# 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 T0353 numbered 1 through 85 Created new target T0353 from T0353.a2m # command:CPU_time= 6.665 sec, elapsed time= 6.724 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qA/T0353-1y8qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y8qA expands to /projects/compbio/data/pdb/1y8q.pdb.gz 1y8qA:# T0353 read from 1y8qA/T0353-1y8qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8qA read from 1y8qA/T0353-1y8qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y8qA to template set # found chain 1y8qA in template set T0353 28 :DDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 265 :DSELLLQIRNDVLDSLGISPDLLPEDFVRYCFS # choosing archetypes in rotamer library T0353 63 :APDEVIEAIK 1y8qA 298 :EMAPVCAVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qA/T0353-1y8qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1y8qA/T0353-1y8qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8qA read from 1y8qA/T0353-1y8qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y8qA in template set T0353 29 :DKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 266 :SELLLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAIK 1y8qA 298 :EMAPVCAVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qA/T0353-1y8qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1y8qA/T0353-1y8qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8qA read from 1y8qA/T0353-1y8qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y8qA in template set T0353 24 :TDVRDDKK 1y8qA 257 :PSSDTYEE T0353 32 :AIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 269 :LLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAI 1y8qA 298 :EMAPVCAVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg5A/T0353-1jg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jg5A expands to /projects/compbio/data/pdb/1jg5.pdb.gz 1jg5A:# T0353 read from 1jg5A/T0353-1jg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg5A read from 1jg5A/T0353-1jg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jg5A to template set # found chain 1jg5A in template set Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)A12 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 2 :QIHVY 1jg5A 2 :YLLIS T0353 9 :YV 1jg5A 7 :TQ T0353 13 :KDGHVMH 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKKA 1jg5A 18 :VGDEHSDPEL T0353 40 :LSSIGEEGAT 1jg5A 28 :MQQLGASKRR T0353 52 :SEECRFC 1jg5A 38 :VLGNNFY T0353 59 :HSQKAPDEVIEAIKQNGYFIYKMEGC 1jg5A 47 :YVNDPPRIVLDKLECRGFRVLSMTGV Number of specific fragments extracted= 7 number of extra gaps= 1 total=14 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 1jg5A/T0353-1jg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1jg5A/T0353-1jg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg5A read from 1jg5A/T0353-1jg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jg5A in template set Warning: unaligning (T0353)V10 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 2 :QIHV 1jg5A 2 :YLLI T0353 7 :DTY 1jg5A 6 :STQ T0353 12 :AKDGHVM 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKKA 1jg5A 18 :VGDEHSDPEL T0353 40 :LSSIG 1jg5A 28 :MQQLG T0353 45 :EEGAT 1jg5A 38 :VLGNN T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEGCN 1jg5A 48 :VNDPPRIVLDKLECRGFRVLSMTGVG Number of specific fragments extracted= 7 number of extra gaps= 1 total=21 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 1jg5A/T0353-1jg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1jg5A/T0353-1jg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg5A read from 1jg5A/T0353-1jg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jg5A in template set Warning: unaligning (T0353)V10 because of BadResidue code BAD_PEPTIDE in next template residue (1jg5A)R10 Warning: unaligning (T0353)K11 because of BadResidue code BAD_PEPTIDE at template residue (1jg5A)R10 T0353 5 :VYDTY 1jg5A 4 :LISTQ T0353 12 :AKDGHVM 1jg5A 11 :MEVGPTM T0353 23 :FTDVRDDKK 1jg5A 18 :VGDEHSDPE T0353 39 :WLSSIGEEGA 1jg5A 27 :LMQQLGASKR T0353 51 :TSEECRFCH 1jg5A 37 :RVLGNNFYE T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEG 1jg5A 48 :VNDPPRIVLDKLECRGFRVLSMTG Number of specific fragments extracted= 6 number of extra gaps= 1 total=27 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 1mdvA/T0353-1mdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mdvA expands to /projects/compbio/data/pdb/1mdv.pdb.gz 1mdvA:# T0353 read from 1mdvA/T0353-1mdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdvA read from 1mdvA/T0353-1mdvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mdvA to template set # found chain 1mdvA in template set T0353 49 :TVTSEECRFCHSQ 1mdvA 73 :NTKFKSCVGCHVE Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 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 1mdvA/T0353-1mdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1mdvA/T0353-1mdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdvA read from 1mdvA/T0353-1mdvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mdvA in template set T0353 49 :TVTSEECRFCHSQKA 1mdvA 73 :NTKFKSCVGCHVEVA T0353 64 :PDEVIE 1mdvA 90 :DAAKKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=30 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 1mdvA/T0353-1mdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1mdvA/T0353-1mdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mdvA read from 1mdvA/T0353-1mdvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mdvA in template set T0353 48 :ATVTSEECRFCHSQKA 1mdvA 72 :KNTKFKSCVGCHVEVA T0353 64 :PDEVIE 1mdvA 90 :DAAKKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=32 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 1is8K/T0353-1is8K-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1is8K expands to /projects/compbio/data/pdb/1is8.pdb.gz 1is8K:# T0353 read from 1is8K/T0353-1is8K-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1is8K read from 1is8K/T0353-1is8K-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1is8K to template set # found chain 1is8K in template set T0353 2 :QIHVYDT 1is8K 3 :YLLISTQ T0353 10 :VKAKDGHV 1is8K 10 :IRMEVGPT T0353 22 :VFTDVRDDKKAIE 1is8K 18 :MVGDEHSDPELMQ T0353 42 :SIG 1is8K 31 :QLG T0353 45 :EEGAT 1is8K 39 :VLGNN T0353 59 :HSQKAPDEVIEAIKQNGYFIYKMEGC 1is8K 48 :YVNDPPRIVLDKLECRGFRVLSMTGV Number of specific fragments extracted= 6 number of extra gaps= 0 total=38 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 1is8K/T0353-1is8K-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1is8K/T0353-1is8K-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1is8K read from 1is8K/T0353-1is8K-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1is8K in template set T0353 2 :QIHVY 1is8K 3 :YLLIS T0353 8 :TYVKAKDGHVM 1is8K 8 :TQIRMEVGPTM T0353 23 :FTDVRDDKKAIE 1is8K 19 :VGDEHSDPELMQ T0353 42 :SIG 1is8K 31 :QLG T0353 45 :EEGAT 1is8K 39 :VLGNN T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEGCN 1is8K 49 :VNDPPRIVLDKLECRGFRVLSMTGVG Number of specific fragments extracted= 6 number of extra gaps= 0 total=44 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 1is8K/T0353-1is8K-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1is8K/T0353-1is8K-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1is8K read from 1is8K/T0353-1is8K-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1is8K in template set T0353 5 :VYDTYVKAKDGHVM 1is8K 5 :LISTQIRMEVGPTM T0353 23 :FTDVRDDKKA 1is8K 19 :VGDEHSDPEL T0353 40 :LSSIGEEGA 1is8K 29 :MQQLGASKR T0353 51 :TSEECRF 1is8K 38 :RVLGNNF T0353 60 :SQKAPDEVIEAIKQNGYFIYKMEG 1is8K 49 :VNDPPRIVLDKLECRGFRVLSMTG Number of specific fragments extracted= 5 number of extra gaps= 0 total=49 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 1wr5A/T0353-1wr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr5A/T0353-1wr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr5A/T0353-1wr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0oA/T0353-1j0oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0oA/T0353-1j0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0oA/T0353-1j0oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cdv/T0353-2cdv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cdv/T0353-2cdv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cdv/T0353-2cdv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtbA/T0353-1wtbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtbA/T0353-1wtbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtbA/T0353-1wtbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iqtA/T0353-1iqtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iqtA/T0353-1iqtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iqtA/T0353-1iqtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cybA/T0353-2cybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cybA expands to /projects/compbio/data/pdb/2cyb.pdb.gz 2cybA:# T0353 read from 2cybA/T0353-2cybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cybA read from 2cybA/T0353-2cybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cybA to template set # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGY T0353 46 :EGATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 211 :DGQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=51 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 2cybA/T0353-2cybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2cybA/T0353-2cybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cybA read from 2cybA/T0353-2cybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGY T0353 46 :EGATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 211 :DGQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=53 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 2cybA/T0353-2cybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2cybA/T0353-2cybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cybA read from 2cybA/T0353-2cybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cybA in template set T0353 21 :DVFTDVRDDKKAIEFAKQWLSSIGEE 2cybA 172 :DLAVGGIDQRKIHMLARENLPRLGYS T0353 47 :GATVTSEECRFCHSQKAPDEVIEAIKQ 2cybA 212 :GQKMSSSKGNYISVRDPPEEVERKIRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=55 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 1t0hB/T0353-1t0hB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0hB expands to /projects/compbio/data/pdb/1t0h.pdb.gz 1t0hB:# T0353 read from 1t0hB/T0353-1t0hB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0hB read from 1t0hB/T0353-1t0hB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0hB to template set # found chain 1t0hB in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t0hB 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=56 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 1t0hB/T0353-1t0hB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1t0hB/T0353-1t0hB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0hB read from 1t0hB/T0353-1t0hB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0hB in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t0hB 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=57 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0hB/T0353-1t0hB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1t0hB/T0353-1t0hB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0hB read from 1t0hB/T0353-1t0hB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0hB in template set Warning: unaligning (T0353)E46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0hB)R424 T0353 20 :FDVFTDVRDDKK 1t0hB 383 :FDVILDENQLED T0353 32 :AIEFAKQWLSSIGE 1t0hB 399 :LADYLEAYWKATHP 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=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2faoA/T0353-2faoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2faoA expands to /projects/compbio/data/pdb/2fao.pdb.gz 2faoA:# T0353 read from 2faoA/T0353-2faoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2faoA read from 2faoA/T0353-2faoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2faoA to template set # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDV 2faoA 700 :FLKTSGGKGMHLLVPLER T0353 27 :RDDKKAIEFAKQWLSSI 2faoA 719 :HGWDEVKDFAQAISQHL 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=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2faoA/T0353-2faoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2faoA/T0353-2faoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2faoA read from 2faoA/T0353-2faoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDV 2faoA 700 :FLKTSGGKGMHLLVPLER T0353 27 :RDDKKAIEFAKQWLSSI 2faoA 719 :HGWDEVKDFAQAISQHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=63 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 2faoA/T0353-2faoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2faoA/T0353-2faoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2faoA read from 2faoA/T0353-2faoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2faoA in template set T0353 9 :YVKAKDGHVMHFDVFTDVR 2faoA 700 :FLKTSGGKGMHLLVPLERR T0353 28 :DDKKAIEFAKQWLSSI 2faoA 720 :GWDEVKDFAQAISQHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=65 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 1r3eA/T0353-1r3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r3eA expands to /projects/compbio/data/pdb/1r3e.pdb.gz 1r3eA:# T0353 read from 1r3eA/T0353-1r3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r3eA read from 1r3eA/T0353-1r3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r3eA to template set # found chain 1r3eA in template set T0353 2 :QIHVYDTYVKAKDGHVMHFDVFTDVRDD 1r3eA 152 :RVKIFKIWDVNIEGRDVSFRVEVSPGTY T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 49 :TVTSEECR 1r3eA 207 :PHTIEESL T0353 58 :CHSQKAPDEVIEA 1r3eA 215 :NVFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 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 1r3eA/T0353-1r3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1r3eA/T0353-1r3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r3eA read from 1r3eA/T0353-1r3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r3eA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDD 1r3eA 151 :KRVKIFKIWDVNIEGRDVSFRVEVSPGTY T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 49 :TVTSEECR 1r3eA 207 :PHTIEESL T0353 58 :CHSQKAPDEVIEA 1r3eA 215 :NVFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 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 1r3eA/T0353-1r3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1r3eA/T0353-1r3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r3eA read from 1r3eA/T0353-1r3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r3eA in template set T0353 4 :HVYDTYV 1r3eA 157 :KIWDVNI T0353 14 :DGHVMHFDVFTDVR 1r3eA 164 :EGRDVSFRVEVSPG T0353 32 :AIEFAKQWLSSIGEE 1r3eA 180 :IRSLCMDIGYKLGCG T0353 48 :ATVTSEECRF 1r3eA 206 :GPHTIEESLN T0353 59 :HSQKAPDEVIEA 1r3eA 216 :VFEAAPEEIENR T0353 78 :IYKMEGC 1r3eA 228 :IIPLEKC Number of specific fragments extracted= 6 number of extra gaps= 0 total=81 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 1ffkI/T0353-1ffkI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ffkI expands to /projects/compbio/data/pdb-ca-mod/1ffk.brk_ca_mod.gz 1ffkI:# T0353 read from 1ffkI/T0353-1ffkI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffkI read from 1ffkI/T0353-1ffkI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ffkI to template set # found chain 1ffkI in template set Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAIE 1ffkI 130 :EVILVDRDHPAIKS Number of specific fragments extracted= 4 number of extra gaps= 3 total=85 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 1ffkI/T0353-1ffkI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1ffkI/T0353-1ffkI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffkI read from 1ffkI/T0353-1ffkI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ffkI in template set Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAIE 1ffkI 130 :EVILVDRDHPAIKS Number of specific fragments extracted= 4 number of extra gaps= 3 total=89 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 1ffkI/T0353-1ffkI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1ffkI/T0353-1ffkI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffkI read from 1ffkI/T0353-1ffkI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ffkI in template set Warning: unaligning (T0353)I3 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)M112 Warning: unaligning (T0353)V5 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)L115 Warning: unaligning (T0353)Y6 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)L115 Warning: unaligning (T0353)V10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ffkI)V120 Warning: unaligning (T0353)K11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ffkI)V120 Warning: unaligning (T0353)H19 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ffkI)F129 Warning: unaligning (T0353)F20 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ffkI)F129 T0353 4 :H 1ffkI 113 :E T0353 7 :DTY 1ffkI 116 :NSY T0353 12 :AKDGHVM 1ffkI 121 :GEDGRYK T0353 21 :DVFTDVRDDKKAI 1ffkI 130 :EVILVDRDHPAIK Number of specific fragments extracted= 4 number of extra gaps= 4 total=93 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 1sgvA/T0353-1sgvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sgvA expands to /projects/compbio/data/pdb/1sgv.pdb.gz 1sgvA:# T0353 read from 1sgvA/T0353-1sgvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sgvA read from 1sgvA/T0353-1sgvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sgvA to template set # found chain 1sgvA in template set T0353 2 :QIH 1sgvA 149 :RID T0353 5 :VYDTYVKAKDG 1sgvA 153 :FELLAARRRDQ T0353 17 :VMHFDVFTDVRDDKKAIEFAKQWLSSIGEE 1sgvA 164 :LIDIDVEIDCSSGTYIRALARDLGDALGVG 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=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sgvA/T0353-1sgvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1sgvA/T0353-1sgvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sgvA read from 1sgvA/T0353-1sgvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sgvA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDDKKAIEFAKQWLSSIGE 1sgvA 148 :IRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGV Number of specific fragments extracted= 1 number of extra gaps= 0 total=97 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 1sgvA/T0353-1sgvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 1sgvA/T0353-1sgvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sgvA read from 1sgvA/T0353-1sgvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sgvA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDDKKAIEFAKQWLSSIGEE 1sgvA 148 :IRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGVG Number of specific fragments extracted= 1 number of extra gaps= 0 total=98 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 2drpA/T0353-2drpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2drpA expands to /projects/compbio/data/pdb/2drp.pdb.gz 2drpA:# T0353 read from 2drpA/T0353-2drpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2drpA read from 2drpA/T0353-2drpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2drpA to template set # found chain 2drpA in template set T0353 14 :DGH 2drpA 116 :CSR T0353 25 :DVRDDKKAIEF 2drpA 119 :VYTHISNFCRH T0353 40 :LSSIG 2drpA 130 :YVTSH T0353 47 :GATVTSEECRFCHSQ 2drpA 135 :KRNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIKQ 2drpA 151 :TRKDNMTAHVKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=103 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 2drpA/T0353-2drpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2drpA/T0353-2drpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2drpA read from 2drpA/T0353-2drpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2drpA in template set T0353 9 :YVKAKDGH 2drpA 111 :YRCKVCSR T0353 25 :DVRDDKKAIE 2drpA 119 :VYTHISNFCR T0353 39 :WLSSIGE 2drpA 129 :HYVTSHK T0353 48 :ATVTSEECRFCHSQ 2drpA 136 :RNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIK 2drpA 151 :TRKDNMTAHVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=108 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2drpA/T0353-2drpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0353 read from 2drpA/T0353-2drpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2drpA read from 2drpA/T0353-2drpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2drpA in template set T0353 27 :RDDKKAIEF 2drpA 121 :THISNFCRH T0353 40 :LSSI 2drpA 130 :YVTS T0353 46 :EGATVTSEECRFCHSQ 2drpA 134 :HKRNVKVYPCPFCFKE T0353 62 :KAPDEVIEAIK 2drpA 151 :TRKDNMTAHVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=112 Will force an alignment to be made, even if fragment is small Number of alignments=33 # command:CPU_time= 12.067 sec, elapsed time= 12.969 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 33 Adding 3570 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.079 sec, elapsed time= 12.980 sec. # command:Reading probabilities from T0353.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 3.000 Optimizing... Probability sum: -169.499, CN propb: -169.499 weights: 0.401 constraints: 137 # command:CPU_time= 12.396 sec, elapsed time= 13.319 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 137 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 137 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 127 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 127 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 2662 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 2662 # command:CPU_time= 12.452 sec, elapsed time= 13.430 sec. # command: