracted= 3 number of extra gaps= 0 total=30 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 1nd6A/T0283-1nd6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nd6A expands to /projects/compbio/data/pdb/1nd6.pdb.gz 1nd6A:# T0283 read from 1nd6A/T0283-1nd6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nd6A read from 1nd6A/T0283-1nd6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nd6A to template set # found chain 1nd6A in template set T0283 3 :FIEKMIGSLNDKREWKAMEARAK 1nd6A 128 :NCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 45 :SGGPTD 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=34 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 1nd6A/T0283-1nd6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1nd6A/T0283-1nd6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nd6A read from 1nd6A/T0283-1nd6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nd6A in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 1nd6A 127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 45 :SGGPTD 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE Number of specific fragments extracted= 4 number of extra gaps= 0 total=38 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 1nd6A/T0283-1nd6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1nd6A/T0283-1nd6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nd6A read from 1nd6A/T0283-1nd6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nd6A in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 1nd6A 127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 1nd6A 151 :PYKDFIATLGK T0283 44 :TSGGPT 1nd6A 162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD 1nd6A 168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 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 2hpaA/T0283-2hpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hpaA expands to /projects/compbio/data/pdb/2hpa.pdb.gz 2hpaA:# T0283 read from 2hpaA/T0283-2hpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hpaA read from 2hpaA/T0283-2hpaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hpaA to template set # found chain 2hpaA in template set T0283 4 :IEKMIGSLNDKREWKAMEARAK 2hpaA 1129 :CPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 2hpaA 1151 :PYKDFIATLGK T0283 45 :SGGPTD 2hpaA 1162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE 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=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hpaA/T0283-2hpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 2hpaA/T0283-2hpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hpaA read from 2hpaA/T0283-2hpaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hpaA in template set T0283 4 :IEKMIGSLNDKREWKAMEARAK 2hpaA 1129 :CPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQK 2hpaA 1151 :PYKDFIATLGK T0283 45 :SGGPTD 2hpaA 1162 :LSGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMK 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSE 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=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hpaA/T0283-2hpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 2hpaA/T0283-2hpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hpaA read from 2hpaA/T0283-2hpaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hpaA in template set T0283 2 :SFIEKMIGSLNDKREWKAMEARAK 2hpaA 1127 :RNCPRFQELESETLKSEEFQKRLH T0283 30 :EYHHAYKAIQKY 2hpaA 1151 :PYKDFIATLGKL T0283 45 :SGGPT 2hpaA 1163 :SGLHG T0283 52 :QDTKRIFGGILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKD 2hpaA 1168 :QDLFGIWSKVYDPLYCESVHNFTLPSWATEDTMTKLRELSEL 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=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tx4A/T0283-1tx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tx4A expands to /projects/compbio/data/pdb/1tx4.pdb.gz 1tx4A:# T0283 read from 1tx4A/T0283-1tx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tx4A read from 1tx4A/T0283-1tx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tx4A to template set # found chain 1tx4A in template set T0283 3 :FIEKMIGS 1tx4A 137 :LYPHVVGF T0283 11 :LNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 147 :IDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 48 :PTDWQDTKRIFGGIL 1tx4A 189 :KMTNTNLAVVFGPNL T0283 81 :EDVAAFCDELMKDTKTW 1tx4A 217 :NPINTFTKFLLDHQGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=58 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 1tx4A/T0283-1tx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1tx4A/T0283-1tx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tx4A read from 1tx4A/T0283-1tx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tx4A in template set T0283 3 :FIEKMIG 1tx4A 137 :LYPHVVG T0283 10 :SLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 146 :NIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 48 :PTDWQDTKRIFGGIL 1tx4A 189 :KMTNTNLAVVFGPNL T0283 81 :EDVAAFCDELMKDTKTW 1tx4A 217 :NPINTFTKFLLDHQGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 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 1tx4A/T0283-1tx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1tx4A/T0283-1tx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tx4A read from 1tx4A/T0283-1tx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tx4A in template set T0283 11 :LNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSG 1tx4A 147 :IDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQIS T0283 47 :GP 1tx4A 189 :KM T0283 50 :DWQDTKRIFGGIL 1tx4A 191 :TNTNLAVVFGPNL T0283 65 :FEEGA 1tx4A 212 :TLKAI T0283 81 :EDVAAFCDELMKDTKT 1tx4A 217 :NPINTFTKFLLDHQGE Number of specific fragments extracted= 5 number of extra gaps= 0 total=67 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 1gk9A/T0283-1gk9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gk9A expands to /projects/compbio/data/pdb/1gk9.pdb.gz 1gk9A:Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 452, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 454, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 456, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 458, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 460, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 462, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 464, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 466, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 468, because occupancy 0.400 <= existing 0.600 in 1gk9A Skipped atom 814, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 816, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 818, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 820, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 822, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 824, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 826, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 828, because occupancy 0.350 <= existing 0.650 in 1gk9A Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1509, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1gk9A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1gk9A # T0283 read from 1gk9A/T0283-1gk9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gk9A read from 1gk9A/T0283-1gk9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gk9A to template set # found chain 1gk9A in template set T0283 10 :SLNDKREWKA 1gk9A 62 :FVKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 31 :YHHAYKAIQK 1gk9A 100 :MNAWIDKVNT T0283 41 :YMWTSGGPTDWQDTKRI 1gk9A 118 :QFNTFGFTPKRWEPFDV T0283 60 :GILDLFEEGAAEGKK 1gk9A 135 :AMIFVGTMANRFSDS T0283 78 :LTGEDVAAFCDELMKD 1gk9A 150 :TSEIDNLALLTALKDK T0283 94 :TKTWMDKYRT 1gk9A 168 :VSQGMAVFNQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=74 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 1gk9A/T0283-1gk9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1gk9A/T0283-1gk9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gk9A read from 1gk9A/T0283-1gk9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gk9A in template set T0283 11 :LNDKREWKA 1gk9A 63 :VKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 31 :YHHAYKAIQK 1gk9A 100 :MNAWIDKVNT T0283 41 :YMWTSGGPTDWQDTKRI 1gk9A 118 :QFNTFGFTPKRWEPFDV T0283 60 :GILDLFEEGAAEGKK 1gk9A 135 :AMIFVGTMANRFSDS T0283 79 :TGEDVAAFCDELMKD 1gk9A 151 :SEIDNLALLTALKDK T0283 94 :TKTWMDKYRT 1gk9A 168 :VSQGMAVFNQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=81 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 1gk9A/T0283-1gk9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1gk9A/T0283-1gk9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gk9A read from 1gk9A/T0283-1gk9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gk9A in template set T0283 9 :GSLNDKREWKA 1gk9A 61 :DFVKFDKDIRR T0283 20 :MEARAKALPKE 1gk9A 78 :IRAQIAALSPE T0283 53 :D 1gk9A 89 :D T0283 55 :KRIFGGIL 1gk9A 90 :MSILQGYA T0283 81 :EDVAAFCDELMKDTKTWMDKYRTKLNDSIGR 1gk9A 98 :DGMNAWIDKVNTNPETLLPKQFNTFGFTPKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=86 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 1csn/T0283-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1csn expands to /projects/compbio/data/pdb/1csn.pdb.gz 1csn:Warning: there is no chain 1csn will retry with 1csnA # T0283 read from 1csn/T0283-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0283-1csn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1csn to template set # found chain 1csn in template set T0283 13 :DKREWKAMEARAKA 1csn 226 :NKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=89 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 1csn/T0283-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1csn/T0283-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0283-1csn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1csn in template set T0283 13 :DKREWKAMEARAKA 1csn 226 :NKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=92 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 1csn/T0283-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1csn/T0283-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1csn read from 1csn/T0283-1csn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1csn in template set T0283 12 :NDKREWKAMEARAKA 1csn 225 :TNKQKYERIGEKKQS T0283 27 :LPKEYHHAYKAIQK 1csn 249 :FPEEFYKYMHYARN T0283 45 :SGGPTDWQDTKRIFGGILD 1csn 265 :FDATPDYDYLQGLFSKVLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 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 1nox/T0283-1nox-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nox expands to /projects/compbio/data/pdb/1nox.pdb.gz 1nox:Warning: there is no chain 1nox will retry with 1noxA # T0283 read from 1nox/T0283-1nox-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nox read from 1nox/T0283-1nox-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nox to template set # found chain 1nox in template set T0283 12 :NDKREWKAMEARAKALPKEYH 1nox 108 :RREAQKQAIQRAFAAMGQEAR T0283 39 :QKYMWT 1nox 129 :KAWASG T0283 53 :DTKRIFGGILDLFEE 1nox 135 :QSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAFC 1nox 163 :ERVRAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=100 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 1nox/T0283-1nox-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1nox/T0283-1nox-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nox read from 1nox/T0283-1nox-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nox in template set T0283 11 :LNDKREWKAMEARAKALPKEYH 1nox 107 :ERREAQKQAIQRAFAAMGQEAR T0283 39 :QKYMWT 1nox 129 :KAWASG T0283 53 :DTKRIFGGILDLFEE 1nox 135 :QSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAFC 1nox 163 :ERVRAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=105 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nox/T0283-1nox-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1nox/T0283-1nox-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nox read from 1nox/T0283-1nox-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nox in template set T0283 10 :SLNDKREWKAMEARAKALPKEYHHAYKA 1nox 106 :GERREAQKQAIQRAFAAMGQEARKAWAS T0283 52 :QDTKRIFGGILDLFEE 1nox 134 :GQSYILLGYLLLLLEA T0283 71 :EGKKVTDLTG 1nox 150 :YGLGSVPMLG T0283 81 :EDVAAF 1nox 163 :ERVRAI Number of specific fragments extracted= 4 number of extra gaps= 0 total=109 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 1am4A/T0283-1am4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1am4A expands to /projects/compbio/data/pdb/1am4.pdb.gz 1am4A:# T0283 read from 1am4A/T0283-1am4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am4A read from 1am4A/T0283-1am4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1am4A to template set # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 3 :FIEKMIGS 1am4A 137 :LYPHVVGF T0283 11 :LNDKREWKAMEARAKALP 1am4A 147 :IDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :PTDWQDTKR 1am4A 189 :KMTNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 71 :EGK 1am4A 207 :KDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKTW 1am4A 223 :TKFLLDHQGEL Number of specific fragments extracted= 11 number of extra gaps= 8 total=120 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 1am4A/T0283-1am4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1am4A/T0283-1am4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am4A read from 1am4A/T0283-1am4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 3 :FIEKMIG 1am4A 137 :LYPHVVG T0283 10 :SLNDKREWKAMEARAKALP 1am4A 146 :NIDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :PTDWQDTKR 1am4A 189 :KMTNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 71 :EGK 1am4A 207 :KDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKTW 1am4A 223 :TKFLLDHQGEL Number of specific fragments extracted= 11 number of extra gaps= 8 total=131 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 1am4A/T0283-1am4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0283 read from 1am4A/T0283-1am4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am4A read from 1am4A/T0283-1am4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1am4A in template set Warning: unaligning (T0283)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)E166 Warning: unaligning (T0283)E30 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)E166 Warning: unaligning (T0283)W43 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)Q180 Warning: unaligning (T0283)T44 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)Q180 Warning: unaligning (T0283)G46 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)A183 Warning: unaligning (T0283)G47 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)A183 Warning: unaligning (T0283)I57 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F199 Warning: unaligning (T0283)F58 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F199 Warning: unaligning (T0283)G60 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)N202 Warning: unaligning (T0283)I61 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N202 Warning: unaligning (T0283)K74 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I211 Warning: unaligning (T0283)V75 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I211 Warning: unaligning (T0283)T76 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)L213 Warning: unaligning (T0283)D77 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)L213 Warning: unaligning (T0283)T79 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)I216 Warning: unaligning (T0283)G80 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)I216 Warning: unaligning (T0283)E81 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)N217 Warning: unaligning (T0283)A85 because of BadResidue code BAD_PEPTIDE in next template residue (1am4A)F222 Warning: unaligning (T0283)F86 because of BadResidue code BAD_PEPTIDE at template residue (1am4A)F222 T0283 11 :LNDKREWKAMEARAKALP 1am4A 147 :IDESQRVPATLQVLQTLP T0283 31 :YHHAYKAIQKYM 1am4A 167 :NYQVLRFLTAFL T0283 45 :S 1am4A 181 :I T0283 48 :P 1am4A 184 :H T0283 50 :DWQDTKR 1am4A 191 :TNTNLAV T0283 59 :G 1am4A 200 :G T0283 62 :L 1am4A 203 :L T0283 70 :AEGK 1am4A 206 :AKDA T0283 78 :L 1am4A 214 :K T0283 82 :DVA 1am4A 218 :PIN T0283 87 :CDELMKDTKT 1am4A 223 :TKFLLDHQGE Number of specific fragments extracted= 11 number of extra gaps= 8 total=142 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 9.714 sec, elapsed time= 10.462 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 6216 constraints to all_contacts Done adding distance constraints # command:CPU_time= 9.728 sec, elapsed time= 10.479 sec. # command:Reading probabilities from T0283.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.530 Optimizing... Probability sum: -175.731, CN propb: -175.731 weights: 0.329 constraints: 134 # command:CPU_time= 9.795 sec, elapsed time= 10.557 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 134 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 134 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 178 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 178 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 5044 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 5044 # command:CPU_time= 9.878 sec, elapsed time= 10.702 sec. # command: