parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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 /projects/compbio/experiments/protein-predict/casp7/T0353/ # command:# Making conformation for sequence T0353 numbered 1 through 85 Created new target T0353 from T0353.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0353/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0353//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0353/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t3lA expands to /projects/compbio/data/pdb/1t3l.pdb.gz 1t3lA:# T0353 read from 1t3lA/merged-good-all-a2m # 1t3lA read from 1t3lA/merged-good-all-a2m # adding 1t3lA to template set # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 Number of alignments=1 # 1t3lA read from 1t3lA/merged-good-all-a2m # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 Number of alignments=2 # 1t3lA read from 1t3lA/merged-good-all-a2m # found chain 1t3lA in template set T0353 20 :FDVFTDVRDDKKAIEFAKQWLSSI 1t3lA 383 :FDVILDENQLEDACEHLADYLEAY Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cthA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2cthA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2cthA/merged-good-all-a2m.gz for input Trying 2cthA/merged-good-all-a2m Error: Couldn't open file 2cthA/merged-good-all-a2m or 2cthA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sgvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sgvA expands to /projects/compbio/data/pdb/1sgv.pdb.gz 1sgvA:# T0353 read from 1sgvA/merged-good-all-a2m # 1sgvA read from 1sgvA/merged-good-all-a2m # adding 1sgvA to template set # found chain 1sgvA in template set T0353 1 :MQIHVYDTYVKAKDGHVMHFDVFTDVRDDKKAIEFAKQWLSSIGE 1sgvA 148 :IRIDRFELLAARRRDQLIDIDVEIDCSSGTYIRALARDLGDALGV Number of specific fragments extracted= 1 number of extra gaps= 0 total=4 Number of alignments=4 # 1sgvA read from 1sgvA/merged-good-all-a2m # 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=7 Number of alignments=5 # 1sgvA read from 1sgvA/merged-good-all-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=8 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a99A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a99A expands to /projects/compbio/data/pdb/1a99.pdb.gz 1a99A:# T0353 read from 1a99A/merged-good-all-a2m # 1a99A read from 1a99A/merged-good-all-a2m # adding 1a99A to template set # found chain 1a99A in template set T0353 12 :AKDGHVMHFDVFT 1a99A 269 :PKEGAMAFFDVFA T0353 25 :DVRDDKKAIEFAKQWLSS 1a99A 285 :DAKNKDEAYQFLNYLLRP T0353 43 :IGE 1a99A 312 :VFY T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Number of alignments=7 # 1a99A read from 1a99A/merged-good-all-a2m # found chain 1a99A in template set T0353 2 :QIHVYD 1a99A 263 :NVSFSI T0353 12 :AKDGHVMHFDVFTDV 1a99A 269 :PKEGAMAFFDVFAMP T0353 27 :RDDKKAIEFAKQWLSS 1a99A 287 :KNKDEAYQFLNYLLRP T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=16 Number of alignments=8 # 1a99A read from 1a99A/merged-good-all-a2m # found chain 1a99A in template set T0353 2 :QIHVY 1a99A 263 :NVSFS T0353 12 :AKDGHVMHFDVFTDVRD 1a99A 269 :PKEGAMAFFDVFAMPAD T0353 29 :DKKAIEFAKQWLSS 1a99A 289 :KDEAYQFLNYLLRP T0353 43 :IGE 1a99A 312 :VFY T0353 55 :CRFCHSQKAPDEVI 1a99A 317 :ANKAATPLVSAEVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=21 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ffkI/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ffkI expands to /projects/compbio/data/pdb-ca-mod/1ffk.brk_ca_mod.gz 1ffkI:# T0353 read from 1ffkI/merged-good-all-a2m # 1ffkI read from 1ffkI/merged-good-all-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=25 # 1ffkI read from 1ffkI/merged-good-all-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=29 # 1ffkI read from 1ffkI/merged-good-all-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=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iqtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1iqtA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1iqtA/merged-good-all-a2m.gz for input Trying 1iqtA/merged-good-all-a2m Error: Couldn't open file 1iqtA/merged-good-all-a2m or 1iqtA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nrfA expands to /projects/compbio/data/pdb/1nrf.pdb.gz 1nrfA:# T0353 read from 1nrfA/merged-good-all-a2m # 1nrfA read from 1nrfA/merged-good-all-a2m # adding 1nrfA to template set # found chain 1nrfA in template set T0353 3 :IHVYDTYVKAKD 1nrfA 551 :AGWFIGYVETAD T0353 16 :HVMHFDVFTDVRDD 1nrfA 563 :NTFFFAVHIQGEKR T0353 30 :KKAIEFAKQWLSSIGE 1nrfA 580 :SSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 Number of alignments=10 # 1nrfA read from 1nrfA/merged-good-all-a2m # found chain 1nrfA in template set T0353 4 :HVYDTYVKAKD 1nrfA 552 :GWFIGYVETAD T0353 16 :HVMHFDVFTDVRDD 1nrfA 563 :NTFFFAVHIQGEKR T0353 30 :KKAIEFAKQWLSSIGE 1nrfA 580 :SSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Number of alignments=11 # 1nrfA read from 1nrfA/merged-good-all-a2m # found chain 1nrfA in template set T0353 5 :VYDTYVKAKDGHVMH 1nrfA 553 :WFIGYVETADNTFFF T0353 20 :FDVFTDVRD 1nrfA 569 :VHIQGEKRA T0353 29 :DKKAIEFAKQWLSSIGE 1nrfA 579 :GSSAAEIALSILDKKGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1j0oA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1j0oA/merged-good-all-a2m.gz for input Trying 1j0oA/merged-good-all-a2m Error: Couldn't open file 1j0oA/merged-good-all-a2m or 1j0oA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8qA expands to /projects/compbio/data/pdb/1y8q.pdb.gz 1y8qA:# T0353 read from 1y8qA/merged-good-all-a2m # 1y8qA read from 1y8qA/merged-good-all-a2m # adding 1y8qA to template set # 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=44 Number of alignments=13 # 1y8qA read from 1y8qA/merged-good-all-a2m # found chain 1y8qA in template set T0353 28 :DDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1y8qA 265 :DSELLLQIRNDVLDSLGISPDLLPEDFVRYCFS T0353 63 :APDEVIEAIK 1y8qA 298 :EMAPVCAVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=46 Number of alignments=14 # 1y8qA read from 1y8qA/merged-good-all-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=49 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1wr5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1wr5A/merged-good-all-a2m.gz for input Trying 1wr5A/merged-good-all-a2m Error: Couldn't open file 1wr5A/merged-good-all-a2m or 1wr5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2mtaC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2mtaC/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2mtaC/merged-good-all-a2m.gz for input Trying 2mtaC/merged-good-all-a2m Error: Couldn't open file 2mtaC/merged-good-all-a2m or 2mtaC/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1is8K/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1is8K expands to /projects/compbio/data/pdb/1is8.pdb.gz 1is8K:# T0353 read from 1is8K/merged-good-all-a2m # 1is8K read from 1is8K/merged-good-all-a2m # adding 1is8K to template set # 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=55 Number of alignments=16 # 1is8K read from 1is8K/merged-good-all-a2m # 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=61 Number of alignments=17 # 1is8K read from 1is8K/merged-good-all-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=66 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1es6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1es6A/merged-good-all-a2m.gz for input Trying 1es6A/merged-good-all-a2m Error: Couldn't open file 1es6A/merged-good-all-a2m or 1es6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 155c/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 155c expands to /projects/compbio/data/pdb/155c.pdb.gz 155c:Warning: there is no chain 155c will retry with 155cA Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X # T0353 read from 155c/merged-good-all-a2m # 155c read from 155c/merged-good-all-a2m # adding 155c to template set # found chain 155c in template set Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 T0353 27 :RDDKKAIEFAKQW 155c 105 :KNQADVVAFLAQD T0353 47 :GATV 155c 118 :DPDA Number of specific fragments extracted= 2 number of extra gaps= 1 total=68 # 155c read from 155c/merged-good-all-a2m # found chain 155c in template set Warning: unaligning (T0353)E45 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)E46 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)G47 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 Warning: unaligning (T0353)A48 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X125 Warning: unaligning (T0353)T49 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X126 Warning: unaligning (T0353)V50 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X127 Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X128 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X129 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X130 Warning: unaligning (T0353)E54 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X131 Warning: unaligning (T0353)C55 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X132 T0353 26 :VRDDKKAIEFAKQW 155c 104 :GKNQADVVAFLAQD T0353 42 :S 155c 120 :D T0353 44 :G 155c 121 :A Number of specific fragments extracted= 3 number of extra gaps= 1 total=71 Number of alignments=19 # 155c read from 155c/merged-good-all-a2m # found chain 155c in template set Warning: unaligning (T0353)E45 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X122 Warning: unaligning (T0353)E46 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X123 Warning: unaligning (T0353)G47 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X124 Warning: unaligning (T0353)A48 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X125 Warning: unaligning (T0353)T49 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X126 Warning: unaligning (T0353)V50 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X127 Warning: unaligning (T0353)T51 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X128 Warning: unaligning (T0353)S52 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X129 Warning: unaligning (T0353)E53 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X130 Warning: unaligning (T0353)E54 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X131 Warning: unaligning (T0353)C55 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X132 Warning: unaligning (T0353)R56 because of BadResidue code NON_STANDARD_RESIDUE at template residue (155c)X133 T0353 26 :VRDDKKAIEFAKQW 155c 104 :GKNQADVVAFLAQD T0353 44 :G 155c 121 :A Number of specific fragments extracted= 2 number of extra gaps= 1 total=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1udzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0353 read from 1udzA/merged-good-all-a2m # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 25 :DVRDDKKAIEFAKQW 1udzA 321 :APAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=75 Number of alignments=20 # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 25 :DVRDDKKAIEFAKQW 1udzA 321 :APAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=77 Number of alignments=21 # 1udzA read from 1udzA/merged-good-all-a2m # found chain 1udzA in training set T0353 9 :YVKAKDGHVMH 1udzA 308 :YVSQEDGTGIV T0353 23 :FTDVRDDKKAIEFAKQW 1udzA 319 :HQAPAFGAEDLETARVY T0353 45 :EEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1udzA 344 :DEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=80 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cybA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cybA expands to /projects/compbio/data/pdb/2cyb.pdb.gz 2cybA:# T0353 read from 2cybA/merged-good-all-a2m # 2cybA read from 2cybA/merged-good-all-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=82 Number of alignments=23 # 2cybA read from 2cybA/merged-good-all-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=84 Number of alignments=24 # 2cybA read from 2cybA/merged-good-all-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=86 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cdv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/2cdv/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/2cdv/merged-good-all-a2m.gz for input Trying 2cdv/merged-good-all-a2m Error: Couldn't open file 2cdv/merged-good-all-a2m or 2cdv/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y9kA expands to /projects/compbio/data/pdb/1y9k.pdb.gz 1y9kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1099, because occupancy 0.5 <= existing 0.500 in 1y9kA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1y9kA 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 # T0353 read from 1y9kA/merged-good-all-a2m # 1y9kA read from 1y9kA/merged-good-all-a2m # adding 1y9kA to template set # found chain 1y9kA in template set T0353 7 :DTYVKAKDGHVMHFDVFTDVRDD 1y9kA 36 :LTYVAKQGGSVIGVYVLLETRPK T0353 30 :KKAIEFAKQWLSSIGEE 1y9kA 78 :KKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKMEG 1y9kA 102 :NSSVSQLALYQKCGFRIFSIDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=89 Number of alignments=26 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set T0353 8 :TYVKAKDGHVMHFDVFTDVRDD 1y9kA 37 :TYVAKQGGSVIGVYVLLETRPK T0353 30 :KKAIEFAKQWLSSIGEE 1y9kA 78 :KKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKMEG 1y9kA 102 :NSSVSQLALYQKCGFRIFSIDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=92 Number of alignments=27 # 1y9kA read from 1y9kA/merged-good-all-a2m # found chain 1y9kA in template set T0353 3 :IHVYDTYVKAKDGHVMHFDVFTDVRD 1y9kA 46 :VIGVYVLLETRPKTMEIMNIAVAEHL T0353 29 :DKKAIEFAKQWLSSIGEE 1y9kA 77 :GKKLLRHAVETAKGYGMS T0353 62 :KAPDEVIEAIKQNGYFIYKME 1y9kA 102 :NSSVSQLALYQKCGFRIFSID Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2drpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2drpA expands to /projects/compbio/data/pdb/2drp.pdb.gz 2drpA:# T0353 read from 2drpA/merged-good-all-a2m # 2drpA read from 2drpA/merged-good-all-a2m # adding 2drpA to template set # 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=100 Number of alignments=29 # 2drpA read from 2drpA/merged-good-all-a2m # 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=105 Number of alignments=30 # 2drpA read from 2drpA/merged-good-all-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=109 Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mdvA expands to /projects/compbio/data/pdb/1mdv.pdb.gz 1mdvA:# T0353 read from 1mdvA/merged-good-all-a2m # 1mdvA read from 1mdvA/merged-good-all-a2m # adding 1mdvA to template set # 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=111 Number of alignments=32 # 1mdvA read from 1mdvA/merged-good-all-a2m # found chain 1mdvA in template set T0353 49 :TVTSEECRFCHSQ 1mdvA 73 :NTKFKSCVGCHVE Number of specific fragments extracted= 1 number of extra gaps= 0 total=112 # 1mdvA read from 1mdvA/merged-good-all-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=114 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2faoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2faoA expands to /projects/compbio/data/pdb/2fao.pdb.gz 2faoA:# T0353 read from 2faoA/merged-good-all-a2m # 2faoA read from 2faoA/merged-good-all-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=116 Number of alignments=34 # 2faoA read from 2faoA/merged-good-all-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=118 Number of alignments=35 # 2faoA read from 2faoA/merged-good-all-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=120 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a26/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a26 expands to /projects/compbio/data/pdb/1a26.pdb.gz 1a26:Warning: there is no chain 1a26 will retry with 1a26A # T0353 read from 1a26/merged-good-all-a2m # 1a26 read from 1a26/merged-good-all-a2m # adding 1a26 to template set # found chain 1a26 in template set T0353 27 :RDDKKAIEF 1a26 664 :KLAKPIQDL T0353 36 :AKQWLSSIGEEGATVTSEECRFCHSQKA 1a26 682 :MKKAMVEFEIDLQKMPLGKLSKRQIQSA T0353 66 :EVIEAIKQNG 1a26 715 :EVQQAVSDGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=123 Number of alignments=37 # 1a26 read from 1a26/merged-good-all-a2m # found chain 1a26 in template set T0353 29 :DKKAIEFAKQWLSSIGEEGA 1a26 706 :IQSAYSILNEVQQAVSDGGS T0353 52 :SEEC 1a26 726 :ESQI T0353 65 :DEVIEAIKQ 1a26 730 :LDLSNRFYT Number of specific fragments extracted= 3 number of extra gaps= 0 total=126 Number of alignments=38 # 1a26 read from 1a26/merged-good-all-a2m # found chain 1a26 in template set T0353 29 :DKKAIEF 1a26 666 :AKPIQDL T0353 36 :AKQWLSSIGEEGATVTSEECRFCHSQKA 1a26 682 :MKKAMVEFEIDLQKMPLGKLSKRQIQSA T0353 66 :EVIEAIKQNG 1a26 715 :EVQQAVSDGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=129 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a7e/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a7e expands to /projects/compbio/data/pdb/1a7e.pdb.gz 1a7e:Warning: there is no chain 1a7e will retry with 1a7eA # T0353 read from 1a7e/merged-good-all-a2m # 1a7e read from 1a7e/merged-good-all-a2m # adding 1a7e to template set # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=131 Number of alignments=40 # 1a7e read from 1a7e/merged-good-all-a2m # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=133 Number of alignments=41 # 1a7e read from 1a7e/merged-good-all-a2m # found chain 1a7e in template set T0353 27 :RDDKKAIEFAKQWLSSIGEEGATVTSEECRFCHS 1a7e 68 :SEVVPHKKMHKDFLEKIGGLSAPVDAKNVDYCKE T0353 66 :EVIEAIKQN 1a7e 102 :WNVNHIKGT Number of specific fragments extracted= 2 number of extra gaps= 0 total=135 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0hB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t0hB expands to /projects/compbio/data/pdb/1t0h.pdb.gz 1t0hB:# T0353 read from 1t0hB/merged-good-all-a2m # 1t0hB read from 1t0hB/merged-good-all-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=136 Number of alignments=43 # 1t0hB read from 1t0hB/merged-good-all-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=137 Number of alignments=44 # 1t0hB read from 1t0hB/merged-good-all-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=139 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jg5A expands to /projects/compbio/data/pdb/1jg5.pdb.gz 1jg5A:# T0353 read from 1jg5A/merged-good-all-a2m # 1jg5A read from 1jg5A/merged-good-all-a2m # adding 1jg5A to template set # 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=146 Number of alignments=46 # 1jg5A read from 1jg5A/merged-good-all-a2m # 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=153 Number of alignments=47 # 1jg5A read from 1jg5A/merged-good-all-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=159 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r3eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r3eA expands to /projects/compbio/data/pdb/1r3e.pdb.gz 1r3eA:# T0353 read from 1r3eA/merged-good-all-a2m # 1r3eA read from 1r3eA/merged-good-all-a2m # adding 1r3eA to template set # 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=164 Number of alignments=49 # 1r3eA read from 1r3eA/merged-good-all-a2m # 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=169 Number of alignments=50 # 1r3eA read from 1r3eA/merged-good-all-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=175 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1wtbA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1wtbA/merged-good-all-a2m.gz for input Trying 1wtbA/merged-good-all-a2m Error: Couldn't open file 1wtbA/merged-good-all-a2m or 1wtbA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wnyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wnyA expands to /projects/compbio/data/pdb/1wny.pdb.gz 1wnyA:# T0353 read from 1wnyA/merged-good-all-a2m # 1wnyA read from 1wnyA/merged-good-all-a2m # adding 1wnyA to template set # found chain 1wnyA in template set T0353 27 :RDDKKAIEFAKQW 1wnyA 323 :AFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFI 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=177 Number of alignments=52 # 1wnyA read from 1wnyA/merged-good-all-a2m # found chain 1wnyA in template set T0353 27 :RDDKKAIEFAKQW 1wnyA 323 :AFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGYFIYK 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKE Number of specific fragments extracted= 2 number of extra gaps= 0 total=179 Number of alignments=53 # 1wnyA read from 1wnyA/merged-good-all-a2m # found chain 1wnyA in template set Warning: unaligning (T0353)G83 because last residue in template chain is (1wnyA)S381 T0353 9 :YVKAKDGHVM 1wnyA 308 :YVSQEDGTGI T0353 22 :VFTDVRDDKKAIEFAKQW 1wnyA 318 :VHQAPAFGAEDLETARVY T0353 43 :IGEEGATVTSEECRFCHSQKAPDEVIEAIKQNGY 1wnyA 342 :TVDEEGKLLVEPFKGLYFREANRAILRDLRGRGL T0353 78 :IYKME 1wnyA 376 :LFKEE Number of specific fragments extracted= 4 number of extra gaps= 0 total=183 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mg2D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0353/1mg2D/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0353/1mg2D/merged-good-all-a2m.gz for input Trying 1mg2D/merged-good-all-a2m Error: Couldn't open file 1mg2D/merged-good-all-a2m or 1mg2D/merged-good-all-a2m.gz for input # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 54 Done printing distance constraints # command: