# 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/T0366/ # command:# Making conformation for sequence T0366 numbered 1 through 106 Created new target T0366 from T0366.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0366/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj6A/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/T0366/1vj6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1vj6A/merged-good-all-a2m.gz for input Trying 1vj6A/merged-good-all-a2m Error: Couldn't open file 1vj6A/merged-good-all-a2m or 1vj6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fneA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fneA expands to /projects/compbio/data/pdb/2fne.pdb.gz 2fneA:Skipped atom 15, because occupancy 0.5 <= existing 0.500 in 2fneA Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fneA # T0366 read from 2fneA/merged-good-all-a2m # 2fneA read from 2fneA/merged-good-all-a2m # adding 2fneA to template set # found chain 2fneA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fneA)M1954 T0366 9 :MGLRTVEMKKG 2fneA 1955 :PQCKSITLERG # choosing archetypes in rotamer library T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 2fneA 1966 :PDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDET Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fneA)M1954 T0366 9 :MGLRTVEMKKG 2fneA 1955 :PQCKSITLERG T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 2fneA 1966 :PDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDET Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (2fneA)M1954 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 1 number of extra gaps= 0 total=5 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bygA/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/T0366/2bygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/2bygA/merged-good-all-a2m.gz for input Trying 2bygA/merged-good-all-a2m Error: Couldn't open file 2bygA/merged-good-all-a2m or 2bygA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8tA expands to /projects/compbio/data/pdb/1y8t.pdb.gz 1y8tA: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 # T0366 read from 1y8tA/merged-good-all-a2m # 1y8tA read from 1y8tA/merged-good-all-a2m # adding 1y8tA to template set # found chain 1y8tA in template set Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :DV 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=13 Number of alignments=4 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :DVS 1y8tA 302 :GGS Number of specific fragments extracted= 8 number of extra gaps= 5 total=21 Number of alignments=5 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :D 1y8tA 302 :G Number of specific fragments extracted= 8 number of extra gaps= 5 total=29 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1qauA/merged-good-all-a2m # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qauA 90 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=7 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1qauA)N14 T0366 11 :LRTVEMKKGPTDSLGISIAGGV 1qauA 15 :VISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 37 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qauA 90 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=8 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDV 1qauA 90 :ETHVVLILRGPEGF Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h2bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h2bA expands to /projects/compbio/data/pdb/2h2b.pdb.gz 2h2bA:# T0366 read from 2h2bA/merged-good-all-a2m # 2h2bA read from 2h2bA/merged-good-all-a2m # adding 2h2bA to template set # found chain 2h2bA in template set T0366 5 :YFQSMGLRTVEMKKGPTDSLGISIAGGV 2h2bA 15 :SHMIWEQHTVTLHRAPGFGFGIAISGGR T0366 33 :GSPLGDVPIFIAMMHPTGVAA 2h2bA 46 :HFQSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGGW T0366 104 :T 2h2bA 117 :T Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 Number of alignments=10 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set Warning: unaligning (T0366)L4 because first residue in template chain is (2h2bA)G14 T0366 5 :YFQSMGLRTVEMKKGPTDSLGISIAGGVGS 2h2bA 15 :SHMIWEQHTVTLHRAPGFGFGIAISGGRDN T0366 35 :PLGDVPIFIAMMHPTGVAA 2h2bA 48 :QSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGG T0366 104 :TSV 2h2bA 116 :RTT Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=11 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set T0366 7 :QSMGLRTVEMKKGPTDSLGISIAGGVG 2h2bA 17 :MIWEQHTVTLHRAPGFGFGIAISGGRD T0366 34 :SPLGDVPIFIAMMHPTGVAA 2h2bA 47 :FQSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGGWRRT Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i16/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i16 expands to /projects/compbio/data/pdb/1i16.pdb.gz 1i16:Warning: there is no chain 1i16 will retry with 1i16A # T0366 read from 1i16/merged-good-all-a2m # 1i16 read from 1i16/merged-good-all-a2m # adding 1i16 to template set # found chain 1i16 in template set T0366 3 :NLYFQ 1i16 19 :DVSVE T0366 11 :LRTVEMKKG 1i16 30 :VCTVTLEKM T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i16 39 :SAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0366 88 :SGSIEMQVVAGGDVSE 1i16 107 :DGPVTIVIRRKSLQSK T0366 105 :S 1i16 125 :T Number of specific fragments extracted= 5 number of extra gaps= 0 total=54 Number of alignments=13 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0366 2 :ENLYFQ 1i16 18 :SDVSVE T0366 11 :LRTVEMKKG 1i16 30 :VCTVTLEKM T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i16 39 :SAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0366 88 :SGSIEMQVVAGGDVS 1i16 107 :DGPVTIVIRRKSLQS T0366 103 :ETS 1i16 123 :ETT Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 Number of alignments=14 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1i16 26 :AEATVCTVTLEKMSAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKALP T0366 89 :GSIEMQVVAGGDVSETS 1i16 108 :GPVTIVIRRKSLQSKET Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v5lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v5lA expands to /projects/compbio/data/pdb/1v5l.pdb.gz 1v5lA:# T0366 read from 1v5lA/merged-good-all-a2m # 1v5lA read from 1v5lA/merged-good-all-a2m # adding 1v5lA to template set # found chain 1v5lA in template set T0366 2 :ENLYFQS 1v5lA 2 :SSGSSGN T0366 14 :VEMKKG 1v5lA 9 :VVLPGP T0366 22 :DSLGISIAGGVGS 1v5lA 15 :APWGFRLSGGIDF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1v5lA 28 :NQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRLW T0366 104 :TS 1v5lA 94 :PQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=67 Number of alignments=16 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0366 2 :ENLYFQS 1v5lA 2 :SSGSSGN T0366 14 :VEMKK 1v5lA 9 :VVLPG T0366 21 :TDSLGISIAGGVG 1v5lA 14 :PAPWGFRLSGGID T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1v5lA 27 :FNQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRL T0366 105 :SV 1v5lA 94 :PQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=73 Number of alignments=17 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0366 17 :KKGPTDSLGISIAGGVG 1v5lA 10 :VLPGPAPWGFRLSGGID T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1v5lA 27 :FNQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRLWSPQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=76 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tp5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tp5A expands to /projects/compbio/data/pdb/1tp5.pdb.gz 1tp5A:# T0366 read from 1tp5A/merged-good-all-a2m # 1tp5A read from 1tp5A/merged-good-all-a2m # adding 1tp5A to template set # found chain 1tp5A in template set Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 1 :TENLYFQSMGLRTVEMKKG 1tp5A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1tp5A 320 :STGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 4 number of extra gaps= 1 total=80 Number of alignments=19 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 1 :TENLYFQSMGLRTVEMKKG 1tp5A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1tp5A 320 :STGLGFNIVGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 4 number of extra gaps= 1 total=84 Number of alignments=20 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 7 :QSMGLRTVEMKKGPTDSLGISIAGGVG 1tp5A 306 :DIPREPRRIVIHRGSTGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=87 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i92A expands to /projects/compbio/data/pdb/1i92.pdb.gz 1i92A:Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i92A # T0366 read from 1i92A/merged-good-all-a2m # 1i92A read from 1i92A/merged-good-all-a2m # adding 1i92A to template set # found chain 1i92A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 9 :MGLRTVEMKKG 1i92A 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGVG 1i92A 21 :PNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVSE 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 5 number of extra gaps= 1 total=92 Number of alignments=22 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 9 :MGLRTVEMKKG 1i92A 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGV 1i92A 21 :PNGYGFHLHGEK T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1i92A 33 :GKLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVS 1i92A 85 :AVRLLVVDPEQDT Number of specific fragments extracted= 5 number of extra gaps= 1 total=97 Number of alignments=23 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVSE 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 4 number of extra gaps= 1 total=101 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bfeA expands to /projects/compbio/data/pdb/1bfe.pdb.gz 1bfeA:# T0366 read from 1bfeA/merged-good-all-a2m # 1bfeA read from 1bfeA/merged-good-all-a2m # adding 1bfeA to template set # found chain 1bfeA in template set Warning: unaligning (T0366)F6 because first residue in template chain is (1bfeA)D306 T0366 7 :QSMGLRTVEMKKG 1bfeA 307 :IPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1bfeA 320 :STGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=104 Number of alignments=25 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set Warning: unaligning (T0366)F6 because first residue in template chain is (1bfeA)D306 T0366 7 :QSMGLRTVEMKKG 1bfeA 307 :IPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1bfeA 320 :STGLGFNIIGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=107 Number of alignments=26 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1bfeA)D306 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1bfeA 307 :IPREPRRIVIHRGSTGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1fc6A/merged-good-all-a2m # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 22 :DSLGISIAGGVGS 1fc6A 161 :TGVGLEITYDGGS T0366 38 :DVPIFIAMMHPTGVAAQTQ 1fc6A 174 :GKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 87 :ASGSIEMQVVAGGD 1fc6A 223 :ADSQVEVVLHAPGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=113 Number of alignments=28 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 21 :TDSLGISIAGGVG 1fc6A 160 :VTGVGLEITYDGG T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1fc6A 173 :SGKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 86 :NASGSIEMQVVAGGDV 1fc6A 222 :EADSQVEVVLHAPGAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=117 Number of alignments=29 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 19 :GPTDSLGISIAGGVG 1fc6A 158 :GSVTGVGLEITYDGG T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1fc6A 173 :SGKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 85 :KNASGSIEMQVVA 1fc6A 221 :GEADSQVEVVLHA Number of specific fragments extracted= 4 number of extra gaps= 0 total=121 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gm1A/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/T0366/1gm1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1gm1A/merged-good-all-a2m.gz for input Trying 1gm1A/merged-good-all-a2m Error: Couldn't open file 1gm1A/merged-good-all-a2m or 1gm1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kefA/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/T0366/1kefA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1kefA/merged-good-all-a2m.gz for input Trying 1kefA/merged-good-all-a2m Error: Couldn't open file 1kefA/merged-good-all-a2m or 1kefA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf3C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf3C expands to /projects/compbio/data/pdb/1nf3.pdb.gz 1nf3C:# T0366 read from 1nf3C/merged-good-all-a2m # 1nf3C read from 1nf3C/merged-good-all-a2m # adding 1nf3C to template set # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 3 :NLYFQSMGLRTVEMKK 1nf3C 147 :DVDILPETHRRVRLCK T0366 19 :GPTDSLGISIAGG 1nf3C 164 :GTEKPLGFYIRDG T0366 32 :VGSPLGD 1nf3C 180 :RVTPHGL T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 190 :PGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=125 Number of alignments=31 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 3 :NLYFQSMGLRTVEMKK 1nf3C 147 :DVDILPETHRRVRLCK T0366 19 :GPTDSLGISIAGGV 1nf3C 164 :GTEKPLGFYIRDGS T0366 33 :GSPLGDV 1nf3C 181 :VTPHGLE T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 191 :GIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=129 Number of alignments=32 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 7 :QSMGLRTVEMKK 1nf3C 151 :LPETHRRVRLCK T0366 19 :GPTDSLGISIAGGVG 1nf3C 164 :GTEKPLGFYIRDGSS T0366 34 :SPLGD 1nf3C 182 :TPHGL T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 190 :PGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=133 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wf7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wf7A expands to /projects/compbio/data/pdb/1wf7.pdb.gz 1wf7A:# T0366 read from 1wf7A/merged-good-all-a2m # 1wf7A read from 1wf7A/merged-good-all-a2m # adding 1wf7A to template set # found chain 1wf7A in template set T0366 7 :QSMGLRTVEMKK 1wf7A 2 :SSGSSGSVSLVG T0366 21 :TDSLGISIAGGVGS 1wf7A 14 :PAPWGFRLQGGKDF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1wf7A 28 :NMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAAK T0366 105 :SV 1wf7A 94 :EP Number of specific fragments extracted= 5 number of extra gaps= 0 total=138 Number of alignments=34 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0366 7 :QSMGLRTVEMKK 1wf7A 2 :SSGSSGSVSLVG T0366 21 :TDSLGISIAGGVG 1wf7A 14 :PAPWGFRLQGGKD T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1wf7A 27 :FNMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAA T0366 103 :ET 1wf7A 95 :PV Number of specific fragments extracted= 5 number of extra gaps= 0 total=143 Number of alignments=35 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0366 12 :RTVEMKKGPTDSLGISIAGGVG 1wf7A 5 :SSGSVSLVGPAPWGFRLQGGKD T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1wf7A 27 :FNMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAAKSEP Number of specific fragments extracted= 3 number of extra gaps= 0 total=146 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1um7A/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/T0366/1um7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1um7A/merged-good-all-a2m.gz for input Trying 1um7A/merged-good-all-a2m Error: Couldn't open file 1um7A/merged-good-all-a2m or 1um7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f0aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f0aA expands to /projects/compbio/data/pdb/2f0a.pdb.gz 2f0aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0366 read from 2f0aA/merged-good-all-a2m # 2f0aA read from 2f0aA/merged-good-all-a2m # adding 2f0aA to template set # found chain 2f0aA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 11 :LRTVEMK 2f0aA 252 :IITVTLN T0366 23 :SLGISIAGG 2f0aA 264 :FLGISIVGQ T0366 33 :GSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 273 :SNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=150 Number of alignments=37 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 11 :LRTVEMK 2f0aA 252 :IITVTLN T0366 23 :SLGISIAG 2f0aA 264 :FLGISIVG T0366 32 :VGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 272 :QSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=154 Number of alignments=38 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 23 :SLGISIAGGVG 2f0aA 264 :FLGISIVGQSN T0366 35 :PLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 3 number of extra gaps= 1 total=157 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n7eA expands to /projects/compbio/data/pdb/1n7e.pdb.gz 1n7eA:# T0366 read from 1n7eA/merged-good-all-a2m # 1n7eA read from 1n7eA/merged-good-all-a2m # adding 1n7eA to template set # found chain 1n7eA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1n7eA)G667 T0366 9 :MGLRTVEMKKG 1n7eA 668 :AIIYTVELKRY T0366 21 :TDSLGISIAGGVGS 1n7eA 679 :GGPLGITISGTEEP T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 3 number of extra gaps= 0 total=160 Number of alignments=40 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1n7eA)G667 T0366 9 :MGLRTVEMKKG 1n7eA 668 :AIIYTVELKRY T0366 21 :TDSLGISIAGGVG 1n7eA 679 :GGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 3 number of extra gaps= 0 total=163 Number of alignments=41 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7eA)G667 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 2 number of extra gaps= 0 total=165 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9A expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M 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 # T0366 read from 1ky9A/merged-good-all-a2m # 1ky9A read from 1ky9A/merged-good-all-a2m # adding 1ky9A to template set # found chain 1ky9A in template set T0366 34 :SPL 1ky9A 282 :VDA T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9A 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEGM 1ky9A 304 :IKAGDVITSLNGKPISSF T0366 78 :TQAVNLLKNA 1ky9A 322 :AALRAQVGTM T0366 88 :SGSIEMQVVAGGDVSETSV 1ky9A 334 :GSKLTLGLLRDGKQVNVNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=43 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9A 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEGM 1ky9A 304 :IKAGDVITSLNGKPISSF T0366 78 :TQAVNLLKNA 1ky9A 322 :AALRAQVGTM T0366 88 :SGSIEMQVVAGGDVS 1ky9A 334 :GSKLTLGLLRDGKQV T0366 105 :S 1ky9A 351 :N Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 Number of alignments=44 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9A 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9A 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLKNA 1ky9A 321 :FAALRAQVGTM T0366 88 :SGSIEMQVVAGGD 1ky9A 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=179 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9B expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9B:# T0366 read from 1ky9B/merged-good-all-a2m # 1ky9B read from 1ky9B/merged-good-all-a2m # adding 1ky9B to template set # found chain 1ky9B in template set Warning: unaligning (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 35 :PL 1ky9B 273 :NS T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 88 :SGSIEMQVVAGGDVSETS 1ky9B 334 :GSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=184 Number of alignments=46 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0366)I28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 24 :L 1ky9B 265 :L T0366 27 :S 1ky9B 266 :G T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9B 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 88 :SGSIEMQVVAGGDVSETS 1ky9B 334 :GSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=190 Number of alignments=47 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 87 :ASGSIEMQVVAGGDVSETS 1ky9B 333 :VGSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 4 number of extra gaps= 0 total=194 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zokA/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/T0366/1zokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1zokA/merged-good-all-a2m.gz for input Trying 1zokA/merged-good-all-a2m Error: Couldn't open file 1zokA/merged-good-all-a2m or 1zokA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mfgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1mfgA/merged-good-all-a2m # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0366)V101 because last residue in template chain is (1mfgA)S1371 T0366 9 :MGLRTVEMKKG 1mfgA 1278 :SMEIRVRVEKD T0366 22 :DSLGISIAGGVGSPL 1mfgA 1289 :PELGFSISGGVGGRG T0366 37 :GDVPIFIAMMHPTGVAA 1mfgA 1309 :DDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1326 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=200 Number of alignments=49 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0366)V101 because last residue in template chain is (1mfgA)S1371 T0366 9 :MGLRTVEMKKG 1mfgA 1278 :SMEIRVRVEKD T0366 22 :DSLGISIAGGV 1mfgA 1289 :PELGFSISGGV T0366 33 :GSPLGDVPIFIAMMHPTGVAA 1mfgA 1305 :PFRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1326 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=206 Number of alignments=50 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 1mfgA 1278 :SMEIRVRVEKDPELGFSISGGVGGRG T0366 37 :GDVPIFIAMMHPTGVA 1mfgA 1309 :DDDGIFVTRVQPEGPA T0366 55 :TQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 5 number of extra gaps= 2 total=211 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b8qA expands to /projects/compbio/data/pdb/1b8q.pdb.gz 1b8qA:# T0366 read from 1b8qA/merged-good-all-a2m # 1b8qA read from 1b8qA/merged-good-all-a2m # adding 1b8qA to template set # found chain 1b8qA in template set T0366 4 :LYFQSMGLRTVEMKKGPTDSLGISIAGGVG 1b8qA 2 :SHMIEPNVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVSE 1b8qA 84 :ETHVVLILRGPEGFTT Number of specific fragments extracted= 3 number of extra gaps= 0 total=214 Number of alignments=52 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set Warning: unaligning (T0366)N3 because first residue in template chain is (1b8qA)G1 T0366 4 :LYFQSMGLRTVEMKKGPTDSLGISIAGGV 1b8qA 2 :SHMIEPNVISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1b8qA 31 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1b8qA 84 :ETHVVLILRGPEGFT T0366 103 :ETSV 1b8qA 100 :HLET Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 Number of alignments=53 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1b8qA 8 :NVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASETHVVLILRGPE Number of specific fragments extracted= 2 number of extra gaps= 0 total=220 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nteA expands to /projects/compbio/data/pdb/1nte.pdb.gz 1nteA:Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 287, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 289, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 291, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1nteA # T0366 read from 1nteA/merged-good-all-a2m # 1nteA read from 1nteA/merged-good-all-a2m # adding 1nteA to template set # found chain 1nteA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1nteA)G192 Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 8 :S 1nteA 193 :A T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=224 Number of alignments=55 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1nteA)G192 Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 8 :S 1nteA 193 :A T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=228 Number of alignments=56 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 1 total=231 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe5A expands to /projects/compbio/data/pdb/2fe5.pdb.gz 2fe5A:Skipped atom 9, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 13, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 15, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 17, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 19, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 47, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 53, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 55, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 57, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 59, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 296, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 298, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 300, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 302, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 317, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 431, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 433, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 435, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 437, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 439, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 441, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 443, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 593, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 597, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 599, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fe5A # T0366 read from 2fe5A/merged-good-all-a2m # 2fe5A read from 2fe5A/merged-good-all-a2m # adding 2fe5A to template set # found chain 2fe5A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fe5A)S221 T0366 9 :MGLRTVEMKKG 2fe5A 222 :MTIMEVNLLKG T0366 21 :TDSLGISIAGGVG 2fe5A 233 :PKGLGFSIAGGIG T0366 34 :SPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 248 :HIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=234 Number of alignments=58 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fe5A)S221 T0366 9 :MGLRTVEMKKG 2fe5A 222 :MTIMEVNLLKG T0366 21 :TDSLGISIAGGVG 2fe5A 233 :PKGLGFSIAGGIG T0366 34 :SPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 248 :HIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=237 Number of alignments=59 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 2fe5A 223 :TIMEVNLLKGPKGLGFSIAGGIGNQH T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 251 :GDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=239 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1r6jA/merged-good-all-a2m # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set Warning: unaligning (T0366)Q7 because first residue in template chain is (1r6jA)G192 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 0 total=242 Number of alignments=61 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set Warning: unaligning (T0366)Q7 because first residue in template chain is (1r6jA)G192 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=245 Number of alignments=62 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0366 9 :MGLRTVEMKKGPTDSLGISIAGG 1r6jA 194 :MDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=248 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavA expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavA:# T0366 read from 1qavA/merged-good-all-a2m # 1qavA read from 1qavA/merged-good-all-a2m # adding 1qavA to template set # found chain 1qavA in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVGS 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGREN T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 103 :KMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=250 Number of alignments=64 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 102 :NKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=252 Number of alignments=65 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 102 :NKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=254 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavB expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavB:# T0366 read from 1qavB/merged-good-all-a2m # 1qavB read from 1qavB/merged-good-all-a2m # adding 1qavB to template set # found chain 1qavB in template set T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVG 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qavB 1090 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=257 Number of alignments=67 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qavB 1037 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qavB 1090 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=260 Number of alignments=68 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1qavB 1014 :NVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGS 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASE T0366 91 :IEMQVVAGGD 1qavB 1093 :VVLILRGPEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=263 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m5zA expands to /projects/compbio/data/pdb/1m5z.pdb.gz 1m5zA:# T0366 read from 1m5zA/merged-good-all-a2m # 1m5zA read from 1m5zA/merged-good-all-a2m # adding 1m5zA to template set # found chain 1m5zA in template set Warning: unaligning (T0366)Y5 because first residue in template chain is (1m5zA)S16 T0366 6 :FQSMGLRTVEMKKGPT 1m5zA 17 :PTPVELHKVTLYKDSG T0366 22 :DSLGISIAGGVG 1m5zA 34 :EDFGFSVADGLL T0366 38 :DVPIFIAMMHPTGVAAQTQ 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=267 Number of alignments=70 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set Warning: unaligning (T0366)Y5 because first residue in template chain is (1m5zA)S16 T0366 6 :FQSMGLRTVEMKKGPT 1m5zA 17 :PTPVELHKVTLYKDSG T0366 22 :DSLGISIAGGV 1m5zA 34 :EDFGFSVADGL T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1m5zA 45 :LEKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=271 Number of alignments=71 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0366 11 :LRTVEMKKGPT 1m5zA 22 :LHKVTLYKDSG T0366 22 :DSLGISIAGGVG 1m5zA 34 :EDFGFSVADGLL T0366 38 :DVPIFIAMMHPTGVAAQTQ 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=275 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1be9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1be9A expands to /projects/compbio/data/pdb/1be9.pdb.gz 1be9A:# T0366 read from 1be9A/merged-good-all-a2m # 1be9A read from 1be9A/merged-good-all-a2m # adding 1be9A to template set # found chain 1be9A in template set T0366 1 :TENLYFQSMGLRTVEMKKG 1be9A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1be9A 320 :STGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=278 Number of alignments=73 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0366 1 :TENLYFQSMGLRTVEMKKG 1be9A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1be9A 320 :STGLGFNIIGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=281 Number of alignments=74 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1be9A 307 :IPREPRRIVIHRGSTGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=283 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5gA/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/T0366/1d5gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1d5gA/merged-good-all-a2m.gz for input Trying 1d5gA/merged-good-all-a2m Error: Couldn't open file 1d5gA/merged-good-all-a2m or 1d5gA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1te0A expands to /projects/compbio/data/pdb/1te0.pdb.gz 1te0A:# T0366 read from 1te0A/merged-good-all-a2m # 1te0A read from 1te0A/merged-good-all-a2m # adding 1te0A to template set # found chain 1te0A in template set Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)S34 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)P35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)L36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 Warning: unaligning (T0366)S102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)T343 Warning: unaligning (T0366)E103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)T343 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGDV 1te0A 328 :GSVIPVVVMRDDKQ Number of specific fragments extracted= 7 number of extra gaps= 7 total=290 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0366)T21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0366)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)V32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)G33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 Warning: unaligning (T0366)S102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)T343 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGDV 1te0A 328 :GSVIPVVVMRDDKQ Number of specific fragments extracted= 7 number of extra gaps= 7 total=297 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)V32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)G33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGD 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=304 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h3lA expands to /projects/compbio/data/pdb/2h3l.pdb.gz 2h3lA:# T0366 read from 2h3lA/merged-good-all-a2m # 2h3lA read from 2h3lA/merged-good-all-a2m # adding 2h3lA to template set # found chain 2h3lA in template set Warning: unaligning (T0366)D100 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0366 3 :NLYFQSMGLRTVEMKKG 2h3lA 1313 :MGHELAKQEIRVRVEKD T0366 22 :DSLGISIAGGVG 2h3lA 1330 :PELGFSISGGVG T0366 34 :SPLGDVPIFIAMMHPTGVAA 2h3lA 1347 :FRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2h3lA 1367 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=308 Number of alignments=76 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set Warning: unaligning (T0366)D100 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0366 3 :NLYFQSMGLRTVEMKKG 2h3lA 1313 :MGHELAKQEIRVRVEKD T0366 22 :DSLGISIAGGV 2h3lA 1330 :PELGFSISGGV T0366 33 :GSPLGDVPIFIAMMHPTGVAA 2h3lA 1346 :PFRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2h3lA 1367 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=312 Number of alignments=77 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 2h3lA 1319 :KQEIRVRVEKDPELGFSISGGVG T0366 34 :SPLGDVPIFIAMMHPTGVA 2h3lA 1347 :FRPDDDGIFVTRVQPEGPA T0366 55 :TQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 2h3lA 1366 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=315 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fcfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fcfA expands to /projects/compbio/data/pdb/2fcf.pdb.gz 2fcfA:Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fcfA # T0366 read from 2fcfA/merged-good-all-a2m # 2fcfA read from 2fcfA/merged-good-all-a2m # adding 2fcfA to template set # found chain 2fcfA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (2fcfA)Q1145 Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=318 Number of alignments=79 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (2fcfA)Q1145 Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=321 Number of alignments=80 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=324 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rgrA/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/T0366/1rgrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1rgrA/merged-good-all-a2m.gz for input Trying 1rgrA/merged-good-all-a2m Error: Couldn't open file 1rgrA/merged-good-all-a2m or 1rgrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lcyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lcyA expands to /projects/compbio/data/pdb/1lcy.pdb.gz 1lcyA:# T0366 read from 1lcyA/merged-good-all-a2m # 1lcyA read from 1lcyA/merged-good-all-a2m # adding 1lcyA to template set # found chain 1lcyA in template set T0366 32 :VGS 1lcyA 252 :PDV T0366 38 :DVPIFIAMMHPTGVAAQTQ 1lcyA 255 :QHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNAS 1lcyA 291 :AEDVYEAVRTQS T0366 90 :SIEMQVVAGGDVSE 1lcyA 303 :QLAVQIRRGRETLT Number of specific fragments extracted= 5 number of extra gaps= 0 total=329 Number of alignments=82 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0366 22 :DSLGISIAG 1lcyA 227 :RYIGVMMLT T0366 31 :GVGSPLG 1lcyA 245 :QLREPSF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1lcyA 255 :QHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNA 1lcyA 291 :AEDVYEAVRTQ T0366 89 :GSIEMQVVAGGDVS 1lcyA 302 :SQLAVQIRRGRETL Number of specific fragments extracted= 6 number of extra gaps= 0 total=335 Number of alignments=83 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0366 32 :VGSPLGDVPIFIAMMHPTGVAAQTQ 1lcyA 249 :PSFPDVQHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNA 1lcyA 291 :AEDVYEAVRTQ T0366 89 :GSIEMQVVAGGD 1lcyA 302 :SQLAVQIRRGRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=339 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f5yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f5yA expands to /projects/compbio/data/pdb/2f5y.pdb.gz 2f5yA:Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2f5yA # T0366 read from 2f5yA/merged-good-all-a2m # 2f5yA read from 2f5yA/merged-good-all-a2m # adding 2f5yA to template set # found chain 2f5yA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)G10 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 11 :LRTVEMKKG 2f5yA 16 :YRQITIPRG T0366 21 :TDSLGISIAG 2f5yA 25 :KDGFGFTICC T0366 38 :DVPIFIAMMHPTGVAAQTQ 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 5 number of extra gaps= 1 total=344 Number of alignments=85 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)G10 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 11 :LRTVEMKKG 2f5yA 16 :YRQITIPRG T0366 21 :TDSLGISIA 2f5yA 25 :KDGFGFTIC T0366 37 :GDVPIFIAMMHPTGVAAQTQ 2f5yA 34 :CDSPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 5 number of extra gaps= 1 total=349 Number of alignments=86 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)L11 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 12 :RTVEMKKGPTDSLGISIAGG 2f5yA 16 :YRQITIPRGKDGFGFTICCD T0366 39 :VPIFIAMMHPTGVAAQTQ 2f5yA 36 :SPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=353 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwaA expands to /projects/compbio/data/pdb/1kwa.pdb.gz 1kwaA:# T0366 read from 1kwaA/merged-good-all-a2m # 1kwaA read from 1kwaA/merged-good-all-a2m # adding 1kwaA to template set # found chain 1kwaA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaA)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaA 488 :SRLVQFQKNTDEPMGITLK T0366 32 :VGSPLG 1kwaA 507 :MNELNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=356 Number of alignments=88 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaA)F574 T0366 11 :LRTVEMKKGPTDSLGISIAGGV 1kwaA 488 :SRLVQFQKNTDEPMGITLKMNE T0366 36 :LGD 1kwaA 510 :LNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=359 Number of alignments=89 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaA)R487 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSP 1kwaA 488 :SRLVQFQKNTDEPMGITLKMNELNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 0 total=361 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwaB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwaB expands to /projects/compbio/data/pdb/1kwa.pdb.gz 1kwaB:# T0366 read from 1kwaB/merged-good-all-a2m # 1kwaB read from 1kwaB/merged-good-all-a2m # adding 1kwaB to template set # found chain 1kwaB in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaB)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 1 total=363 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaB)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 1 total=365 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)G31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPS Number of specific fragments extracted= 2 number of extra gaps= 1 total=367 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pdr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pdr expands to /projects/compbio/data/pdb/1pdr.pdb.gz 1pdr:Warning: there is no chain 1pdr will retry with 1pdrA # T0366 read from 1pdr/merged-good-all-a2m # 1pdr read from 1pdr/merged-good-all-a2m # adding 1pdr to template set # found chain 1pdr in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1pdr)I460 T0366 8 :SMGLRTVEMKKG 1pdr 461 :TREPRKVVLHRG T0366 21 :TDSLGISIAGGVG 1pdr 473 :STGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=370 Number of alignments=91 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1pdr)I460 T0366 8 :SMGLRTVEMKKG 1pdr 461 :TREPRKVVLHRG T0366 21 :TDSLGISIAGGV 1pdr 473 :STGLGFNIVGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 485 :DGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=373 Number of alignments=92 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1pdr)I460 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVG 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=375 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iu0A/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/T0366/1iu0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1iu0A/merged-good-all-a2m.gz for input Trying 1iu0A/merged-good-all-a2m Error: Couldn't open file 1iu0A/merged-good-all-a2m or 1iu0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n99A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n99A expands to /projects/compbio/data/pdb/1n99.pdb.gz 1n99A: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 # T0366 read from 1n99A/merged-good-all-a2m # 1n99A read from 1n99A/merged-good-all-a2m # adding 1n99A to template set # found chain 1n99A in template set Warning: unaligning (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAGG 1n99A 113 :REVILCKDQDGKIGLRLKSI T0366 38 :DVPIFIAMMHPTGVAAQTQ 1n99A 133 :DNGIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGGDVSE 1n99A 191 :RDRPFERT Number of specific fragments extracted= 5 number of extra gaps= 1 total=380 Number of alignments=94 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAG 1n99A 113 :REVILCKDQDGKIGLRLKS T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1n99A 132 :IDNGIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGGDVS 1n99A 191 :RDRPFER Number of specific fragments extracted= 5 number of extra gaps= 1 total=385 Number of alignments=95 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAGGVG 1n99A 113 :REVILCKDQDGKIGLRLKSIDN T0366 40 :PIFIAMMHPTGVAAQTQ 1n99A 135 :GIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGG 1n99A 191 :RDRP Number of specific fragments extracted= 5 number of extra gaps= 1 total=390 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g9oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1g9oA/merged-good-all-a2m # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0366)T104 because last residue in template chain is (1g9oA)L99 T0366 9 :MGLRTVEMKKG 1g9oA 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGVG 1g9oA 21 :PNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=394 Number of alignments=97 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0366)T104 because last residue in template chain is (1g9oA)L99 T0366 9 :MGLRTVEMKKG 1g9oA 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGV 1g9oA 21 :PNGYGFHLHGEK T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1g9oA 33 :GKLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=398 Number of alignments=98 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=401 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l6oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l6oA expands to /projects/compbio/data/pdb/1l6o.pdb.gz 1l6oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0366 read from 1l6oA/merged-good-all-a2m # 1l6oA read from 1l6oA/merged-good-all-a2m # adding 1l6oA to template set # found chain 1l6oA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)S34 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=414 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)V32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=427 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)V32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=440 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1q3oA/merged-good-all-a2m # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 1q3oA 589 :EKTVLLQKKDSEGFGFVLRGAKAQTP T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1q3oA 624 :FPALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=443 Number of alignments=100 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVGSPLG 1q3oA 588 :KEKTVLLQKKDSEGFGFVLRGAKAQTPI T0366 38 :DVPIFIAMMHPTGVAAQTQ 1q3oA 625 :PALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=446 Number of alignments=101 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 12 :RTVEMKKGPTDSLGISIAGGVGSPL 1q3oA 590 :KTVLLQKKDSEGFGFVLRGAKAQTP T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1q3oA 624 :FPALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=449 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1n7fA/merged-good-all-a2m # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 10 :GLRTVEMKKG 1n7fA 669 :IIYTVELKRY T0366 21 :TDSLGISIAGGVGS 1n7fA 679 :GGPLGITISGTEEP T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=452 Number of alignments=103 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 10 :GLRTVEMKKG 1n7fA 669 :IIYTVELKRY T0366 21 :TDSLGISIAGGVG 1n7fA 679 :GGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=455 Number of alignments=104 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1n7fA 669 :IIYTVELKRYGGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=457 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1ihjA/merged-good-all-a2m # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0366)L36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVGSP 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGEVKD T0366 39 :V 1ihjA 43 :T T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 3 number of extra gaps= 1 total=460 Number of alignments=106 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0366)S34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)P35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)L36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGE T0366 33 :G 1ihjA 39 :D T0366 37 :GD 1ihjA 43 :TK T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 1 total=464 Number of alignments=107 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)S34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)P35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGE T0366 36 :LGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 43 :TKTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 2 number of extra gaps= 1 total=466 Number of alignments=108 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0366/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0366)V65.CB, (T0366)V96.CB) [> 3.4422 = 5.7370 < 7.4581] w=1.0000 to align # Constraint # added constraint: constraint((T0366)M46.CB, (T0366)V60.CB) [> 3.8664 = 6.4440 < 8.3771] w=1.0000 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)I64.CB) [> 4.0472 = 6.7453 < 8.7690] w=1.0000 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)D62.CB) [> 2.8532 = 4.7553 < 6.1819] w=1.0000 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)G61.CA) [> 3.2854 = 5.4757 < 7.1184] w=1.0000 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)V60.CB) [> 3.5483 = 5.9139 < 7.6880] w=1.0000 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)G61.CA) [> 3.1235 = 5.2058 < 6.7675] w=1.0000 to align # Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V96.CB) [> 2.8516 = 4.7527 < 6.1785] w=0.9904 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)I91.CB) [> 3.5563 = 5.9272 < 7.7054] w=0.9904 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)E92.CB) [> 3.2639 = 5.4398 < 7.0718] w=0.9904 to align # Constraint # added constraint: constraint((T0366)M46.CB, (T0366)L58.CB) [> 3.5459 = 5.9099 < 7.6828] w=0.9714 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)L58.CB) [> 3.6100 = 6.0166 < 7.8216] w=0.9714 to align # Constraint # added constraint: constraint((T0366)V65.CB, (T0366)V95.CB) [> 3.9793 = 6.6322 < 8.6219] w=0.9713 to align # Constraint # added constraint: constraint((T0366)I64.CB, (T0366)V95.CB) [> 3.4944 = 5.8240 < 7.5712] w=0.9713 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)R63.CB) [> 3.2024 = 5.3373 < 6.9385] w=0.9713 to align # Constraint # added constraint: constraint((T0366)A44.CB, (T0366)V60.CB) [> 3.9987 = 6.6645 < 8.6638] w=0.9713 to align # Constraint # added constraint: constraint((T0366)M45.CB, (T0366)V60.CB) [> 3.8954 = 6.4924 < 8.4401] w=0.9713 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)R59.CB) [> 4.1684 = 6.9474 < 9.0316] w=0.9684 to align # Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V95.CB) [> 3.8363 = 6.3938 < 8.3120] w=0.9617 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)I91.CB) [> 3.5938 = 5.9897 < 7.7866] w=0.9617 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)M46.CB) [> 3.9249 = 6.5414 < 8.5038] w=0.9564 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)H47.CB) [> 2.4566 = 4.0943 < 5.3225] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)I43.CB) [> 3.2216 = 5.3694 < 6.9802] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)M46.CB) [> 3.1060 = 5.1767 < 6.7297] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)H47.CB) [> 4.0485 = 6.7475 < 8.7718] w=0.9564 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)I43.CB) [> 4.2578 = 7.0964 < 9.2253] w=0.9564 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)A44.CB) [> 2.8511 = 4.7518 < 6.1774] w=0.9564 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)M45.CB) [> 2.6069 = 4.3449 < 5.6483] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)F42.CB) [> 4.0001 = 6.6668 < 8.6668] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I43.CB) [> 3.6469 = 6.0782 < 7.9017] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)A44.CB) [> 3.7977 = 6.3296 < 8.2285] w=0.9564 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I64.CB) [> 4.1365 = 6.8941 < 8.9623] w=0.9564 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)F42.CB) [> 3.3199 = 5.5332 < 7.1931] w=0.9564 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)A44.CB) [> 2.7013 = 4.5021 < 5.8527] w=0.9564 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)D62.CB) [> 4.0717 = 6.7862 < 8.8221] w=0.9497 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)I64.CB) [> 4.3234 = 7.2056 < 9.3673] w=0.9470 to align # Constraint # added constraint: constraint((T0366)T70.CB, (T0366)L83.CB) [> 3.6198 = 6.0330 < 7.8428] w=0.9427 to align # Constraint # added constraint: constraint((T0366)D62.CB, (T0366)V95.CB) [> 2.5854 = 4.3091 < 5.6018] w=0.9426 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)L83.CB) [> 3.4477 = 5.7461 < 7.4700] w=0.9426 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)T72.CB) [> 3.2535 = 5.4225 < 7.0493] w=0.9426 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)I64.CB) [> 2.9027 = 4.8378 < 6.2892] w=0.9426 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)M93.CB) [> 3.0937 = 5.1561 < 6.7030] w=0.9426 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)V51.CB) [> 3.2908 = 5.4847 < 7.1301] w=0.9351 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A52.CB) [> 3.3374 = 5.5623 < 7.2309] w=0.9349 to align # Constraint # added constraint: constraint((T0366)I64.CB, (T0366)M93.CB) [> 3.5422 = 5.9036 < 7.6747] w=0.9330 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)M93.CB) [> 4.1737 = 6.9562 < 9.0431] w=0.9330 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)E92.CB) [> 3.9965 = 6.6609 < 8.6591] w=0.9330 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)L58.CB) [> 3.7777 = 6.2962 < 8.1851] w=0.9279 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)G50.CA) [> 3.0521 = 5.0868 < 6.6129] w=0.9279 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)A52.CB) [> 2.7053 = 4.5088 < 5.8615] w=0.9277 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)A52.CB) [> 2.8606 = 4.7676 < 6.1979] w=0.9277 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)M45.CB) [> 3.9893 = 6.6488 < 8.6434] w=0.9277 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)L84.CB) [> 3.8911 = 6.4851 < 8.4306] w=0.9140 to align # Constraint # added constraint: constraint((T0366)D62.CB, (T0366)A97.CB) [> 3.4215 = 5.7026 < 7.4134] w=0.9140 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)Q94.CB) [> 2.4052 = 4.0086 < 5.2112] w=0.9139 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)R63.CB) [> 4.0885 = 6.8142 < 8.8584] w=0.9139 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)A80.CB) [> 3.0167 = 5.0278 < 6.5361] w=0.9139 to align # Constraint # added constraint: constraint((T0366)A44.CB, (T0366)G61.CA) [> 4.3816 = 7.3027 < 9.4935] w=0.9139 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)H77.CB) [> 3.2974 = 5.4957 < 7.1444] w=0.9087 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)F42.CB) [> 3.6874 = 6.1458 < 7.9895] w=0.9087 to align # Constraint # added constraint: constraint((T0366)V65.CB, (T0366)Q94.CB) [> 2.8287 = 4.7146 < 6.1289] w=0.9043 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)V51.CB) [> 3.4986 = 5.8310 < 7.5804] w=0.8992 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)I41.CB) [> 4.4217 = 7.3695 < 9.5803] w=0.8990 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I41.CB) [> 3.1655 = 5.2759 < 6.8586] w=0.8990 to align # Constraint # added constraint: constraint((T0366)I64.CB, (T0366)A80.CB) [> 4.1527 = 6.9212 < 8.9976] w=0.8852 to align # Constraint # added constraint: constraint((T0366)I64.CB, (T0366)Q94.CB) [> 4.3989 = 7.3315 < 9.5310] w=0.8852 to align # Constraint # added constraint: constraint((T0366)M46.CB, (T0366)R59.CB) [> 4.1137 = 6.8562 < 8.9131] w=0.8852 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)H77.CB) [> 3.9974 = 6.6623 < 8.6610] w=0.8833 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)I91.CB) [> 3.8268 = 6.3781 < 8.2915] w=0.8800 to align # Constraint # added constraint: constraint((T0366)G69.CA, (T0366)E92.CB) [> 4.2090 = 7.0150 < 9.1195] w=0.8758 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)A80.CB) [> 3.6975 = 6.1624 < 8.0112] w=0.8703 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)A87.CB) [> 3.4470 = 5.7450 < 7.4684] w=0.8609 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)I41.CB) [> 3.3408 = 5.5679 < 7.2383] w=0.8514 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)L84.CB) [> 3.9772 = 6.6286 < 8.6172] w=0.8488 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)I91.CB) [> 3.1371 = 5.2285 < 6.7970] w=0.8418 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)E92.CB) [> 4.2632 = 7.1053 < 9.2369] w=0.8322 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)A87.CB) [> 4.1132 = 6.8553 < 8.9119] w=0.8322 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)V81.CB) [> 4.1244 = 6.8740 < 8.9361] w=0.8321 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)Q94.CB) [> 4.3766 = 7.2943 < 9.4826] w=0.8278 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)R63.CB) [> 4.6430 = 7.7384 < 10.0599] w=0.8278 to align # Constraint # added constraint: constraint((T0366)K17.CB, (T0366)S90.CB) [> 3.4025 = 5.6709 < 7.3721] w=0.8227 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)H77.CB) [> 4.0521 = 6.7535 < 8.7796] w=0.8130 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)S90.CB) [> 4.1263 = 6.8771 < 8.9403] w=0.8035 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)P40.CB) [> 4.0032 = 6.6721 < 8.6737] w=0.8035 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)V95.CB) [> 3.8122 = 6.3536 < 8.2597] w=0.7940 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V95.CB) [> 3.4351 = 5.7252 < 7.4427] w=0.7844 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)M93.CB) [> 3.1524 = 5.2540 < 6.8302] w=0.7844 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)M93.CB) [> 4.0868 = 6.8113 < 8.8547] w=0.7844 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)H77.CB) [> 4.2889 = 7.1482 < 9.2926] w=0.7843 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)A53.CB) [> 4.2513 = 7.0856 < 9.2113] w=0.7843 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V96.CB) [> 3.3573 = 5.5954 < 7.2741] w=0.7748 to align # Constraint # added constraint: constraint((T0366)K18.CB, (T0366)V51.CB) [> 3.6158 = 6.0263 < 7.8342] w=0.7748 to align # Constraint # added constraint: constraint((T0366)K18.CB, (T0366)G89.CA) [> 3.1680 = 5.2801 < 6.8641] w=0.7748 to align # Constraint # added constraint: constraint((T0366)I43.CB, (T0366)V95.CB) [> 4.4851 = 7.4752 < 9.7177] w=0.7747 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)R63.CB) [> 3.0007 = 5.0012 < 6.5015] w=0.7704 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)Q94.CB) [> 3.3938 = 5.6564 < 7.3533] w=0.7653 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)E92.CB) [> 4.3326 = 7.2209 < 9.3872] w=0.7653 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)Q94.CB) [> 4.2751 = 7.1252 < 9.2627] w=0.7366 to align # Constraint # added constraint: constraint((T0366)K18.CB, (T0366)I91.CB) [> 3.9704 = 6.6172 < 8.6024] w=0.7366 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)A52.CB) [> 3.7683 = 6.2805 < 8.1646] w=0.7270 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)V51.CB) [> 3.0837 = 5.1396 < 6.6814] w=0.7270 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)L58.CB) [> 3.6904 = 6.1507 < 7.9959] w=0.7270 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)I91.CB) [> 4.3295 = 7.2159 < 9.3807] w=0.7174 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)L83.CB) [> 4.0837 = 6.8062 < 8.8480] w=0.7174 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)E92.CB) [> 4.6424 = 7.7373 < 10.0585] w=0.7106 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)I41.CB) [> 3.7722 = 6.2870 < 8.1731] w=0.7079 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)P40.CB) [> 3.8635 = 6.4392 < 8.3709] w=0.7079 to align # Constraint # added constraint: constraint((T0366)S23.CB, (T0366)V51.CB) [> 4.3590 = 7.2651 < 9.4446] w=0.6983 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)E92.CB) [> 3.8543 = 6.4239 < 8.3510] w=0.6983 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)L84.CB) [> 4.4545 = 7.4241 < 9.6513] w=0.6887 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)S90.CB) [> 3.6558 = 6.0931 < 7.9210] w=0.6887 to align # Constraint # added constraint: constraint((T0366)T72.CB, (T0366)L83.CB) [> 4.0704 = 6.7840 < 8.8192] w=0.6843 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)H77.CB) [> 3.1583 = 5.2639 < 6.8431] w=0.6792 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)M93.CB) [> 4.2734 = 7.1223 < 9.2590] w=0.6792 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)M93.CB) [> 4.3124 = 7.1873 < 9.3435] w=0.6696 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V95.CB) [> 4.2296 = 7.0493 < 9.1641] w=0.6600 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)V65.CB) [> 4.1601 = 6.9335 < 9.0135] w=0.6505 to align # Constraint # added constraint: constraint((T0366)K17.CB, (T0366)G89.CA) [> 3.6955 = 6.1592 < 8.0070] w=0.6505 to align # Constraint # added constraint: constraint((T0366)K18.CB, (T0366)S90.CB) [> 4.1618 = 6.9363 < 9.0172] w=0.6409 to align # Constraint # added constraint: constraint((T0366)K17.CB, (T0366)I91.CB) [> 4.2277 = 7.0462 < 9.1601] w=0.6122 to align # Constraint # added constraint: constraint((T0366)G69.CA, (T0366)Q94.CB) [> 4.3643 = 7.2738 < 9.4560] w=0.6079 to align # Constraint # added constraint: constraint((T0366)G19.CA, (T0366)V51.CB) [> 3.5582 = 5.9304 < 7.7095] w=0.6026 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)M46.CB) [> 4.6155 = 7.6925 < 10.0003] w=0.5907 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)T55.CB) [> 3.4120 = 5.6867 < 7.3927] w=0.5835 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V96.CB) [> 4.1935 = 6.9892 < 9.0859] w=0.5739 to align # Constraint # added constraint: constraint((T0366)I67.CB, (T0366)A80.CB) [> 4.1745 = 6.9575 < 9.0447] w=0.5695 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)Q94.CB) [> 4.2798 = 7.1329 < 9.2728] w=0.5644 to align # Constraint # added constraint: constraint((T0366)S23.CB, (T0366)H47.CB) [> 4.4343 = 7.3904 < 9.6076] w=0.5644 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)V39.CB) [> 3.5975 = 5.9958 < 7.7946] w=0.5548 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V95.CB) [> 4.3213 = 7.2021 < 9.3628] w=0.5548 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)A97.CB) [> 3.9167 = 6.5278 < 8.4861] w=0.5548 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)G50.CA) [> 4.5147 = 7.5245 < 9.7818] w=0.5261 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)A44.CB) [> 4.6104 = 7.6840 < 9.9892] w=0.4974 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)T76.CB) [> 3.4759 = 5.7932 < 7.5311] w=0.4879 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)K57.CB) [> 2.9730 = 4.9550 < 6.4415] w=0.4879 to align # Constraint # added constraint: constraint((T0366)G10.CA, (T0366)A97.CB) [> 3.4440 = 5.7399 < 7.4619] w=0.4879 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)T55.CB) [> 4.0093 = 6.6821 < 8.6868] w=0.4879 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)A80.CB) [> 3.9880 = 6.6467 < 8.6407] w=0.4496 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)T72.CB) [> 4.1387 = 6.8979 < 8.9672] w=0.4261 to align # Constraint # added constraint: constraint((T0366)D22.CB, (T0366)V51.CB) [> 3.9655 = 6.6091 < 8.5919] w=0.4018 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)L58.CB) [> 4.4856 = 7.4759 < 9.7187] w=0.4018 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)I64.CB) [> 4.1956 = 6.9927 < 9.0905] w=0.3974 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)M93.CB) [> 4.4432 = 7.4053 < 9.6268] w=0.3946 to align # Constraint # added constraint: constraint((T0366)V32.CB, (T0366)H77.CB) [> 4.0420 = 6.7367 < 8.7578] w=0.3922 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)A97.CB) [> 4.2641 = 7.1069 < 9.2389] w=0.3922 to align # Constraint # added constraint: constraint((T0366)M9.CB, (T0366)A97.CB) [> 3.6382 = 6.0637 < 7.8828] w=0.3826 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)H47.CB) [> 4.4285 = 7.3808 < 9.5950] w=0.3801 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)I43.CB) [> 4.5852 = 7.6419 < 9.9345] w=0.3157 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)V65.CB) [> 4.1308 = 6.8847 < 8.9502] w=0.3113 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)K57.CB) [> 4.1083 = 6.8472 < 8.9014] w=0.3061 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)A80.CB) [> 4.6215 = 7.7024 < 10.0132] w=0.3061 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)F42.CB) [> 3.3106 = 5.5176 < 7.1729] w=0.3061 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)S88.CB) [> 4.3509 = 7.2515 < 9.4269] w=0.2870 to align # Constraint # added constraint: constraint((T0366)G33.CA, (T0366)H77.CB) [> 4.2754 = 7.1257 < 9.2634] w=0.2487 to align # Constraint # added constraint: constraint((T0366)I64.CB, (T0366)L84.CB) [> 4.6750 = 7.7916 < 10.1291] w=0.2296 to align # Constraint # added constraint: constraint((T0366)D38.CB, (T0366)E73.CB) [> 4.2245 = 7.0409 < 9.1532] w=0.2296 to align # Constraint # added constraint: constraint((T0366)P20.CB, (T0366)G89.CA) [> 3.9628 = 6.6047 < 8.5861] w=0.2296 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)A52.CB) [> 4.5827 = 7.6378 < 9.9291] w=0.2200 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A87.CB) [> 4.5528 = 7.5879 < 9.8643] w=0.2009 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)K57.CB) [> 3.7538 = 6.2564 < 8.1333] w=0.1913 to align # Constraint # added constraint: constraint((T0366)G19.CA, (T0366)S90.CB) [> 4.1695 = 6.9492 < 9.0340] w=0.1913 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)D62.CB) [> 4.6037 = 7.6728 < 9.9746] w=0.1913 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)G25.CA) [> 4.6122 = 7.6870 < 9.9931] w=0.1913 to align # Constraint # added constraint: constraint((T0366)M9.CB, (T0366)G99.CA) [> 4.1789 = 6.9648 < 9.0542] w=0.1817 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)K57.CB) [> 3.6002 = 6.0003 < 7.8004] w=0.1722 to align # Constraint # added constraint: constraint((T0366)S8.CB, (T0366)A97.CB) [> 3.9239 = 6.5398 < 8.5017] w=0.1722 to align # Constraint # added constraint: constraint((T0366)T21.CB, (T0366)G89.CA) [> 4.0935 = 6.8224 < 8.8692] w=0.1722 to align # Constraint # added constraint: constraint((T0366)C68.CB, (T0366)L84.CB) [> 3.9851 = 6.6418 < 8.6344] w=0.1722 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)M75.CB) [> 4.1586 = 6.9310 < 9.0103] w=0.1722 to align # Constraint # added constraint: constraint((T0366)V65.CB, (T0366)M93.CB) [> 4.7283 = 7.8804 < 10.2445] w=0.1650 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)V65.CB) [> 4.3642 = 7.2736 < 9.4557] w=0.1464 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)T66.CB) [> 4.5833 = 7.6388 < 9.9305] w=0.1435 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)V95.CB) [> 3.9297 = 6.5495 < 8.5143] w=0.1435 to align # Constraint # added constraint: constraint((T0366)S23.CB, (T0366)K85.CB) [> 4.1235 = 6.8725 < 8.9342] w=0.1435 to align # Constraint # added constraint: constraint((T0366)V39.CB, (T0366)T72.CB) [> 4.0709 = 6.7849 < 8.8203] w=0.1435 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)V96.CB) [> 4.4896 = 7.4826 < 9.7274] w=0.1391 to align # Constraint # added constraint: constraint((T0366)M16.CB, (T0366)I26.CB) [> 4.4733 = 7.4556 < 9.6922] w=0.1339 to align # Constraint # added constraint: constraint((T0366)K17.CB, (T0366)Q54.CB) [> 4.5766 = 7.6277 < 9.9160] w=0.1244 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)V39.CB) [> 4.5790 = 7.6317 < 9.9212] w=0.1148 to align # Constraint # added constraint: constraint((T0366)G37.CA, (T0366)T76.CB) [> 4.0945 = 6.8242 < 8.8714] w=0.1148 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)G98.CA) [> 4.5504 = 7.5839 < 9.8591] w=0.1148 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)A44.CB) [> 4.7274 = 7.8790 < 10.2427] w=0.1148 to align # Constraint # added constraint: constraint((T0366)G31.CA, (T0366)R63.CB) [> 4.0158 = 6.6929 < 8.7008] w=0.1148 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V96.CB) [> 4.2115 = 7.0191 < 9.1248] w=0.1148 to align # Constraint # added constraint: constraint((T0366)V39.CB, (T0366)R63.CB) [> 3.1193 = 5.1989 < 6.7586] w=0.1148 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)M45.CB) [> 4.7064 = 7.8440 < 10.1972] w=0.1148 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)V81.CB) [> 4.4082 = 7.3470 < 9.5510] w=0.1147 to align # Constraint # added constraint: constraint((T0366)I41.CB, (T0366)Q79.CB) [> 4.3560 = 7.2600 < 9.4379] w=0.1104 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)V65.CB) [> 3.9341 = 6.5568 < 8.5239] w=0.1052 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)A97.CB) [> 4.2192 = 7.0321 < 9.1417] w=0.1052 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)Q94.CB) [> 4.2689 = 7.1148 < 9.2492] w=0.1052 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)R59.CB) [> 4.5299 = 7.5498 < 9.8147] w=0.1052 to align # Constraint # added constraint: constraint((T0366)S34.CB, (T0366)H77.CB) [> 3.1091 = 5.1819 < 6.7365] w=0.0957 to align # Constraint # added constraint: constraint((T0366)V39.CB, (T0366)H77.CB) [> 4.2378 = 7.0630 < 9.1819] w=0.0861 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)L58.CB) [> 4.7511 = 7.9185 < 10.2940] w=0.0861 to align # Constraint # added constraint: constraint((T0366)V39.CB, (T0366)I64.CB) [> 3.8764 = 6.4607 < 8.3989] w=0.0861 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)I64.CB) [> 4.6436 = 7.7393 < 10.0611] w=0.0861 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)T49.CB) [> 4.1056 = 6.8426 < 8.8954] w=0.0861 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)L84.CB) [> 4.2800 = 7.1333 < 9.2733] w=0.0861 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)A80.CB) [> 3.3182 = 5.5303 < 7.1894] w=0.0860 to align # Constraint # added constraint: constraint((T0366)P40.CB, (T0366)H77.CB) [> 3.2652 = 5.4419 < 7.0745] w=0.0860 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)G98.CA) [> 3.4288 = 5.7146 < 7.4290] w=0.0765 to align # Constraint # added constraint: constraint((T0366)R63.CB, (T0366)V101.CB) [> 4.0117 = 6.6862 < 8.6920] w=0.0670 to align # Constraint # added constraint: constraint((T0366)V32.CB, (T0366)T78.CB) [> 3.8641 = 6.4402 < 8.3723] w=0.0574 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)M45.CB) [> 4.5827 = 7.6378 < 9.9291] w=0.0574 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)D62.CB) [> 4.5234 = 7.5390 < 9.8007] w=0.0574 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)I91.CB) [> 4.7338 = 7.8897 < 10.2566] w=0.0574 to align # Constraint # added constraint: constraint((T0366)G69.CA, (T0366)M93.CB) [> 4.5219 = 7.5364 < 9.7973] w=0.0574 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)V60.CB) [> 4.2982 = 7.1637 < 9.3128] w=0.0574 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)H47.CB) [> 4.6749 = 7.7914 < 10.1289] w=0.0574 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)I67.CB) [> 4.7666 = 7.9443 < 10.3275] w=0.0574 to align # Constraint # added constraint: constraint((T0366)I28.CB, (T0366)T72.CB) [> 3.9837 = 6.6396 < 8.6314] w=0.0574 to align # Constraint # added constraint: constraint((T0366)T70.CB, (T0366)A80.CB) [> 2.9156 = 4.8593 < 6.3171] w=0.0574 to align # Constraint # added constraint: constraint((T0366)S71.CB, (T0366)A80.CB) [> 4.6479 = 7.7464 < 10.0703] w=0.0574 to align # Constraint # added constraint: constraint((T0366)I26.CB, (T0366)V51.CB) [> 4.5163 = 7.5271 < 9.7852] w=0.0574 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)V81.CB) [> 4.0298 = 6.7164 < 8.7313] w=0.0574 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)H77.CB) [> 4.3274 = 7.2123 < 9.3760] w=0.0511 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)D62.CB) [> 4.6393 = 7.7322 < 10.0518] w=0.0383 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)T66.CB) [> 4.7474 = 7.9122 < 10.2859] w=0.0383 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)E73.CB) [> 4.4694 = 7.4489 < 9.6836] w=0.0383 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)A80.CB) [> 4.5880 = 7.6467 < 9.9408] w=0.0357 to align # Constraint # added constraint: constraint((T0366)P35.CB, (T0366)H77.CB) [> 4.5556 = 7.5927 < 9.8705] w=0.0287 to align # Constraint # added constraint: constraint((T0366)T13.CB, (T0366)V65.CB) [> 4.5076 = 7.5127 < 9.7665] w=0.0287 to align # Constraint # added constraint: constraint((T0366)S8.CB, (T0366)D100.CB) [> 4.5121 = 7.5201 < 9.7761] w=0.0287 to align # Constraint # added constraint: constraint((T0366)L11.CB, (T0366)T66.CB) [> 4.1562 = 6.9271 < 9.0052] w=0.0287 to align # Constraint # added constraint: constraint((T0366)V32.CB, (T0366)F42.CB) [> 4.4781 = 7.4634 < 9.7024] w=0.0287 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)Q54.CB) [> 4.6537 = 7.7561 < 10.0829] w=0.0287 to align # Constraint # added constraint: constraint((T0366)G69.CA, (T0366)I91.CB) [> 4.3116 = 7.1859 < 9.3417] w=0.0287 to align # Constraint # added constraint: constraint((T0366)T70.CB, (T0366)V81.CB) [> 4.5367 = 7.5611 < 9.8294] w=0.0287 to align # Constraint # added constraint: constraint((T0366)V14.CB, (T0366)A97.CB) [> 3.4841 = 5.8069 < 7.5490] w=0.0287 to align # Constraint # added constraint: constraint((T0366)S23.CB, (T0366)P48.CB) [> 3.3988 = 5.6646 < 7.3640] w=0.0287 to align # Constraint # added constraint: constraint((T0366)L24.CB, (T0366)I67.CB) [> 4.5676 = 7.6126 < 9.8964] w=0.0287 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)P48.CB) [> 2.4418 = 4.0697 < 5.2906] w=0.0287 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)T72.CB) [> 3.6341 = 6.0568 < 7.8738] w=0.0287 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V96.CB) [> 3.7612 = 6.2686 < 8.1492] w=0.0287 to align # Constraint # added constraint: constraint((T0366)G30.CA, (T0366)M75.CB) [> 4.1352 = 6.8920 < 8.9596] w=0.0287 to align # Constraint # added constraint: constraint((T0366)A29.CB, (T0366)A80.CB) [> 4.6582 = 7.7637 < 10.0928] w=0.0287 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V101.CB) [> 4.4040 = 7.3401 < 9.5421] w=0.0235 to align # Constraint # added constraint: constraint((T0366)V32.CB, (T0366)A80.CB) [> 4.1280 = 6.8801 < 8.9441] w=0.0191 to align # Constraint # added constraint: constraint((T0366)G33.CA, (T0366)A44.CB) [> 4.6252 = 7.7087 < 10.0214] w=0.0191 to align # Constraint # added constraint: constraint((T0366)R12.CB, (T0366)M93.CB) [> 4.7051 = 7.8418 < 10.1944] w=0.0191 to align # Constraint # added constraint: constraint((T0366)M9.CB, (T0366)G61.CA) [> 4.7957 = 7.9928 < 10.3906] w=0.0191 to align # Constraint # added constraint: constraint((T0366)T66.CB, (T0366)V95.CB) [> 3.6683 = 6.1138 < 7.9480] w=0.0124 to align # Constraint # added constraint: constraint((T0366)G25.CA, (T0366)T55.CB) [> 4.7910 = 7.9850 < 10.3805] w=0.0096 to align # Constraint # added constraint: constraint((T0366)E15.CB, (T0366)T66.CB) [> 4.3720 = 7.2867 < 9.4726] w=0.0096 to align # Constraint # added constraint: constraint((T0366)L36.CB, (T0366)A80.CB) [> 4.0259 = 6.7099 < 8.7229] w=0.0096 to align # Constraint # added constraint: constraint((T0366)L36.CB, (T0366)H77.CB) [> 4.2067 = 7.0112 < 9.1145] w=0.0096 to align # Constraint # added constraint: constraint((T0366)V65.CB, (T0366)A97.CB) [> 4.0203 = 6.7006 < 8.7107] w=0.0096 to align # Constraint # added constraint: constraint((T0366)S34.CB, (T0366)V65.CB) [> 4.1976 = 6.9960 < 9.0947] w=0.0096 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)G50.CA) [> 2.3813 = 3.9688 < 5.1595] w=0.0072 to align # Constraint # added constraint: constraint((T0366)S27.CB, (T0366)A52.CB) [> 2.6350 = 4.3916 < 5.7091] w=0.0072 to align # Constraint # added constraint: constraint((T0366)M46.CB, (T0366)D62.CB) [> 4.6962 = 7.8271 < 10.1752] w=0.0029 to align # Constraint # added constraint: constraint((T0366)F42.CB, (T0366)M75.CB) [> 3.8088 = 6.3480 < 8.2524] w=0.0019 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0366/decoys/ # ReadConformPDB reading from PDB file tr366.gromacs0.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr366.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr366.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr366.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr366-1g9oA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-tr366-1g9oA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr366-1tp5A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-tr366-1tp5A # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 20 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 Skipped atom 211, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 9 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 9 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 326, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0366)M9.N and (T0366)P20.N only 0.000 apart, marking (T0366)P20.N as missing WARNING: atoms too close: (T0366)M9.CA and (T0366)P20.CA only 0.000 apart, marking (T0366)P20.CA as missing WARNING: atoms too close: (T0366)M9.CB and (T0366)P20.CB only 0.000 apart, marking (T0366)P20.CB as missing WARNING: atoms too close: (T0366)M9.O and (T0366)P20.O only 0.000 apart, marking (T0366)P20.O as missing WARNING: atoms too close: (T0366)M9.C and (T0366)P20.C only 0.000 apart, marking (T0366)P20.C as missing # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0366 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.7298 model score -0.7389 model score -0.7327 model score -0.7378 model score -0.7388 model score -0.7389 model score -0.6165 model score -0.6729 model score -0.6689 model score -0.6423 model score -0.6326 model score -0.5336 model score -0.6137 model score -0.5961 model score -0.5961 model score -0.6893 model score -0.6730 model score -0.6609 model score -0.6171 model score -0.6595 model score -0.5860 model score -0.7226 model score -0.7309 model score -0.7177 model score -0.7165 model score -0.7142 model score 1.3091 model score 1.8232 model score 1.6260 model score 1.0017 model score 1.1779 model score -0.7390 model score -0.7309 model score -0.7358 model score -0.6451 model score -0.5429 model score -0.5963 model score -0.6891 model score -0.5043 model score -0.6018 model score -0.6712 model score -0.5957 model score -0.6576 model score -0.7108 model score 0.4308 model score -0.6814 model score -0.6305 model score -0.2184 model score 1.2663 model score 1.2626 model score 1.2660 model score 1.2615 model score 1.2650 model score -0.6963 model score -0.6731 model score -0.6229 model score -0.2037 model score -0.5544 model score -0.6744 model score -0.6697 model score -0.5951 model score -0.6018 model score -0.6652 model score -0.7226 model score -0.6473 model score -0.7309 model score -0.7177 model score -0.7148 model score 1.2657 model score 1.2611 model score 1.2647 model score 1.2702 model score 1.2620 model score 1.2647 model score 1.2657 model score 1.2606 model score 1.2620 model score 1.2702 model score 2.2518 model score 2.0015 model score 2.0403 model score 2.1255 model score 2.3217 model score -0.6603 model score -0.7151 model score -0.6166 model score 0.2891 model score -0.6005 model score 1.2607 model score 1.2608 model score 1.2612 model score 1.2743 model score 1.2613 model score -0.6652 model score -0.6697 model score -0.6785 model score -0.6865 model score -0.5951 model score -0.7052 model score -0.6133 model score -0.5541 model score -0.6411 model score -0.5985 model score -0.6532 model score -0.7159 model score -0.6383 model score -0.5676 model score -0.5698 model score -0.7549 model score -0.7549 model score -0.6915 model score -0.5199 model score -0.6236 model score -0.6931 model score -0.3740 model score -0.7175 model score -0.6962 model score -0.6703 model score -0.5613 model score -0.1196 model score 1.2607 model score -0.7186 model score -0.7344 model score -0.7270 model score -0.7262 model score -0.7173 model score -0.7186 model score -0.7270 model score -0.7230 model score -0.7478 model score -0.7173 model score -0.7123 model score -0.7044 model score -0.7121 model score -0.7319 model score -0.7075 model score -0.5610 model score -0.6918 model score -0.6621 model score -0.6807 model score -0.6685 model score -0.6603 model score -0.7046 model score -0.6858 model score -0.6634 model score -0.6802 model score -0.5817 model score -0.7200 model score -0.6947 model score -0.7317 model score -0.5721 model score -0.6678 model score -0.4807 model score -0.6365 model score -0.6365 model score -0.6365 model score -0.6365 model score -0.6365 model score -0.7131 model score -0.7087 model score -0.6968 model score -0.4247 model score -0.7200 model score -0.7111 model score -0.7176 model score -0.7093 model score -0.7011 model score -0.6572 model score -0.6442 model score -0.6442 model score -0.6442 model score -0.6361 model score -0.6361 model score -0.6947 model score -0.6947 model score -0.6947 model score -0.6775 model score -0.6775 model score -0.6968 model score -0.7107 model score -0.7131 model score -0.6842 model score -0.7110 model score -0.7363 model score -0.7216 model score -0.5842 model score -0.5293 model score -0.3796 model score 1.2631 model 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min: -0.7549 max: 2.3217 USE_META, weight: 0.9638 cost: -0.6311 min: -0.7549 max: 2.3217 USE_META, weight: 0.9104 cost: -0.4487 min: -0.7549 max: 2.3217 USE_META, weight: 0.9485 cost: -0.5789 min: -0.7549 max: 2.3217 USE_META, weight: 0.9720 cost: -0.6593 min: -0.7549 max: 2.3217 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 0.9952 eval: 0.0021 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 0.9952 eval: 0.0021 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 0.9952 eval: 0.0021 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.3831 Number of contacts in models: 263 Number of contacts in alignments: 108 NUMB_ALIGNS: 108 Adding 2241 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -187.5347, CN propb: -187.5347 weights: 0.5046 constraints: 270 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 270 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 270 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 1971 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 1971 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2241 # command: