# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0639 numbered 1 through 128 Created new target T0639 from T0639.a2m # command:CPU_time= 5.792 sec, elapsed time= 6.814 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avxA/T0639-2avxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2avxA expands to /projects/compbio/data/pdb/2avx.pdb.gz 2avxA:# T0639 read from 2avxA/T0639-2avxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avxA read from 2avxA/T0639-2avxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2avxA to template set # found chain 2avxA in template set T0639 5 :ETLNDIKKILINVGLYQGFDL 2avxA 21 :ETAEEVYHEIELQAQQLEYDY # choosing archetypes in rotamer library T0639 31 :SEEVNHETANMKWIKDYT 2avxA 47 :RHPVPFTRPKVAFYTNYP T0639 58 :KEDLKNFLD 2avxA 65 :EAWVSYYQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avxA/T0639-2avxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2avxA/T0639-2avxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avxA read from 2avxA/T0639-2avxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2avxA in template set T0639 5 :ETLNDIKKILINVGLYQGFDL 2avxA 21 :ETAEEVYHEIELQAQQLEYDY T0639 31 :SEEVNHETANMKWIKDYTSD 2avxA 47 :RHPVPFTRPKVAFYTNYPEA T0639 53 :W 2avxA 67 :W T0639 61 :LKNFLD 2avxA 68 :VSYYQA Number of specific fragments extracted= 4 number of extra gaps= 0 total=7 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 2avxA/T0639-2avxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2avxA/T0639-2avxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avxA read from 2avxA/T0639-2avxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2avxA in template set T0639 7 :LNDIKKILINVGLYQGFDL 2avxA 23 :AEEVYHEIELQAQQLEYDY T0639 31 :SEEVNHETANMKWIKDYT 2avxA 47 :RHPVPFTRPKVAFYTNYP T0639 55 :NEFKEDL 2avxA 65 :EAWVSYY T0639 65 :L 2avxA 72 :Q Number of specific fragments extracted= 4 number of extra gaps= 0 total=11 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 1yz4A/T0639-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yz4A expands to /projects/compbio/data/pdb/1yz4.pdb.gz 1yz4A:# T0639 read from 1yz4A/T0639-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0639-1yz4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yz4A to template set # found chain 1yz4A in template set T0639 12 :KILINVGLYQGFDLTDPKV 1yz4A 24 :DQLGRNKITHIISIHESPQ T0639 36 :HETANMKWIK 1yz4A 43 :PLLQDITYLR T0639 46 :DYTSDGNWD 1yz4A 54 :PVADTPEVP T0639 57 :FKED 1yz4A 63 :IKKH T0639 64 :FLDYMEVCQLALNDK 1yz4A 67 :FKECINFIHCCRLNG T0639 79 :NFKIASNSLFMAMIYAG 1yz4A 90 :AGISRSTTIVTAYVMTV T0639 96 :NLSLIFDSIKT 1yz4A 110 :GWRDVLEAIKA T0639 107 :DISTLLS 1yz4A 130 :GFRQQLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=19 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 1yz4A/T0639-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1yz4A/T0639-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0639-1yz4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yz4A in template set T0639 12 :KILINVGLYQGFDLTDPKVS 1yz4A 24 :DQLGRNKITHIISIHESPQP T0639 37 :ETANMKWIK 1yz4A 44 :LLQDITYLR T0639 46 :DYTSDGNWDNE 1yz4A 56 :ADTPEVPIKKH T0639 64 :FLDYMEVCQLALNDK 1yz4A 67 :FKECINFIHCCRLNG T0639 79 :NFKIASNSLFMAMIYAG 1yz4A 90 :AGISRSTTIVTAYVMTV T0639 96 :NLSLIFDSIKTD 1yz4A 110 :GWRDVLEAIKAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=25 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 1yz4A/T0639-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1yz4A/T0639-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yz4A read from 1yz4A/T0639-1yz4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yz4A in template set T0639 12 :KILINVGLYQGFDL 1yz4A 24 :DQLGRNKITHIISI T0639 31 :SEEVNHETANMKWIK 1yz4A 38 :HESPQPLLQDITYLR T0639 46 :DYTSDGNWDNEFKE 1yz4A 56 :ADTPEVPIKKHFKE T0639 67 :YMEVCQLALNDK 1yz4A 70 :CINFIHCCRLNG T0639 79 :NFKIASNSLFMAMIYAG 1yz4A 90 :AGISRSTTIVTAYVMTV T0639 96 :NLSLIFDSIKT 1yz4A 110 :GWRDVLEAIKA 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=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vytE/T0639-1vytE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vytE expands to /projects/compbio/data/pdb/1vyt.pdb.gz 1vytE:# T0639 read from 1vytE/T0639-1vytE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vytE read from 1vytE/T0639-1vytE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vytE to template set # found chain 1vytE in template set T0639 55 :NEFKEDLKNFLDYMEV 1vytE 428 :QQLEEDLKGYLDWITQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 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 1vytE/T0639-1vytE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1vytE/T0639-1vytE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vytE read from 1vytE/T0639-1vytE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vytE in template set T0639 54 :DNEFKEDLKNFLDYMEV 1vytE 427 :KQQLEEDLKGYLDWITQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=33 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 1vytE/T0639-1vytE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1vytE/T0639-1vytE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vytE read from 1vytE/T0639-1vytE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vytE in template set T0639 55 :NEFKEDLKNFLDYMEV 1vytE 428 :QQLEEDLKGYLDWITQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=34 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 3ix3A/T0639-3ix3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ix3A expands to /projects/compbio/data/pdb/3ix3.pdb.gz 3ix3A:# T0639 read from 3ix3A/T0639-3ix3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ix3A read from 3ix3A/T0639-3ix3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ix3A to template set # found chain 3ix3A in template set T0639 5 :ETLNDIKKILINVGLYQ 3ix3A 96 :RKQHEFFEEASAAGLVY Number of specific fragments extracted= 1 number of extra gaps= 0 total=35 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 3ix3A/T0639-3ix3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 3ix3A/T0639-3ix3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ix3A read from 3ix3A/T0639-3ix3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ix3A in template set T0639 6 :TLNDIKKILINVGLYQGFDL 3ix3A 15 :GKLEWSAILQKMASDLGFSK T0639 31 :SEEVNHETANMKWIKDYT 3ix3A 40 :LPKDSQDYENAFIVGNYP T0639 58 :KEDLKNFLD 3ix3A 58 :AAWREHYDR T0639 68 :MEVCQLALNDKNFKIASN 3ix3A 73 :DPTVSHCTQSVLPIFWEP T0639 126 :L 3ix3A 91 :S Number of specific fragments extracted= 5 number of extra gaps= 0 total=40 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 3ix3A/T0639-3ix3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 3ix3A/T0639-3ix3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ix3A read from 3ix3A/T0639-3ix3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ix3A in template set T0639 6 :TLNDIKKILINVGLYQGFD 3ix3A 15 :GKLEWSAILQKMASDLGFS T0639 34 :VNHETANMK 3ix3A 40 :LPKDSQDYE T0639 43 :WIKDYT 3ix3A 52 :IVGNYP T0639 58 :KEDLKNFLDY 3ix3A 58 :AAWREHYDRA T0639 68 :MEVCQLALNDKNFKIASNSLF 3ix3A 73 :DPTVSHCTQSVLPIFWEPSIY T0639 95 :GNLSLIFDSIKT 3ix3A 96 :RKQHEFFEEASA Number of specific fragments extracted= 6 number of extra gaps= 0 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 1wrmA/T0639-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wrmA expands to /projects/compbio/data/pdb/1wrm.pdb.gz 1wrmA:# T0639 read from 1wrmA/T0639-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0639-1wrmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wrmA to template set # found chain 1wrmA in template set T0639 12 :KILINVGLYQGFD 1wrmA 24 :EQLSKNKVTHILS T0639 30 :VSEEVNHETANMKWIK 1wrmA 37 :VHDSARPMLEGVKYLC T0639 46 :DYTSDGNWD 1wrmA 54 :PAADSPSQN T0639 57 :FKED 1wrmA 63 :LTRH T0639 64 :FLDYMEVCQLALNDKN 1wrmA 67 :FKESIKFIHECRLRGE T0639 80 :FKIASNSLFMAMIYAG 1wrmA 91 :GVSRSVTLVIAYIMTV T0639 96 :NLSLIFDSIKTD 1wrmA 110 :GWEDALHTVRAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=53 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 1wrmA/T0639-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1wrmA/T0639-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0639-1wrmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrmA in template set T0639 12 :KILINVGLYQGFD 1wrmA 24 :EQLSKNKVTHILS T0639 30 :VSEEVNHETANMKWIK 1wrmA 37 :VHDSARPMLEGVKYLC T0639 46 :DYTSDGNWD 1wrmA 54 :PAADSPSQN T0639 57 :FKEDLKN 1wrmA 63 :LTRHFKE T0639 67 :YMEVCQLALNDKN 1wrmA 70 :SIKFIHECRLRGE T0639 80 :FKIASNSLFMAMIYAGN 1wrmA 91 :GVSRSVTLVIAYIMTVT T0639 97 :LSLIFDSIKTD 1wrmA 111 :WEDALHTVRAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=60 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 1wrmA/T0639-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1wrmA/T0639-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wrmA read from 1wrmA/T0639-1wrmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wrmA in template set T0639 12 :KILINVGLY 1wrmA 24 :EQLSKNKVT T0639 30 :VSEEVNHETANMKWIK 1wrmA 37 :VHDSARPMLEGVKYLC T0639 46 :DYTSDGNWDNEFKED 1wrmA 56 :ADSPSQNLTRHFKES T0639 68 :MEVCQLALNDKN 1wrmA 71 :IKFIHECRLRGE T0639 80 :FKIASNSLFMAMIYAG 1wrmA 91 :GVSRSVTLVIAYIMTV T0639 96 :NLSLIFDSIKTD 1wrmA 110 :GWEDALHTVRAG Number of specific fragments extracted= 6 number of extra gaps= 0 total=66 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 1wt4A/T0639-1wt4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wt4A expands to /projects/compbio/data/pdb/1wt4.pdb.gz 1wt4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0639 read from 1wt4A/T0639-1wt4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wt4A read from 1wt4A/T0639-1wt4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wt4A to template set # found chain 1wt4A in template set Warning: unaligning (T0639)T48 because first residue in template chain is (1wt4A)G54 T0639 49 :SDGNWDNEFKEDLKNFLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDSIKT 1wt4A 55 :PLGSDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQ T0639 107 :DISTLLSA 1wt4A 117 :PVFQMLLT Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 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 1wt4A/T0639-1wt4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1wt4A/T0639-1wt4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wt4A read from 1wt4A/T0639-1wt4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wt4A in template set T0639 51 :GNWDNEFKEDLKNFLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDSIKTD 1wt4A 57 :GSDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQT T0639 108 :ISTLLSA 1wt4A 118 :VFQMLLT Number of specific fragments extracted= 2 number of extra gaps= 0 total=70 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 1wt4A/T0639-1wt4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1wt4A/T0639-1wt4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wt4A read from 1wt4A/T0639-1wt4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wt4A in template set T0639 49 :SDGNWDNEFKEDLKNFLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDSIKT 1wt4A 55 :PLGSDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQ T0639 107 :DISTLLSA 1wt4A 117 :PVFQMLLT Number of specific fragments extracted= 2 number of extra gaps= 0 total=72 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 2hwjA/T0639-2hwjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hwjA expands to /projects/compbio/data/pdb/2hwj.pdb.gz 2hwjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0639 read from 2hwjA/T0639-2hwjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hwjA read from 2hwjA/T0639-2hwjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hwjA to template set # found chain 2hwjA in template set Warning: unaligning (T0639)I92 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hwjA)R166 Warning: unaligning (T0639)Y93 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hwjA)R166 T0639 8 :NDIKKILINVGLYQGFDLTDPKVS 2hwjA 97 :DEFWSVMDHRNLIYPFDAQGLRRQ T0639 32 :EEVNHE 2hwjA 122 :GDIPKN T0639 44 :IKDYTSD 2hwjA 128 :IHDLEDD T0639 60 :DLKNF 2hwjA 135 :PFRSL T0639 67 :YMEVCQLALNDKNFKIASNSLFMAM 2hwjA 140 :AGALRMAGGYAKVIIPFSEFGWADF T0639 94 :AG 2hwjA 167 :RR T0639 96 :NLSLIFDSIKTDISTLLSAEYKKNS 2hwjA 173 :LLSDSFDDALAEAMKLAKSREARHL Number of specific fragments extracted= 7 number of extra gaps= 1 total=79 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 2hwjA/T0639-2hwjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2hwjA/T0639-2hwjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hwjA read from 2hwjA/T0639-2hwjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hwjA in template set Warning: unaligning (T0639)I92 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hwjA)R166 Warning: unaligning (T0639)Y93 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hwjA)R166 T0639 8 :NDIKKILINVGLYQGFDLTDPKVS 2hwjA 97 :DEFWSVMDHRNLIYPFDAQGLRRQ T0639 32 :EEVNHE 2hwjA 122 :GDIPKN T0639 44 :IKDYTSD 2hwjA 128 :IHDLEDD T0639 60 :DLKNF 2hwjA 135 :PFRSL T0639 67 :YMEVCQLALNDKNFKIASNSLFMAM 2hwjA 140 :AGALRMAGGYAKVIIPFSEFGWADF T0639 94 :AG 2hwjA 167 :RR T0639 96 :NLSLIFDSIKTDISTLLSAEYKKN 2hwjA 173 :LLSDSFDDALAEAMKLAKSREARH Number of specific fragments extracted= 7 number of extra gaps= 1 total=86 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 2hwjA/T0639-2hwjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2hwjA/T0639-2hwjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hwjA read from 2hwjA/T0639-2hwjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hwjA in template set Warning: unaligning (T0639)I92 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hwjA)R166 Warning: unaligning (T0639)Y93 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hwjA)R166 Warning: unaligning (T0639)W123 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hwjA)C201 T0639 8 :NDIKKILINVGLYQGFDLTDPKVS 2hwjA 97 :DEFWSVMDHRNLIYPFDAQGLRRQ T0639 32 :EEVNHE 2hwjA 122 :GDIPKN T0639 44 :IKDYTSD 2hwjA 128 :IHDLEDD T0639 60 :DLKNF 2hwjA 135 :PFRSL T0639 67 :YMEVCQLALNDKNFKIASNSLFMAM 2hwjA 140 :AGALRMAGGYAKVIIPFSEFGWADF T0639 94 :AGNLSLIFDSIKTDISTLLSAEYKKNSFS 2hwjA 171 :RDLLSDSFDDALAEAMKLAKSREARHLPG Number of specific fragments extracted= 6 number of extra gaps= 2 total=92 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 1cipA/T0639-1cipA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cipA expands to /projects/compbio/data/pdb/1cip.pdb.gz 1cipA:# T0639 read from 1cipA/T0639-1cipA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cipA read from 1cipA/T0639-1cipA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cipA to template set # found chain 1cipA in template set Warning: unaligning (T0639)L112 because last residue in template chain is (1cipA)N347 T0639 44 :IKDYTSDGNWDNEFKEDLKNFLDYMEVC 1cipA 283 :LTICYPEYAGSNTYEEAAAYIQCQFEDL T0639 76 :NDKNFKI 1cipA 313 :RKDTKEI T0639 94 :AGNLSLIFDSIKTDISTL 1cipA 329 :TKNVQFVFDAVTDVIIKN Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cipA/T0639-1cipA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1cipA/T0639-1cipA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cipA read from 1cipA/T0639-1cipA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cipA in template set T0639 1 :SNAMETLNDIKKILINVGL 1cipA 75 :SNTIQSIIAIIRAMGRLKI T0639 24 :DLTDPKV 1cipA 94 :DFGDAAR T0639 58 :KE 1cipA 101 :AD T0639 64 :FLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDS 1cipA 103 :DARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNR Number of specific fragments extracted= 4 number of extra gaps= 0 total=99 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 1cipA/T0639-1cipA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 1cipA/T0639-1cipA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cipA read from 1cipA/T0639-1cipA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cipA in template set T0639 2 :NAMETLNDIKKILINVGL 1cipA 76 :NTIQSIIAIIRAMGRLKI T0639 24 :DLTDPKVSE 1cipA 94 :DFGDAARAD T0639 53 :WDNEFKEDLKNFLD 1cipA 103 :DARQLFVLAGAAEE T0639 67 :YMEVCQLALNDKNFKIASNSLFM 1cipA 123 :LAGVIKRLWKDSGVQACFNRSRE T0639 93 :YAGNLSLIFDSIK 1cipA 148 :LNDSAAYYLNDLD T0639 110 :T 1cipA 161 :R Number of specific fragments extracted= 6 number of extra gaps= 0 total=105 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 2uv0E/T0639-2uv0E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2uv0E expands to /projects/compbio/data/pdb/2uv0.pdb.gz 2uv0E:Skipped atom 123, because occupancy 0.5 <= existing 0.500 in 2uv0E Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 998, because occupancy 0.500 <= existing 0.500 in 2uv0E Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0639 read from 2uv0E/T0639-2uv0E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uv0E read from 2uv0E/T0639-2uv0E-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2uv0E to template set # found chain 2uv0E in template set T0639 4 :METLNDIKKILINVGLYQGFD 2uv0E 13 :SSGKLEWSAILQKMASDLGFS T0639 25 :L 2uv0E 39 :L T0639 31 :SEEVNHETANMKWIKDYT 2uv0E 40 :LPKDSQDYENAFIVGNYP T0639 58 :KEDLKNFLDY 2uv0E 58 :AAWREHYDRA T0639 69 :EVCQLALNDKNFKIASNSL 2uv0E 74 :PTVSHCTQSVLPIFWEPSI T0639 94 :AGNLSLIFDSIKT 2uv0E 95 :TRKQHEFFEEASA Number of specific fragments extracted= 6 number of extra gaps= 0 total=111 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 2uv0E/T0639-2uv0E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2uv0E/T0639-2uv0E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uv0E read from 2uv0E/T0639-2uv0E-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uv0E in template set T0639 6 :TLNDIKKILINVGLYQG 2uv0E 97 :KQHEFFEEASAAGLVYG T0639 23 :FD 2uv0E 116 :MP T0639 34 :VNHETANMKWIKDYTSDGN 2uv0E 118 :LHGARGELGALSLSVEAEN T0639 54 :DNEFKEDLKNFLD 2uv0E 137 :RAEANRFMESVLP T0639 79 :NFKIASNSLFMAMIYA 2uv0E 150 :TLWMLKDYALQSGAGL Number of specific fragments extracted= 5 number of extra gaps= 0 total=116 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 2uv0E/T0639-2uv0E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2uv0E/T0639-2uv0E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uv0E read from 2uv0E/T0639-2uv0E-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uv0E in template set T0639 6 :TLNDIKKILINVGLYQGFD 2uv0E 15 :GKLEWSAILQKMASDLGFS T0639 25 :LTDPKVSEE 2uv0E 40 :LPKDSQDYE T0639 40 :NMKWIKDYT 2uv0E 49 :NAFIVGNYP T0639 58 :KEDLKNFLDY 2uv0E 58 :AAWREHYDRA T0639 68 :MEVCQLALNDKNFKIASNSLF 2uv0E 73 :DPTVSHCTQSVLPIFWEPSIY T0639 95 :GNLSLIFDSIKT 2uv0E 96 :RKQHEFFEEASA Number of specific fragments extracted= 6 number of extra gaps= 0 total=122 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 2imgA/T0639-2imgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2imgA expands to /projects/compbio/data/pdb/2img.pdb.gz 2imgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0639 read from 2imgA/T0639-2imgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imgA read from 2imgA/T0639-2imgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2imgA to template set # found chain 2imgA in template set T0639 8 :NDIKKILINVGLYQGFDLTDPKVSE 2imgA 25 :PAHYQFLLDLGVRHLVSLTERGPPH T0639 35 :NHETANMKWIKDYTSDGNWDN 2imgA 50 :SDSCPGLTLHRLRIPDFCPPA T0639 58 :KEDLKNFLDYMEV 2imgA 71 :PDQIDRFVQIVDE T0639 74 :ALNDK 2imgA 84 :ANARG T0639 79 :NFKIASNSLFMAMIYAG 2imgA 97 :LGFGRTGTMLACYLVKE T0639 96 :NLSLIFDSIKTD 2imgA 117 :AAGDAIAEIRRL T0639 108 :ISTLLSAEYK 2imgA 138 :QEKAVFQFYQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=129 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 2imgA/T0639-2imgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2imgA/T0639-2imgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imgA read from 2imgA/T0639-2imgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2imgA in template set T0639 9 :DIKKILINVGLYQGFDLTDPKVSEE 2imgA 26 :AHYQFLLDLGVRHLVSLTERGPPHS T0639 36 :HETANMKWIKDYTSDGNWDN 2imgA 51 :DSCPGLTLHRLRIPDFCPPA T0639 58 :KEDLKNFLDYMEV 2imgA 71 :PDQIDRFVQIVDE T0639 74 :ALNDK 2imgA 84 :ANARG T0639 79 :NFKIASNSLFMAMIYAG 2imgA 97 :LGFGRTGTMLACYLVKE T0639 96 :NLSLIFDSIKTD 2imgA 117 :AAGDAIAEIRRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=135 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 2imgA/T0639-2imgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0639 read from 2imgA/T0639-2imgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imgA read from 2imgA/T0639-2imgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2imgA in template set T0639 8 :NDIKKILINVGLYQGFDLTDPKVSEEVNHETANMKWI 2imgA 25 :PAHYQFLLDLGVRHLVSLTERGPPHSDSCPGLTLHRL T0639 46 :DYTSDGNWD 2imgA 62 :RIPDFCPPA T0639 58 :KEDLKNFLDYMEV 2imgA 71 :PDQIDRFVQIVDE T0639 74 :ALNDK 2imgA 84 :ANARG T0639 79 :NFKIASNSLFMAMIYAG 2imgA 97 :LGFGRTGTMLACYLVKE T0639 96 :NLSLIFDSIKTD 2imgA 117 :AAGDAIAEIRRL T0639 108 :ISTLLSA 2imgA 138 :QEKAVFQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=142 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.930 sec, elapsed time= 15.925 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 681 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.950 sec, elapsed time= 15.945 sec. # command:Reading probabilities from T0639.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.764 Optimizing... Probability sum: -225.030, CN propb: -225.030 weights: 0.326 constraints: 172 # command:CPU_time= 20.201 sec, elapsed time= 25.263 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 172 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 172 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 509 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 509 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 20.212 sec, elapsed time= 26.833 sec. # command: