# 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 T0349 numbered 1 through 75 Created new target T0349 from T0349.a2m # command:CPU_time= 6.316 sec, elapsed time= 6.370 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhvA/T0349-1zhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zhvA expands to /projects/compbio/data/pdb/1zhv.pdb.gz 1zhvA:# T0349 read from 1zhvA/T0349-1zhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhvA read from 1zhvA/T0349-1zhvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zhvA to template set # found chain 1zhvA in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNM 1zhvA 79 :IVLSVISPLSTNGIGIFVVSTFD # choosing archetypes in rotamer library T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHELRSD 1zhvA 102 :GDHLLVRSNDLEKTADLLANAGHSLLLEHH Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 1zhvA/T0349-1zhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1zhvA/T0349-1zhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhvA read from 1zhvA/T0349-1zhvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zhvA in template set T0349 13 :LSAVGALLDGADIGHLVLDQNM 1zhvA 80 :VLSVISPLSTNGIGIFVVSTFD T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAH 1zhvA 102 :GDHLLVRSNDLEKTADLLANAGHSL Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 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 1zhvA/T0349-1zhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1zhvA/T0349-1zhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zhvA read from 1zhvA/T0349-1zhvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zhvA in template set T0349 9 :DAVLLSAVGALLDGADIGHLVLDQ 1zhvA 76 :ETGIVLSVISPLSTNGIGIFVVST T0349 37 :LEG 1zhvA 100 :FDG T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHELRS 1zhvA 103 :DHLLVRSNDLEKTADLLANAGHSLLLEH Number of specific fragments extracted= 3 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 1vjqA/T0349-1vjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjqA expands to /projects/compbio/data/pdb/1vjq.pdb.gz 1vjqA:Skipped atom 292, because occupancy 0.5 <= existing 0.500 in 1vjqA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 1vjqA 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 # T0349 read from 1vjqA/T0349-1vjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjqA read from 1vjqA/T0349-1vjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjqA to template set # found chain 1vjqA in template set Warning: unaligning (T0349)G26 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)H27 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)L28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 5 :LRTNDAVLLSAVGALLDGADI 1vjqA 6 :IVPTNEEQVAFLEALAKQDEL T0349 30 :L 1vjqA 30 :W T0349 32 :QNMSILEGS 1vjqA 31 :QNPPTEPGQ T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1vjqA 40 :PVVILIPSDMVEWFLEMLKAKGIPFT Number of specific fragments extracted= 4 number of extra gaps= 1 total=11 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 1vjqA/T0349-1vjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1vjqA/T0349-1vjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjqA read from 1vjqA/T0349-1vjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjqA in template set Warning: unaligning (T0349)G26 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)L28 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 9 :DAVLLSAVGALLDGADI 1vjqA 10 :NEEQVAFLEALAKQDEL T0349 30 :LDQNMS 1vjqA 30 :WQNPPT T0349 38 :EGS 1vjqA 37 :PGQ T0349 45 :PRRVLVHEDDLAGARRLLTDAGLA 1vjqA 40 :PVVILIPSDMVEWFLEMLKAKGIP Number of specific fragments extracted= 4 number of extra gaps= 1 total=15 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 1vjqA/T0349-1vjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1vjqA/T0349-1vjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjqA read from 1vjqA/T0349-1vjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjqA in template set Warning: unaligning (T0349)N33 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)S35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 4 :LLRTNDAVLLSAVGALLDGAD 1vjqA 5 :VIVPTNEEQVAFLEALAKQDE T0349 32 :Q 1vjqA 26 :L T0349 36 :ILEGS 1vjqA 30 :WQNPP T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLA 1vjqA 36 :EPGQPVVILIPSDMVEWFLEMLKAKGIP Number of specific fragments extracted= 4 number of extra gaps= 1 total=19 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 1yj7A/T0349-1yj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yj7A expands to /projects/compbio/data/pdb/1yj7.pdb.gz 1yj7A:Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1yj7A # T0349 read from 1yj7A/T0349-1yj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yj7A read from 1yj7A/T0349-1yj7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yj7A to template set # found chain 1yj7A in template set T0349 10 :AVLLSAVGALLDGADIGHL 1yj7A 30 :EKEANQMQALLLSNDVNVS T0349 29 :VLDQNMS 1yj7A 50 :EMDKSGN T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1yj7A 57 :MTLSVAAADFVRAITILNNNGFPKKK 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=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yj7A/T0349-1yj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1yj7A/T0349-1yj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yj7A read from 1yj7A/T0349-1yj7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yj7A in template set T0349 13 :LSAVGALLDGADIGH 1yj7A 33 :ANQMQALLLSNDVNV T0349 28 :LVLDQNMS 1yj7A 49 :KEMDKSGN T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1yj7A 57 :MTLSVAAADFVRAITILNNNGFPKKK 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=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yj7A/T0349-1yj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1yj7A/T0349-1yj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yj7A read from 1yj7A/T0349-1yj7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yj7A in template set T0349 1 :MRELLRTN 1yj7A 20 :MKEQLYTG T0349 9 :DAVLLSAVGALLDGADIG 1yj7A 29 :TEKEANQMQALLLSNDVN T0349 30 :LDQN 1yj7A 51 :MDKS T0349 39 :G 1yj7A 55 :G T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1yj7A 56 :NMTLSVAAADFVRAITILNNNGFPKK T0349 74 :D 1yj7A 82 :K Number of specific fragments extracted= 6 number of extra gaps= 0 total=31 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 1g61A/T0349-1g61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g61A expands to /projects/compbio/data/pdb/1g61.pdb.gz 1g61A:# T0349 read from 1g61A/T0349-1g61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g61A read from 1g61A/T0349-1g61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g61A to template set # found chain 1g61A in template set Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 9 :DAVLLSAVGALLD 1g61A 2033 :DKDDVNEVSEVLE T0349 25 :IGHLVLDQN 1g61A 2046 :TKCLQTNIG T0349 36 :ILEGSLGVI 1g61A 2057 :SLVGSLSVA T0349 45 :PRRVL 1g61A 2067 :KYGLL T0349 50 :VHEDDLAGARRLLTDAGLAHE 1g61A 2076 :VEDEELDRIKNFLKENNLDLN Number of specific fragments extracted= 5 number of extra gaps= 1 total=36 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 1g61A/T0349-1g61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1g61A/T0349-1g61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g61A read from 1g61A/T0349-1g61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g61A in template set Warning: unaligning (T0349)N33 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 13 :LSAVGALLD 1g61A 2037 :VNEVSEVLE T0349 25 :IGHLVLD 1g61A 2046 :TKCLQTN T0349 32 :Q 1g61A 2054 :G T0349 35 :SILEGSLGVIPRRVL 1g61A 2057 :SLVGSLSVANKYGLL T0349 50 :VHEDDLAGARRLLTDAGLAH 1g61A 2076 :VEDEELDRIKNFLKENNLDL Number of specific fragments extracted= 5 number of extra gaps= 1 total=41 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 1g61A/T0349-1g61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1g61A/T0349-1g61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g61A read from 1g61A/T0349-1g61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g61A in template set Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 12 :LLSAVGALLD 1g61A 2036 :DVNEVSEVLE T0349 25 :IGHLVLDQN 1g61A 2046 :TKCLQTNIG T0349 36 :ILEGSLG 1g61A 2057 :SLVGSLS T0349 43 :VIPRRVL 1g61A 2065 :ANKYGLL T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1g61A 2076 :VEDEELDRIKNFLKENNLDLNV Number of specific fragments extracted= 5 number of extra gaps= 1 total=46 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 1kwmA/T0349-1kwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kwmA expands to /projects/compbio/data/pdb/1kwm.pdb.gz 1kwmA:Skipped atom 268, because occupancy 0.470 <= existing 0.530 in 1kwmA Skipped atom 270, because occupancy 0.470 <= existing 0.530 in 1kwmA Skipped atom 272, because occupancy 0.470 <= existing 0.530 in 1kwmA WARNING: atom 790 has residue number 4 < previous residue 95A in 1kwmA Skipped atom 1086, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1088, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1090, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1311, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1313, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1315, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1317, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1319, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1321, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1961, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1963, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1965, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1967, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1969, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1971, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1973, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 2225, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2227, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2229, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2231, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2315, because occupancy 0.340 <= existing 0.660 in 1kwmA Skipped atom 2317, because occupancy 0.340 <= existing 0.660 in 1kwmA # T0349 read from 1kwmA/T0349-1kwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kwmA read from 1kwmA/T0349-1kwmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kwmA to template set # found chain 1kwmA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGHLVLDQNMSI 1kwmA 15A:VNVEDENHINIIRELASTTQIDFWKPDSVTQI T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLAHE 1kwmA 47A:KPHSTVDFRVKAEDTVTVENVLKQNELQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=48 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 1kwmA/T0349-1kwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1kwmA/T0349-1kwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kwmA read from 1kwmA/T0349-1kwmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kwmA in template set T0349 9 :DAVLLSAVGALLDGADIGHLVLDQNMSI 1kwmA 19A:DENHINIIRELASTTQIDFWKPDSVTQI T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLA 1kwmA 47A:KPHSTVDFRVKAEDTVTVENVLKQNELQ Number of specific fragments extracted= 2 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 1kwmA/T0349-1kwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1kwmA/T0349-1kwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kwmA read from 1kwmA/T0349-1kwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kwmA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGHLV 1kwmA 15A:VNVEDENHINIIRELASTTQIDFWK T0349 34 :MSILEGSLGVIPRRVLVHEDDLAGARRLLTDAGLA 1kwmA 40A:PDSVTQIKPHSTVDFRVKAEDTVTVENVLKQNELQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=52 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 1dzkA/T0349-1dzkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dzkA expands to /projects/compbio/data/pdb/1dzk.pdb.gz 1dzkA:Skipped atom 83, because occupancy 0.280 <= existing 0.720 in 1dzkA Skipped atom 239, because occupancy 0.310 <= existing 0.730 in 1dzkA Skipped atom 241, because occupancy 0.090 <= existing 0.470 in 1dzkA Skipped atom 243, because occupancy 0.110 <= existing 0.540 in 1dzkA Skipped atom 847, because occupancy 0.280 <= existing 0.360 in 1dzkA Skipped atom 849, because occupancy 0.100 <= existing 0.190 in 1dzkA Skipped atom 959, because occupancy 0.240 <= existing 0.650 in 1dzkA Skipped atom 961, because occupancy 0.320 <= existing 0.970 in 1dzkA Skipped atom 1003, because occupancy 0.260 <= existing 0.410 in 1dzkA Skipped atom 1114, because occupancy 0.280 <= existing 0.620 in 1dzkA # T0349 read from 1dzkA/T0349-1dzkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dzkA read from 1dzkA/T0349-1dzkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dzkA to template set # found chain 1dzkA in template set T0349 35 :SILEGSLGV 1dzkA 112 :TIMTGLLGK T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1dzkA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=54 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 1dzkA/T0349-1dzkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1dzkA/T0349-1dzkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dzkA read from 1dzkA/T0349-1dzkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dzkA in template set T0349 42 :GVIPRRVL 1dzkA 112 :TIMTGLLG T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1dzkA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=56 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 1dzkA/T0349-1dzkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1dzkA/T0349-1dzkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dzkA read from 1dzkA/T0349-1dzkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dzkA in template set T0349 50 :VHEDDLAGARRLLTDAGLAHE 1dzkA 124 :IEDQDLEKFKEVTRENGIPEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=57 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f06A/T0349-2f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f06A expands to /projects/compbio/data/pdb/2f06.pdb.gz 2f06A: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 22, because occupancy 0.500 <= existing 0.500 in 2f06A 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 26, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 2f06A 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 850, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 854, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2f06A 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 1051, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1057, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f06A # T0349 read from 2f06A/T0349-2f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f06A read from 2f06A/T0349-2f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f06A to template set # found chain 2f06A in template set Warning: unaligning (T0349)L12 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)R16 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE in next template residue (2f06A)I44 Warning: unaligning (T0349)I36 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)I44 Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 13 :LSAVGALLDGADIGHLVLD 2f06A 17 :LTEVTEVLAKENINLSALC T0349 32 :QNM 2f06A 40 :ADF T0349 37 :L 2f06A 45 :L T0349 49 :LVH 2f06A 48 :IVS T0349 54 :DLAGARRLLTDAGLAHE 2f06A 51 :DPDKAYKALKDNHFAVN Number of specific fragments extracted= 5 number of extra gaps= 3 total=62 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 2f06A/T0349-2f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2f06A/T0349-2f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f06A read from 2f06A/T0349-2f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f06A in template set Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 13 :LSAVGALLDGADIGHLVLD 2f06A 17 :LTEVTEVLAKENINLSALC T0349 43 :VIP 2f06A 36 :IAE T0349 46 :R 2f06A 45 :L T0349 49 :LVH 2f06A 48 :IVS T0349 54 :DLAGARRLLTDAGLA 2f06A 51 :DPDKAYKALKDNHFA Number of specific fragments extracted= 5 number of extra gaps= 1 total=67 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 2f06A/T0349-2f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2f06A/T0349-2f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f06A read from 2f06A/T0349-2f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f06A in template set Warning: unaligning (T0349)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)S14 Warning: unaligning (T0349)A10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)S14 Warning: unaligning (T0349)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G15 Warning: unaligning (T0349)L12 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)R16 Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 8 :N 2f06A 12 :N T0349 13 :LSAVGALLDGADIGH 2f06A 17 :LTEVTEVLAKENINL T0349 32 :QNMSILEGSL 2f06A 32 :SALCIAENAD T0349 46 :R 2f06A 45 :L T0349 49 :LVHE 2f06A 48 :IVSD T0349 55 :LAGARRLLTDAGLA 2f06A 52 :PDKAYKALKDNHFA Number of specific fragments extracted= 6 number of extra gaps= 2 total=73 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 1zvpA/T0349-1zvpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zvpA expands to /projects/compbio/data/pdb/1zvp.pdb.gz 1zvpA:# T0349 read from 1zvpA/T0349-1zvpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvpA read from 1zvpA/T0349-1zvpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zvpA to template set # found chain 1zvpA in template set T0349 13 :LSAVGALLDGADIGHLVL 1zvpA 87 :TAAFATKLAEHGISANVI T0349 38 :E 1zvpA 105 :A T0349 42 :GVIPRRVLVHEDDLAGARRLLT 1zvpA 106 :GYYHDHIFVQKEKAQQALQALG Number of specific fragments extracted= 3 number of extra gaps= 0 total=76 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 1zvpA/T0349-1zvpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1zvpA/T0349-1zvpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvpA read from 1zvpA/T0349-1zvpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zvpA in template set T0349 15 :AVGALLDGADIGH 1zvpA 89 :AFATKLAEHGISA T0349 35 :SILEG 1zvpA 102 :NVIAG T0349 43 :VIPRRVLVHEDDLAGARRLLTD 1zvpA 107 :YYHDHIFVQKEKAQQALQALGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=79 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 1zvpA/T0349-1zvpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1zvpA/T0349-1zvpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zvpA read from 1zvpA/T0349-1zvpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zvpA in template set T0349 14 :SAVGALLDGADIG 1zvpA 88 :AAFATKLAEHGIS T0349 34 :MSILEG 1zvpA 101 :ANVIAG T0349 43 :VIPRRVLVHEDDLAGARRLLT 1zvpA 107 :YYHDHIFVQKEKAQQALQALG Number of specific fragments extracted= 3 number of extra gaps= 0 total=82 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 1nm2A/T0349-1nm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nm2A expands to /projects/compbio/data/pdb/1nm2.pdb.gz 1nm2A:# T0349 read from 1nm2A/T0349-1nm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nm2A read from 1nm2A/T0349-1nm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nm2A to template set # found chain 1nm2A in template set T0349 13 :LSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 257 :WDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=84 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 1nm2A/T0349-1nm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1nm2A/T0349-1nm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nm2A read from 1nm2A/T0349-1nm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nm2A in template set T0349 13 :LSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 257 :WDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=86 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 1nm2A/T0349-1nm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1nm2A/T0349-1nm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nm2A read from 1nm2A/T0349-1nm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nm2A in template set T0349 8 :NDAVLLSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 252 :ANPVRWDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=88 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 1hdoA/T0349-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1hdoA/T0349-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0349-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set T0349 4 :LLRTNDAVLLSAVGALLD 1hdoA 8 :IFGATGQTGLTTLAQAVQ T0349 23 :ADIGHLVLDQNMSILEGSL 1hdoA 26 :AGYEVTVLVRDSSRLPSEG T0349 43 :VIPRRVLVHE 1hdoA 45 :PRPAHVVVGD T0349 53 :DDLAGARRLL 1hdoA 56 :LQAADVDKTV Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 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 1hdoA/T0349-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1hdoA/T0349-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0349-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0349)V50 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0349)A65 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0349)G66 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0349 11 :VLLSAVGALLDGADIGHLVLDQNMSILEGSL 1hdoA 89 :EGARNIVAAMKAHGVDKVVACTSAFLLWDPT T0349 51 :HEDDLA 1hdoA 122 :PPRLQA T0349 57 :GARRLLTD 1hdoA 134 :RMHKVLRE T0349 67 :L 1hdoA 144 :L Number of specific fragments extracted= 4 number of extra gaps= 2 total=96 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 1hdoA/T0349-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1hdoA/T0349-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0349-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0349)V43 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0349)A65 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0349)G66 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0349 12 :LLSAVGALLDGADIGHLVLDQNMSILEGSL 1hdoA 90 :GARNIVAAMKAHGVDKVVACTSAFLLWDPT T0349 44 :IPRR 1hdoA 122 :PPRL T0349 49 :LVHEDDLAGARRLLTD 1hdoA 126 :QAVTDDHIRMHKVLRE T0349 67 :LA 1hdoA 144 :LK Number of specific fragments extracted= 4 number of extra gaps= 2 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6sA/T0349-1v6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v6sA expands to /projects/compbio/data/pdb/1v6s.pdb.gz 1v6sA:# T0349 read from 1v6sA/T0349-1v6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6sA read from 1v6sA/T0349-1v6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v6sA to template set # found chain 1v6sA in template set T0349 13 :LSAVGALL 1v6sA 199 :IGVIESLL T0349 23 :ADIGHLVLDQNMS 1v6sA 207 :PRIDRLLIGGAMA T0349 36 :ILEGSLGVI 1v6sA 225 :ALGGEVGRS T0349 49 :LVHEDDLAGARRLLTDA 1v6sA 234 :LVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=104 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6sA/T0349-1v6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1v6sA/T0349-1v6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6sA read from 1v6sA/T0349-1v6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6sA in template set T0349 13 :LSAVGALLD 1v6sA 199 :IGVIESLLP T0349 24 :DIGHLVLDQNMS 1v6sA 208 :RIDRLLIGGAMA T0349 36 :ILEGSLGVI 1v6sA 225 :ALGGEVGRS T0349 49 :LVHEDDLAGARRLLTDA 1v6sA 234 :LVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=108 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6sA/T0349-1v6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1v6sA/T0349-1v6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6sA read from 1v6sA/T0349-1v6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6sA in template set T0349 13 :LSAVGALLD 1v6sA 199 :IGVIESLLP T0349 24 :DIGHLVLDQNMS 1v6sA 208 :RIDRLLIGGAMA T0349 36 :ILEGSLG 1v6sA 225 :ALGGEVG T0349 47 :RVLVHEDDLAGARRLLTDA 1v6sA 232 :RSLVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=112 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/T0349-1ve1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ve1A expands to /projects/compbio/data/pdb/1ve1.pdb.gz 1ve1A:# T0349 read from 1ve1A/T0349-1ve1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve1A read from 1ve1A/T0349-1ve1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ve1A to template set # found chain 1ve1A in template set T0349 8 :NDAVLLSAVGALLDG 1ve1A 176 :TGGTITGVGRYLKER T0349 23 :ADIGHLVLD 1ve1A 192 :PHVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=117 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/T0349-1ve1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1ve1A/T0349-1ve1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve1A read from 1ve1A/T0349-1ve1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ve1A in template set T0349 9 :DAVLLSAVGALLDG 1ve1A 177 :GGTITGVGRYLKER T0349 23 :ADIGHLVLD 1ve1A 192 :PHVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=122 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/T0349-1ve1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1ve1A/T0349-1ve1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve1A read from 1ve1A/T0349-1ve1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ve1A in template set T0349 7 :TNDAVLLSAVGALLDGA 1ve1A 174 :SGTGGTITGVGRYLKER T0349 24 :DIGHLVLD 1ve1A 193 :HVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=127 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gnkA/T0349-1gnkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gnkA expands to /projects/compbio/data/pdb/1gnk.pdb.gz 1gnkA:# T0349 read from 1gnkA/T0349-1gnkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gnkA read from 1gnkA/T0349-1gnkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gnkA to template set # found chain 1gnkA in template set Warning: unaligning (T0349)L41 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gnkA)V53 T0349 16 :VGALLDGADIGHLVLD 1gnkA 16 :VREALSSIGIQGLTVT T0349 42 :GVIPR 1gnkA 54 :NFLPK T0349 47 :RVLVHEDDLAGARRLLTDAG 1gnkA 62 :DVAIADDQLDEVIDIVSKAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=130 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gnkA/T0349-1gnkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1gnkA/T0349-1gnkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gnkA read from 1gnkA/T0349-1gnkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gnkA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLA 1gnkA 6 :VIIKPFKLEDVREALSSIGIQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=131 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gnkA/T0349-1gnkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1gnkA/T0349-1gnkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gnkA read from 1gnkA/T0349-1gnkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gnkA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLAH 1gnkA 6 :VIIKPFKLEDVREALSSIGIQG Number of specific fragments extracted= 1 number of extra gaps= 0 total=132 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jbeA/T0349-1jbeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1jbeA/T0349-1jbeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jbeA read from 1jbeA/T0349-1jbeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 5 :LRTNDAV 1jbeA 34 :EEAEDGV T0349 15 :AVGALLDGADIGHLVLDQNMS 1jbeA 41 :DALNKLQAGGYGFVISDWNMP T0349 43 :VIPRRVLV 1jbeA 80 :ALPVLMVT T0349 51 :HEDDLAGARR 1jbeA 91 :KKENIIAAAQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=136 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jbeA/T0349-1jbeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1jbeA/T0349-1jbeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jbeA read from 1jbeA/T0349-1jbeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 16 :VGALLDGADIGHLVLDQNMS 1jbeA 42 :ALNKLQAGGYGFVISDWNMP T0349 43 :VIPRRVLV 1jbeA 80 :ALPVLMVT T0349 51 :HEDDLAGARR 1jbeA 91 :KKENIIAAAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=139 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jbeA/T0349-1jbeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1jbeA/T0349-1jbeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jbeA read from 1jbeA/T0349-1jbeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 16 :VGALLDGADIGHLVLDQNMSIL 1jbeA 42 :ALNKLQAGGYGFVISDWNMPNM T0349 43 :VIPRRVLVH 1jbeA 80 :ALPVLMVTA T0349 52 :EDDLAGARR 1jbeA 92 :KENIIAAAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pba/T0349-1pba-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pba expands to /projects/compbio/data/pdb/1pba.pdb.gz 1pba:Warning: there is no chain 1pba will retry with 1pbaA # T0349 read from 1pba/T0349-1pba-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pba read from 1pba/T0349-1pba-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pba to template set # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 5 :LRTNDAVLLSAVGALLDGADIGHL 1pba 15 :VNVEDENDISELHELASTRQIDFW T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GS 1pba 49 :HS T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHELR 1pba 51 :TVDFRVKAEDILAVEDFLEQNELQYEVL Number of specific fragments extracted= 4 number of extra gaps= 1 total=146 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pba/T0349-1pba-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1pba/T0349-1pba-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pba read from 1pba/T0349-1pba-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 9 :DAVLLSAVGALLDGADIGH 1pba 19 :DENDISELHELASTRQIDF T0349 31 :D 1pba 38 :W T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GS 1pba 49 :HS T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1pba 51 :TVDFRVKAEDILAVEDFLEQNELQYE Number of specific fragments extracted= 5 number of extra gaps= 1 total=151 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pba/T0349-1pba-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1pba/T0349-1pba-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pba read from 1pba/T0349-1pba-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 5 :LRTNDAVLLSAVGALLDGADIG 1pba 15 :VNVEDENDISELHELASTRQID T0349 30 :LD 1pba 37 :FW T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GSL 1pba 49 :HST T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHE 1pba 52 :VDFRVKAEDILAVEDFLEQNELQYE Number of specific fragments extracted= 5 number of extra gaps= 1 total=156 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvlA/T0349-2cvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cvlA expands to /projects/compbio/data/pdb/2cvl.pdb.gz 2cvlA: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 # T0349 read from 2cvlA/T0349-2cvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvlA read from 2cvlA/T0349-2cvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cvlA to template set # found chain 2cvlA in template set T0349 6 :RTNDAVLLSAVGALLDGADIGH 2cvlA 46 :RVQTERVMENLKAVLEAAGSGL T0349 28 :LVLD 2cvlA 70 :VVQT T0349 46 :RRVLVHEDDLAGARRLLTDA 2cvlA 74 :TCFLADMEDFPGFNEVYARY T0349 67 :LAH 2cvlA 94 :FTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=160 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvlA/T0349-2cvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2cvlA/T0349-2cvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvlA read from 2cvlA/T0349-2cvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvlA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGH 2cvlA 45 :IRVQTERVMENLKAVLEAAGSGL T0349 42 :GVIP 2cvlA 69 :RVVQ T0349 46 :RRVLVHEDDLAGARRLLTDA 2cvlA 74 :TCFLADMEDFPGFNEVYARY T0349 67 :LAHE 2cvlA 94 :FTPP Number of specific fragments extracted= 4 number of extra gaps= 0 total=164 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvlA/T0349-2cvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2cvlA/T0349-2cvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvlA read from 2cvlA/T0349-2cvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvlA in template set T0349 11 :VLLSAVGALLDGADIG 2cvlA 51 :RVMENLKAVLEAAGSG T0349 37 :LEGSLG 2cvlA 67 :LSRVVQ T0349 45 :PRRVLVHEDDLAGARRLLTDA 2cvlA 73 :TTCFLADMEDFPGFNEVYARY Number of specific fragments extracted= 3 number of extra gaps= 0 total=167 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt1A/T0349-1gt1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gt1A expands to /projects/compbio/data/pdb/1gt1.pdb.gz 1gt1A:# T0349 read from 1gt1A/T0349-1gt1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gt1A read from 1gt1A/T0349-1gt1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gt1A to template set # found chain 1gt1A in template set T0349 31 :DQNMSILEGSLGV 1gt1A 107 :DKHGQTTELTELF T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1gt1A 120 :VKLNVEDEDLEKFWKLTEDKGIDKKN Number of specific fragments extracted= 2 number of extra gaps= 0 total=169 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt1A/T0349-1gt1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1gt1A/T0349-1gt1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gt1A read from 1gt1A/T0349-1gt1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gt1A in template set T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1gt1A 124 :VEDEDLEKFWKLTEDKGIDKKN Number of specific fragments extracted= 1 number of extra gaps= 0 total=170 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt1A/T0349-1gt1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1gt1A/T0349-1gt1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gt1A read from 1gt1A/T0349-1gt1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gt1A in template set T0349 50 :VHEDDLAGARRLLTDAGLAHE 1gt1A 124 :VEDEDLEKFWKLTEDKGIDKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=171 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gukA/T0349-2gukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gukA expands to /projects/compbio/data/pdb/2guk.pdb.gz 2gukA: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 271, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 273, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 275, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 277, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 279, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2gukA 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 589, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2gukA 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 930, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2gukA # T0349 read from 2gukA/T0349-2gukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gukA read from 2gukA/T0349-2gukA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gukA to template set # found chain 2gukA in template set T0349 9 :DAVLLSAVGALLDGAD 2gukA 10 :LRVFMHHIYEFEKGVR T0349 40 :S 2gukA 26 :S T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 2gukA 27 :MVLATLANDDIPYAEERLRSRQIPYF Number of specific fragments extracted= 3 number of extra gaps= 0 total=174 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gukA/T0349-2gukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2gukA/T0349-2gukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gukA read from 2gukA/T0349-2gukA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gukA in template set T0349 10 :AVLLSAVGALLDGAD 2gukA 11 :RVFMHHIYEFEKGVR T0349 40 :SL 2gukA 26 :SM T0349 46 :RRVLVHEDDLAGARRLLTDAGLA 2gukA 28 :VLATLANDDIPYAEERLRSRQIP Number of specific fragments extracted= 3 number of extra gaps= 0 total=177 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gukA/T0349-2gukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 2gukA/T0349-2gukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gukA read from 2gukA/T0349-2gukA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gukA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLA 2gukA 30 :ATLANDDIPYAEERLRSRQIP Number of specific fragments extracted= 1 number of extra gaps= 0 total=178 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qd9A/T0349-1qd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qd9A expands to /projects/compbio/data/pdb/1qd9.pdb.gz 1qd9A:Skipped atom 598, because occupancy 0.230 <= existing 0.770 in 1qd9A Skipped atom 600, because occupancy 0.230 <= existing 0.770 in 1qd9A Skipped atom 602, because occupancy 0.230 <= existing 0.770 in 1qd9A # T0349 read from 1qd9A/T0349-1qd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qd9A read from 1qd9A/T0349-1qd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qd9A to template set # found chain 1qd9A in template set T0349 9 :DAVLLSAVGALLDGADIGHL 1qd9A 50 :THQVFSNLKAVLEEAGASFE T0349 35 :SILEG 1qd9A 70 :TVVKA T0349 46 :RRVLVHEDDLAGARRLLTDA 1qd9A 75 :TVFIADMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=181 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qd9A/T0349-1qd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1qd9A/T0349-1qd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qd9A read from 1qd9A/T0349-1qd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qd9A in template set T0349 6 :RTNDAVLLSAVGALLDGADIGH 1qd9A 47 :KEQTHQVFSNLKAVLEEAGASF T0349 42 :GVIPRRVLV 1qd9A 70 :TVVKATVFI T0349 51 :HEDDLAGARRLLTDA 1qd9A 80 :DMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=184 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qd9A/T0349-1qd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1qd9A/T0349-1qd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qd9A read from 1qd9A/T0349-1qd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qd9A in template set T0349 11 :VLLSAVGALLDGADIG 1qd9A 52 :QVFSNLKAVLEEAGAS T0349 37 :LEGSLGV 1qd9A 68 :FETVVKA T0349 46 :RRVLVHEDDLAGARRLLTDA 1qd9A 75 :TVFIADMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=187 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oo0A/T0349-1oo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oo0A expands to /projects/compbio/data/pdb/1oo0.pdb.gz 1oo0A:# T0349 read from 1oo0A/T0349-1oo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oo0A read from 1oo0A/T0349-1oo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oo0A to template set # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=188 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oo0A/T0349-1oo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1oo0A/T0349-1oo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oo0A read from 1oo0A/T0349-1oo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=189 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oo0A/T0349-1oo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0349 read from 1oo0A/T0349-1oo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oo0A read from 1oo0A/T0349-1oo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=190 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 11.878 sec, elapsed time= 13.144 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 2775 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.893 sec, elapsed time= 13.160 sec. # command:Reading probabilities from T0349.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 9.024 Optimizing... Probability sum: -143.255, CN propb: -143.255 weights: 0.285 constraints: 192 # command:CPU_time= 13.421 sec, elapsed time= 14.702 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 192 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 192 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 315 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 315 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 1704 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 1704 # command:CPU_time= 13.457 sec, elapsed time= 14.800 sec. # command: