parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0363/ # command:# Making conformation for sequence T0363 numbered 1 through 97 Created new target T0363 from T0363.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0363/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yqbA expands to /projects/compbio/data/pdb/1yqb.pdb.gz 1yqbA:# T0363 read from 1yqbA/merged-good-all-a2m # 1yqbA read from 1yqbA/merged-good-all-a2m # adding 1yqbA to template set # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG # choosing archetypes in rotamer library T0363 11 :NQINIEIA 1yqbA 20 :HLIKVTVK T0363 21 :FPER 1yqbA 28 :TPKD T0363 27 :LKSFQVDEGITVQTAITQS 1yqbA 32 :KEDFSVTDTCTIQQLKEEI T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEI 1yqbA 81 :VRDGLTVHL Number of specific fragments extracted= 7 number of extra gaps= 2 total=7 Number of alignments=1 # 1yqbA read from 1yqbA/merged-good-all-a2m # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG T0363 11 :NQINIEIA 1yqbA 20 :HLIKVTVK T0363 21 :FPER 1yqbA 28 :TPKD T0363 27 :LKSFQVDEGITVQTAITQS 1yqbA 32 :KEDFSVTDTCTIQQLKEEI T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEIY 1yqbA 81 :VRDGLTVHLV Number of specific fragments extracted= 7 number of extra gaps= 2 total=14 Number of alignments=2 # 1yqbA read from 1yqbA/merged-good-all-a2m # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG T0363 11 :NQINIEI 1yqbA 20 :HLIKVTV T0363 20 :AFPERY 1yqbA 27 :KTPKDK T0363 28 :KSFQVDEGITVQTAITQ 1yqbA 33 :EDFSVTDTCTIQQLKEE T0363 47 :ILSQF 1yqbA 50 :ISQRF T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEI 1yqbA 81 :VRDGLTVHL Number of specific fragments extracted= 8 number of extra gaps= 2 total=22 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uwmA expands to /projects/compbio/data/pdb/1uwm.pdb.gz 1uwmA:Skipped atom 119, because occupancy 0.25 <= existing 0.750 in 1uwmA Skipped atom 121, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 123, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 125, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 127, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 129, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 131, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 189, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 191, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 193, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 195, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 197, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 199, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 201, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 203, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 205, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 207, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 209, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 211, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 213, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 215, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 217, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 219, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 221, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 330, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 332, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 334, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 336, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 338, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 340, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 342, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 344, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 346, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 348, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 350, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 717, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 719, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 721, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 723, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 725, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 727, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 729, because occupancy 0.600 <= existing 0.800 in 1uwmA # T0363 read from 1uwmA/merged-good-all-a2m # 1uwmA read from 1uwmA/merged-good-all-a2m # adding 1uwmA to template set # found chain 1uwmA in template set T0363 14 :NIEIA 1uwmA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1uwmA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1uwmA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 Number of alignments=4 # 1uwmA read from 1uwmA/merged-good-all-a2m # found chain 1uwmA in template set T0363 14 :NIEIA 1uwmA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSG 1uwmA 7 :EHNGTRHEVEAKPGLTVMEAARDNG T0363 51 :FPEIDLST 1uwmA 32 :VPGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=28 Number of alignments=5 # 1uwmA read from 1uwmA/merged-good-all-a2m # found chain 1uwmA in template set T0363 17 :IAYAFPERY 1uwmA 3 :IIFIEHNGT T0363 27 :LKSFQVDEGITVQTAITQSG 1uwmA 12 :RHEVEAKPGLTVMEAARDNG T0363 51 :FPEIDLSTN 1uwmA 32 :VPGIDADCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=31 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e9mA expands to /projects/compbio/data/pdb/1e9m.pdb.gz 1e9mA:# T0363 read from 1e9mA/merged-good-all-a2m # 1e9mA read from 1e9mA/merged-good-all-a2m # adding 1e9mA to template set # found chain 1e9mA in template set T0363 14 :NIEIA 1e9mA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1e9mA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1e9mA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=34 Number of alignments=7 # 1e9mA read from 1e9mA/merged-good-all-a2m # found chain 1e9mA in template set T0363 14 :NIEIA 1e9mA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1e9mA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1e9mA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=37 Number of alignments=8 # 1e9mA read from 1e9mA/merged-good-all-a2m # found chain 1e9mA in template set T0363 17 :IAYAFPERY 1e9mA 3 :IIFIEHNGT T0363 27 :LKSFQVDEGITVQTAITQSGI 1e9mA 12 :RHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLSTN 1e9mA 33 :PGIDADCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z2mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z2mA expands to /projects/compbio/data/pdb/1z2m.pdb.gz 1z2mA:# T0363 read from 1z2mA/merged-good-all-a2m # 1z2mA read from 1z2mA/merged-good-all-a2m # adding 1z2mA to template set # found chain 1z2mA in template set T0363 5 :HHHHSLNQINIE 1z2mA 76 :DKSDEPLSILVR T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1z2mA 88 :NNKGRSSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYR 1z2mA 142 :LKPLSTVFMNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=44 Number of alignments=10 # 1z2mA read from 1z2mA/merged-good-all-a2m # found chain 1z2mA in template set T0363 5 :HHHHSLNQINIE 1z2mA 76 :DKSDEPLSILVR T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1z2mA 88 :NNKGRSSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYRP 1z2mA 142 :LKPLSTVFMNLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 Number of alignments=11 # 1z2mA read from 1z2mA/merged-good-all-a2m # found chain 1z2mA in template set T0363 7 :HHSLNQINIEIA 1z2mA 76 :DKSDEPLSILVR T0363 20 :AFPER 1z2mA 88 :NNKGR T0363 27 :LKSFQVDEGITVQTAITQSGILS 1z2mA 93 :SSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYR 1z2mA 142 :LKPLSTVFMNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=53 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ogwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1ogwA/merged-good-all-a2m # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 Warning: unaligning (T0363)R79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)H68 Warning: unaligning (T0363)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)H68 T0363 12 :QINIEI 1ogwA 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ogwA 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDV 1ogwA 52 :DGRT T0363 74 :LKEGD 1ogwA 61 :IQKES T0363 82 :IYRPLL 1ogwA 69 :LVLRLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=59 Number of alignments=13 # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 Warning: unaligning (T0363)R79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)H68 Warning: unaligning (T0363)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)H68 T0363 12 :QINIEI 1ogwA 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ogwA 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDV 1ogwA 52 :DGRT T0363 74 :LKEGD 1ogwA 61 :IQKES T0363 82 :IYRPLL 1ogwA 69 :LVLRLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=65 Number of alignments=14 # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 T0363 13 :INIE 1ogwA 3 :IFVK T0363 20 :AFPER 1ogwA 7 :TLTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1ogwA 12 :TITLEVEPSDTIENVKAKIQDKE T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDVLK 1ogwA 52 :DGRTLS Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1frd expands to /projects/compbio/data/pdb/1frd.pdb.gz 1frd:Warning: there is no chain 1frd will retry with 1frdA # T0363 read from 1frd/merged-good-all-a2m # 1frd read from 1frd/merged-good-all-a2m # adding 1frd to template set # found chain 1frd in template set T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGI T0363 48 :LSQFPEIDLSTNKIGIFSRPIKLTDV 1frd 38 :PFSCHSGSCSSCVGKVVEGEVDQSDQ T0363 86 :LLADPKEIRR 1frd 64 :IFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=74 Number of alignments=16 # 1frd read from 1frd/merged-good-all-a2m # found chain 1frd in template set Warning: unaligning (T0363)N11 because first residue in template chain is (1frd)A1 T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGI T0363 49 :SQFPEIDLSTNKIGIFSRPIKLTDV 1frd 39 :FSCHSGSCSSCVGKVVEGEVDQSDQ T0363 86 :LLADPKEIRR 1frd 64 :IFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=78 Number of alignments=17 # 1frd read from 1frd/merged-good-all-a2m # found chain 1frd in template set T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGIELPFSCHSGSCSS T0363 63 :IFSRPIKLTDVLKE 1frd 49 :CVGKVVEGEVDQSD T0363 85 :PLLADPKEIRR 1frd 63 :QIFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1awd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1awd expands to /projects/compbio/data/pdb/1awd.pdb.gz 1awd:Warning: there is no chain 1awd will retry with 1awdA Skipped atom 116, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 118, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 120, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 122, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 142, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 144, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 146, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 148, because occupancy 0.450 <= existing 0.550 in 1awd # T0363 read from 1awd/merged-good-all-a2m # 1awd read from 1awd/merged-good-all-a2m # adding 1awd to template set # found chain 1awd in template set T0363 12 :QINIE 1awd 2 :KVTLK T0363 21 :FPERY 1awd 7 :TPSGE T0363 28 :KSFQVDEGITVQTAITQSGI 1awd 12 :ETIECPEDTYILDAAEEAGL T0363 53 :EIDLSTN 1awd 32 :DLPYSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=86 Number of alignments=19 # 1awd read from 1awd/merged-good-all-a2m # found chain 1awd in template set T0363 14 :NIEI 1awd 2 :KVTL T0363 20 :AFPERYY 1awd 6 :KTPSGEE T0363 29 :SFQVDEGITVQTAITQSGI 1awd 13 :TIECPEDTYILDAAEEAGL T0363 53 :EIDLSTN 1awd 32 :DLPYSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=90 Number of alignments=20 # 1awd read from 1awd/merged-good-all-a2m # found chain 1awd in template set T0363 17 :IAYAFPERYY 1awd 3 :VTLKTPSGEE T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1awd 13 :TIECPEDTYILDAAEEAGLDLPYSCRAGACSS T0363 63 :IFSRPIKLT 1awd 45 :CAGKVESGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rwsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rwsA expands to /projects/compbio/data/pdb/1rws.pdb.gz 1rwsA:# T0363 read from 1rwsA/merged-good-all-a2m # 1rwsA read from 1rwsA/merged-good-all-a2m # adding 1rwsA to template set # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 31 :Q 1rwsA 18 :E T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSGI 1rwsA 25 :VRDILRAVGF T0363 55 :DLSTNKIGIFSRPIKLTD 1rwsA 35 :NTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :EI 1rwsA 61 :EV Number of specific fragments extracted= 6 number of extra gaps= 4 total=99 Number of alignments=22 # 1rwsA read from 1rwsA/merged-good-all-a2m # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 31 :Q 1rwsA 18 :E T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSG 1rwsA 25 :VRDILRAVG T0363 54 :IDLSTNKIGIFSRPIKLTD 1rwsA 34 :FNTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :E 1rwsA 61 :E Number of specific fragments extracted= 6 number of extra gaps= 4 total=105 Number of alignments=23 # 1rwsA read from 1rwsA/merged-good-all-a2m # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSG 1rwsA 25 :VRDILRAVG T0363 54 :IDLSTNKIGIFSRPIKLTD 1rwsA 34 :FNTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :E 1rwsA 61 :E Number of specific fragments extracted= 5 number of extra gaps= 4 total=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c1yB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c1yB expands to /projects/compbio/data/pdb/1c1y.pdb.gz 1c1yB:Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 1c1yB # T0363 read from 1c1yB/merged-good-all-a2m # 1c1yB read from 1c1yB/merged-good-all-a2m # adding 1c1yB to template set # found chain 1c1yB in template set T0363 11 :NQINIEI 1c1yB 56 :NTIRVFL T0363 22 :PERYY 1c1yB 63 :PNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :SGI 1c1yB 86 :LKV T0363 52 :PEIDLSTNKIGIF 1c1yB 89 :RGLQPECCAVFRL T0363 65 :SRPIKLTDVLKE 1c1yB 109 :KARLDWNTDAAS T0363 77 :GDRIEI 1c1yB 123 :GEELQV Number of specific fragments extracted= 7 number of extra gaps= 0 total=117 Number of alignments=24 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0363 11 :NQINIEI 1c1yB 56 :NTIRVFL T0363 22 :PERYY 1c1yB 63 :PNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :S 1c1yB 85 :A T0363 47 :I 1c1yB 88 :V T0363 52 :PEIDLSTNKIGIF 1c1yB 89 :RGLQPECCAVFRL T0363 65 :SRPIKLTDVLK 1c1yB 109 :KARLDWNTDAA T0363 76 :EGDRIEI 1c1yB 122 :IGEELQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=125 Number of alignments=25 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0363 11 :NQINIE 1c1yB 56 :NTIRVF T0363 21 :FPERYY 1c1yB 62 :LPNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :S 1c1yB 85 :A T0363 48 :LS 1c1yB 86 :LK T0363 51 :FPEIDLSTNK 1c1yB 88 :VRGLQPECCA T0363 63 :IFSRPIKLTD 1c1yB 98 :VFRLLHEHKG T0363 73 :VLKEG 1c1yB 111 :RLDWN Number of specific fragments extracted= 8 number of extra gaps= 0 total=133 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bpsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bpsA expands to /projects/compbio/data/pdb/2bps.pdb.gz 2bpsA:# T0363 read from 2bpsA/merged-good-all-a2m # 2bpsA read from 2bpsA/merged-good-all-a2m # adding 2bpsA to template set # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAYA 2bpsA 0 :GSYIDITIDLK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 11 :HYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGI 2bpsA 44 :PREGHWIRV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=138 Number of alignments=27 # 2bpsA read from 2bpsA/merged-good-all-a2m # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAY 2bpsA 0 :GSYIDITIDL T0363 21 :FPERYYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 10 :KHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGI 2bpsA 44 :PREGHWIRV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=143 Number of alignments=28 # 2bpsA read from 2bpsA/merged-good-all-a2m # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAYAFPE 2bpsA 0 :GSYIDITIDLKHYN T0363 25 :YYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 14 :GSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGIF 2bpsA 44 :PREGHWIRVV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=148 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1put/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1put expands to /projects/compbio/data/pdb/1put.pdb.gz 1put:Warning: there is no chain 1put will retry with 1putA # T0363 read from 1put/merged-good-all-a2m # 1put read from 1put/merged-good-all-a2m # adding 1put to template set # found chain 1put in template set T0363 17 :IAYAFPERY 1put 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1put 12 :RRQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 70 :LTDVLKEGDRI 1put 74 :VTAELKPNSRL T0363 83 :YRPLLADP 1put 85 :CCQIIMTP Number of specific fragments extracted= 5 number of extra gaps= 0 total=153 Number of alignments=30 # 1put read from 1put/merged-good-all-a2m # found chain 1put in template set T0363 17 :IAYAFPERY 1put 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1put 12 :RRQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 70 :LTDVLKEGDRI 1put 74 :VTAELKPNSRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=157 Number of alignments=31 # 1put read from 1put/merged-good-all-a2m # found chain 1put in template set T0363 17 :IAYAFPERYY 1put 3 :VVYVSHDGTR T0363 28 :KSFQVDEGITVQTAITQSGILSQFPEID 1put 13 :RQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 69 :KLTDVLKEGDRI 1put 73 :CVTAELKPNSRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=161 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nddA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nddA expands to /projects/compbio/data/pdb/1ndd.pdb.gz 1nddA:# T0363 read from 1nddA/merged-good-all-a2m # 1nddA read from 1nddA/merged-good-all-a2m # adding 1nddA to template set # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nddA 7 :TLTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEI 1nddA 61 :ILGGSVLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=165 Number of alignments=33 # 1nddA read from 1nddA/merged-good-all-a2m # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 21 :F 1nddA 7 :T T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1nddA 8 :LTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPL 1nddA 61 :ILGGSVLHLVLAL Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=34 # 1nddA read from 1nddA/merged-good-all-a2m # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 20 :AFPER 1nddA 7 :TLTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1nddA 12 :EIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEI 1nddA 61 :ILGGSVLHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lfdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lfdA expands to /projects/compbio/data/pdb/1lfd.pdb.gz 1lfdA:# T0363 read from 1lfdA/merged-good-all-a2m # 1lfdA read from 1lfdA/merged-good-all-a2m # adding 1lfdA to template set # found chain 1lfdA in template set T0363 12 :QINIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGI 1lfdA 16 :CCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQ T0363 67 :PIKLTD 1lfdA 68 :IISEDH T0363 73 :VLKEGD 1lfdA 76 :KIPENA Number of specific fragments extracted= 3 number of extra gaps= 0 total=178 Number of alignments=36 # 1lfdA read from 1lfdA/merged-good-all-a2m # found chain 1lfdA in template set T0363 12 :QINIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGI 1lfdA 16 :CCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQ T0363 67 :PIKLTD 1lfdA 68 :IISEDH T0363 73 :VLKEGDR 1lfdA 76 :KIPENAN Number of specific fragments extracted= 3 number of extra gaps= 0 total=181 Number of alignments=37 # 1lfdA read from 1lfdA/merged-good-all-a2m # found chain 1lfdA in template set T0363 13 :INIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIG 1lfdA 17 :CIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELL T0363 66 :RPIKLTD 1lfdA 67 :QIISEDH T0363 73 :VLKEGDR 1lfdA 76 :KIPENAN Number of specific fragments extracted= 3 number of extra gaps= 0 total=184 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zud2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zud2 expands to /projects/compbio/data/pdb/1zud.pdb.gz 1zud2:# T0363 read from 1zud2/merged-good-all-a2m # 1zud2 read from 1zud2/merged-good-all-a2m # adding 1zud2 to template set # found chain 1zud2 in template set T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRP 1zud2 50 :IVQDGDQILLFQV Number of specific fragments extracted= 3 number of extra gaps= 0 total=187 Number of alignments=39 # 1zud2 read from 1zud2/merged-good-all-a2m # found chain 1zud2 in template set T0363 22 :PE 1zud2 6 :ND T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRP 1zud2 50 :IVQDGDQILLFQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=191 Number of alignments=40 # 1zud2 read from 1zud2/merged-good-all-a2m # found chain 1zud2 in template set T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRPL 1zud2 50 :IVQDGDQILLFQVI Number of specific fragments extracted= 3 number of extra gaps= 0 total=194 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ubi/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ubi expands to /projects/compbio/data/pdb/1ubi.pdb.gz 1ubi:Warning: there is no chain 1ubi will retry with 1ubiA # T0363 read from 1ubi/merged-good-all-a2m # 1ubi read from 1ubi/merged-good-all-a2m # adding 1ubi to template set # found chain 1ubi in template set T0363 12 :QINIEI 1ubi 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ubi 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1ubi 35 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1ubi 61 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=198 Number of alignments=42 # 1ubi read from 1ubi/merged-good-all-a2m # found chain 1ubi in template set T0363 12 :QINIEI 1ubi 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ubi 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1ubi 35 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPL 1ubi 61 :IQKESTLHLVLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=43 # 1ubi read from 1ubi/merged-good-all-a2m # found chain 1ubi in template set T0363 12 :QINIE 1ubi 2 :QIFVK T0363 20 :AFPERY 1ubi 7 :TLTGKT T0363 28 :KSFQVDEGITVQTAITQSGILS 1ubi 13 :ITLEVEPSDTIENVKAKIQDKE T0363 53 :EIDLSTNKIGIFSRPIKLTDVLK 1ubi 35 :GIPPDQQRLIFAGKQLEDGRTLS Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oqqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1oqqA/merged-good-all-a2m # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERY 1oqqA 2 :KVVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEIDL 1oqqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGDCGG Number of specific fragments extracted= 2 number of extra gaps= 0 total=208 Number of alignments=45 # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERY 1oqqA 2 :KVVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1oqqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGDCG Number of specific fragments extracted= 2 number of extra gaps= 0 total=210 Number of alignments=46 # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERYY 1oqqA 2 :KVVYVSHDGTR T0363 28 :KSFQVDEGITVQTAITQSGILS 1oqqA 13 :RELDVADGVSLMQAAVSNGIYD T0363 54 :IDLS 1oqqA 35 :IVGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=213 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1euvB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1euvB expands to /projects/compbio/data/pdb/1euv.pdb.gz 1euvB:# T0363 read from 1euvB/merged-good-all-a2m # 1euvB read from 1euvB/merged-good-all-a2m # adding 1euvB to template set # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEIA 1euvB 21 :ETHINLKVS T0363 21 :FPERYYLKSFQ 1euvB 30 :DGSSEIFFKIK T0363 34 :EGITVQTAITQS 1euvB 41 :KTTPLRRLMEAF T0363 52 :PEIDLSTNKIGIFSRPIK 1euvB 56 :QGKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRPLL 1euvB 83 :MEDNDIIEAHREQI Number of specific fragments extracted= 6 number of extra gaps= 1 total=219 Number of alignments=48 # 1euvB read from 1euvB/merged-good-all-a2m # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEIA 1euvB 21 :ETHINLKVS T0363 21 :FPERYYLKSFQ 1euvB 30 :DGSSEIFFKIK T0363 34 :EGITVQTAITQSGIL 1euvB 41 :KTTPLRRLMEAFAKR T0363 52 :PEIDLSTNKIGIFSRPIK 1euvB 56 :QGKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRP 1euvB 83 :MEDNDIIEAHRE Number of specific fragments extracted= 6 number of extra gaps= 1 total=225 Number of alignments=49 # 1euvB read from 1euvB/merged-good-all-a2m # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEI 1euvB 21 :ETHINLKV T0363 20 :AFPERYYLKSF 1euvB 29 :SDGSSEIFFKI T0363 33 :DEGITVQTAITQS 1euvB 40 :KKTTPLRRLMEAF T0363 48 :LSQF 1euvB 53 :AKRQ T0363 53 :EIDLSTNKIGIFSRPIK 1euvB 57 :GKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRPL 1euvB 83 :MEDNDIIEAHREQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=232 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bb6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bb6A expands to /projects/compbio/data/pdb/2bb6.pdb.gz 2bb6A:# T0363 read from 2bb6A/merged-good-all-a2m # 2bb6A read from 2bb6A/merged-good-all-a2m # adding 2bb6A to template set # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 54 :IDLSTNKI 2bb6A 361 :ASLSGPFL T0363 62 :GIFSRPIK 2bb6A 370 :SVLGRKAG T0363 71 :TDVLKEGDRIEIY 2bb6A 398 :DYRPKDGETIELR Number of specific fragments extracted= 6 number of extra gaps= 2 total=238 Number of alignments=51 # 2bb6A read from 2bb6A/merged-good-all-a2m # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 53 :EIDLSTNKI 2bb6A 360 :QASLSGPFL T0363 62 :GIFSRPIKL 2bb6A 370 :SVLGRKAGE T0363 72 :DVLKEGDRIEIY 2bb6A 399 :YRPKDGETIELR Number of specific fragments extracted= 6 number of extra gaps= 2 total=244 Number of alignments=52 # 2bb6A read from 2bb6A/merged-good-all-a2m # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 53 :EIDLSTNKI 2bb6A 360 :QASLSGPFL T0363 62 :GIFSRPIK 2bb6A 370 :SVLGRKAG T0363 70 :LTDVLKEGDRIEI 2bb6A 397 :ADYRPKDGETIEL Number of specific fragments extracted= 6 number of extra gaps= 2 total=250 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nbfD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nbfD expands to /projects/compbio/data/pdb/1nbf.pdb.gz 1nbfD:# T0363 read from 1nbfD/merged-good-all-a2m # 1nbfD read from 1nbfD/merged-good-all-a2m # adding 1nbfD to template set # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nbfD 307 :TLTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1nbfD 361 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=254 Number of alignments=54 # 1nbfD read from 1nbfD/merged-good-all-a2m # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nbfD 307 :TLTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1nbfD 361 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=258 Number of alignments=55 # 1nbfD read from 1nbfD/merged-good-all-a2m # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 20 :AFPERY 1nbfD 307 :TLTGKT T0363 28 :KSFQVDEGITVQTAITQSGI 1nbfD 313 :ITLEVEPSDTIENVKAKIQD T0363 50 :QF 1nbfD 333 :KE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1nbfD 361 :IQKESTLHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=264 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fm0D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1fm0D/merged-good-all-a2m # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set Warning: unaligning (T0363)D89 because last residue in template chain is (1fm0D)G81 T0363 29 :SFQVDEGI 1fm0D 18 :ATEVAADF T0363 37 :TVQTAITQS 1fm0D 27 :TVEALRQHM T0363 54 :IDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1fm0D 46 :LEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTG Number of specific fragments extracted= 3 number of extra gaps= 0 total=267 Number of alignments=57 # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1fm0D)M1 T0363 13 :INIEI 1fm0D 2 :IKVLF T0363 22 :PERYY 1fm0D 15 :GTDAT T0363 31 :QVDEGI 1fm0D 20 :EVAADF T0363 37 :TVQTAITQS 1fm0D 27 :TVEALRQHM T0363 54 :IDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLL 1fm0D 46 :LEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVT Number of specific fragments extracted= 5 number of extra gaps= 0 total=272 Number of alignments=58 # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set T0363 29 :SFQVDEGI 1fm0D 18 :ATEVAADF T0363 37 :TVQTAITQSGILSQ 1fm0D 27 :TVEALRQHMAAQSD T0363 55 :DLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1fm0D 47 :EDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTG Number of specific fragments extracted= 3 number of extra gaps= 0 total=275 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bt0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bt0A expands to /projects/compbio/data/pdb/1bt0.pdb.gz 1bt0A:# T0363 read from 1bt0A/merged-good-all-a2m # 1bt0A read from 1bt0A/merged-good-all-a2m # adding 1bt0A to template set # found chain 1bt0A in template set Warning: unaligning (T0363)N11 because first residue in template chain is (1bt0A)M1 T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1bt0A 7 :TLTGKEIEIDIEPTDTIDRIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEIY 1bt0A 61 :IEGGSVLHLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=279 Number of alignments=60 # 1bt0A read from 1bt0A/merged-good-all-a2m # found chain 1bt0A in template set Warning: unaligning (T0363)L86 because last residue in template chain is (1bt0A)L73 T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1bt0A 7 :TLTGKEIEIDIEPTDTIDRIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEIYRP 1bt0A 61 :IEGGSVLHLVLA Number of specific fragments extracted= 4 number of extra gaps= 0 total=283 Number of alignments=61 # 1bt0A read from 1bt0A/merged-good-all-a2m # found chain 1bt0A in template set T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 21 :FPER 1bt0A 8 :LTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1bt0A 12 :EIEIDIEPTDTIDRIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEI 1bt0A 61 :IEGGSVLHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=288 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yj1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yj1A expands to /projects/compbio/data/pdb/1yj1.pdb.gz 1yj1A:Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1yj1A # T0363 read from 1yj1A/merged-good-all-a2m # 1yj1A read from 1yj1A/merged-good-all-a2m # adding 1yj1A to template set # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 7 :TLTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1yj1A 61 :IQKESTLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=292 Number of alignments=63 # 1yj1A read from 1yj1A/merged-good-all-a2m # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 7 :TLTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1yj1A 61 :IQKESTLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=296 Number of alignments=64 # 1yj1A read from 1yj1A/merged-good-all-a2m # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 21 :F 1yj1A 7 :T T0363 23 :ERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 8 :LTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGD 1yj1A 61 :IQKES Number of specific fragments extracted= 5 number of extra gaps= 0 total=301 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xlqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xlqA expands to /projects/compbio/data/pdb/1xlq.pdb.gz 1xlqA:# T0363 read from 1xlqA/merged-good-all-a2m # 1xlqA read from 1xlqA/merged-good-all-a2m # adding 1xlqA to template set # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPE 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGD T0363 54 :IDLSTNKIGI 1xlqA 43 :ASCATCHVYV Number of specific fragments extracted= 3 number of extra gaps= 0 total=304 Number of alignments=66 # 1xlqA read from 1xlqA/merged-good-all-a2m # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPE 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGD T0363 54 :IDLSTNKIGIF 1xlqA 41 :GSASCATCHVY Number of specific fragments extracted= 3 number of extra gaps= 0 total=307 Number of alignments=67 # 1xlqA read from 1xlqA/merged-good-all-a2m # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQF 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIV T0363 52 :PEIDLSTNKIGIFS 1xlqA 39 :CGGSASCATCHVYV Number of specific fragments extracted= 3 number of extra gaps= 0 total=310 Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ryjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ryjA expands to /projects/compbio/data/pdb/1ryj.pdb.gz 1ryjA:# T0363 read from 1ryjA/merged-good-all-a2m # 1ryjA read from 1ryjA/merged-good-all-a2m # adding 1ryjA to template set # found chain 1ryjA in template set Warning: unaligning (T0363)H7 because first residue in template chain is (1ryjA)M4 T0363 8 :HSLNQINIE 1ryjA 5 :VIGMKFTVI T0363 21 :FPERYYLKSF 1ryjA 14 :TDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRVIYG Number of specific fragments extracted= 4 number of extra gaps= 0 total=314 Number of alignments=69 # 1ryjA read from 1ryjA/merged-good-all-a2m # found chain 1ryjA in template set Warning: unaligning (T0363)H7 because first residue in template chain is (1ryjA)M4 T0363 8 :HSLNQINIE 1ryjA 5 :VIGMKFTVI T0363 21 :FPERYYLKSF 1ryjA 14 :TDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLL 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRVIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=318 Number of alignments=70 # 1ryjA read from 1ryjA/merged-good-all-a2m # found chain 1ryjA in template set T0363 13 :INIEI 1ryjA 8 :MKFTV T0363 20 :AFPERYYLKSF 1ryjA 13 :ITDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRP 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=322 Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cu3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cu3A expands to /projects/compbio/data/pdb/2cu3.pdb.gz 2cu3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0363 read from 2cu3A/merged-good-all-a2m # 2cu3A read from 2cu3A/merged-good-all-a2m # adding 2cu3A to template set # found chain 2cu3A in template set T0363 16 :EI 2cu3A 3 :WL T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIKL 2cu3A 25 :VELKGVAVLLNEEAFLG T0363 71 :TDVLKEGDRIEI 2cu3A 46 :DRPLRDGDVVEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=327 Number of alignments=72 # 2cu3A read from 2cu3A/merged-good-all-a2m # found chain 2cu3A in template set T0363 16 :EI 2cu3A 3 :WL T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIKL 2cu3A 25 :VELKGVAVLLNEEAFLG T0363 71 :TDVLKEGDRIEI 2cu3A 46 :DRPLRDGDVVEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=332 Number of alignments=73 # 2cu3A read from 2cu3A/merged-good-all-a2m # found chain 2cu3A in template set T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIK 2cu3A 25 :VELKGVAVLLNEEAFL T0363 70 :LTDVLKEGDRIEIY 2cu3A 45 :PDRPLRDGDVVEVV Number of specific fragments extracted= 4 number of extra gaps= 0 total=336 Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bwfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bwfA expands to /projects/compbio/data/pdb/2bwf.pdb.gz 2bwfA:# T0363 read from 2bwfA/merged-good-all-a2m # 2bwfA read from 2bwfA/merged-good-all-a2m # adding 2bwfA to template set # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 24 :RYYLKSFQVDEGITVQTAITQSGILS 2bwfA 10 :GQDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=340 Number of alignments=75 # 2bwfA read from 2bwfA/merged-good-all-a2m # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 24 :RYYLKSFQVDEGITVQTAITQSGILS 2bwfA 10 :GQDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=344 Number of alignments=76 # 2bwfA read from 2bwfA/merged-good-all-a2m # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 22 :P 2bwfA 10 :G T0363 25 :YYLKSFQVDEGITVQTAITQSGILS 2bwfA 11 :QDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=349 Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1frrA expands to /projects/compbio/data/pdb/1frr.pdb.gz 1frrA:# T0363 read from 1frrA/merged-good-all-a2m # 1frrA read from 1frrA/merged-good-all-a2m # adding 1frrA to template set # found chain 1frrA in template set T0363 13 :INIE 1frrA 4 :TVLK T0363 21 :FPERY 1frrA 8 :TPSGE T0363 28 :KSFQVDEGITVQTAITQSGI 1frrA 13 :FTLDVPEGTTILDAAEEAGY T0363 53 :EIDLSTN 1frrA 33 :DLPFSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=353 Number of alignments=78 # 1frrA read from 1frrA/merged-good-all-a2m # found chain 1frrA in template set T0363 17 :IAYAFPERYY 1frrA 4 :TVLKTPSGEF T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDL 1frrA 14 :TLDVPEGTTILDAAEEAGYDLPFSCRAG T0363 57 :STNKIGIFSRPIKLTDV 1frrA 44 :SSCLGKVVSGSVDESEG T0363 86 :LLADPKEIR 1frrA 61 :SFLDDGQME Number of specific fragments extracted= 4 number of extra gaps= 0 total=357 Number of alignments=79 # 1frrA read from 1frrA/merged-good-all-a2m # found chain 1frrA in template set T0363 17 :IAYAFPERYY 1frrA 4 :TVLKTPSGEF T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1frrA 14 :TLDVPEGTTILDAAEEAGYDLPFSCRAGACSS T0363 63 :IFSRPIKLT 1frrA 46 :CLGKVVSGS Number of specific fragments extracted= 3 number of extra gaps= 0 total=360 Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bkrB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bkrB expands to /projects/compbio/data/pdb/2bkr.pdb.gz 2bkrB:# T0363 read from 2bkrB/merged-good-all-a2m # 2bkrB read from 2bkrB/merged-good-all-a2m # adding 2bkrB to template set # found chain 2bkrB in template set Warning: unaligning (T0363)D89 because last residue in template chain is (2bkrB)G76 T0363 11 :NQINIEI 2bkrB 1 :MLIKVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 2bkrB 8 :LTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLLA 2bkrB 61 :ILGGSVLHLVLALRG Number of specific fragments extracted= 4 number of extra gaps= 0 total=364 Number of alignments=81 # 2bkrB read from 2bkrB/merged-good-all-a2m # found chain 2bkrB in template set T0363 12 :QINIEI 2bkrB 2 :LIKVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQSGILS 2bkrB 8 :LTGKEIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLLA 2bkrB 61 :ILGGSVLHLVLALRG Number of specific fragments extracted= 4 number of extra gaps= 0 total=368 Number of alignments=82 # 2bkrB read from 2bkrB/merged-good-all-a2m # found chain 2bkrB in template set T0363 13 :INIEIAY 2bkrB 1 :MLIKVKT T0363 21 :FPER 2bkrB 8 :LTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 2bkrB 12 :EIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLL 2bkrB 61 :ILGGSVLHLVLALR Number of specific fragments extracted= 5 number of extra gaps= 0 total=373 Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wm3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1wm3A/merged-good-all-a2m # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1wm3A 24 :GQDGSVVQFKIKRHTPLSKLMKAY T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=377 Number of alignments=84 # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1wm3A 24 :GQDGSVVQFKIKRHTPLSKLMKAY T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=381 Number of alignments=85 # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 21 :F 1wm3A 24 :G T0363 23 :ERYYLKSFQVDEGITVQTAITQSG 1wm3A 25 :QDGSVVQFKIKRHTPLSKLMKAYC T0363 49 :SQF 1wm3A 49 :ERQ T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 6 number of extra gaps= 0 total=387 Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1vjkA/merged-good-all-a2m # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAY 1vjkA 2 :VKVKVKY T0363 24 :RYYLKSFQVDEGITVQTAITQS 1vjkA 17 :GVDEEEIELPEGARVRDLIEEI T0363 48 :LSQFPEIDL 1vjkA 39 :KKRHEKFKE T0363 57 :STNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 58 :ADVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 4 number of extra gaps= 1 total=391 Number of alignments=87 # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAY 1vjkA 2 :VKVKVKY T0363 24 :RYYLKSFQVDEGITVQTAITQS 1vjkA 17 :GVDEEEIELPEGARVRDLIEEI T0363 48 :LSQFPEIDL 1vjkA 42 :HEKFKEEVF T0363 57 :STNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 58 :ADVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 4 number of extra gaps= 1 total=395 Number of alignments=88 # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAYAF 1vjkA 2 :VKVKVKYFA T0363 27 :LKSFQVDEGITVQTAITQSG 1vjkA 20 :EEEIELPEGARVRDLIEEIK T0363 47 :ILSQFPEID 1vjkA 41 :RHEKFKEEV T0363 56 :L 1vjkA 57 :D T0363 58 :TNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 59 :DVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 5 number of extra gaps= 1 total=400 Number of alignments=89 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 89 Done printing distance constraints # command: