# 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 T0319 numbered 1 through 135 Created new target T0319 from T0319.a2m # command:CPU_time= 6.199 sec, elapsed time= 6.269 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/T0319-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rlyA expands to /projects/compbio/data/pdb/1rly.pdb.gz 1rlyA:# T0319 read from 1rlyA/T0319-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0319-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rlyA to template set # found chain 1rlyA in template set T0319 68 :NNALP 1rlyA 7 :LDALP # choosing archetypes in rotamer library T0319 73 :PTKPSFPS 1rlyA 13 :VTCPNHPD T0319 83 :QELTDDD 1rlyA 21 :AILVEDY T0319 106 :AEGEMKCRNCGHI 1rlyA 28 :RAGDMICPECGLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 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 1rlyA/T0319-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rlyA/T0319-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0319-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rlyA in template set T0319 69 :NALP 1rlyA 8 :DALP T0319 73 :PTKPSFPSS 1rlyA 13 :VTCPNHPDA T0319 82 :IQELTDDD 1rlyA 24 :VEDYRAGD T0319 110 :MKCRNCGHI 1rlyA 32 :MICPECGLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 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 1rlyA/T0319-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rlyA/T0319-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0319-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rlyA in template set T0319 69 :NALPPTKPSFPSSIQELTDD 1rlyA 10 :LPRVTCPNHPDAILVEDYRA T0319 108 :GEMKCRNCGHI 1rlyA 30 :GDMICPECGLV 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=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/T0319-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1yk4A/T0319-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0319-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1yk4A 3 :KLSCKICGYIYDEDEGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/T0319-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1yk4A/T0319-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0319-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1yk4A 3 :KLSCKICGYIYDEDEGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=12 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 1yk4A/T0319-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1yk4A/T0319-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0319-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training set T0319 109 :EMKCRNCGHIYYIKNGIP 1yk4A 3 :KLSCKICGYIYDEDEGDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=13 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 1vq0A/T0319-1vq0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vq0A expands to /projects/compbio/data/pdb/1vq0.pdb.gz 1vq0A:# T0319 read from 1vq0A/T0319-1vq0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq0A read from 1vq0A/T0319-1vq0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vq0A to template set # found chain 1vq0A in template set T0319 6 :TNFLKCSVKACDTS 1vq0A 142 :YYFAVSEQIPSAFS T0319 23 :FPLQYDGSKCQL 1vq0A 156 :IGVLVDSDGVKI T0319 35 :VQDESIEFNPEF 1vq0A 173 :VQIIDRTLEQEK T0319 47 :LLNIVDRVDWPAVLTVAA 1vq0A 198 :ISKLFQEAEPLDVLERIF T0319 68 :NNALPP 1vq0A 216 :GEKVGF T0319 74 :TKPSFPSSIQELT 1vq0A 230 :KCDCNREKAKNAL T0319 87 :DDDMAILNDLHTL 1vq0A 244 :VLDKKELEDMRKE T0319 106 :AEGEMKCRNCGHIYYIK 1vq0A 257 :GKGEVVCKWCNTRYVFS Number of specific fragments extracted= 8 number of extra gaps= 0 total=21 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 1vq0A/T0319-1vq0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1vq0A/T0319-1vq0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq0A read from 1vq0A/T0319-1vq0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vq0A in template set T0319 4 :LTTNFLKCSVKACDTS 1vq0A 140 :LAYYFAVSEQIPSAFS T0319 23 :FPLQYDGSKCQL 1vq0A 156 :IGVLVDSDGVKI T0319 35 :VQDESIEFNPEF 1vq0A 173 :VQIIDRTLEQEK T0319 47 :LLNIVDRVDWPAVLTVAA 1vq0A 198 :ISKLFQEAEPLDVLERIF T0319 68 :NNALPPT 1vq0A 216 :GEKVGFV T0319 77 :SFPSSIQE 1vq0A 230 :KCDCNREK T0319 85 :LTDDDMAILNDLH 1vq0A 242 :LLVLDKKELEDMR T0319 106 :AEGEMKCRNCGHIYYIK 1vq0A 257 :GKGEVVCKWCNTRYVFS Number of specific fragments extracted= 8 number of extra gaps= 0 total=29 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 1vq0A/T0319-1vq0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1vq0A/T0319-1vq0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq0A read from 1vq0A/T0319-1vq0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vq0A in template set T0319 27 :YDGSKCQLVQD 1vq0A 219 :VGFVETAEIKY T0319 39 :SIEFNPEFLLNIVDRVDWPAVLTVAAE 1vq0A 230 :KCDCNREKAKNALLVLDKKELEDMRKE T0319 67 :G 1vq0A 257 :G T0319 107 :EGEMKCRNCGHIYYIK 1vq0A 258 :KGEVVCKWCNTRYVFS Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 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 1iro/T0319-1iro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1iro/T0319-1iro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iro read from 1iro/T0319-1iro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iro in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1iro 4 :YTCTVCGYIYNPEDGDPDNGVNPGTD 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=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iro/T0319-1iro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1iro/T0319-1iro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iro read from 1iro/T0319-1iro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iro in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1iro 4 :YTCTVCGYIYNPEDGDPDNGVNPGTD 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=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iro/T0319-1iro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1iro/T0319-1iro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iro read from 1iro/T0319-1iro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iro in training set T0319 110 :MKCRNCGHIYYIKNGIP 1iro 4 :YTCTVCGYIYNPEDGDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=36 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 1zin/T0319-1zin-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zin expands to /projects/compbio/data/pdb/1zin.pdb.gz 1zin:Warning: there is no chain 1zin will retry with 1zinA # T0319 read from 1zin/T0319-1zin-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zin read from 1zin/T0319-1zin-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zin to template set # found chain 1zin in template set T0319 45 :EFLLNIVDR 1zin 66 :GIVRERLSK T0319 56 :WPAVLTVAAELGNN 1zin 93 :AEALETMLADIGRK T0319 71 :LP 1zin 107 :LD T0319 84 :EL 1zin 114 :DV T0319 89 :DMAILNDLHT 1zin 116 :RQDVLMERLT T0319 108 :GEMKCRNCGHIYY 1zin 126 :GRRICRNCGATYH Number of specific fragments extracted= 6 number of extra gaps= 0 total=42 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 1zin/T0319-1zin-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1zin/T0319-1zin-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zin read from 1zin/T0319-1zin-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zin in template set T0319 45 :EFLLNIVDR 1zin 66 :GIVRERLSK T0319 56 :WPAVLTVAAELGNN 1zin 93 :AEALETMLADIGRK T0319 71 :LP 1zin 107 :LD T0319 89 :DMAILNDLHT 1zin 116 :RQDVLMERLT T0319 108 :GEMKCRNCGHIYY 1zin 126 :GRRICRNCGATYH Number of specific fragments extracted= 5 number of extra gaps= 0 total=47 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 1zin/T0319-1zin-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1zin/T0319-1zin-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zin read from 1zin/T0319-1zin-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zin in template set T0319 56 :WPAVLTVAAELGN 1zin 93 :AEALETMLADIGR T0319 77 :SFP 1zin 106 :KLD T0319 89 :DMAIL 1zin 116 :RQDVL T0319 97 :HTLLL 1zin 121 :MERLT T0319 108 :GEMKCRNCGHIY 1zin 126 :GRRICRNCGATY Number of specific fragments extracted= 5 number of extra gaps= 0 total=52 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1woyA/T0319-1woyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1woyA expands to /projects/compbio/data/pdb/1woy.pdb.gz 1woyA:# T0319 read from 1woyA/T0319-1woyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woyA read from 1woyA/T0319-1woyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1woyA to template set # found chain 1woyA in template set T0319 44 :PEFLLNIVDR 1woyA 68 :KAFVDRVSGR T0319 59 :VLTVAAELGNN 1woyA 78 :FKRAWDLLGIA T0319 82 :IQE 1woyA 89 :YDD T0319 85 :LTDDDMAILNDLHTLLLQT 1woyA 96 :TEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHL 1woyA 135 :TEKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 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 1woyA/T0319-1woyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1woyA/T0319-1woyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woyA read from 1woyA/T0319-1woyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1woyA in template set T0319 44 :PEFLLNIVDR 1woyA 68 :KAFVDRVSGR T0319 59 :VLTVAAELGNNA 1woyA 78 :FKRAWDLLGIAY T0319 83 :QE 1woyA 90 :DD T0319 85 :LTDDDMAILNDLHTLLLQT 1woyA 96 :TEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHL 1woyA 135 :TEKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=66 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 1woyA/T0319-1woyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1woyA/T0319-1woyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woyA read from 1woyA/T0319-1woyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1woyA in template set T0319 4 :LTTNFLKC 1woyA 44 :FFLTGTDE T0319 27 :YDGSKCQLVQDESIE 1woyA 52 :HGETVYRAAQAAGED T0319 43 :NPEFLLNIVDR 1woyA 67 :PKAFVDRVSGR T0319 59 :VLTVAAELGN 1woyA 78 :FKRAWDLLGI T0319 77 :SFPSSIQELTDDDMAILNDLHTLLLQT 1woyA 88 :AYDDFIRTTEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHLV 1woyA 135 :TEKEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=74 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 1dx8A/T0319-1dx8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dx8A expands to /projects/compbio/data/pdb/1dx8.pdb.gz 1dx8A:# T0319 read from 1dx8A/T0319-1dx8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dx8A read from 1dx8A/T0319-1dx8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dx8A to template set # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE T0319 121 :IKNGIPNLLLPPH 1dx8A 28 :IPPGTPFVDLSDS Number of specific fragments extracted= 2 number of extra gaps= 0 total=76 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 1dx8A/T0319-1dx8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1dx8A/T0319-1dx8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dx8A read from 1dx8A/T0319-1dx8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE T0319 121 :IKNGIPNLLLPPH 1dx8A 28 :IPPGTPFVDLSDS Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 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 1dx8A/T0319-1dx8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1dx8A/T0319-1dx8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dx8A read from 1dx8A/T0319-1dx8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE Number of specific fragments extracted= 1 number of extra gaps= 0 total=79 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 1rb9/T0319-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rb9/T0319-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0319-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rb9 in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rb9 4 :YVCTVCGYEYDPAEGDPDNGVKPGTS Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 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 1rb9/T0319-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rb9/T0319-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0319-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rb9 in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rb9 4 :YVCTVCGYEYDPAEGDPDNGVKPGTS Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 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 1rb9/T0319-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rb9/T0319-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0319-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rb9 in training set T0319 111 :KCRNCGHIYYIKNG 1rb9 5 :VCTVCGYEYDPAEG Number of specific fragments extracted= 1 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdg/T0319-1rdg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rdg expands to /projects/compbio/data/pdb/1rdg.pdb.gz 1rdg:Warning: there is no chain 1rdg will retry with 1rdgA # T0319 read from 1rdg/T0319-1rdg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdg read from 1rdg/T0319-1rdg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rdg to template set # found chain 1rdg in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rdg 4 :YVCTVCGYEYDPAKGDPDSGIKPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=83 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 1rdg/T0319-1rdg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rdg/T0319-1rdg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdg read from 1rdg/T0319-1rdg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdg in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rdg 4 :YVCTVCGYEYDPAKGDPDSGIKPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=84 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 1rdg/T0319-1rdg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1rdg/T0319-1rdg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdg read from 1rdg/T0319-1rdg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdg in template set T0319 111 :KCRNCGHIYYIKNG 1rdg 5 :VCTVCGYEYDPAKG Number of specific fragments extracted= 1 number of extra gaps= 0 total=85 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 1weoA/T0319-1weoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1weoA expands to /projects/compbio/data/pdb/1weo.pdb.gz 1weoA:# T0319 read from 1weoA/T0319-1weoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1weoA read from 1weoA/T0319-1weoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1weoA to template set # found chain 1weoA in template set T0319 12 :SVKACDTSNDNFPLQ 1weoA 22 :CGDQIGLTVEGDLFV T0319 34 :LVQDESIEFNPEFLLNIVDRVD 1weoA 37 :ACNECGFPACRPCYEYERREGT T0319 67 :GNNAL 1weoA 64 :CKTRY T0319 72 :PPTKPSF 1weoA 71 :LRGSPRV T0319 80 :SSIQELTDDD 1weoA 78 :EGDEDEEDID Number of specific fragments extracted= 5 number of extra gaps= 0 total=90 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 1weoA/T0319-1weoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1weoA/T0319-1weoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1weoA read from 1weoA/T0319-1weoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1weoA in template set T0319 12 :SVKACDTSNDNFPL 1weoA 22 :CGDQIGLTVEGDLF T0319 33 :QLVQDESIEFNPEFLLNIVDRV 1weoA 36 :VACNECGFPACRPCYEYERREG T0319 66 :LG 1weoA 63 :QC T0319 68 :NNALPPTKPSFPSSIQELTDD 1weoA 67 :RYKRLRGSPRVEGDEDEEDID Number of specific fragments extracted= 4 number of extra gaps= 0 total=94 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 1weoA/T0319-1weoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0319 read from 1weoA/T0319-1weoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1weoA read from 1weoA/T0319-1weoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1weoA in template set T0319 13 :VKACDTSNDNFPL 1weoA 25 :QIGLTVEGDLFVA T0319 35 :VQDESIEFNPEFLLNIVDRVD 1weoA 38 :CNECGFPACRPCYEYERREGT T0319 69 :NALPPTKPSFP 1weoA 59 :QNCPQCKTRYK T0319 81 :SIQ 1weoA 70 :RLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=98 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.036 sec, elapsed time= 10.684 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 9045 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.057 sec, elapsed time= 10.708 sec. # command:Reading probabilities from T0319.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 7.489 Optimizing... Probability sum: -291.618, CN propb: -291.618 weights: 0.132 constraints: 174 # command:CPU_time= 10.511 sec, elapsed time= 11.182 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 174 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 174 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 241 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 241 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 7586 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 7586 # command:CPU_time= 10.649 sec, elapsed time= 11.448 sec. # command: