# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0304//projects/compbio/experiments/protein-predict/casp7/T0304/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0304//projects/compbio/experiments/protein-predict/casp7/T0304/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0304/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0304/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)A101.CB) [> 4.3384 = 7.2306 < 9.3998] w=1.0000 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)A101.CB) [> 3.2206 = 5.3677 < 6.9780] w=1.0000 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)K100.CB) [> 3.3431 = 5.5718 < 7.2433] w=0.8534 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)K100.CB) [> 4.2956 = 7.1594 < 9.3072] w=0.8127 to align # Constraint # added constraint: constraint((T0304)L92.CB, (T0304)A101.CB) [> 4.0955 = 6.8258 < 8.8736] w=0.7597 to align # Constraint # added constraint: constraint((T0304)C99.CB, (T0304)A113.CB) [> 3.8991 = 6.4986 < 8.4482] w=0.7141 to align # Constraint # added constraint: constraint((T0304)A45.CB, (T0304)F54.CB) [> 3.6103 = 6.0173 < 7.8224] w=0.6652 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)F54.CB) [> 4.0285 = 6.7142 < 8.7284] w=0.6652 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)K100.CB) [> 3.8898 = 6.4830 < 8.4280] w=0.6255 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)D102.CB) [> 3.1891 = 5.3151 < 6.9096] w=0.6110 to align # Constraint # added constraint: constraint((T0304)H86.CB, (T0304)T98.CB) [> 4.1786 = 6.9644 < 9.0537] w=0.6083 to align # Constraint # added constraint: constraint((T0304)H86.CB, (T0304)C99.CB) [> 3.6040 = 6.0066 < 7.8086] w=0.6083 to align # Constraint # added constraint: constraint((T0304)Q87.CB, (T0304)T98.CB) [> 4.1065 = 6.8442 < 8.8974] w=0.6083 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)L97.CB) [> 3.6231 = 6.0385 < 7.8500] w=0.6083 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)C99.CB) [> 4.0664 = 6.7773 < 8.8105] w=0.6083 to align # Constraint # added constraint: constraint((T0304)M70.CB, (T0304)L82.CB) [> 4.5566 = 7.5944 < 9.8727] w=0.5995 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)Y43.CB) [> 3.6246 = 6.0410 < 7.8533] w=0.5677 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)R51.CB) [> 4.2994 = 7.1656 < 9.3153] w=0.5677 to align # Constraint # added constraint: constraint((T0304)G52.CA, (T0304)L62.CB) [> 3.7046 = 6.1744 < 8.0267] w=0.5677 to align # Constraint # added constraint: constraint((T0304)L41.CB, (T0304)F66.CB) [> 4.1260 = 6.8766 < 8.9396] w=0.5575 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)A59.CB) [> 3.7292 = 6.2153 < 8.0798] w=0.5427 to align # Constraint # added constraint: constraint((T0304)M70.CB, (T0304)A113.CB) [> 3.6561 = 6.0934 < 7.9215] w=0.5416 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)D102.CB) [> 3.6864 = 6.1440 < 7.9872] w=0.5416 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)T103.CB) [> 3.9181 = 6.5302 < 8.4892] w=0.5416 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)Y109.CB) [> 4.3917 = 7.3195 < 9.5153] w=0.5416 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)Y111.CB) [> 4.6530 = 7.7551 < 10.0816] w=0.5416 to align # Constraint # added constraint: constraint((T0304)T98.CB, (T0304)L112.CB) [> 3.8232 = 6.3720 < 8.2837] w=0.5416 to align # Constraint # added constraint: constraint((T0304)T98.CB, (T0304)A113.CB) [> 3.2234 = 5.3724 < 6.9840] w=0.5416 to align # Constraint # added constraint: constraint((T0304)C99.CB, (T0304)L112.CB) [> 3.1022 = 5.1703 < 6.7214] w=0.5416 to align # Constraint # added constraint: constraint((T0304)K100.CB, (T0304)V110.CB) [> 4.0906 = 6.8176 < 8.8629] w=0.5416 to align # Constraint # added constraint: constraint((T0304)K100.CB, (T0304)Y111.CB) [> 3.3411 = 5.5685 < 7.2391] w=0.5416 to align # Constraint # added constraint: constraint((T0304)A101.CB, (T0304)V110.CB) [> 3.7826 = 6.3043 < 8.1957] w=0.5416 to align # Constraint # added constraint: constraint((T0304)A101.CB, (T0304)Y111.CB) [> 3.9828 = 6.6380 < 8.6294] w=0.5416 to align # Constraint # added constraint: constraint((T0304)D102.CB, (T0304)Y111.CB) [> 3.9901 = 6.6502 < 8.6453] w=0.5416 to align # Constraint # added constraint: constraint((T0304)L53.CB, (T0304)Q64.CB) [> 3.8319 = 6.3864 < 8.3024] w=0.5344 to align # Constraint # added constraint: constraint((T0304)Q36.CB, (T0304)F54.CB) [> 3.8517 = 6.4194 < 8.3453] w=0.5276 to align # Constraint # added constraint: constraint((T0304)L82.CB, (T0304)T103.CB) [> 3.3767 = 5.6278 < 7.3162] w=0.5198 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)G52.CA) [> 3.7235 = 6.2059 < 8.0677] w=0.5096 to align # Constraint # added constraint: constraint((T0304)Y43.CB, (T0304)A59.CB) [> 3.8063 = 6.3438 < 8.2469] w=0.4895 to align # Constraint # added constraint: constraint((T0304)T98.CB, (T0304)Y115.CB) [> 3.7017 = 6.1695 < 8.0203] w=0.4792 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)Y115.CB) [> 3.5348 = 5.8913 < 7.6586] w=0.4792 to align # Constraint # added constraint: constraint((T0304)G96.CA, (T0304)Y115.CB) [> 3.0114 = 5.0190 < 6.5247] w=0.4792 to align # Constraint # added constraint: constraint((T0304)L73.CB, (T0304)A101.CB) [> 3.8795 = 6.4659 < 8.4057] w=0.4531 to align # Constraint # added constraint: constraint((T0304)E81.CB, (T0304)P116.CB) [> 3.7177 = 6.1962 < 8.0551] w=0.4365 to align # Constraint # added constraint: constraint((T0304)G38.CA, (T0304)M70.CB) [> 4.6377 = 7.7295 < 10.0484] w=0.3976 to align # Constraint # added constraint: constraint((T0304)L73.CB, (T0304)L82.CB) [> 4.0001 = 6.6668 < 8.6669] w=0.3816 to align # Constraint # added constraint: constraint((T0304)L92.CB, (T0304)Y109.CB) [> 4.4300 = 7.3833 < 9.5983] w=0.3717 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)T103.CB) [> 4.6475 = 7.7459 < 10.0696] w=0.3706 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)T103.CB) [> 3.3013 = 5.5022 < 7.1528] w=0.3706 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)V90.CB) [> 3.5232 = 5.8720 < 7.6336] w=0.3706 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)I50.CB) [> 3.1726 = 5.2877 < 6.8740] w=0.3664 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)R51.CB) [> 4.3042 = 7.1737 < 9.3259] w=0.3664 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)G52.CA) [> 3.6559 = 6.0931 < 7.9211] w=0.3664 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)G52.CA) [> 3.2862 = 5.4770 < 7.1201] w=0.3664 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)F54.CB) [> 3.9038 = 6.5063 < 8.4581] w=0.3664 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)D102.CB) [> 2.6659 = 4.4432 < 5.7761] w=0.3544 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)A101.CB) [> 4.6266 = 7.7111 < 10.0244] w=0.3544 to align # Constraint # added constraint: constraint((T0304)S79.CB, (T0304)D102.CB) [> 3.9514 = 6.5856 < 8.5613] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L77.CB, (T0304)L104.CB) [> 3.2959 = 5.4932 < 7.1411] w=0.3544 to align # Constraint # added constraint: constraint((T0304)E74.CB, (T0304)Y111.CB) [> 2.8106 = 4.6843 < 6.0896] w=0.3544 to align # Constraint # added constraint: constraint((T0304)E74.CB, (T0304)D102.CB) [> 4.4721 = 7.4535 < 9.6896] w=0.3544 to align # Constraint # added constraint: constraint((T0304)K71.CB, (T0304)A113.CB) [> 4.7131 = 7.8552 < 10.2117] w=0.3544 to align # Constraint # added constraint: constraint((T0304)M70.CB, (T0304)L112.CB) [> 4.3145 = 7.1908 < 9.3480] w=0.3544 to align # Constraint # added constraint: constraint((T0304)M70.CB, (T0304)Y111.CB) [> 3.2106 = 5.3509 < 6.9562] w=0.3544 to align # Constraint # added constraint: constraint((T0304)P67.CB, (T0304)A113.CB) [> 3.2127 = 5.3545 < 6.9608] w=0.3544 to align # Constraint # added constraint: constraint((T0304)F54.CB, (T0304)P116.CB) [> 4.4327 = 7.3879 < 9.6042] w=0.3544 to align # Constraint # added constraint: constraint((T0304)F54.CB, (T0304)Y115.CB) [> 2.7665 = 4.6109 < 5.9941] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L53.CB, (T0304)T117.CB) [> 3.2140 = 5.3567 < 6.9637] w=0.3544 to align # Constraint # added constraint: constraint((T0304)C99.CB, (T0304)Y111.CB) [> 3.7247 = 6.2078 < 8.0702] w=0.3544 to align # Constraint # added constraint: constraint((T0304)C99.CB, (T0304)V110.CB) [> 3.2916 = 5.4860 < 7.1318] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)P116.CB) [> 4.3401 = 7.2335 < 9.4036] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)V114.CB) [> 2.9388 = 4.8980 < 6.3674] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)A113.CB) [> 3.6803 = 6.1338 < 7.9739] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)L112.CB) [> 2.9748 = 4.9579 < 6.4453] w=0.3544 to align # Constraint # added constraint: constraint((T0304)G96.CA, (T0304)P116.CB) [> 2.9716 = 4.9527 < 6.4386] w=0.3544 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)Y111.CB) [> 4.0862 = 6.8103 < 8.8533] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L82.CB, (T0304)T98.CB) [> 3.0359 = 5.0598 < 6.5778] w=0.3544 to align # Constraint # added constraint: constraint((T0304)L82.CB, (T0304)L112.CB) [> 4.6190 = 7.6984 < 10.0079] w=0.3544 to align # Constraint # added constraint: constraint((T0304)N83.CB, (T0304)T98.CB) [> 4.3969 = 7.3282 < 9.5267] w=0.3544 to align # Constraint # added constraint: constraint((T0304)N83.CB, (T0304)K100.CB) [> 4.1015 = 6.8359 < 8.8867] w=0.3544 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)V114.CB) [> 4.2510 = 7.0850 < 9.2105] w=0.3334 to align # Constraint # added constraint: constraint((T0304)R40.CB, (T0304)G52.CA) [> 4.0265 = 6.7108 < 8.7241] w=0.3297 to align # Constraint # added constraint: constraint((T0304)Y43.CB, (T0304)G52.CA) [> 3.2861 = 5.4769 < 7.1199] w=0.3297 to align # Constraint # added constraint: constraint((T0304)Y43.CB, (T0304)L53.CB) [> 3.5135 = 5.8558 < 7.6126] w=0.3297 to align # Constraint # added constraint: constraint((T0304)Y43.CB, (T0304)F54.CB) [> 2.9346 = 4.8911 < 6.3584] w=0.3297 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)S55.CB) [> 4.4994 = 7.4990 < 9.7487] w=0.3297 to align # Constraint # added constraint: constraint((T0304)A45.CB, (T0304)S55.CB) [> 3.4124 = 5.6873 < 7.3935] w=0.3297 to align # Constraint # added constraint: constraint((T0304)A101.CB, (T0304)L112.CB) [> 4.2891 = 7.1485 < 9.2931] w=0.2919 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)A48.CB) [> 4.5264 = 7.5439 < 9.8071] w=0.2877 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)G49.CA) [> 4.2160 = 7.0266 < 9.1346] w=0.2847 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)I50.CB) [> 4.0260 = 6.7100 < 8.7230] w=0.2847 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)R51.CB) [> 4.1781 = 6.9635 < 9.0526] w=0.2847 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)G52.CA) [> 3.8822 = 6.4703 < 8.4115] w=0.2847 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)L53.CB) [> 3.2582 = 5.4303 < 7.0593] w=0.2847 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)A113.CB) [> 2.9227 = 4.8712 < 6.3326] w=0.2802 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)V114.CB) [> 3.0054 = 5.0090 < 6.5117] w=0.2802 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)A113.CB) [> 4.0135 = 6.6891 < 8.6959] w=0.2802 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)Y115.CB) [> 3.4245 = 5.7075 < 7.4198] w=0.2802 to align # Constraint # added constraint: constraint((T0304)L69.CB, (T0304)L92.CB) [> 4.1243 = 6.8738 < 8.9359] w=0.2659 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)S106.CB) [> 3.8330 = 6.3883 < 8.3048] w=0.2659 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)S106.CB) [> 3.7019 = 6.1698 < 8.0207] w=0.2659 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)S106.CB) [> 1.8705 = 3.1175 < 4.0527] w=0.2659 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)R51.CB) [> 3.9835 = 6.6392 < 8.6310] w=0.2617 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)L44.CB) [> 3.9460 = 6.5766 < 8.5496] w=0.2617 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)A45.CB) [> 2.8319 = 4.7198 < 6.1357] w=0.2617 to align # Constraint # added constraint: constraint((T0304)Q87.CB, (T0304)C99.CB) [> 3.5152 = 5.8587 < 7.6163] w=0.2539 to align # Constraint # added constraint: constraint((T0304)R85.CB, (T0304)A101.CB) [> 2.4406 = 4.0676 < 5.2879] w=0.2539 to align # Constraint # added constraint: constraint((T0304)P84.CB, (T0304)K100.CB) [> 4.6654 = 7.7757 < 10.1084] w=0.2539 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)C99.CB) [> 3.3422 = 5.5704 < 7.2415] w=0.2511 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)T91.CB) [> 4.5414 = 7.5690 < 9.8397] w=0.2442 to align # Constraint # added constraint: constraint((T0304)L69.CB, (T0304)L97.CB) [> 4.0823 = 6.8038 < 8.8450] w=0.2418 to align # Constraint # added constraint: constraint((T0304)F66.CB, (T0304)C99.CB) [> 3.8796 = 6.4660 < 8.4057] w=0.2418 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)Y93.CB) [> 2.8339 = 4.7231 < 6.1400] w=0.2124 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)T91.CB) [> 4.1069 = 6.8448 < 8.8982] w=0.2124 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)Y93.CB) [> 3.0392 = 5.0654 < 6.5849] w=0.2124 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)T91.CB) [> 3.7054 = 6.1757 < 8.0285] w=0.2124 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)L92.CB) [> 3.9145 = 6.5242 < 8.4815] w=0.2124 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)V90.CB) [> 3.4345 = 5.7242 < 7.4414] w=0.2124 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)L92.CB) [> 4.6460 = 7.7433 < 10.0663] w=0.2124 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)V90.CB) [> 3.4720 = 5.7867 < 7.5227] w=0.2124 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)A45.CB) [> 4.2375 = 7.0626 < 9.1813] w=0.1894 to align # Constraint # added constraint: constraint((T0304)R85.CB, (T0304)S105.CB) [> 4.5360 = 7.5601 < 9.8281] w=0.1872 to align # Constraint # added constraint: constraint((T0304)M76.CB, (T0304)Y111.CB) [> 4.6338 = 7.7229 < 10.0398] w=0.1872 to align # Constraint # added constraint: constraint((T0304)L69.CB, (T0304)A113.CB) [> 2.9609 = 4.9348 < 6.4153] w=0.1872 to align # Constraint # added constraint: constraint((T0304)Q87.CB, (T0304)S105.CB) [> 4.7649 = 7.9416 < 10.3240] w=0.1872 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)A101.CB) [> 3.6963 = 6.1605 < 8.0086] w=0.1872 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)T103.CB) [> 3.9964 = 6.6607 < 8.6589] w=0.1872 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)L104.CB) [> 3.7382 = 6.2303 < 8.0994] w=0.1872 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)L104.CB) [> 3.4428 = 5.7379 < 7.4593] w=0.1872 to align # Constraint # added constraint: constraint((T0304)T98.CB, (T0304)V114.CB) [> 3.2905 = 5.4841 < 7.1294] w=0.1872 to align # Constraint # added constraint: constraint((T0304)C99.CB, (T0304)V114.CB) [> 4.7165 = 7.8608 < 10.2191] w=0.1872 to align # Constraint # added constraint: constraint((T0304)K100.CB, (T0304)L112.CB) [> 3.4923 = 5.8204 < 7.5666] w=0.1872 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)I50.CB) [> 3.2974 = 5.4957 < 7.1444] w=0.1864 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)G52.CA) [> 3.3800 = 5.6334 < 7.3234] w=0.1864 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)M76.CB) [> 4.0696 = 6.7827 < 8.8176] w=0.1800 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)L77.CB) [> 4.7141 = 7.8569 < 10.2139] w=0.1800 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)L69.CB) [> 4.0496 = 6.7493 < 8.7740] w=0.1800 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)M76.CB) [> 4.4665 = 7.4441 < 9.6773] w=0.1800 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)A48.CB) [> 4.7530 = 7.9216 < 10.2981] w=0.1800 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)I50.CB) [> 2.6621 = 4.4368 < 5.7679] w=0.1800 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)A65.CB) [> 3.4160 = 5.6933 < 7.4013] w=0.1800 to align # Constraint # added constraint: constraint((T0304)E37.CB, (T0304)F54.CB) [> 3.0378 = 5.0631 < 6.5820] w=0.1800 to align # Constraint # added constraint: constraint((T0304)N39.CB, (T0304)H61.CB) [> 4.4432 = 7.4053 < 9.6269] w=0.1800 to align # Constraint # added constraint: constraint((T0304)K100.CB, (T0304)V114.CB) [> 3.6146 = 6.0244 < 7.8317] w=0.1725 to align # Constraint # added constraint: constraint((T0304)K100.CB, (T0304)A113.CB) [> 3.5387 = 5.8978 < 7.6671] w=0.1725 to align # Constraint # added constraint: constraint((T0304)L92.CB, (T0304)A113.CB) [> 3.9653 = 6.6088 < 8.5914] w=0.1725 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)Y115.CB) [> 4.3051 = 7.1751 < 9.3276] w=0.1725 to align # Constraint # added constraint: constraint((T0304)H86.CB, (T0304)Y115.CB) [> 4.1695 = 6.9491 < 9.0339] w=0.1725 to align # Constraint # added constraint: constraint((T0304)E81.CB, (T0304)P118.CB) [> 4.7014 = 7.8357 < 10.1865] w=0.1725 to align # Constraint # added constraint: constraint((T0304)E81.CB, (T0304)T117.CB) [> 1.8844 = 3.1407 < 4.0830] w=0.1725 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)T117.CB) [> 3.9432 = 6.5719 < 8.5435] w=0.1725 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)G38.CA) [> 4.2384 = 7.0639 < 9.1831] w=0.1693 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)L41.CB) [> 3.6428 = 6.0713 < 7.8927] w=0.1693 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)G38.CA) [> 2.5922 = 4.3203 < 5.6164] w=0.1693 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)N39.CB) [> 2.8349 = 4.7248 < 6.1423] w=0.1693 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)R40.CB) [> 2.7952 = 4.6587 < 6.0563] w=0.1693 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)L41.CB) [> 4.2386 = 7.0643 < 9.1836] w=0.1693 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)L69.CB) [> 3.7341 = 6.2235 < 8.0906] w=0.1612 to align # Constraint # added constraint: constraint((T0304)Q36.CB, (T0304)D58.CB) [> 4.0542 = 6.7570 < 8.7840] w=0.1612 to align # Constraint # added constraint: constraint((T0304)R40.CB, (T0304)I50.CB) [> 3.0578 = 5.0963 < 6.6252] w=0.1612 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)L112.CB) [> 4.6710 = 7.7850 < 10.1205] w=0.1609 to align # Constraint # added constraint: constraint((T0304)E37.CB, (T0304)L73.CB) [> 4.6294 = 7.7158 < 10.0305] w=0.1599 to align # Constraint # added constraint: constraint((T0304)G21.CA, (T0304)N39.CB) [> 4.0289 = 6.7148 < 8.7292] w=0.1599 to align # Constraint # added constraint: constraint((T0304)W20.CB, (T0304)R40.CB) [> 3.8674 = 6.4457 < 8.3794] w=0.1599 to align # Constraint # added constraint: constraint((T0304)W20.CB, (T0304)E37.CB) [> 3.5298 = 5.8831 < 7.6480] w=0.1599 to align # Constraint # added constraint: constraint((T0304)W20.CB, (T0304)Q36.CB) [> 4.5810 = 7.6350 < 9.9254] w=0.1599 to align # Constraint # added constraint: constraint((T0304)D46.CB, (T0304)A57.CB) [> 3.1901 = 5.3168 < 6.9119] w=0.1599 to align # Constraint # added constraint: constraint((T0304)A45.CB, (T0304)F66.CB) [> 4.3743 = 7.2905 < 9.4776] w=0.1599 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)L68.CB) [> 4.2669 = 7.1115 < 9.2450] w=0.1599 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)A65.CB) [> 2.1480 = 3.5799 < 4.6539] w=0.1599 to align # Constraint # added constraint: constraint((T0304)L41.CB, (T0304)Y60.CB) [> 4.7557 = 7.9262 < 10.3041] w=0.1599 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)A65.CB) [> 4.4375 = 7.3959 < 9.6147] w=0.1599 to align # Constraint # added constraint: constraint((T0304)Y43.CB, (T0304)A65.CB) [> 4.5805 = 7.6342 < 9.9244] w=0.1599 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)Y60.CB) [> 2.0917 = 3.4862 < 4.5320] w=0.1599 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)V110.CB) [> 2.9385 = 4.8975 < 6.3667] w=0.1579 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)H88.CB) [> 3.8166 = 6.3610 < 8.2693] w=0.1365 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)L92.CB) [> 4.0686 = 6.7811 < 8.8154] w=0.1365 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)T91.CB) [> 3.0446 = 5.0743 < 6.5966] w=0.1365 to align # Constraint # added constraint: constraint((T0304)T25.CB, (T0304)V90.CB) [> 4.4678 = 7.4464 < 9.6803] w=0.1365 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)L92.CB) [> 2.8670 = 4.7784 < 6.2119] w=0.1365 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)T91.CB) [> 4.3573 = 7.2621 < 9.4407] w=0.1365 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)V90.CB) [> 3.6418 = 6.0697 < 7.8906] w=0.1365 to align # Constraint # added constraint: constraint((T0304)L22.CB, (T0304)Y93.CB) [> 3.5515 = 5.9191 < 7.6949] w=0.1365 to align # Constraint # added constraint: constraint((T0304)L22.CB, (T0304)L92.CB) [> 3.4911 = 5.8185 < 7.5641] w=0.1365 to align # Constraint # added constraint: constraint((T0304)W19.CB, (T0304)K95.CB) [> 3.6528 = 6.0879 < 7.9143] w=0.1365 to align # Constraint # added constraint: constraint((T0304)W19.CB, (T0304)Y93.CB) [> 3.2329 = 5.3882 < 7.0046] w=0.1365 to align # Constraint # added constraint: constraint((T0304)R17.CB, (T0304)K95.CB) [> 2.4118 = 4.0196 < 5.2255] w=0.1365 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)T89.CB) [> 4.1988 = 6.9980 < 9.0975] w=0.1365 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)V90.CB) [> 3.3802 = 5.6337 < 7.3238] w=0.1365 to align # Constraint # added constraint: constraint((T0304)T27.CB, (T0304)T91.CB) [> 4.2470 = 7.0783 < 9.2018] w=0.1365 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)A65.CB) [> 2.7939 = 4.6564 < 6.0534] w=0.1365 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)F66.CB) [> 3.2785 = 5.4642 < 7.1034] w=0.1365 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)H88.CB) [> 3.4169 = 5.6948 < 7.4033] w=0.1365 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)T89.CB) [> 4.4432 = 7.4053 < 9.6269] w=0.1365 to align # Constraint # added constraint: constraint((T0304)F66.CB, (T0304)H88.CB) [> 3.6352 = 6.0586 < 7.8762] w=0.1365 to align # Constraint # added constraint: constraint((T0304)K95.CB, (T0304)Y115.CB) [> 3.7722 = 6.2870 < 8.1731] w=0.1248 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)V90.CB) [> 4.0430 = 6.7383 < 8.7598] w=0.1077 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)T89.CB) [> 4.1111 = 6.8518 < 8.9073] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)H88.CB) [> 3.7403 = 6.2339 < 8.1040] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L34.CB, (T0304)T89.CB) [> 2.9533 = 4.9222 < 6.3988] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)Q87.CB) [> 4.2522 = 7.0870 < 9.2131] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)H88.CB) [> 3.1360 = 5.2268 < 6.7948] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L41.CB, (T0304)T89.CB) [> 4.2878 = 7.1463 < 9.2903] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L44.CB, (T0304)Q72.CB) [> 4.1130 = 6.8550 < 8.9115] w=0.1077 to align # Constraint # added constraint: constraint((T0304)R47.CB, (T0304)L69.CB) [> 4.5491 = 7.5819 < 9.8565] w=0.1077 to align # Constraint # added constraint: constraint((T0304)R47.CB, (T0304)Q72.CB) [> 3.4249 = 5.7081 < 7.4205] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A48.CB, (T0304)A65.CB) [> 3.9700 = 6.6167 < 8.6017] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L22.CB, (T0304)R33.CB) [> 3.6622 = 6.1036 < 7.9347] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L22.CB, (T0304)L34.CB) [> 4.0844 = 6.8074 < 8.8496] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L22.CB, (T0304)L41.CB) [> 4.6473 = 7.7456 < 10.0692] w=0.1077 to align # Constraint # added constraint: constraint((T0304)P23.CB, (T0304)A32.CB) [> 4.3636 = 7.2727 < 9.4545] w=0.1077 to align # Constraint # added constraint: constraint((T0304)P23.CB, (T0304)R33.CB) [> 3.0209 = 5.0348 < 6.5452] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)R33.CB) [> 4.7535 = 7.9225 < 10.2992] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C24.CB, (T0304)A45.CB) [> 2.8670 = 4.7783 < 6.2119] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)A45.CB) [> 4.0340 = 6.7234 < 8.7404] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)A48.CB) [> 2.9798 = 4.9663 < 6.4562] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)Y93.CB) [> 4.7809 = 7.9682 < 10.3586] w=0.1077 to align # Constraint # added constraint: constraint((T0304)T27.CB, (T0304)Y60.CB) [> 4.2058 = 7.0096 < 9.1125] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)A59.CB) [> 3.6941 = 6.1568 < 8.0039] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)L62.CB) [> 4.6853 = 7.8089 < 10.1515] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)Y93.CB) [> 3.3409 = 5.5681 < 7.2386] w=0.1077 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)A94.CB) [> 3.0086 = 5.0143 < 6.5186] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)A59.CB) [> 4.4785 = 7.4641 < 9.7034] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)L62.CB) [> 3.4171 = 5.6952 < 7.4037] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)A65.CB) [> 3.5409 = 5.9015 < 7.6720] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)T91.CB) [> 3.8733 = 6.4556 < 8.3923] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)L92.CB) [> 4.2843 = 7.1405 < 9.2826] w=0.1077 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)A94.CB) [> 4.6455 = 7.7426 < 10.0654] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A32.CB, (T0304)T89.CB) [> 3.1127 = 5.1878 < 6.7441] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L73.CB, (T0304)P84.CB) [> 4.3193 = 7.1989 < 9.3586] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L73.CB, (T0304)V114.CB) [> 3.8948 = 6.4913 < 8.4387] w=0.1077 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)A113.CB) [> 3.9232 = 6.5387 < 8.5003] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)Y111.CB) [> 4.1109 = 6.8515 < 8.9069] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)L112.CB) [> 4.3126 = 7.1877 < 9.3440] w=0.1077 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)Y111.CB) [> 4.4995 = 7.4992 < 9.7489] w=0.1077 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)L112.CB) [> 2.8785 = 4.7975 < 6.2368] w=0.1077 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)A113.CB) [> 4.7648 = 7.9412 < 10.3236] w=0.1077 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)V114.CB) [> 4.0582 = 6.7637 < 8.7928] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L92.CB, (T0304)V110.CB) [> 4.3273 = 7.2121 < 9.3757] w=0.1077 to align # Constraint # added constraint: constraint((T0304)Y93.CB, (T0304)Y109.CB) [> 4.5921 = 7.6534 < 9.9494] w=0.1077 to align # Constraint # added constraint: constraint((T0304)Y93.CB, (T0304)V110.CB) [> 3.5435 = 5.9059 < 7.6776] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A94.CB, (T0304)C107.CB) [> 4.7783 = 7.9638 < 10.3529] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A94.CB, (T0304)D108.CB) [> 3.2974 = 5.4956 < 7.1443] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A94.CB, (T0304)Y109.CB) [> 3.1974 = 5.3290 < 6.9277] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A94.CB, (T0304)V110.CB) [> 4.4903 = 7.4838 < 9.7290] w=0.1077 to align # Constraint # added constraint: constraint((T0304)G96.CA, (T0304)D108.CB) [> 3.8906 = 6.4843 < 8.4296] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L97.CB, (T0304)C107.CB) [> 3.1773 = 5.2954 < 6.8841] w=0.1077 to align # Constraint # added constraint: constraint((T0304)A48.CB, (T0304)L68.CB) [> 4.1802 = 6.9670 < 9.0570] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L62.CB, (T0304)A94.CB) [> 4.2624 = 7.1039 < 9.2351] w=0.1077 to align # Constraint # added constraint: constraint((T0304)D63.CB, (T0304)L112.CB) [> 4.0556 = 6.7594 < 8.7872] w=0.1077 to align # Constraint # added constraint: constraint((T0304)D63.CB, (T0304)V110.CB) [> 3.9727 = 6.6212 < 8.6075] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L62.CB, (T0304)L112.CB) [> 3.9856 = 6.6426 < 8.6354] w=0.1077 to align # Constraint # added constraint: constraint((T0304)L62.CB, (T0304)V110.CB) [> 2.7520 = 4.5867 < 5.9628] w=0.1077 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)G80.CA) [> 3.0911 = 5.1519 < 6.6975] w=0.1047 to align # Constraint # added constraint: constraint((T0304)V35.CB, (T0304)T78.CB) [> 4.5839 = 7.6399 < 9.9318] w=0.1047 to align # Constraint # added constraint: constraint((T0304)E37.CB, (T0304)T78.CB) [> 4.6131 = 7.6885 < 9.9951] w=0.1047 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)I50.CB) [> 2.9251 = 4.8751 < 6.3377] w=0.1047 to align # Constraint # added constraint: constraint((T0304)V26.CB, (T0304)G52.CA) [> 4.3035 = 7.1725 < 9.3243] w=0.1047 to align # Constraint # added constraint: constraint((T0304)T27.CB, (T0304)I50.CB) [> 4.7531 = 7.9218 < 10.2983] w=0.1047 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)G49.CA) [> 3.3730 = 5.6217 < 7.3082] w=0.1047 to align # Constraint # added constraint: constraint((T0304)P28.CB, (T0304)I50.CB) [> 2.4791 = 4.1318 < 5.3713] w=0.1047 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)A48.CB) [> 2.4906 = 4.1511 < 5.3964] w=0.1047 to align # Constraint # added constraint: constraint((T0304)F30.CB, (T0304)I50.CB) [> 4.5495 = 7.5824 < 9.8572] w=0.1047 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)G49.CA) [> 2.9448 = 4.9080 < 6.3803] w=0.1047 to align # Constraint # added constraint: constraint((T0304)G31.CA, (T0304)A94.CB) [> 4.1762 = 6.9603 < 9.0484] w=0.1047 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)G49.CA) [> 3.2740 = 5.4566 < 7.0936] w=0.1047 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)S79.CB) [> 4.1054 = 6.8423 < 8.8950] w=0.1047 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)G80.CA) [> 2.9597 = 4.9328 < 6.4127] w=0.1047 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)T91.CB) [> 3.1387 = 5.2311 < 6.8005] w=0.1047 to align # Constraint # added constraint: constraint((T0304)R33.CB, (T0304)L104.CB) [> 4.2942 = 7.1570 < 9.3042] w=0.1047 to align # Constraint # added constraint: constraint((T0304)T78.CB, (T0304)L104.CB) [> 4.1871 = 6.9786 < 9.0721] w=0.1047 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)T103.CB) [> 4.0890 = 6.8150 < 8.8595] w=0.1047 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)L104.CB) [> 2.9353 = 4.8922 < 6.3598] w=0.1047 to align # Constraint # added constraint: constraint((T0304)G80.CA, (T0304)S105.CB) [> 2.5457 = 4.2429 < 5.5157] w=0.1047 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)L104.CB) [> 4.3470 = 7.2450 < 9.4185] w=0.1047 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)C107.CB) [> 4.5083 = 7.5138 < 9.7680] w=0.1047 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)L104.CB) [> 3.3612 = 5.6020 < 7.2826] w=0.1047 to align # Constraint # added constraint: constraint((T0304)L73.CB, (T0304)C107.CB) [> 3.4930 = 5.8216 < 7.5681] w=0.1047 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)F54.CB) [> 4.1668 = 6.9447 < 9.0281] w=0.0817 to align # Constraint # added constraint: constraint((T0304)P84.CB, (T0304)V114.CB) [> 4.3674 = 7.2790 < 9.4627] w=0.0532 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)S106.CB) [> 4.6121 = 7.6868 < 9.9929] w=0.0532 to align # Constraint # added constraint: constraint((T0304)H42.CB, (T0304)D102.CB) [> 3.2367 = 5.3945 < 7.0128] w=0.0532 to align # Constraint # added constraint: constraint((T0304)L41.CB, (T0304)S106.CB) [> 4.1394 = 6.8990 < 8.9687] w=0.0532 to align # Constraint # added constraint: constraint((T0304)G38.CA, (T0304)S106.CB) [> 2.2826 = 3.8043 < 4.9456] w=0.0532 to align # Constraint # added constraint: constraint((T0304)E37.CB, (T0304)C107.CB) [> 2.9282 = 4.8804 < 6.3445] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T8.CB, (T0304)R17.CB) [> 4.2991 = 7.1652 < 9.3147] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)Y109.CB) [> 3.0326 = 5.0543 < 6.5705] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)D108.CB) [> 4.2156 = 7.0261 < 9.1339] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T91.CB, (T0304)C107.CB) [> 4.3738 = 7.2896 < 9.4765] w=0.0532 to align # Constraint # added constraint: constraint((T0304)V90.CB, (T0304)Y109.CB) [> 3.9267 = 6.5446 < 8.5080] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)Y111.CB) [> 2.8641 = 4.7736 < 6.2056] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)V110.CB) [> 3.9403 = 6.5672 < 8.5373] w=0.0532 to align # Constraint # added constraint: constraint((T0304)T89.CB, (T0304)Y109.CB) [> 3.5087 = 5.8478 < 7.6021] w=0.0532 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)Y111.CB) [> 4.5082 = 7.5137 < 9.7678] w=0.0532 to align # Constraint # added constraint: constraint((T0304)R85.CB, (T0304)V114.CB) [> 3.7766 = 6.2944 < 8.1827] w=0.0532 to align # Constraint # added constraint: constraint((T0304)H88.CB, (T0304)V110.CB) [> 4.7700 = 7.9500 < 10.3351] w=0.0532 to align # Constraint # added constraint: constraint((T0304)C29.CB, (T0304)F66.CB) [> 4.2401 = 7.0668 < 9.1868] w=0.0455 to align # Constraint # added constraint: constraint((T0304)L10.CB, (T0304)G96.CA) [> 3.9616 = 6.6027 < 8.5835] w=0.0455 to align # Constraint # added constraint: constraint((T0304)L10.CB, (T0304)K95.CB) [> 4.7380 = 7.8967 < 10.2657] w=0.0455 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0304/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0304/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 25, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 27, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 121, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 123, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 449, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 451, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 25, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 27, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 121, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 123, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 449, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 451, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 45 < previous residue 122 in servers/POMYSL_TS4.pdb.gz # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 32 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0304)C99.CA and (T0304)L104.CA only 0.000 apart, marking (T0304)L104.CA as missing WARNING: atoms too close: (T0304)K100.CA and (T0304)S105.CA only 0.000 apart, marking (T0304)S105.CA as missing WARNING: atoms too close: (T0304)A101.CA and (T0304)S106.CA only 0.000 apart, marking (T0304)S106.CA as missing # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0304)P6.O and (T0304)G7.N only 0.000 apart, marking (T0304)G7.N as missing # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0304)C24.O and (T0304)T25.N only 0.000 apart, marking (T0304)T25.N as missing # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0304 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.9870 model score 1.8484 model score 1.6074 model score 1.6638 model score 1.6852 model score 1.5331 model score 1.3759 model score 1.3759 model score 1.5837 model score 1.5837 model score 2.1247 model score 1.3883 model score 2.0323 model score 2.0463 model score 1.8549 model score 1.0966 model score 1.8546 model score 1.2985 model score 2.4032 model score 2.1203 model score 1.0966 model score 1.2985 model score 1.2585 model score 1.1420 model score 1.1136 model score 1.8407 model score 1.5338 model score 1.7061 model score 1.8574 model score 1.8365 model score 1.7639 model score 1.7936 model score 1.8202 model score 1.6390 model score 1.8564 model score 1.8981 model score 1.4886 model score 1.6755 model score 1.7457 model score 2.1070 model score 2.1952 model score 1.2794 model score 1.2793 model score 1.2794 model score 1.2794 model score 1.2795 model score 1.6390 model score 1.7086 model score 1.6206 model score 1.5056 model score 2.0600 model score 1.8981 model score 1.4985 model score 1.8564 model score 1.7936 model score 1.6390 model score 1.7850 model score 1.9148 model score 1.5651 model score 2.2418 model score 2.0133 model score 1.2800 model score 1.2771 model score 1.2796 model score 1.2789 model score 1.2797 model score 1.2800 model score 1.2771 model score 1.2796 model score 1.2771 model score 1.2789 model score 1.9407 model score 1.7801 model score 1.8598 model score 2.3560 model score 1.6629 model score 1.6161 model score 2.0684 model score 1.4496 model score 2.1902 model score 1.8968 model score 1.2794 model score 1.2795 model score 1.2780 model score 1.2771 model score 1.2793 model score 1.2958 model score 1.4985 model score 1.6582 model score 1.8081 model score 2.0154 model score 2.0526 model score 1.8884 model score 1.9390 model score 1.3762 model score 2.0836 model score 2.5926 model score 2.7106 model score 2.6772 model score 2.0857 model score 1.6769 model score 1.5106 model score 1.8517 model score 1.7149 model score 1.7872 model score 1.3394 model score 1.0727 model score 1.6049 model score 1.5726 model score 1.2771 model score 1.3341 model score 1.5349 model score 1.3655 model score 1.6672 model score 1.8297 model score 1.1740 model score 1.4990 model score 1.4063 model score 1.0683 model score 1.3927 model score 2.0038 model score 1.7482 model score 1.7814 model score 2.1016 model score 1.6230 model score 2.0403 model score 1.5719 model score 1.5800 model score 1.5432 model score 1.5934 model score 1.7478 model score 1.5974 model score 2.2070 model score 1.7645 model score 2.1845 model score 2.1858 model score 2.0770 model score 1.7310 model score 1.9415 model score 1.2340 model score 1.3789 model score 1.3623 model score 1.7918 model score 1.5400 model score 1.7308 model score 1.5610 model score 1.7306 model score 1.2340 model score 1.2697 model score 1.2689 model score 1.6226 model score 1.3657 model score 1.3557 model score 2.5956 model score 2.3183 model score 1.7896 model score 2.0874 model score 1.2251 model score 1.8406 model score 1.9856 model score 1.4706 model score 2.0228 model score 1.1991 model score 1.8376 model score 1.9728 model score 1.4027 model score 2.1367 model score 1.4614 model score 1.2697 model score 1.2689 model score 1.3657 model score 1.2390 model score 1.2794 model score 1.2760 model score 1.2790 model score 1.2771 model score 1.2786 model score 1.2798 model score 1.2783 model score 1.2771 model score 1.2771 model score 1.2790 model score 2.0453 model score 1.2895 model score 1.3749 model score 2.0516 model score 1.6388 model score 1.8499 model score 1.8800 model score 1.6790 model score 1.7760 model score 1.9959 model score 1.7950 model score 1.8800 model score 1.8053 model score 1.6299 model score 1.1708 model score 1.9550 model score 2.4555 model score 2.2616 model score 2.0045 model score 2.1269 model score 1.2771 model score 1.2771 model score 1.2784 model score 1.2771 model score 1.2771 model score 1.0461 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.1086 model score 0.9617 model score 1.1600 model score 0.9504 model score 1.0352 model score 1.5713 model score 1.7413 model score 1.2799 model score 1.2771 model score 1.2771 model score 1.2790 model score 1.2771 model score 1.8910 model score 1.8538 model score 1.7482 model score 1.6881 model score 2.1699 model score 1.7053 model score 2.0561 model score 1.7552 model score 1.8212 model score 2.0646 model score 1.6307 model score 1.7158 model score 1.7560 model score 1.4977 model score 1.8173 model score 2.0900 model score 2.1955 model score 2.1246 model score 2.0999 model score 2.0910 model score 1.7693 model score 2.0038 model score 1.8519 model score 1.9881 model score 2.0239 model score 2.1080 model score 1.4701 model score 1.2628 USE_META, weight: 0.4700 cost: 1.9870 min: 0.9504 max: 2.7106 USE_META, weight: 0.5408 cost: 1.8484 min: 0.9504 max: 2.7106 USE_META, weight: 0.6641 cost: 1.6074 min: 0.9504 max: 2.7106 USE_META, weight: 0.6352 cost: 1.6638 min: 0.9504 max: 2.7106 USE_META, weight: 0.6243 cost: 1.6852 min: 0.9504 max: 2.7106 USE_META, weight: 0.7020 cost: 1.5331 min: 0.9504 max: 2.7106 USE_META, weight: 0.7824 cost: 1.3759 min: 0.9504 max: 2.7106 USE_META, weight: 0.7824 cost: 1.3759 min: 0.9504 max: 2.7106 USE_META, weight: 0.6762 cost: 1.5837 min: 0.9504 max: 2.7106 USE_META, weight: 0.6762 cost: 1.5837 min: 0.9504 max: 2.7106 USE_META, weight: 0.3996 cost: 2.1247 min: 0.9504 max: 2.7106 USE_META, weight: 0.7761 cost: 1.3883 min: 0.9504 max: 2.7106 USE_META, weight: 0.4468 cost: 2.0323 min: 0.9504 max: 2.7106 USE_META, weight: 0.4397 cost: 2.0463 min: 0.9504 max: 2.7106 USE_META, weight: 0.5375 cost: 1.8549 min: 0.9504 max: 2.7106 USE_META, weight: 0.9252 cost: 1.0966 min: 0.9504 max: 2.7106 USE_META, weight: 0.5377 cost: 1.8546 min: 0.9504 max: 2.7106 USE_META, weight: 0.8220 cost: 1.2985 min: 0.9504 max: 2.7106 USE_META, weight: 0.2572 cost: 2.4032 min: 0.9504 max: 2.7106 USE_META, weight: 0.4018 cost: 2.1203 min: 0.9504 max: 2.7106 USE_META, weight: 0.9252 cost: 1.0966 min: 0.9504 max: 2.7106 USE_META, weight: 0.8220 cost: 1.2985 min: 0.9504 max: 2.7106 USE_META, weight: 0.8424 cost: 1.2585 min: 0.9504 max: 2.7106 USE_META, weight: 0.9020 cost: 1.1420 min: 0.9504 max: 2.7106 USE_META, weight: 0.9166 cost: 1.1136 min: 0.9504 max: 2.7106 USE_META, weight: 0.5448 cost: 1.8407 min: 0.9504 max: 2.7106 USE_META, weight: 0.7017 cost: 1.5338 min: 0.9504 max: 2.7106 USE_META, weight: 0.6136 cost: 1.7061 min: 0.9504 max: 2.7106 USE_META, weight: 0.5362 cost: 1.8574 min: 0.9504 max: 2.7106 USE_META, weight: 0.5469 cost: 1.8365 min: 0.9504 max: 2.7106 USE_META, weight: 0.5840 cost: 1.7639 min: 0.9504 max: 2.7106 USE_META, weight: 0.5688 cost: 1.7936 min: 0.9504 max: 2.7106 USE_META, weight: 0.5553 cost: 1.8202 min: 0.9504 max: 2.7106 USE_META, weight: 0.6479 cost: 1.6390 min: 0.9504 max: 2.7106 USE_META, weight: 0.5367 cost: 1.8564 min: 0.9504 max: 2.7106 USE_META, weight: 0.5154 cost: 1.8981 min: 0.9504 max: 2.7106 USE_META, weight: 0.7248 cost: 1.4886 min: 0.9504 max: 2.7106 USE_META, weight: 0.6292 cost: 1.6755 min: 0.9504 max: 2.7106 USE_META, weight: 0.5934 cost: 1.7457 min: 0.9504 max: 2.7106 USE_META, weight: 0.4086 cost: 2.1070 min: 0.9504 max: 2.7106 USE_META, weight: 0.3635 cost: 2.1952 min: 0.9504 max: 2.7106 USE_META, weight: 0.8318 cost: 1.2794 min: 0.9504 max: 2.7106 USE_META, weight: 0.8318 cost: 1.2793 min: 0.9504 max: 2.7106 USE_META, weight: 0.8317 cost: 1.2794 min: 0.9504 max: 2.7106 USE_META, weight: 0.8317 cost: 1.2794 min: 0.9504 max: 2.7106 USE_META, weight: 0.8317 cost: 1.2795 min: 0.9504 max: 2.7106 USE_META, weight: 0.6479 cost: 1.6390 min: 0.9504 max: 2.7106 USE_META, weight: 0.6123 cost: 1.7086 min: 0.9504 max: 2.7106 USE_META, weight: 0.6573 cost: 1.6206 min: 0.9504 max: 2.7106 USE_META, weight: 0.7161 cost: 1.5056 min: 0.9504 max: 2.7106 USE_META, weight: 0.4326 cost: 2.0600 min: 0.9504 max: 2.7106 USE_META, weight: 0.5154 cost: 1.8981 min: 0.9504 max: 2.7106 USE_META, weight: 0.7198 cost: 1.4985 min: 0.9504 max: 2.7106 USE_META, weight: 0.5367 cost: 1.8564 min: 0.9504 max: 2.7106 USE_META, weight: 0.5688 cost: 1.7936 min: 0.9504 max: 2.7106 USE_META, weight: 0.6479 cost: 1.6390 min: 0.9504 max: 2.7106 USE_META, weight: 0.5733 cost: 1.7850 min: 0.9504 max: 2.7106 USE_META, weight: 0.5069 cost: 1.9148 min: 0.9504 max: 2.7106 USE_META, weight: 0.6857 cost: 1.5651 min: 0.9504 max: 2.7106 USE_META, weight: 0.3397 cost: 2.2418 min: 0.9504 max: 2.7106 USE_META, weight: 0.4565 cost: 2.0133 min: 0.9504 max: 2.7106 USE_META, weight: 0.8315 cost: 1.2800 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8316 cost: 1.2796 min: 0.9504 max: 2.7106 USE_META, weight: 0.8320 cost: 1.2789 min: 0.9504 max: 2.7106 USE_META, weight: 0.8316 cost: 1.2797 min: 0.9504 max: 2.7106 USE_META, weight: 0.8315 cost: 1.2800 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8316 cost: 1.2796 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8320 cost: 1.2789 min: 0.9504 max: 2.7106 USE_META, weight: 0.4936 cost: 1.9407 min: 0.9504 max: 2.7106 USE_META, weight: 0.5757 cost: 1.7801 min: 0.9504 max: 2.7106 USE_META, weight: 0.5350 cost: 1.8598 min: 0.9504 max: 2.7106 USE_META, weight: 0.2813 cost: 2.3560 min: 0.9504 max: 2.7106 USE_META, weight: 0.6357 cost: 1.6629 min: 0.9504 max: 2.7106 USE_META, weight: 0.6596 cost: 1.6161 min: 0.9504 max: 2.7106 USE_META, weight: 0.4283 cost: 2.0684 min: 0.9504 max: 2.7106 USE_META, weight: 0.7447 cost: 1.4496 min: 0.9504 max: 2.7106 USE_META, weight: 0.3661 cost: 2.1902 min: 0.9504 max: 2.7106 USE_META, weight: 0.5161 cost: 1.8968 min: 0.9504 max: 2.7106 USE_META, weight: 0.8318 cost: 1.2794 min: 0.9504 max: 2.7106 USE_META, weight: 0.8317 cost: 1.2795 min: 0.9504 max: 2.7106 USE_META, weight: 0.8325 cost: 1.2780 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8318 cost: 1.2793 min: 0.9504 max: 2.7106 USE_META, weight: 0.8234 cost: 1.2958 min: 0.9504 max: 2.7106 USE_META, weight: 0.7198 cost: 1.4985 min: 0.9504 max: 2.7106 USE_META, weight: 0.6381 cost: 1.6582 min: 0.9504 max: 2.7106 USE_META, weight: 0.5614 cost: 1.8081 min: 0.9504 max: 2.7106 USE_META, weight: 0.4554 cost: 2.0154 min: 0.9504 max: 2.7106 USE_META, weight: 0.4364 cost: 2.0526 min: 0.9504 max: 2.7106 USE_META, weight: 0.5204 cost: 1.8884 min: 0.9504 max: 2.7106 USE_META, weight: 0.4945 cost: 1.9390 min: 0.9504 max: 2.7106 USE_META, weight: 0.7823 cost: 1.3762 min: 0.9504 max: 2.7106 USE_META, weight: 0.4206 cost: 2.0836 min: 0.9504 max: 2.7106 USE_META, weight: 0.1603 cost: 2.5926 min: 0.9504 max: 2.7106 USE_META, weight: 0.1000 cost: 2.7106 min: 0.9504 max: 2.7106 USE_META, weight: 0.1171 cost: 2.6772 min: 0.9504 max: 2.7106 USE_META, weight: 0.4195 cost: 2.0857 min: 0.9504 max: 2.7106 USE_META, weight: 0.6285 cost: 1.6769 min: 0.9504 max: 2.7106 USE_META, weight: 0.7136 cost: 1.5106 min: 0.9504 max: 2.7106 USE_META, weight: 0.5391 cost: 1.8517 min: 0.9504 max: 2.7106 USE_META, weight: 0.6091 cost: 1.7149 min: 0.9504 max: 2.7106 USE_META, weight: 0.5721 cost: 1.7872 min: 0.9504 max: 2.7106 USE_META, weight: 0.8011 cost: 1.3394 min: 0.9504 max: 2.7106 USE_META, weight: 0.9375 cost: 1.0727 min: 0.9504 max: 2.7106 USE_META, weight: 0.6653 cost: 1.6049 min: 0.9504 max: 2.7106 USE_META, weight: 0.6819 cost: 1.5726 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8038 cost: 1.3341 min: 0.9504 max: 2.7106 USE_META, weight: 0.7011 cost: 1.5349 min: 0.9504 max: 2.7106 USE_META, weight: 0.7877 cost: 1.3655 min: 0.9504 max: 2.7106 USE_META, weight: 0.6335 cost: 1.6672 min: 0.9504 max: 2.7106 USE_META, weight: 0.5504 cost: 1.8297 min: 0.9504 max: 2.7106 USE_META, weight: 0.8856 cost: 1.1740 min: 0.9504 max: 2.7106 USE_META, weight: 0.7195 cost: 1.4990 min: 0.9504 max: 2.7106 USE_META, weight: 0.7669 cost: 1.4063 min: 0.9504 max: 2.7106 USE_META, weight: 0.9397 cost: 1.0683 min: 0.9504 max: 2.7106 USE_META, weight: 0.7739 cost: 1.3927 min: 0.9504 max: 2.7106 USE_META, weight: 0.4614 cost: 2.0038 min: 0.9504 max: 2.7106 USE_META, weight: 0.5921 cost: 1.7482 min: 0.9504 max: 2.7106 USE_META, weight: 0.5751 cost: 1.7814 min: 0.9504 max: 2.7106 USE_META, weight: 0.4114 cost: 2.1016 min: 0.9504 max: 2.7106 USE_META, weight: 0.6561 cost: 1.6230 min: 0.9504 max: 2.7106 USE_META, weight: 0.4427 cost: 2.0403 min: 0.9504 max: 2.7106 USE_META, weight: 0.6822 cost: 1.5719 min: 0.9504 max: 2.7106 USE_META, weight: 0.6780 cost: 1.5800 min: 0.9504 max: 2.7106 USE_META, weight: 0.6969 cost: 1.5432 min: 0.9504 max: 2.7106 USE_META, weight: 0.6712 cost: 1.5934 min: 0.9504 max: 2.7106 USE_META, weight: 0.5923 cost: 1.7478 min: 0.9504 max: 2.7106 USE_META, weight: 0.6692 cost: 1.5974 min: 0.9504 max: 2.7106 USE_META, weight: 0.3575 cost: 2.2070 min: 0.9504 max: 2.7106 USE_META, weight: 0.5837 cost: 1.7645 min: 0.9504 max: 2.7106 USE_META, weight: 0.3690 cost: 2.1845 min: 0.9504 max: 2.7106 USE_META, weight: 0.3683 cost: 2.1858 min: 0.9504 max: 2.7106 USE_META, weight: 0.4240 cost: 2.0770 min: 0.9504 max: 2.7106 USE_META, weight: 0.6009 cost: 1.7310 min: 0.9504 max: 2.7106 USE_META, weight: 0.4932 cost: 1.9415 min: 0.9504 max: 2.7106 USE_META, weight: 0.8550 cost: 1.2340 min: 0.9504 max: 2.7106 USE_META, weight: 0.7809 cost: 1.3789 min: 0.9504 max: 2.7106 USE_META, weight: 0.7894 cost: 1.3623 min: 0.9504 max: 2.7106 USE_META, weight: 0.5698 cost: 1.7918 min: 0.9504 max: 2.7106 USE_META, weight: 0.6985 cost: 1.5400 min: 0.9504 max: 2.7106 USE_META, weight: 0.6010 cost: 1.7308 min: 0.9504 max: 2.7106 USE_META, weight: 0.6878 cost: 1.5610 min: 0.9504 max: 2.7106 USE_META, weight: 0.6011 cost: 1.7306 min: 0.9504 max: 2.7106 USE_META, weight: 0.8550 cost: 1.2340 min: 0.9504 max: 2.7106 USE_META, weight: 0.8367 cost: 1.2697 min: 0.9504 max: 2.7106 USE_META, weight: 0.8371 cost: 1.2689 min: 0.9504 max: 2.7106 USE_META, weight: 0.6563 cost: 1.6226 min: 0.9504 max: 2.7106 USE_META, weight: 0.7877 cost: 1.3657 min: 0.9504 max: 2.7106 USE_META, weight: 0.7928 cost: 1.3557 min: 0.9504 max: 2.7106 USE_META, weight: 0.1588 cost: 2.5956 min: 0.9504 max: 2.7106 USE_META, weight: 0.3006 cost: 2.3183 min: 0.9504 max: 2.7106 USE_META, weight: 0.5709 cost: 1.7896 min: 0.9504 max: 2.7106 USE_META, weight: 0.4186 cost: 2.0874 min: 0.9504 max: 2.7106 USE_META, weight: 0.8595 cost: 1.2251 min: 0.9504 max: 2.7106 USE_META, weight: 0.5448 cost: 1.8406 min: 0.9504 max: 2.7106 USE_META, weight: 0.4707 cost: 1.9856 min: 0.9504 max: 2.7106 USE_META, weight: 0.7340 cost: 1.4706 min: 0.9504 max: 2.7106 USE_META, weight: 0.4517 cost: 2.0228 min: 0.9504 max: 2.7106 USE_META, weight: 0.8728 cost: 1.1991 min: 0.9504 max: 2.7106 USE_META, weight: 0.5464 cost: 1.8376 min: 0.9504 max: 2.7106 USE_META, weight: 0.4772 cost: 1.9728 min: 0.9504 max: 2.7106 USE_META, weight: 0.7687 cost: 1.4027 min: 0.9504 max: 2.7106 USE_META, weight: 0.3934 cost: 2.1367 min: 0.9504 max: 2.7106 USE_META, weight: 0.7387 cost: 1.4614 min: 0.9504 max: 2.7106 USE_META, weight: 0.8367 cost: 1.2697 min: 0.9504 max: 2.7106 USE_META, weight: 0.8371 cost: 1.2689 min: 0.9504 max: 2.7106 USE_META, weight: 0.7877 cost: 1.3657 min: 0.9504 max: 2.7106 USE_META, weight: 0.8524 cost: 1.2390 min: 0.9504 max: 2.7106 USE_META, weight: 0.8318 cost: 1.2794 min: 0.9504 max: 2.7106 USE_META, weight: 0.8335 cost: 1.2760 min: 0.9504 max: 2.7106 USE_META, weight: 0.8320 cost: 1.2790 min: 0.9504 max: 2.7106 USE_META, weight: 0.8329 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8322 cost: 1.2786 min: 0.9504 max: 2.7106 USE_META, weight: 0.8316 cost: 1.2798 min: 0.9504 max: 2.7106 USE_META, weight: 0.8323 cost: 1.2783 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8320 cost: 1.2790 min: 0.9504 max: 2.7106 USE_META, weight: 0.4401 cost: 2.0453 min: 0.9504 max: 2.7106 USE_META, weight: 0.8266 cost: 1.2895 min: 0.9504 max: 2.7106 USE_META, weight: 0.7829 cost: 1.3749 min: 0.9504 max: 2.7106 USE_META, weight: 0.4370 cost: 2.0516 min: 0.9504 max: 2.7106 USE_META, weight: 0.6480 cost: 1.6388 min: 0.9504 max: 2.7106 USE_META, weight: 0.5401 cost: 1.8499 min: 0.9504 max: 2.7106 USE_META, weight: 0.5247 cost: 1.8800 min: 0.9504 max: 2.7106 USE_META, weight: 0.6275 cost: 1.6790 min: 0.9504 max: 2.7106 USE_META, weight: 0.5779 cost: 1.7760 min: 0.9504 max: 2.7106 USE_META, weight: 0.4654 cost: 1.9959 min: 0.9504 max: 2.7106 USE_META, weight: 0.5681 cost: 1.7950 min: 0.9504 max: 2.7106 USE_META, weight: 0.5247 cost: 1.8800 min: 0.9504 max: 2.7106 USE_META, weight: 0.5628 cost: 1.8053 min: 0.9504 max: 2.7106 USE_META, weight: 0.6525 cost: 1.6299 min: 0.9504 max: 2.7106 USE_META, weight: 0.8873 cost: 1.1708 min: 0.9504 max: 2.7106 USE_META, weight: 0.4863 cost: 1.9550 min: 0.9504 max: 2.7106 USE_META, weight: 0.2304 cost: 2.4555 min: 0.9504 max: 2.7106 USE_META, weight: 0.3296 cost: 2.2616 min: 0.9504 max: 2.7106 USE_META, weight: 0.4610 cost: 2.0045 min: 0.9504 max: 2.7106 USE_META, weight: 0.3984 cost: 2.1269 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8323 cost: 1.2784 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8329 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.9510 cost: 1.0461 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.9191 cost: 1.1086 min: 0.9504 max: 2.7106 USE_META, weight: 0.9942 cost: 0.9617 min: 0.9504 max: 2.7106 USE_META, weight: 0.8928 cost: 1.1600 min: 0.9504 max: 2.7106 USE_META, weight: 1.0000 cost: 0.9504 min: 0.9504 max: 2.7106 USE_META, weight: 0.9566 cost: 1.0352 min: 0.9504 max: 2.7106 USE_META, weight: 0.6825 cost: 1.5713 min: 0.9504 max: 2.7106 USE_META, weight: 0.5956 cost: 1.7413 min: 0.9504 max: 2.7106 USE_META, weight: 0.8315 cost: 1.2799 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.8320 cost: 1.2790 min: 0.9504 max: 2.7106 USE_META, weight: 0.8330 cost: 1.2771 min: 0.9504 max: 2.7106 USE_META, weight: 0.5191 cost: 1.8910 min: 0.9504 max: 2.7106 USE_META, weight: 0.5381 cost: 1.8538 min: 0.9504 max: 2.7106 USE_META, weight: 0.5920 cost: 1.7482 min: 0.9504 max: 2.7106 USE_META, weight: 0.6228 cost: 1.6881 min: 0.9504 max: 2.7106 USE_META, weight: 0.3765 cost: 2.1699 min: 0.9504 max: 2.7106 USE_META, weight: 0.6140 cost: 1.7053 min: 0.9504 max: 2.7106 USE_META, weight: 0.4347 cost: 2.0561 min: 0.9504 max: 2.7106 USE_META, weight: 0.5885 cost: 1.7552 min: 0.9504 max: 2.7106 USE_META, weight: 0.5547 cost: 1.8212 min: 0.9504 max: 2.7106 USE_META, weight: 0.4303 cost: 2.0646 min: 0.9504 max: 2.7106 USE_META, weight: 0.6521 cost: 1.6307 min: 0.9504 max: 2.7106 USE_META, weight: 0.6086 cost: 1.7158 min: 0.9504 max: 2.7106 USE_META, weight: 0.5881 cost: 1.7560 min: 0.9504 max: 2.7106 USE_META, weight: 0.7201 cost: 1.4977 min: 0.9504 max: 2.7106 USE_META, weight: 0.5567 cost: 1.8173 min: 0.9504 max: 2.7106 USE_META, weight: 0.4173 cost: 2.0900 min: 0.9504 max: 2.7106 USE_META, weight: 0.3634 cost: 2.1955 min: 0.9504 max: 2.7106 USE_META, weight: 0.3996 cost: 2.1246 min: 0.9504 max: 2.7106 USE_META, weight: 0.4123 cost: 2.0999 min: 0.9504 max: 2.7106 USE_META, weight: 0.4168 cost: 2.0910 min: 0.9504 max: 2.7106 USE_META, weight: 0.5813 cost: 1.7693 min: 0.9504 max: 2.7106 USE_META, weight: 0.4614 cost: 2.0038 min: 0.9504 max: 2.7106 USE_META, weight: 0.5390 cost: 1.8519 min: 0.9504 max: 2.7106 USE_META, weight: 0.4694 cost: 1.9881 min: 0.9504 max: 2.7106 USE_META, weight: 0.4511 cost: 2.0239 min: 0.9504 max: 2.7106 USE_META, weight: 0.4081 cost: 2.1080 min: 0.9504 max: 2.7106 USE_META, weight: 0.7343 cost: 1.4701 min: 0.9504 max: 2.7106 USE_META, weight: 0.8403 cost: 1.2628 min: 0.9504 max: 2.7106 USE_EVALUE, weight: 0.5002 eval: 33.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.5002 eval: 33.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.5002 eval: 33.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3521 eval: 39.7310 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3521 eval: 39.7310 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3521 eval: 39.7310 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4610 eval: 34.9280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4610 eval: 34.9280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4610 eval: 34.9280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1970 eval: 46.5720 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1970 eval: 46.5720 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1970 eval: 46.5720 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3385 eval: 40.3280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3385 eval: 40.3280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3385 eval: 40.3280 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4775 eval: 34.1980 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4775 eval: 34.1980 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4775 eval: 34.1980 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3245 eval: 40.9480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3245 eval: 40.9480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3245 eval: 40.9480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4964 eval: 33.3640 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4964 eval: 33.3640 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4964 eval: 33.3640 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1804 eval: 47.3000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1804 eval: 47.3000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4548 eval: 35.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4548 eval: 35.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4548 eval: 35.2000 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3007 eval: 41.9960 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3007 eval: 41.9960 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3007 eval: 41.9960 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 1.0000 eval: 11.1560 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 1.0000 eval: 11.1560 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1000 eval: 50.8480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1000 eval: 50.8480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1000 eval: 50.8480 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2567 eval: 43.9350 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2567 eval: 43.9350 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2567 eval: 43.9350 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7479 eval: 22.2730 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7479 eval: 22.2730 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7479 eval: 22.2730 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4308 eval: 36.2600 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4308 eval: 36.2600 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.4308 eval: 36.2600 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7317 eval: 22.9880 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7317 eval: 22.9880 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.7317 eval: 22.9880 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1945 eval: 46.6790 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1945 eval: 46.6790 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.1945 eval: 46.6790 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2026 eval: 46.3230 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2026 eval: 46.3230 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.2026 eval: 46.3230 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3199 eval: 41.1500 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3199 eval: 41.1500 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.3199 eval: 41.1500 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.9301 eval: 14.2390 min: 11.1560 max: 50.8480 USE_EVALUE, weight: 0.9301 eval: 14.2390 min: 11.1560 max: 50.8480 Number of contacts in models: 253 Number of contacts in alignments: 60 NUMB_ALIGNS: 60 Adding 5914 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -242.3536, CN propb: -242.3536 weights: 0.2665 constraints: 442 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 442 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 442 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 5472 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 5472 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 5914 # command: