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/T0304/ # command:# Making conformation for sequence T0304 numbered 1 through 122 Created new target T0304 from T0304.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0304/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0304//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0304/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0304//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0304/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0304/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0304/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1glv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1glv expands to /projects/compbio/data/pdb/1glv.pdb.gz 1glv:Warning: there is no chain 1glv will retry with 1glvA Skipped atom 2, because occupancy 0.5 <= existing 0.500 in 1glv Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 1glv Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 1glv # T0304 read from 1glv/merged-good-all-a2m # 1glv read from 1glv/merged-good-all-a2m # adding 1glv to template set # found chain 1glv in template set Warning: unaligning (T0304)K71 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)Q257 Warning: unaligning (T0304)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1glv)Q257 Warning: unaligning (T0304)A94 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)I275 T0304 64 :QAFPLLM 1glv 249 :ESDWKIA # choosing archetypes in rotamer library T0304 73 :LELMLTSGEL 1glv 258 :IGPTLKEKGL T0304 88 :HTVTLY 1glv 268 :IFVGLD T0304 95 :KGLTCKADTLSS 1glv 276 :GDRLTEINVTSP Number of specific fragments extracted= 4 number of extra gaps= 2 total=4 Number of alignments=1 # 1glv read from 1glv/merged-good-all-a2m # found chain 1glv in template set Warning: unaligning (T0304)K71 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)Q257 Warning: unaligning (T0304)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1glv)Q257 Warning: unaligning (T0304)A94 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)I275 T0304 64 :QAFPLLM 1glv 249 :ESDWKIA T0304 73 :LELMLTSGEL 1glv 258 :IGPTLKEKGL T0304 88 :HTVTLY 1glv 268 :IFVGLD T0304 95 :KGLTCKADTLSS 1glv 276 :GDRLTEINVTSP Number of specific fragments extracted= 4 number of extra gaps= 2 total=8 Number of alignments=2 # 1glv read from 1glv/merged-good-all-a2m # found chain 1glv in template set Warning: unaligning (T0304)K71 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)Q257 Warning: unaligning (T0304)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1glv)Q257 Warning: unaligning (T0304)A94 because of BadResidue code BAD_PEPTIDE in next template residue (1glv)I275 T0304 65 :AFPLLM 1glv 250 :SDWKIA T0304 73 :LELMLTSGEL 1glv 258 :IGPTLKEKGL T0304 88 :HTVTLY 1glv 268 :IFVGLD T0304 95 :KGLTCKADTLSS 1glv 276 :GDRLTEINVTSP Number of specific fragments extracted= 4 number of extra gaps= 2 total=12 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vpkA expands to /projects/compbio/data/pdb/1vpk.pdb.gz 1vpkA:Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1961, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1977, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2409, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2411, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2413, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2415, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2800, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2804, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2806, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2810, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2812, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2814, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2816, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2818, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2820, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2822, because occupancy 0.500 <= existing 0.500 in 1vpkA # T0304 read from 1vpkA/merged-good-all-a2m # 1vpkA read from 1vpkA/merged-good-all-a2m # adding 1vpkA to template set # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAVY 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVMP Number of specific fragments extracted= 2 number of extra gaps= 0 total=14 Number of alignments=4 # 1vpkA read from 1vpkA/merged-good-all-a2m # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAVY 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVMP Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 Number of alignments=5 # 1vpkA read from 1vpkA/merged-good-all-a2m # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAV 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVM Number of specific fragments extracted= 2 number of extra gaps= 0 total=18 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gulA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gulA expands to /projects/compbio/data/pdb/1gul.pdb.gz 1gulA:# T0304 read from 1gulA/merged-good-all-a2m # 1gulA read from 1gulA/merged-good-all-a2m # adding 1gulA to template set # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=20 # 1gulA read from 1gulA/merged-good-all-a2m # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=22 # 1gulA read from 1gulA/merged-good-all-a2m # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zemA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zemA expands to /projects/compbio/data/pdb/1zem.pdb.gz 1zemA:# T0304 read from 1zemA/merged-good-all-a2m # 1zemA read from 1zemA/merged-good-all-a2m # adding 1zemA to template set # found chain 1zemA in template set T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=26 Number of alignments=7 # 1zemA read from 1zemA/merged-good-all-a2m # found chain 1zemA in template set T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=28 Number of alignments=8 # 1zemA read from 1zemA/merged-good-all-a2m # found chain 1zemA in template set T0304 31 :GARLVQEG 1zemA 33 :AIALLDMN T0304 39 :NRLHYLADR 1zemA 42 :EALEKAEAS T0304 48 :AGIRGLF 1zemA 54 :KGVEARS T0304 55 :SDAD 1zemA 64 :DVTS T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 6 number of extra gaps= 0 total=34 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qwtA expands to /projects/compbio/data/pdb/1qwt.pdb.gz 1qwtA:# T0304 read from 1qwtA/merged-good-all-a2m # 1qwtA read from 1qwtA/merged-good-all-a2m # adding 1qwtA to template set # found chain 1qwtA in template set T0304 23 :PCTVTPCFGARLVQEGNR 1qwtA 217 :QQTISCPEGLRLVGSEVG T0304 48 :AGIRGLFSDADAYHLDQAFPLLMKQLELMLTSG 1qwtA 239 :PGWPVTLPDPGMSLTDRGVMSYVRHVLSCLGGG T0304 90 :VTLYAKGLTCKADTLSSCD 1qwtA 272 :LALWRAGQWLWAQRLGHCH T0304 110 :VYLAVYPTPEMKN 1qwtA 291 :TYWAVSEELLPNS Number of specific fragments extracted= 4 number of extra gaps= 0 total=38 Number of alignments=10 # 1qwtA read from 1qwtA/merged-good-all-a2m # found chain 1qwtA in template set T0304 23 :PCTVTPCFGARLVQEGNR 1qwtA 217 :QQTISCPEGLRLVGSEVG T0304 48 :AGIRGLFSDADAYHLDQAFPLLMKQLELMLTSG 1qwtA 239 :PGWPVTLPDPGMSLTDRGVMSYVRHVLSCLGGG T0304 90 :VTLYAKGLTCKADTLSSCD 1qwtA 272 :LALWRAGQWLWAQRLGHCH T0304 110 :VYLAVYPTPEMKN 1qwtA 291 :TYWAVSEELLPNS Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 Number of alignments=11 # 1qwtA read from 1qwtA/merged-good-all-a2m # found chain 1qwtA in template set T0304 23 :PCTVTPCFGARLVQEGNR 1qwtA 217 :QQTISCPEGLRLVGSEVG T0304 48 :AGIRGLFSDADAYHLDQAFPLLMKQLELMLTSG 1qwtA 239 :PGWPVTLPDPGMSLTDRGVMSYVRHVLSCLGGG T0304 90 :VTLYAKGLTCKADTLSSCD 1qwtA 272 :LALWRAGQWLWAQRLGHCH T0304 110 :VYLAVYPTPEMKN 1qwtA 291 :TYWAVSEELLPNS Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h9sB/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/T0304/1h9sB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0304/1h9sB/merged-good-all-a2m.gz for input Trying 1h9sB/merged-good-all-a2m Error: Couldn't open file 1h9sB/merged-good-all-a2m or 1h9sB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o7lA/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/T0304/1o7lA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0304/1o7lA/merged-good-all-a2m.gz for input Trying 1o7lA/merged-good-all-a2m Error: Couldn't open file 1o7lA/merged-good-all-a2m or 1o7lA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f9lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f9lA expands to /projects/compbio/data/pdb/2f9l.pdb.gz 2f9lA:# T0304 read from 2f9lA/merged-good-all-a2m # 2f9lA read from 2f9lA/merged-good-all-a2m # adding 2f9lA to template set # found chain 2f9lA in template set Warning: unaligning (T0304)N83 because last residue in template chain is (2f9lA)A182 T0304 29 :CFGARLVQEGN 2f9lA 116 :NIVIMLVGNKS T0304 40 :RLHYLADRAGIRGL 2f9lA 138 :EARAFAEKNNLSFI T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTSGEL 2f9lA 153 :TSALDSTNVEEAFKNILTEIYRIVSQKQI Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=13 # 2f9lA read from 2f9lA/merged-good-all-a2m # found chain 2f9lA in template set Warning: unaligning (T0304)N83 because last residue in template chain is (2f9lA)A182 T0304 29 :CFGARLVQEGN 2f9lA 116 :NIVIMLVGNKS T0304 40 :RLHYLADRAGIRGL 2f9lA 138 :EARAFAEKNNLSFI T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTSGEL 2f9lA 153 :TSALDSTNVEEAFKNILTEIYRIVSQKQI Number of specific fragments extracted= 3 number of extra gaps= 0 total=52 Number of alignments=14 # 2f9lA read from 2f9lA/merged-good-all-a2m # found chain 2f9lA in template set Warning: unaligning (T0304)N83 because last residue in template chain is (2f9lA)A182 T0304 29 :CFGARLVQEGN 2f9lA 116 :NIVIMLVGNKS T0304 40 :RLHYLADRAGIRGL 2f9lA 138 :EARAFAEKNNLSFI T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTSGEL 2f9lA 153 :TSALDSTNVEEAFKNILTEIYRIVSQKQI Number of specific fragments extracted= 3 number of extra gaps= 0 total=55 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0304 read from 1kaeA/merged-good-all-a2m # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set Warning: unaligning (T0304)R17 because of BadResidue code BAD_PEPTIDE at template residue (1kaeA)T61 T0304 18 :PWWGLPCT 1kaeA 62 :TVTALKVS T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYHLD 1kaeA 80 :LSDELKQAMA T0304 68 :LLMKQLELMLTSGELNPRHQH 1kaeA 90 :VAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPEM 1kaeA 122 :RPVASVGLYIPGGSAP Number of specific fragments extracted= 6 number of extra gaps= 1 total=61 Number of alignments=16 # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set Warning: unaligning (T0304)R17 because of BadResidue code BAD_PEPTIDE at template residue (1kaeA)T61 T0304 18 :PWWGLPCT 1kaeA 62 :TVTALKVS T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYHLD 1kaeA 80 :LSDELKQAMA T0304 68 :LLMKQLELMLTSGELNPRHQH 1kaeA 90 :VAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPEM 1kaeA 122 :RPVASVGLYIPGGSAP Number of specific fragments extracted= 6 number of extra gaps= 1 total=67 Number of alignments=17 # 1kaeA read from 1kaeA/merged-good-all-a2m # found chain 1kaeA in training set T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYH 1kaeA 80 :LSDELKQA T0304 66 :FPLLMKQLELMLTSGELNPRHQH 1kaeA 88 :MAVAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPE 1kaeA 122 :RPVASVGLYIPGGSA Number of specific fragments extracted= 5 number of extra gaps= 0 total=72 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u69A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0304 read from 1u69A/merged-good-all-a2m # 1u69A read from 1u69A/merged-good-all-a2m # found chain 1u69A in training set T0304 80 :GELNPRHQHTVTLYAKGLTCK 1u69A 42 :PSGKEGDVLTVEFRVMGIPCL T0304 113 :AVYPTPEMK 1u69A 63 :GLNGGPAFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=74 Number of alignments=19 # 1u69A read from 1u69A/merged-good-all-a2m # found chain 1u69A in training set T0304 80 :GELNPRHQHTVTLYAKGLTCK 1u69A 42 :PSGKEGDVLTVEFRVMGIPCL T0304 113 :AVYPTPEMK 1u69A 63 :GLNGGPAFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=76 Number of alignments=20 # 1u69A read from 1u69A/merged-good-all-a2m # found chain 1u69A in training set T0304 80 :GELNPRHQHTVTLYAKGLTCK 1u69A 42 :PSGKEGDVLTVEFRVMGIPCL T0304 113 :AVYPTPEMK 1u69A 63 :GLNGGPAFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z9lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z9lA expands to /projects/compbio/data/pdb/1z9l.pdb.gz 1z9lA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0304 read from 1z9lA/merged-good-all-a2m # 1z9lA read from 1z9lA/merged-good-all-a2m # adding 1z9lA to template set # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=79 Number of alignments=22 # 1z9lA read from 1z9lA/merged-good-all-a2m # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 Number of alignments=23 # 1z9lA read from 1z9lA/merged-good-all-a2m # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i42A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i42A expands to /projects/compbio/data/pdb/1i42.pdb.gz 1i42A:# T0304 read from 1i42A/merged-good-all-a2m # 1i42A read from 1i42A/merged-good-all-a2m # adding 1i42A to template set # found chain 1i42A in template set T0304 88 :HTVTLYAKG 1i42A 296 :TNIQIRLAD T0304 97 :LTCK 1i42A 308 :LVQK Number of specific fragments extracted= 2 number of extra gaps= 0 total=83 Number of alignments=25 # 1i42A read from 1i42A/merged-good-all-a2m # found chain 1i42A in template set T0304 88 :HTVTLYAKG 1i42A 296 :TNIQIRLAD T0304 97 :LTCK 1i42A 308 :LVQK Number of specific fragments extracted= 2 number of extra gaps= 0 total=85 Number of alignments=26 # 1i42A read from 1i42A/merged-good-all-a2m # found chain 1i42A in template set T0304 88 :HTVTLYAKG 1i42A 296 :TNIQIRLAD Number of specific fragments extracted= 1 number of extra gaps= 0 total=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aroL/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aroL expands to /projects/compbio/data/pdb/1aro.pdb.gz 1aroL:# T0304 read from 1aroL/merged-good-all-a2m # 1aroL read from 1aroL/merged-good-all-a2m # adding 1aroL to template set # found chain 1aroL in template set T0304 29 :CFGARLVQEGNR 1aroL 1074 :HNSIGVCLVGGI T0304 46 :DRAGIRGLFSDADAYHLDQAFPLLMKQL 1aroL 1087 :DKGKFDANFTPAQMQSLRSLLVTLLAKY T0304 95 :KGLTCKAD 1aroL 1115 :EGAVLRAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=89 Number of alignments=27 # 1aroL read from 1aroL/merged-good-all-a2m # found chain 1aroL in template set T0304 29 :CFGARLVQEGNR 1aroL 1074 :HNSIGVCLVGGI T0304 46 :DRAGIRGLFSDADAYHLDQAFPLLMKQL 1aroL 1087 :DKGKFDANFTPAQMQSLRSLLVTLLAKY T0304 95 :KGLTCKAD 1aroL 1115 :EGAVLRAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=92 Number of alignments=28 # 1aroL read from 1aroL/merged-good-all-a2m # found chain 1aroL in template set T0304 47 :RAGIRGLFSDADAYHLDQAFPLLMKQL 1aroL 1088 :KGKFDANFTPAQMQSLRSLLVTLLAKY T0304 95 :KGLTCKAD 1aroL 1115 :EGAVLRAH Number of specific fragments extracted= 2 number of extra gaps= 0 total=94 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rw2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rw2A expands to /projects/compbio/data/pdb/1rw2.pdb.gz 1rw2A:# T0304 read from 1rw2A/merged-good-all-a2m # 1rw2A read from 1rw2A/merged-good-all-a2m # adding 1rw2A to template set # found chain 1rw2A in template set T0304 4 :TLPGTTLPDDNHDRPWWGLP 1rw2A 15 :GAHFSVSSLAEGSVTSVGSV T0304 36 :QEGNRLHYLAD 1rw2A 35 :NPAENFRVLVK T0304 57 :ADAYHLDQAFPLLMKQLELMLTSGE 1rw2A 46 :QKKASFEEASNQLINHIEQFLDTNE Number of specific fragments extracted= 3 number of extra gaps= 0 total=97 Number of alignments=30 # 1rw2A read from 1rw2A/merged-good-all-a2m # found chain 1rw2A in template set T0304 4 :TLPGTTLPDDNHDRPWWGLP 1rw2A 15 :GAHFSVSSLAEGSVTSVGSV T0304 36 :QEGNRLHYLAD 1rw2A 35 :NPAENFRVLVK T0304 57 :ADAYHLDQAFPLLMKQLELMLTSGE 1rw2A 46 :QKKASFEEASNQLINHIEQFLDTNE Number of specific fragments extracted= 3 number of extra gaps= 0 total=100 Number of alignments=31 # 1rw2A read from 1rw2A/merged-good-all-a2m # found chain 1rw2A in template set T0304 3 :DTLPGTTLPDDNHDRPWWGLP 1rw2A 14 :GGAHFSVSSLAEGSVTSVGSV T0304 36 :QEGNRLHYLAD 1rw2A 35 :NPAENFRVLVK T0304 57 :ADAYHLDQAFPLLMKQLELMLTSGE 1rw2A 46 :QKKASFEEASNQLINHIEQFLDTNE Number of specific fragments extracted= 3 number of extra gaps= 0 total=103 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rybA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0304 read from 1rybA/merged-good-all-a2m # 1rybA read from 1rybA/merged-good-all-a2m # found chain 1rybA in training set T0304 53 :LFSDADAYHLDQAFPLLMKQLELML 1rybA 11 :NPGNKYYGTRHNVGFEMVDRIAAEE T0304 79 :SGELN 1rybA 36 :GITMN T0304 86 :HQH 1rybA 41 :TIQ T0304 95 :KGLTCKADTLSSCDYVYLAVYPTP 1rybA 44 :SKSLLGIGSIGEVPVLVVKPQSYM Number of specific fragments extracted= 4 number of extra gaps= 0 total=107 Number of alignments=33 # 1rybA read from 1rybA/merged-good-all-a2m # found chain 1rybA in training set T0304 53 :LFSDADAYHLDQAFPLLMKQLELML 1rybA 11 :NPGNKYYGTRHNVGFEMVDRIAAEE T0304 79 :SGELN 1rybA 36 :GITMN T0304 86 :HQH 1rybA 41 :TIQ T0304 95 :KGLTCKADTLSSCDYVYLAVYPTP 1rybA 44 :SKSLLGIGSIGEVPVLVVKPQSYM Number of specific fragments extracted= 4 number of extra gaps= 0 total=111 Number of alignments=34 # 1rybA read from 1rybA/merged-good-all-a2m # found chain 1rybA in training set Number of specific fragments extracted= 0 number of extra gaps= 0 total=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e3dB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e3dB expands to /projects/compbio/data/pdb/1e3d.pdb.gz 1e3dB:Skipped atom 4481, because occupancy 0.400 <= existing 0.600 in 1e3dB Skipped atom 4483, because occupancy 0.400 <= existing 0.600 in 1e3dB Skipped atom 5526, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 5528, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 5530, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 5532, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 10512, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 10514, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 10516, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 10518, because occupancy 0.450 <= existing 0.550 in 1e3dB Skipped atom 12117, because occupancy 0.160 <= existing 0.700 in 1e3dB Skipped atom 12118, because occupancy 0.140 <= existing 0.700 in 1e3dB Skipped atom 12120, because occupancy 0.160 <= existing 0.700 in 1e3dB Skipped atom 12121, because occupancy 0.140 <= existing 0.700 in 1e3dB # T0304 read from 1e3dB/merged-good-all-a2m # 1e3dB read from 1e3dB/merged-good-all-a2m # adding 1e3dB to template set # found chain 1e3dB in template set T0304 2 :SDTLPGTTLPDDNHDRPWWGL 1e3dB 345 :EGETNPHFTFMGDTDKYSWNK T0304 27 :TPCFGARLVQEGNRLHYL 1e3dB 366 :APRYDGHAVETGPLAQML T0304 45 :ADRAGIRG 1e3dB 385 :AYGHNHKT T0304 53 :LFSDADAYH 1e3dB 405 :NLGPEALFS T0304 62 :LDQAFPLLMKQLELMLTSG 1e3dB 428 :IAQQMENWLNEYENNIVKD T0304 81 :ELNPRHQHTVT 1e3dB 454 :AVPTSARGVGF T0304 101 :ADTLSSCDYVYLAVY 1e3dB 465 :ADVSRGGLSHWMTIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=118 Number of alignments=35 # 1e3dB read from 1e3dB/merged-good-all-a2m # found chain 1e3dB in template set T0304 2 :SDTLPGTTLPDDNHDRPWWGL 1e3dB 345 :EGETNPHFTFMGDTDKYSWNK T0304 27 :TPCFGARLVQEGNRLHYL 1e3dB 366 :APRYDGHAVETGPLAQML T0304 45 :ADRAGIRG 1e3dB 385 :AYGHNHKT T0304 53 :LFSDADAYH 1e3dB 405 :NLGPEALFS T0304 62 :LDQAFPLLMKQLELMLTSG 1e3dB 428 :IAQQMENWLNEYENNIVKD T0304 81 :ELNPRHQHTVT 1e3dB 454 :AVPTSARGVGF T0304 101 :ADTLSSCDYVYLAVY 1e3dB 465 :ADVSRGGLSHWMTIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=125 Number of alignments=36 # 1e3dB read from 1e3dB/merged-good-all-a2m # found chain 1e3dB in template set T0304 2 :SDTLPGTTLPDDNHDRPWWGL 1e3dB 345 :EGETNPHFTFMGDTDKYSWNK T0304 27 :TPCFGARLVQEGNRLHYL 1e3dB 366 :APRYDGHAVETGPLAQML T0304 45 :ADRAGIRG 1e3dB 385 :AYGHNHKT T0304 53 :LFSDADAYH 1e3dB 405 :NLGPEALFS T0304 62 :LDQAFPLLMKQLELMLTSG 1e3dB 428 :IAQQMENWLNEYENNIVKD T0304 81 :ELNPRHQHTVT 1e3dB 454 :AVPTSARGVGF T0304 101 :ADTLSSCDYVYLAVY 1e3dB 465 :ADVSRGGLSHWMTIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=132 Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i1qA expands to /projects/compbio/data/pdb/1i1q.pdb.gz 1i1qA:# T0304 read from 1i1qA/merged-good-all-a2m # 1i1qA read from 1i1qA/merged-good-all-a2m # adding 1i1qA to template set # found chain 1i1qA in template set T0304 12 :DDNHDRPWWGLPCTVTP 1i1qA 224 :PPLPVTPVPDMRCECNQ T0304 55 :S 1i1qA 241 :S T0304 63 :DQAFPLLMKQLELMLTSGELN 1i1qA 242 :DDAFGAVVRQLQKAIRAGEIF T0304 85 :RHQHTVTLYAKG 1i1qA 265 :VPSRRFSLPCPS T0304 105 :SSCDYVYLAVYPT 1i1qA 288 :NPSPYMFFMQDND Number of specific fragments extracted= 5 number of extra gaps= 0 total=137 Number of alignments=38 # 1i1qA read from 1i1qA/merged-good-all-a2m # found chain 1i1qA in template set T0304 12 :DDNHDRPWWGLPCTVTP 1i1qA 224 :PPLPVTPVPDMRCECNQ T0304 55 :S 1i1qA 241 :S T0304 63 :DQAFPLLMKQLELMLTSGELN 1i1qA 242 :DDAFGAVVRQLQKAIRAGEIF T0304 85 :RHQHTVTLYAKG 1i1qA 265 :VPSRRFSLPCPS T0304 105 :SSCDYVYLAVYPT 1i1qA 288 :NPSPYMFFMQDND Number of specific fragments extracted= 5 number of extra gaps= 0 total=142 Number of alignments=39 # 1i1qA read from 1i1qA/merged-good-all-a2m # found chain 1i1qA in template set T0304 4 :TLPGTTL 1i1qA 222 :PAPPLPV T0304 17 :RPWWGLPCTVTPC 1i1qA 229 :TPVPDMRCECNQS T0304 63 :DQAFPLLMKQLELMLTSGELN 1i1qA 242 :DDAFGAVVRQLQKAIRAGEIF T0304 85 :RHQHTVTLYAKG 1i1qA 265 :VPSRRFSLPCPS T0304 105 :SSCDYVYLAVYPT 1i1qA 288 :NPSPYMFFMQDND Number of specific fragments extracted= 5 number of extra gaps= 0 total=147 Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gumA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gumA expands to /projects/compbio/data/pdb/1gum.pdb.gz 1gumA:# T0304 read from 1gumA/merged-good-all-a2m # 1gumA read from 1gumA/merged-good-all-a2m # adding 1gumA to template set # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=149 Number of alignments=41 # 1gumA read from 1gumA/merged-good-all-a2m # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=151 Number of alignments=42 # 1gumA read from 1gumA/merged-good-all-a2m # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=153 Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cigA/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/T0304/2cigA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0304/2cigA/merged-good-all-a2m.gz for input Trying 2cigA/merged-good-all-a2m Error: Couldn't open file 2cigA/merged-good-all-a2m or 2cigA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lj2A expands to /projects/compbio/data/pdb/1lj2.pdb.gz 1lj2A:# T0304 read from 1lj2A/merged-good-all-a2m # 1lj2A read from 1lj2A/merged-good-all-a2m # adding 1lj2A to template set # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=154 Number of alignments=44 # 1lj2A read from 1lj2A/merged-good-all-a2m # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=155 Number of alignments=45 # 1lj2A read from 1lj2A/merged-good-all-a2m # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=156 Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bmeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bmeA expands to /projects/compbio/data/pdb/2bme.pdb.gz 2bmeA:Skipped atom 858, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 862, because occupancy 0.400 <= existing 0.600 in 2bmeA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2bmeA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2bmeA # T0304 read from 2bmeA/merged-good-all-a2m # 2bmeA read from 2bmeA/merged-good-all-a2m # adding 2bmeA to template set # found chain 2bmeA in template set Warning: unaligning (T0304)L53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0304)G80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E179 Warning: unaligning (T0304)E81 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E179 T0304 30 :FGARLVQEGNR 2bmeA 116 :IVIILCGNKKD T0304 41 :LHYLADRAGIRG 2bmeA 138 :ASRFAQENELMF T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTS 2bmeA 152 :TSALTGENVEEAFVQCARKILNKIES Number of specific fragments extracted= 3 number of extra gaps= 2 total=159 # 2bmeA read from 2bmeA/merged-good-all-a2m # found chain 2bmeA in template set Warning: unaligning (T0304)L53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0304)G80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E179 Warning: unaligning (T0304)E81 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E179 T0304 30 :FGARLVQEGNR 2bmeA 116 :IVIILCGNKKD T0304 41 :LHYLADRAGIRG 2bmeA 138 :ASRFAQENELMF T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTS 2bmeA 152 :TSALTGENVEEAFVQCARKILNKIES Number of specific fragments extracted= 3 number of extra gaps= 2 total=162 # 2bmeA read from 2bmeA/merged-good-all-a2m # found chain 2bmeA in template set Warning: unaligning (T0304)L53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E151 Warning: unaligning (T0304)G80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bmeA)E179 Warning: unaligning (T0304)E81 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bmeA)E179 T0304 29 :CFGARLVQEGNR 2bmeA 115 :NIVIILCGNKKD T0304 41 :LHYLADRAGIRG 2bmeA 138 :ASRFAQENELMF T0304 54 :FSDADAYHLDQAFPLLMKQLELMLTS 2bmeA 152 :TSALTGENVEEAFVQCARKILNKIES Number of specific fragments extracted= 3 number of extra gaps= 2 total=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gaiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gaiA expands to /projects/compbio/data/pdb/2gai.pdb.gz 2gaiA:Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1549, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2019, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2025, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2462, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2464, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2466, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2468, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2631, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2633, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2635, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3105, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3107, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3109, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3383, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3385, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3387, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4164, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4166, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4168, because occupancy 0.500 <= existing 0.500 in 2gaiA # T0304 read from 2gaiA/merged-good-all-a2m # 2gaiA read from 2gaiA/merged-good-all-a2m # adding 2gaiA to template set # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=167 Number of alignments=47 # 2gaiA read from 2gaiA/merged-good-all-a2m # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=169 Number of alignments=48 # 2gaiA read from 2gaiA/merged-good-all-a2m # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=171 Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ld4M/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ld4M expands to /projects/compbio/data/pdb/1ld4.pdb.gz 1ld4M:# T0304 read from 1ld4M/merged-good-all-a2m # 1ld4M read from 1ld4M/merged-good-all-a2m # adding 1ld4M to template set # found chain 1ld4M in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=171 # 1ld4M read from 1ld4M/merged-good-all-a2m # found chain 1ld4M in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=171 # 1ld4M read from 1ld4M/merged-good-all-a2m # found chain 1ld4M in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=171 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z8yB/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/T0304/1z8yB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0304/1z8yB/merged-good-all-a2m.gz for input Trying 1z8yB/merged-good-all-a2m Error: Couldn't open file 1z8yB/merged-good-all-a2m or 1z8yB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y74A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y74A expands to /projects/compbio/data/pdb/1y74.pdb.gz 1y74A:# T0304 read from 1y74A/merged-good-all-a2m # 1y74A read from 1y74A/merged-good-all-a2m # adding 1y74A to template set # found chain 1y74A in template set T0304 61 :HLDQAFPLLMKQLELMLTSGELNP 1y74A 18 :GLERDVSRAVELLERLQRSGELPP Number of specific fragments extracted= 1 number of extra gaps= 0 total=172 Number of alignments=50 # 1y74A read from 1y74A/merged-good-all-a2m # found chain 1y74A in template set T0304 61 :HLDQAFPLLMKQLELMLTSGELNP 1y74A 18 :GLERDVSRAVELLERLQRSGELPP Number of specific fragments extracted= 1 number of extra gaps= 0 total=173 Number of alignments=51 # 1y74A read from 1y74A/merged-good-all-a2m # found chain 1y74A in template set T0304 61 :HLDQAFPLLMKQLELMLTSGELNP 1y74A 18 :GLERDVSRAVELLERLQRSGELPP Number of specific fragments extracted= 1 number of extra gaps= 0 total=174 Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rypB expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1rypB:# T0304 read from 1rypB/merged-good-all-a2m # 1rypB read from 1rypB/merged-good-all-a2m # adding 1rypB to template set # found chain 1rypB in template set T0304 9 :TLPDDNHDRPWWGLPCTVTPCFGARLVQEGNRLHYLADRA 1rypB 50 :KSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKS T0304 56 :DADAYHLDQAFPLLMKQLELMLTSGELNPRHQHTVTLYAKGL 1rypB 101 :YGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEF T0304 107 :CDYVYLAVY 1rypB 143 :NGFSLYQVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=177 Number of alignments=53 # 1rypB read from 1rypB/merged-good-all-a2m # found chain 1rypB in template set T0304 9 :TLPDDNHDRPWWGLPCTVTPCFGARLVQEGNRLHYLADRA 1rypB 50 :KSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKS T0304 56 :DADAYHLDQAFPLLMKQLELMLTSGELNPRHQHTVTLYAKGL 1rypB 101 :YGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEF T0304 107 :CDYVYLAVY 1rypB 143 :NGFSLYQVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=180 Number of alignments=54 # 1rypB read from 1rypB/merged-good-all-a2m # found chain 1rypB in template set T0304 9 :TLPDDNHDRPWWGLPCTVTPCFGARLVQEGNRLHYLADRA 1rypB 50 :KSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKS T0304 56 :DADAYHLDQAFPLLMKQLELMLTSGELNPRHQHTVTLYAKGL 1rypB 101 :YGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEF T0304 107 :CDYVYLAVY 1rypB 143 :NGFSLYQVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=183 Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k3yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0304 read from 1k3yA/merged-good-all-a2m # 1k3yA read from 1k3yA/merged-good-all-a2m # found chain 1k3yA in training set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1k3yA 64 :KLVQTRAILNYIASKYNLYGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1k3yA 85 :DIKERALIDMYIEGIADLGEMILL Number of specific fragments extracted= 2 number of extra gaps= 0 total=185 Number of alignments=56 # 1k3yA read from 1k3yA/merged-good-all-a2m # found chain 1k3yA in training set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1k3yA 64 :KLVQTRAILNYIASKYNLYGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1k3yA 85 :DIKERALIDMYIEGIADLGEMILL Number of specific fragments extracted= 2 number of extra gaps= 0 total=187 Number of alignments=57 # 1k3yA read from 1k3yA/merged-good-all-a2m # found chain 1k3yA in training set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1k3yA 64 :KLVQTRAILNYIASKYNLYGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1k3yA 85 :DIKERALIDMYIEGIADLGEMILL Number of specific fragments extracted= 2 number of extra gaps= 0 total=189 Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1womA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1womA expands to /projects/compbio/data/pdb/1wom.pdb.gz 1womA:Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 1womA # T0304 read from 1womA/merged-good-all-a2m # 1womA read from 1womA/merged-good-all-a2m # adding 1womA to template set # found chain 1womA in template set T0304 27 :TPCFGARLVQEGNRLHYLADRAGIRGLFSDADAYHLDQAFPL 1womA 109 :RPELFSHLVMVGPSPCYLNDPPEYYGGFEEEQLLGLLEMMEK T0304 69 :LMKQLELM 1womA 155 :WATVFAAT Number of specific fragments extracted= 2 number of extra gaps= 0 total=191 Number of alignments=59 # 1womA read from 1womA/merged-good-all-a2m # found chain 1womA in template set T0304 27 :TPCFGARLVQEGNRLHYLADRAGIRGLFSDADAYHLDQAFPL 1womA 109 :RPELFSHLVMVGPSPCYLNDPPEYYGGFEEEQLLGLLEMMEK T0304 69 :LMKQLELM 1womA 155 :WATVFAAT Number of specific fragments extracted= 2 number of extra gaps= 0 total=193 Number of alignments=60 # 1womA read from 1womA/merged-good-all-a2m # found chain 1womA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=193 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b9bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b9bA expands to /projects/compbio/data/pdb/1b9b.pdb.gz 1b9bA:# T0304 read from 1b9bA/merged-good-all-a2m # 1b9bA read from 1b9bA/merged-good-all-a2m # adding 1b9bA to template set # found chain 1b9bA in template set T0304 59 :AYHLDQAFPLLMKQLELML 1b9bA 181 :PQQAQEVHAFIRKLLSEMY Number of specific fragments extracted= 1 number of extra gaps= 0 total=194 # 1b9bA read from 1b9bA/merged-good-all-a2m # found chain 1b9bA in template set T0304 59 :AYHLDQAFPLLMKQLELML 1b9bA 181 :PQQAQEVHAFIRKLLSEMY Number of specific fragments extracted= 1 number of extra gaps= 0 total=195 # 1b9bA read from 1b9bA/merged-good-all-a2m # found chain 1b9bA in template set T0304 59 :AYHLDQAFPLLMKQLELML 1b9bA 181 :PQQAQEVHAFIRKLLSEMY Number of specific fragments extracted= 1 number of extra gaps= 0 total=196 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 60 Done printing distance constraints # command: