# 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 T0335 numbered 1 through 85 Created new target T0335 from T0335.a2m # command:CPU_time= 6.384 sec, elapsed time= 6.428 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/T0335-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t3wA expands to /projects/compbio/data/pdb/1t3w.pdb.gz 1t3wA: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 # T0335 read from 1t3wA/T0335-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0335-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t3wA to template set # found chain 1t3wA in template set T0335 2 :ISNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 543 :FDSLLELRQEELIARERTHGLSNEERLELWTLNQE # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 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 1t3wA/T0335-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1t3wA/T0335-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0335-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3wA in template set T0335 2 :ISNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 543 :FDSLLELRQEELIARERTHGLSNEERLELWTLNQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 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 1t3wA/T0335-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1t3wA/T0335-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0335-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3wA in template set T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 544 :DSLLELRQEELIARERTHGLSNEERLELWTLNQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 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 1b5sA/T0335-1b5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b5sA expands to /projects/compbio/data/pdb/1b5s.pdb.gz 1b5sA:# T0335 read from 1b5sA/T0335-1b5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5sA read from 1b5sA/T0335-1b5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b5sA to template set # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=4 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 1b5sA/T0335-1b5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1b5sA/T0335-1b5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5sA read from 1b5sA/T0335-1b5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=5 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 1b5sA/T0335-1b5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1b5sA/T0335-1b5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5sA read from 1b5sA/T0335-1b5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=6 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 1il1A/T0335-1il1A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1il1A expands to /projects/compbio/data/pdb/1il1.pdb.gz 1il1A:# T0335 read from 1il1A/T0335-1il1A-t06-local-adpstyle5.a2m # 1il1A read from 1il1A/T0335-1il1A-t06-local-adpstyle5.a2m # adding 1il1A to template set # found chain 1il1A in template set T0335 33 :LRQEYLKGFRSSMKNTLKSVKIIDPEGNDVTP 1il1A 29 :IKDYYIHWVRQRPEQGLEWIGWLDPENGDTES Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 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 1qokA/T0335-1qokA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qokA expands to /projects/compbio/data/pdb/1qok.pdb.gz 1qokA:# T0335 read from 1qokA/T0335-1qokA-t06-local-adpstyle5.a2m # 1qokA read from 1qokA/T0335-1qokA-t06-local-adpstyle5.a2m # adding 1qokA to template set # found chain 1qokA in template set T0335 33 :LRQEYLKGFRSSMKNTLKSVKIIDPEGNDVT 1qokA 55 :IKDSYMHWLRQGPEQGLEWIGWIDPENGDTE Number of specific fragments extracted= 1 number of extra gaps= 0 total=8 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 1y96B/T0335-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y96B expands to /projects/compbio/data/pdb/1y96.pdb.gz 1y96B:# T0335 read from 1y96B/T0335-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0335-1y96B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y96B to template set # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFRS 1y96B 59 :RAALRERYLRSLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=10 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 1y96B/T0335-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1y96B/T0335-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0335-1y96B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFRS 1y96B 59 :RAALRERYLRSLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=12 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 1y96B/T0335-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1y96B/T0335-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y96B read from 1y96B/T0335-1y96B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFR 1y96B 59 :RAALRERYLRSLL T0335 47 :NTL 1y96B 72 :AMV T0335 50 :KSVKIIDPEGNDV 1y96B 76 :HQVSFTLHEGVRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=16 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 1r2uA/T0335-1r2uA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r2uA expands to /projects/compbio/data/pdb/1r2u.pdb.gz 1r2uA:# T0335 read from 1r2uA/T0335-1r2uA-t06-local-adpstyle5.a2m # 1r2uA read from 1r2uA/T0335-1r2uA-t06-local-adpstyle5.a2m # adding 1r2uA to template set # found chain 1r2uA in template set T0335 16 :KAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLKSVKIIDPEGNDVTPEKLKREQRNNK 1r2uA 6 :KAAVEQLTDEQKNEFKAAFDIFIQDAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVD Number of specific fragments extracted= 1 number of extra gaps= 0 total=17 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 1f47B/T0335-1f47B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f47B expands to /projects/compbio/data/pdb/1f47.pdb.gz 1f47B:# T0335 read from 1f47B/T0335-1f47B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f47B read from 1f47B/T0335-1f47B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f47B to template set # found chain 1f47B in template set T0335 33 :LRQEYLKGF 1f47B 97 :LFKLMLQSA T0335 43 :SSMKNTL 1f47B 106 :QHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKL 1f47B 113 :GGVVLDDQRRMMTPQKLREYQDIIRE 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=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f47B/T0335-1f47B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1f47B/T0335-1f47B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f47B read from 1f47B/T0335-1f47B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f47B in template set T0335 26 :EKA 1f47B 94 :ELQ T0335 33 :LRQEYLKGFR 1f47B 97 :LFKLMLQSAQ T0335 44 :SMKNTL 1f47B 107 :HIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKLHLE 1f47B 113 :GGVVLDDQRRMMTPQKLREYQDIIREVKD Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f47B/T0335-1f47B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1f47B/T0335-1f47B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f47B read from 1f47B/T0335-1f47B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f47B in template set T0335 32 :KLRQEYLKGFR 1f47B 96 :QLFKLMLQSAQ T0335 44 :SMKNTL 1f47B 107 :HIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQR 1f47B 113 :GGVVLDDQRRMMTPQKLREYQD Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 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 1t95A/T0335-1t95A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t95A expands to /projects/compbio/data/pdb/1t95.pdb.gz 1t95A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M 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 # T0335 read from 1t95A/T0335-1t95A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t95A read from 1t95A/T0335-1t95A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t95A to template set # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAE 1t95A 92 :QITAEQRRE T0335 30 :QQKLRQEYLKGFRSS 1t95A 102 :LEAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHH 1t95A 127 :PPSRIERALEEAKVHIDIF Number of specific fragments extracted= 8 number of extra gaps= 2 total=35 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 1t95A/T0335-1t95A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1t95A/T0335-1t95A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t95A read from 1t95A/T0335-1t95A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAEQ 1t95A 92 :QITAEQRREM T0335 31 :QKLRQEYLKGFRSS 1t95A 103 :EAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHH 1t95A 127 :PPSRIERALEEAKVHIDIF Number of specific fragments extracted= 8 number of extra gaps= 2 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t95A/T0335-1t95A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1t95A/T0335-1t95A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t95A read from 1t95A/T0335-1t95A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAEQ 1t95A 92 :QITAEQRREM T0335 31 :QKLRQEYLKGFRSS 1t95A 103 :EAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHHH 1t95A 127 :PPSRIERALEEAKVHIDIFK Number of specific fragments extracted= 8 number of extra gaps= 2 total=51 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 1xhdA/T0335-1xhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xhdA expands to /projects/compbio/data/pdb/1xhd.pdb.gz 1xhdA:Skipped atom 2, because occupancy 0.31 <= existing 0.690 in 1xhdA Skipped atom 4, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 6, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 8, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 10, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 12, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 14, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 16, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 18, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 20, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 22, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 24, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 26, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 28, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 1xhdA 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 118, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 120, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 122, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 124, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 126, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 1xhdA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1xhdA Skipped atom 295, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 297, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 299, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 301, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 303, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 759, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 761, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 763, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 765, because occupancy 0.450 <= existing 0.550 in 1xhdA 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 973, because occupancy 0.490 <= existing 0.510 in 1xhdA Skipped atom 975, because occupancy 0.490 <= existing 0.510 in 1xhdA Skipped atom 1164, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1166, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1168, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1170, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1172, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1206, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1208, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1210, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1212, because occupancy 0.420 <= existing 0.580 in 1xhdA 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 # T0335 read from 1xhdA/T0335-1xhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhdA read from 1xhdA/T0335-1xhdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xhdA to template set # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL Number of specific fragments extracted= 1 number of extra gaps= 0 total=52 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 1xhdA/T0335-1xhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1xhdA/T0335-1xhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhdA read from 1xhdA/T0335-1xhdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL Number of specific fragments extracted= 1 number of extra gaps= 0 total=53 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 1xhdA/T0335-1xhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1xhdA/T0335-1xhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhdA read from 1xhdA/T0335-1xhdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL Number of specific fragments extracted= 1 number of extra gaps= 0 total=54 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 2fzfA/T0335-2fzfA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fzfA expands to /projects/compbio/data/pdb/2fzf.pdb.gz 2fzfA:# T0335 read from 2fzfA/T0335-2fzfA-t06-local-adpstyle5.a2m # 2fzfA read from 2fzfA/T0335-2fzfA-t06-local-adpstyle5.a2m # adding 2fzfA to template set # found chain 2fzfA in template set T0335 7 :IARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRS 2fzfA 43 :AEKIKIEALKEKINWLAEEEKKHEALLRKLYSQMFPG Number of specific fragments extracted= 1 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aexA/T0335-2aexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aexA expands to /projects/compbio/data/pdb/2aex.pdb.gz 2aexA:Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1520, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2095, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2099, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2101, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2103, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2105, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2175, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2177, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2179, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2183, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2187, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2189, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2323, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2325, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2327, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2333, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2335, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2337, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2476, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2478, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2480, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2482, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2484, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2486, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2653, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2655, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2657, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2659, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2661, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2663, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2722, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2724, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2726, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2728, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2730, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2732, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2734, because occupancy 0.500 <= existing 0.500 in 2aexA # T0335 read from 2aexA/T0335-2aexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aexA read from 2aexA/T0335-2aexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aexA to template set # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQ 2aexA 367 :PLVKKHCDDSFTPQEKLWQQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 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 2aexA/T0335-2aexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 2aexA/T0335-2aexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aexA read from 2aexA/T0335-2aexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQKLRQEYL 2aexA 367 :PLVKKHCDDSFTPQEKLWQQLRRGRYV Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 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 2aexA/T0335-2aexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 2aexA/T0335-2aexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aexA read from 2aexA/T0335-2aexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQKLRQEYL 2aexA 367 :PLVKKHCDDSFTPQEKLWQQLRRGRYV Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 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 1ap4/T0335-1ap4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ap4 expands to /projects/compbio/data/pdb/1ap4.pdb.gz 1ap4:Warning: there is no chain 1ap4 will retry with 1ap4A # T0335 read from 1ap4/T0335-1ap4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ap4 read from 1ap4/T0335-1ap4-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ap4 to template set # found chain 1ap4 in template set T0335 3 :SNAKIARINE 1ap4 2 :DDIYKAAVEQ T0335 22 :ITEEEKA 1ap4 12 :LTEEQKN T0335 40 :GFRSSMKNTLKSV 1ap4 19 :EFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLE 1ap4 32 :EDGCISTKELGKVMRMLGQNPT Number of specific fragments extracted= 4 number of extra gaps= 0 total=65 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 1ap4/T0335-1ap4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1ap4/T0335-1ap4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ap4 read from 1ap4/T0335-1ap4-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ap4 in template set T0335 6 :K 1ap4 5 :Y T0335 16 :KAKAGVITEEEKA 1ap4 6 :KAAVEQLTEEQKN T0335 40 :GFRSSMKNTLKSV 1ap4 19 :EFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLEH 1ap4 32 :EDGCISTKELGKVMRMLGQNPTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=69 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 1ap4/T0335-1ap4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1ap4/T0335-1ap4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ap4 read from 1ap4/T0335-1ap4-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ap4 in template set T0335 3 :SNAKIARI 1ap4 2 :DDIYKAAV T0335 20 :GVITEEEK 1ap4 10 :EQLTEEQK T0335 39 :KGFRSSMKNTLKSV 1ap4 18 :NEFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLEH 1ap4 32 :EDGCISTKELGKVMRMLGQNPTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=73 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 1lj9A/T0335-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0335 read from 1lj9A/T0335-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0335-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lj9A to template set # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLK 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=74 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 1lj9A/T0335-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1lj9A/T0335-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0335-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKN 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEF Number of specific fragments extracted= 1 number of extra gaps= 0 total=75 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 1lj9A/T0335-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1lj9A/T0335-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0335-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLK 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=76 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 2au5A/T0335-2au5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2au5A expands to /projects/compbio/data/pdb/2au5.pdb.gz 2au5A: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 15, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2au5A 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 379, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 2au5A 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 569, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2au5A 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 # T0335 read from 2au5A/T0335-2au5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2au5A read from 2au5A/T0335-2au5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2au5A to template set # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 Warning: unaligning (T0335)S51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2au5A)S132 T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 82 :LKGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=78 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 2au5A/T0335-2au5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 2au5A/T0335-2au5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2au5A read from 2au5A/T0335-2au5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 82 :LKGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=80 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 2au5A/T0335-2au5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 2au5A/T0335-2au5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2au5A read from 2au5A/T0335-2au5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 Warning: unaligning (T0335)S51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2au5A)S132 T0335 4 :NAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 83 :KGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=82 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 1wdtA/T0335-1wdtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wdtA expands to /projects/compbio/data/pdb/1wdt.pdb.gz 1wdtA:# T0335 read from 1wdtA/T0335-1wdtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdtA read from 1wdtA/T0335-1wdtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wdtA to template set # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRS 1wdtA 192 :EVPPEERERVQRFRQEVLEAIVE T0335 44 :SMKNTLKS 1wdtA 218 :GLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 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 1wdtA/T0335-1wdtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1wdtA/T0335-1wdtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdtA read from 1wdtA/T0335-1wdtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFR 1wdtA 192 :EVPPEERERVQRFRQEVLEAIV T0335 43 :SSMKNTLKS 1wdtA 217 :EGLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=88 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 1wdtA/T0335-1wdtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1wdtA/T0335-1wdtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wdtA read from 1wdtA/T0335-1wdtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRS 1wdtA 192 :EVPPEERERVQRFRQEVLEAIVE T0335 44 :SMKNTLKS 1wdtA 218 :GLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=91 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 1f46A/T0335-1f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f46A expands to /projects/compbio/data/pdb/1f46.pdb.gz 1f46A:# T0335 read from 1f46A/T0335-1f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f46A read from 1f46A/T0335-1f46A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f46A to template set # found chain 1f46A in template set T0335 37 :YLKGFRSSMKNTLK 1f46A 97 :LFKLMLQSAQHIAD T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNK 1f46A 113 :GGVVLDDQRRMMTPQKLREYQDIIR Number of specific fragments extracted= 2 number of extra gaps= 0 total=93 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 1f46A/T0335-1f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1f46A/T0335-1f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f46A read from 1f46A/T0335-1f46A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f46A in template set T0335 28 :AEQQKLRQ 1f46A 96 :QLFKLMLQ T0335 37 :YLKGFRSSM 1f46A 104 :SAQHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKLHLE 1f46A 113 :GGVVLDDQRRMMTPQKLREYQDIIREVKD Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 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 1f46A/T0335-1f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1f46A/T0335-1f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f46A read from 1f46A/T0335-1f46A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f46A in template set T0335 33 :LRQEYLKGF 1f46A 97 :LFKLMLQSA T0335 43 :SSMKNTL 1f46A 106 :QHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQR 1f46A 113 :GGVVLDDQRRMMTPQKLREYQD Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 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 1gzqA/T0335-1gzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gzqA expands to /projects/compbio/data/pdb/1gzq.pdb.gz 1gzqA:# T0335 read from 1gzqA/T0335-1gzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzqA read from 1gzqA/T0335-1gzqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gzqA to template set # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKS 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzqA/T0335-1gzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1gzqA/T0335-1gzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzqA read from 1gzqA/T0335-1gzqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKS 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=101 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 1gzqA/T0335-1gzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1gzqA/T0335-1gzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gzqA read from 1gzqA/T0335-1gzqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKSV 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGDF Number of specific fragments extracted= 1 number of extra gaps= 0 total=102 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 1wmhA/T0335-1wmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wmhA expands to /projects/compbio/data/pdb/1wmh.pdb.gz 1wmhA:# T0335 read from 1wmhA/T0335-1wmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmhA read from 1wmhA/T0335-1wmhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wmhA to template set # found chain 1wmhA in template set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQRNNKLH 1wmhA 73 :SQLELEEAFRLYELN Number of specific fragments extracted= 3 number of extra gaps= 0 total=105 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 1wmhA/T0335-1wmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1wmhA/T0335-1wmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmhA read from 1wmhA/T0335-1wmhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wmhA in template set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQRNNKLH 1wmhA 73 :SQLELEEAFRLYELN Number of specific fragments extracted= 3 number of extra gaps= 0 total=108 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 1wmhA/T0335-1wmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1wmhA/T0335-1wmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wmhA read from 1wmhA/T0335-1wmhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wmhA in template set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQR 1wmhA 73 :SQLELEEAFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=111 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 1byb/T0335-1byb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1byb expands to /projects/compbio/data/pdb/1byb.pdb.gz 1byb:Warning: there is no chain 1byb will retry with 1bybA # T0335 read from 1byb/T0335-1byb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byb read from 1byb/T0335-1byb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1byb to template set # found chain 1byb in template set T0335 55 :IDPEGNDVTPEKLKREQRN 1byb 23 :VNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=112 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 1byb/T0335-1byb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1byb/T0335-1byb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byb read from 1byb/T0335-1byb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1byb in template set T0335 54 :IIDPEGNDVTPEKLKREQRN 1byb 22 :VVNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=113 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 1byb/T0335-1byb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0335 read from 1byb/T0335-1byb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1byb read from 1byb/T0335-1byb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1byb in template set T0335 54 :IIDPEGNDVTPEKLKREQR 1byb 22 :VVNVDNVFEDPDGLKEQLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=114 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 1xupO/T0335-1xupO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xupO expands to /projects/compbio/data/pdb/1xup.pdb.gz 1xupO:# T0335 read from 1xupO/T0335-1xupO-t06-local-adpstyle5.a2m # 1xupO read from 1xupO/T0335-1xupO-t06-local-adpstyle5.a2m # adding 1xupO to template set # found chain 1xupO in template set T0335 28 :AEQQKLRQEYLKGFRSSMKNTLKSVKIIDPEGNDVTPEKLKREQRN 1xupO 437 :LETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDN Number of specific fragments extracted= 1 number of extra gaps= 0 total=115 Will force an alignment to be made, even if fragment is small Number of alignments=50 # command:CPU_time= 11.989 sec, elapsed time= 26.223 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 50 Adding 3570 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.002 sec, elapsed time= 26.236 sec. # command:Reading probabilities from T0335.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 6.891 Optimizing... Probability sum: -118.718, CN propb: -118.718 weights: 0.295 constraints: 60 # command:CPU_time= 12.093 sec, elapsed time= 26.339 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 60 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 60 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 123 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 123 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 2743 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 2743 # command:CPU_time= 12.147 sec, elapsed time= 26.462 sec. # command: