# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0363/ # command:# Making conformation for sequence T0363 numbered 1 through 97 Created new target T0363 from T0363.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0363/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yqbA expands to /projects/compbio/data/pdb/1yqb.pdb.gz 1yqbA:# T0363 read from 1yqbA/merged-good-all-a2m # 1yqbA read from 1yqbA/merged-good-all-a2m # adding 1yqbA to template set # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG # choosing archetypes in rotamer library T0363 11 :NQINIEIA 1yqbA 20 :HLIKVTVK T0363 21 :FPER 1yqbA 28 :TPKD T0363 27 :LKSFQVDEGITVQTAITQS 1yqbA 32 :KEDFSVTDTCTIQQLKEEI T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEI 1yqbA 81 :VRDGLTVHL Number of specific fragments extracted= 7 number of extra gaps= 2 total=7 Number of alignments=1 # 1yqbA read from 1yqbA/merged-good-all-a2m # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG T0363 11 :NQINIEIA 1yqbA 20 :HLIKVTVK T0363 21 :FPER 1yqbA 28 :TPKD T0363 27 :LKSFQVDEGITVQTAITQS 1yqbA 32 :KEDFSVTDTCTIQQLKEEI T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEIY 1yqbA 81 :VRDGLTVHLV Number of specific fragments extracted= 7 number of extra gaps= 2 total=14 Number of alignments=2 # 1yqbA read from 1yqbA/merged-good-all-a2m # found chain 1yqbA in template set Warning: unaligning (T0363)A2 because first residue in template chain is (1yqbA)S11 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE in next template residue (1yqbA)P19 Warning: unaligning (T0363)L10 because of BadResidue code BAD_PEPTIDE at template residue (1yqbA)P19 Warning: unaligning (T0363)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yqbA)L61 Warning: unaligning (T0363)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yqbA)L61 T0363 3 :HHHHHH 1yqbA 12 :GLVPRG T0363 11 :NQINIEI 1yqbA 20 :HLIKVTV T0363 20 :AFPERY 1yqbA 27 :KTPKDK T0363 28 :KSFQVDEGITVQTAITQ 1yqbA 33 :EDFSVTDTCTIQQLKEE T0363 47 :ILSQF 1yqbA 50 :ISQRF T0363 53 :EIDLS 1yqbA 55 :KAHPD T0363 60 :KIGIFSRPIKLTDV 1yqbA 62 :VLIFAGKILKDPDS T0363 74 :LKEGDRIEI 1yqbA 81 :VRDGLTVHL Number of specific fragments extracted= 8 number of extra gaps= 2 total=22 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uwmA expands to /projects/compbio/data/pdb/1uwm.pdb.gz 1uwmA:Skipped atom 119, because occupancy 0.25 <= existing 0.750 in 1uwmA Skipped atom 121, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 123, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 125, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 127, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 129, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 131, because occupancy 0.250 <= existing 0.750 in 1uwmA Skipped atom 189, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 191, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 193, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 195, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 197, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 199, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 201, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 203, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 205, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 207, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 209, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 211, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 213, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 215, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 217, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 219, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 221, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 330, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 332, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 334, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 336, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 338, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 340, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 342, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 344, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 346, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 348, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 350, because occupancy 0.400 <= existing 0.600 in 1uwmA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1uwmA Skipped atom 717, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 719, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 721, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 723, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 725, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 727, because occupancy 0.600 <= existing 0.800 in 1uwmA Skipped atom 729, because occupancy 0.600 <= existing 0.800 in 1uwmA # T0363 read from 1uwmA/merged-good-all-a2m # 1uwmA read from 1uwmA/merged-good-all-a2m # adding 1uwmA to template set # found chain 1uwmA in template set T0363 14 :NIEIA 1uwmA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1uwmA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1uwmA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 Number of alignments=4 # 1uwmA read from 1uwmA/merged-good-all-a2m # found chain 1uwmA in template set T0363 14 :NIEIA 1uwmA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSG 1uwmA 7 :EHNGTRHEVEAKPGLTVMEAARDNG T0363 51 :FPEIDLST 1uwmA 32 :VPGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=28 Number of alignments=5 # 1uwmA read from 1uwmA/merged-good-all-a2m # found chain 1uwmA in template set T0363 17 :IAYAFPERY 1uwmA 3 :IIFIEHNGT T0363 27 :LKSFQVDEGITVQTAITQSG 1uwmA 12 :RHEVEAKPGLTVMEAARDNG T0363 51 :FPEIDLSTN 1uwmA 32 :VPGIDADCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=31 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e9mA expands to /projects/compbio/data/pdb/1e9m.pdb.gz 1e9mA:# T0363 read from 1e9mA/merged-good-all-a2m # 1e9mA read from 1e9mA/merged-good-all-a2m # adding 1e9mA to template set # found chain 1e9mA in template set T0363 14 :NIEIA 1e9mA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1e9mA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1e9mA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=34 Number of alignments=7 # 1e9mA read from 1e9mA/merged-good-all-a2m # found chain 1e9mA in template set T0363 14 :NIEIA 1e9mA 2 :KIIFI T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1e9mA 7 :EHNGTRHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLST 1e9mA 33 :PGIDADC Number of specific fragments extracted= 3 number of extra gaps= 0 total=37 Number of alignments=8 # 1e9mA read from 1e9mA/merged-good-all-a2m # found chain 1e9mA in template set T0363 17 :IAYAFPERY 1e9mA 3 :IIFIEHNGT T0363 27 :LKSFQVDEGITVQTAITQSGI 1e9mA 12 :RHEVEAKPGLTVMEAARDNGV T0363 52 :PEIDLSTN 1e9mA 33 :PGIDADCG Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z2mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z2mA expands to /projects/compbio/data/pdb/1z2m.pdb.gz 1z2mA:# T0363 read from 1z2mA/merged-good-all-a2m # 1z2mA read from 1z2mA/merged-good-all-a2m # adding 1z2mA to template set # found chain 1z2mA in template set T0363 5 :HHHHSLNQINIE 1z2mA 76 :DKSDEPLSILVR T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1z2mA 88 :NNKGRSSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYR 1z2mA 142 :LKPLSTVFMNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=44 Number of alignments=10 # 1z2mA read from 1z2mA/merged-good-all-a2m # found chain 1z2mA in template set T0363 5 :HHHHSLNQINIE 1z2mA 76 :DKSDEPLSILVR T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1z2mA 88 :NNKGRSSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYRP 1z2mA 142 :LKPLSTVFMNLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 Number of alignments=11 # 1z2mA read from 1z2mA/merged-good-all-a2m # found chain 1z2mA in template set T0363 7 :HHSLNQINIEIA 1z2mA 76 :DKSDEPLSILVR T0363 20 :AFPER 1z2mA 88 :NNKGR T0363 27 :LKSFQVDEGITVQTAITQSGILS 1z2mA 93 :SSTYEVRLTQTVAHLKQQVSGLE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1z2mA 116 :GVQDDLFWLTFEGKPLEDQLP T0363 74 :LKEGDRIEIYR 1z2mA 142 :LKPLSTVFMNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=53 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ogwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1ogwA/merged-good-all-a2m # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 Warning: unaligning (T0363)R79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)H68 Warning: unaligning (T0363)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)H68 T0363 12 :QINIEI 1ogwA 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ogwA 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDV 1ogwA 52 :DGRT T0363 74 :LKEGD 1ogwA 61 :IQKES T0363 82 :IYRPLL 1ogwA 69 :LVLRLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=59 Number of alignments=13 # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 Warning: unaligning (T0363)R79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)H68 Warning: unaligning (T0363)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)H68 T0363 12 :QINIEI 1ogwA 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ogwA 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDV 1ogwA 52 :DGRT T0363 74 :LKEGD 1ogwA 61 :IQKES T0363 82 :IYRPLL 1ogwA 69 :LVLRLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=65 Number of alignments=14 # 1ogwA read from 1ogwA/merged-good-all-a2m # found chain 1ogwA in training set Warning: unaligning (T0363)P67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ogwA)E51 Warning: unaligning (T0363)K69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ogwA)E51 T0363 13 :INIE 1ogwA 3 :IFVK T0363 20 :AFPER 1ogwA 7 :TLTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1ogwA 12 :TITLEVEPSDTIENVKAKIQDKE T0363 53 :EIDLSTNKIGIFSR 1ogwA 35 :GIPPDQQRLIFAGK T0363 70 :LTDVLK 1ogwA 52 :DGRTLS Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1frd expands to /projects/compbio/data/pdb/1frd.pdb.gz 1frd:Warning: there is no chain 1frd will retry with 1frdA # T0363 read from 1frd/merged-good-all-a2m # 1frd read from 1frd/merged-good-all-a2m # adding 1frd to template set # found chain 1frd in template set T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGI T0363 48 :LSQFPEIDLSTNKIGIFSRPIKLTDV 1frd 38 :PFSCHSGSCSSCVGKVVEGEVDQSDQ T0363 86 :LLADPKEIRR 1frd 64 :IFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=74 Number of alignments=16 # 1frd read from 1frd/merged-good-all-a2m # found chain 1frd in template set Warning: unaligning (T0363)N11 because first residue in template chain is (1frd)A1 T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGI 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGI T0363 49 :SQFPEIDLSTNKIGIFSRPIKLTDV 1frd 39 :FSCHSGSCSSCVGKVVEGEVDQSDQ T0363 86 :LLADPKEIRR 1frd 64 :IFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=78 Number of alignments=17 # 1frd read from 1frd/merged-good-all-a2m # found chain 1frd in template set T0363 12 :QINIEIAY 1frd 2 :SYQVRLIN T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1frd 10 :KKQDIDTTIEIDEETTILDGAEENGIELPFSCHSGSCSS T0363 63 :IFSRPIKLTDVLKE 1frd 49 :CVGKVVEGEVDQSD T0363 85 :PLLADPKEIRR 1frd 63 :QIFLDDEQMGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1awd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1awd expands to /projects/compbio/data/pdb/1awd.pdb.gz 1awd:Warning: there is no chain 1awd will retry with 1awdA Skipped atom 116, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 118, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 120, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 122, because occupancy 0.350 <= existing 0.650 in 1awd Skipped atom 142, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 144, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 146, because occupancy 0.450 <= existing 0.550 in 1awd Skipped atom 148, because occupancy 0.450 <= existing 0.550 in 1awd # T0363 read from 1awd/merged-good-all-a2m # 1awd read from 1awd/merged-good-all-a2m # adding 1awd to template set # found chain 1awd in template set T0363 12 :QINIE 1awd 2 :KVTLK T0363 21 :FPERY 1awd 7 :TPSGE T0363 28 :KSFQVDEGITVQTAITQSGI 1awd 12 :ETIECPEDTYILDAAEEAGL T0363 53 :EIDLSTN 1awd 32 :DLPYSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=86 Number of alignments=19 # 1awd read from 1awd/merged-good-all-a2m # found chain 1awd in template set T0363 14 :NIEI 1awd 2 :KVTL T0363 20 :AFPERYY 1awd 6 :KTPSGEE T0363 29 :SFQVDEGITVQTAITQSGI 1awd 13 :TIECPEDTYILDAAEEAGL T0363 53 :EIDLSTN 1awd 32 :DLPYSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=90 Number of alignments=20 # 1awd read from 1awd/merged-good-all-a2m # found chain 1awd in template set T0363 17 :IAYAFPERYY 1awd 3 :VTLKTPSGEE T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1awd 13 :TIECPEDTYILDAAEEAGLDLPYSCRAGACSS T0363 63 :IFSRPIKLT 1awd 45 :CAGKVESGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rwsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rwsA expands to /projects/compbio/data/pdb/1rws.pdb.gz 1rwsA:# T0363 read from 1rwsA/merged-good-all-a2m # 1rwsA read from 1rwsA/merged-good-all-a2m # adding 1rwsA to template set # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 31 :Q 1rwsA 18 :E T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSGI 1rwsA 25 :VRDILRAVGF T0363 55 :DLSTNKIGIFSRPIKLTD 1rwsA 35 :NTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :EI 1rwsA 61 :EV Number of specific fragments extracted= 6 number of extra gaps= 4 total=99 Number of alignments=22 # 1rwsA read from 1rwsA/merged-good-all-a2m # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 31 :Q 1rwsA 18 :E T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSG 1rwsA 25 :VRDILRAVG T0363 54 :IDLSTNKIGIFSRPIKLTD 1rwsA 34 :FNTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :E 1rwsA 61 :E Number of specific fragments extracted= 6 number of extra gaps= 4 total=105 Number of alignments=23 # 1rwsA read from 1rwsA/merged-good-all-a2m # found chain 1rwsA in template set Warning: unaligning (T0363)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)R20 Warning: unaligning (T0363)D33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)R20 Warning: unaligning (T0363)I36 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)K24 Warning: unaligning (T0363)T37 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)K24 Warning: unaligning (T0363)V73 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rwsA)V54 Warning: unaligning (T0363)L74 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V54 Warning: unaligning (T0363)D78 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1rwsA)F59 Warning: unaligning (T0363)R79 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1rwsA)F59 Warning: unaligning (T0363)I80 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rwsA)V60 T0363 34 :EG 1rwsA 21 :EG T0363 38 :VQTAITQSG 1rwsA 25 :VRDILRAVG T0363 54 :IDLSTNKIGIFSRPIKLTD 1rwsA 34 :FNTESAIAKVNGKVVLEDD T0363 75 :KEG 1rwsA 55 :KDG T0363 81 :E 1rwsA 61 :E Number of specific fragments extracted= 5 number of extra gaps= 4 total=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c1yB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c1yB expands to /projects/compbio/data/pdb/1c1y.pdb.gz 1c1yB:Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 1c1yB # T0363 read from 1c1yB/merged-good-all-a2m # 1c1yB read from 1c1yB/merged-good-all-a2m # adding 1c1yB to template set # found chain 1c1yB in template set T0363 11 :NQINIEI 1c1yB 56 :NTIRVFL T0363 22 :PERYY 1c1yB 63 :PNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :SGI 1c1yB 86 :LKV T0363 52 :PEIDLSTNKIGIF 1c1yB 89 :RGLQPECCAVFRL T0363 65 :SRPIKLTDVLKE 1c1yB 109 :KARLDWNTDAAS T0363 77 :GDRIEI 1c1yB 123 :GEELQV Number of specific fragments extracted= 7 number of extra gaps= 0 total=117 Number of alignments=24 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0363 11 :NQINIEI 1c1yB 56 :NTIRVFL T0363 22 :PERYY 1c1yB 63 :PNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :S 1c1yB 85 :A T0363 47 :I 1c1yB 88 :V T0363 52 :PEIDLSTNKIGIF 1c1yB 89 :RGLQPECCAVFRL T0363 65 :SRPIKLTDVLK 1c1yB 109 :KARLDWNTDAA T0363 76 :EGDRIEI 1c1yB 122 :IGEELQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=125 Number of alignments=25 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0363 11 :NQINIE 1c1yB 56 :NTIRVF T0363 21 :FPERYY 1c1yB 62 :LPNKQR T0363 28 :KSFQVDEGITVQTAIT 1c1yB 68 :TVVNVRNGMSLHDCLM T0363 45 :S 1c1yB 85 :A T0363 48 :LS 1c1yB 86 :LK T0363 51 :FPEIDLSTNK 1c1yB 88 :VRGLQPECCA T0363 63 :IFSRPIKLTD 1c1yB 98 :VFRLLHEHKG T0363 73 :VLKEG 1c1yB 111 :RLDWN Number of specific fragments extracted= 8 number of extra gaps= 0 total=133 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bpsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bpsA expands to /projects/compbio/data/pdb/2bps.pdb.gz 2bpsA:# T0363 read from 2bpsA/merged-good-all-a2m # 2bpsA read from 2bpsA/merged-good-all-a2m # adding 2bpsA to template set # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAYA 2bpsA 0 :GSYIDITIDLK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 11 :HYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGI 2bpsA 44 :PREGHWIRV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=138 Number of alignments=27 # 2bpsA read from 2bpsA/merged-good-all-a2m # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAY 2bpsA 0 :GSYIDITIDL T0363 21 :FPERYYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 10 :KHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGI 2bpsA 44 :PREGHWIRV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=143 Number of alignments=28 # 2bpsA read from 2bpsA/merged-good-all-a2m # found chain 2bpsA in template set Warning: unaligning (T0363)E53 because of BadResidue code BAD_PEPTIDE in next template residue (2bpsA)P43 Warning: unaligning (T0363)I54 because of BadResidue code BAD_PEPTIDE at template residue (2bpsA)P43 T0363 10 :LNQINIEIAYAFPE 2bpsA 0 :GSYIDITIDLKHYN T0363 25 :YYLKSFQVDEGITVQTAITQSGILSQFP 2bpsA 14 :GSVFDLRLSDYHPVKKVIDIAWQAQSVS T0363 55 :DLSTNKIGIF 2bpsA 44 :PREGHWIRVV T0363 65 :SRPIKLTDV 2bpsA 56 :DKVFSGECK T0363 74 :LKEGDRIEI 2bpsA 70 :ITNGDRLEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=148 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1put/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1put expands to /projects/compbio/data/pdb/1put.pdb.gz 1put:Warning: there is no chain 1put will retry with 1putA # T0363 read from 1put/merged-good-all-a2m # 1put read from 1put/merged-good-all-a2m # adding 1put to template set # found chain 1put in template set T0363 17 :IAYAFPERY 1put 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1put 12 :RRQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 70 :LTDVLKEGDRI 1put 74 :VTAELKPNSRL T0363 83 :YRPLLADP 1put 85 :CCQIIMTP Number of specific fragments extracted= 5 number of extra gaps= 0 total=153 Number of alignments=30 # 1put read from 1put/merged-good-all-a2m # found chain 1put in template set T0363 17 :IAYAFPERY 1put 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1put 12 :RRQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 70 :LTDVLKEGDRI 1put 74 :VTAELKPNSRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=157 Number of alignments=31 # 1put read from 1put/merged-good-all-a2m # found chain 1put in template set T0363 17 :IAYAFPERYY 1put 3 :VVYVSHDGTR T0363 28 :KSFQVDEGITVQTAITQSGILSQFPEID 1put 13 :RQLDVADGVSLMQAAVSNGIYDIVGDCG T0363 56 :LSTNKIGIFSRPI 1put 43 :ASCATCHVYVNEA T0363 69 :KLTDVLKEGDRI 1put 73 :CVTAELKPNSRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=161 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nddA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nddA expands to /projects/compbio/data/pdb/1ndd.pdb.gz 1nddA:# T0363 read from 1nddA/merged-good-all-a2m # 1nddA read from 1nddA/merged-good-all-a2m # adding 1nddA to template set # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nddA 7 :TLTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEI 1nddA 61 :ILGGSVLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=165 Number of alignments=33 # 1nddA read from 1nddA/merged-good-all-a2m # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 21 :F 1nddA 7 :T T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1nddA 8 :LTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPL 1nddA 61 :ILGGSVLHLVLAL Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=34 # 1nddA read from 1nddA/merged-good-all-a2m # found chain 1nddA in template set T0363 12 :QINIE 1nddA 2 :LIKVK T0363 20 :AFPER 1nddA 7 :TLTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1nddA 12 :EIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nddA 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEI 1nddA 61 :ILGGSVLHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lfdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lfdA expands to /projects/compbio/data/pdb/1lfd.pdb.gz 1lfdA:# T0363 read from 1lfdA/merged-good-all-a2m # 1lfdA read from 1lfdA/merged-good-all-a2m # adding 1lfdA to template set # found chain 1lfdA in template set T0363 12 :QINIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGI 1lfdA 16 :CCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQ T0363 67 :PIKLTD 1lfdA 68 :IISEDH T0363 73 :VLKEGD 1lfdA 76 :KIPENA Number of specific fragments extracted= 3 number of extra gaps= 0 total=178 Number of alignments=36 # 1lfdA read from 1lfdA/merged-good-all-a2m # found chain 1lfdA in template set T0363 12 :QINIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIGI 1lfdA 16 :CCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQ T0363 67 :PIKLTD 1lfdA 68 :IISEDH T0363 73 :VLKEGDR 1lfdA 76 :KIPENAN Number of specific fragments extracted= 3 number of extra gaps= 0 total=181 Number of alignments=37 # 1lfdA read from 1lfdA/merged-good-all-a2m # found chain 1lfdA in template set T0363 13 :INIEIAYAFPERYYLKSFQVDEGITVQTAITQSGILSQFPEIDLSTNKIG 1lfdA 17 :CIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELL T0363 66 :RPIKLTD 1lfdA 67 :QIISEDH T0363 73 :VLKEGDR 1lfdA 76 :KIPENAN Number of specific fragments extracted= 3 number of extra gaps= 0 total=184 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zud2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zud2 expands to /projects/compbio/data/pdb/1zud.pdb.gz 1zud2:# T0363 read from 1zud2/merged-good-all-a2m # 1zud2 read from 1zud2/merged-good-all-a2m # adding 1zud2 to template set # found chain 1zud2 in template set T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRP 1zud2 50 :IVQDGDQILLFQV Number of specific fragments extracted= 3 number of extra gaps= 0 total=187 Number of alignments=39 # 1zud2 read from 1zud2/merged-good-all-a2m # found chain 1zud2 in template set T0363 22 :PE 1zud2 6 :ND T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRP 1zud2 50 :IVQDGDQILLFQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=191 Number of alignments=40 # 1zud2 read from 1zud2/merged-good-all-a2m # found chain 1zud2 in template set T0363 28 :KSFQVDEGITVQTAITQS 1zud2 8 :QAMQCAAGQTVHELLEQL T0363 53 :EIDLSTNKIGIFSRPIKLTD 1zud2 26 :DQRQAGAALAINQQIVPREQ T0363 73 :VLKEGDRIEIYRPL 1zud2 50 :IVQDGDQILLFQVI Number of specific fragments extracted= 3 number of extra gaps= 0 total=194 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ubi/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ubi expands to /projects/compbio/data/pdb/1ubi.pdb.gz 1ubi:Warning: there is no chain 1ubi will retry with 1ubiA # T0363 read from 1ubi/merged-good-all-a2m # 1ubi read from 1ubi/merged-good-all-a2m # adding 1ubi to template set # found chain 1ubi in template set T0363 12 :QINIEI 1ubi 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ubi 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1ubi 35 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1ubi 61 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=198 Number of alignments=42 # 1ubi read from 1ubi/merged-good-all-a2m # found chain 1ubi in template set T0363 12 :QINIEI 1ubi 2 :QIFVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 1ubi 8 :LTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1ubi 35 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPL 1ubi 61 :IQKESTLHLVLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=43 # 1ubi read from 1ubi/merged-good-all-a2m # found chain 1ubi in template set T0363 12 :QINIE 1ubi 2 :QIFVK T0363 20 :AFPERY 1ubi 7 :TLTGKT T0363 28 :KSFQVDEGITVQTAITQSGILS 1ubi 13 :ITLEVEPSDTIENVKAKIQDKE T0363 53 :EIDLSTNKIGIFSRPIKLTDVLK 1ubi 35 :GIPPDQQRLIFAGKQLEDGRTLS Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oqqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1oqqA/merged-good-all-a2m # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERY 1oqqA 2 :KVVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEIDL 1oqqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGDCGG Number of specific fragments extracted= 2 number of extra gaps= 0 total=208 Number of alignments=45 # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERY 1oqqA 2 :KVVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPEID 1oqqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGDCG Number of specific fragments extracted= 2 number of extra gaps= 0 total=210 Number of alignments=46 # 1oqqA read from 1oqqA/merged-good-all-a2m # found chain 1oqqA in training set T0363 16 :EIAYAFPERYY 1oqqA 2 :KVVYVSHDGTR T0363 28 :KSFQVDEGITVQTAITQSGILS 1oqqA 13 :RELDVADGVSLMQAAVSNGIYD T0363 54 :IDLS 1oqqA 35 :IVGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=213 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1euvB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1euvB expands to /projects/compbio/data/pdb/1euv.pdb.gz 1euvB:# T0363 read from 1euvB/merged-good-all-a2m # 1euvB read from 1euvB/merged-good-all-a2m # adding 1euvB to template set # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEIA 1euvB 21 :ETHINLKVS T0363 21 :FPERYYLKSFQ 1euvB 30 :DGSSEIFFKIK T0363 34 :EGITVQTAITQS 1euvB 41 :KTTPLRRLMEAF T0363 52 :PEIDLSTNKIGIFSRPIK 1euvB 56 :QGKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRPLL 1euvB 83 :MEDNDIIEAHREQI Number of specific fragments extracted= 6 number of extra gaps= 1 total=219 Number of alignments=48 # 1euvB read from 1euvB/merged-good-all-a2m # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEIA 1euvB 21 :ETHINLKVS T0363 21 :FPERYYLKSFQ 1euvB 30 :DGSSEIFFKIK T0363 34 :EGITVQTAITQSGIL 1euvB 41 :KTTPLRRLMEAFAKR T0363 52 :PEIDLSTNKIGIFSRPIK 1euvB 56 :QGKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRP 1euvB 83 :MEDNDIIEAHRE Number of specific fragments extracted= 6 number of extra gaps= 1 total=225 Number of alignments=49 # 1euvB read from 1euvB/merged-good-all-a2m # found chain 1euvB in template set Warning: unaligning (T0363)S9 because first residue in template chain is (1euvB)P20 Warning: unaligning (T0363)L70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1euvB)D75 Warning: unaligning (T0363)T71 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1euvB)D75 T0363 10 :LNQINIEI 1euvB 21 :ETHINLKV T0363 20 :AFPERYYLKSF 1euvB 29 :SDGSSEIFFKI T0363 33 :DEGITVQTAITQS 1euvB 40 :KKTTPLRRLMEAF T0363 48 :LSQF 1euvB 53 :AKRQ T0363 53 :EIDLSTNKIGIFSRPIK 1euvB 57 :GKEMDSLRFLYDGIRIQ T0363 72 :DV 1euvB 76 :QT T0363 74 :LKEGDRIEIYRPL 1euvB 83 :MEDNDIIEAHREQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=232 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bb6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bb6A expands to /projects/compbio/data/pdb/2bb6.pdb.gz 2bb6A:# T0363 read from 2bb6A/merged-good-all-a2m # 2bb6A read from 2bb6A/merged-good-all-a2m # adding 2bb6A to template set # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 54 :IDLSTNKI 2bb6A 361 :ASLSGPFL T0363 62 :GIFSRPIK 2bb6A 370 :SVLGRKAG T0363 71 :TDVLKEGDRIEIY 2bb6A 398 :DYRPKDGETIELR Number of specific fragments extracted= 6 number of extra gaps= 2 total=238 Number of alignments=51 # 2bb6A read from 2bb6A/merged-good-all-a2m # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 53 :EIDLSTNKI 2bb6A 360 :QASLSGPFL T0363 62 :GIFSRPIKL 2bb6A 370 :SVLGRKAGE T0363 72 :DVLKEGDRIEIY 2bb6A 399 :YRPKDGETIELR Number of specific fragments extracted= 6 number of extra gaps= 2 total=244 Number of alignments=52 # 2bb6A read from 2bb6A/merged-good-all-a2m # found chain 2bb6A in template set Warning: unaligning (T0363)H7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)K312 Warning: unaligning (T0363)H8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)K312 Warning: unaligning (T0363)S9 because of BadResidue code BAD_PEPTIDE at template residue (2bb6A)V313 Warning: unaligning (T0363)P22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bb6A)S327 Warning: unaligning (T0363)E23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bb6A)S327 T0363 1 :MAHHHH 2bb6A 305 :LETPPQ T0363 10 :LNQINIEIAYAF 2bb6A 314 :PKFIDVLLKVSG T0363 24 :RYYLKSFQVDEGITVQTAITQSGILSQFP 2bb6A 328 :PSYRHSVSVPAGSSLEDILKNAQEHGRFR T0363 53 :EIDLSTNKI 2bb6A 360 :QASLSGPFL T0363 62 :GIFSRPIK 2bb6A 370 :SVLGRKAG T0363 70 :LTDVLKEGDRIEI 2bb6A 397 :ADYRPKDGETIEL Number of specific fragments extracted= 6 number of extra gaps= 2 total=250 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nbfD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nbfD expands to /projects/compbio/data/pdb/1nbf.pdb.gz 1nbfD:# T0363 read from 1nbfD/merged-good-all-a2m # 1nbfD read from 1nbfD/merged-good-all-a2m # adding 1nbfD to template set # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nbfD 307 :TLTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1nbfD 361 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=254 Number of alignments=54 # 1nbfD read from 1nbfD/merged-good-all-a2m # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1nbfD 307 :TLTGKTITLEVEPSDTIENVKAKI T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEIYRPLL 1nbfD 361 :IQKESTLHLVLRLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=258 Number of alignments=55 # 1nbfD read from 1nbfD/merged-good-all-a2m # found chain 1nbfD in template set T0363 12 :QINIE 1nbfD 302 :QIFVK T0363 20 :AFPERY 1nbfD 307 :TLTGKT T0363 28 :KSFQVDEGITVQTAITQSGI 1nbfD 313 :ITLEVEPSDTIENVKAKIQD T0363 50 :QF 1nbfD 333 :KE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1nbfD 335 :GIPPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1nbfD 361 :IQKESTLHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=264 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fm0D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1fm0D/merged-good-all-a2m # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set Warning: unaligning (T0363)D89 because last residue in template chain is (1fm0D)G81 T0363 29 :SFQVDEGI 1fm0D 18 :ATEVAADF T0363 37 :TVQTAITQS 1fm0D 27 :TVEALRQHM T0363 54 :IDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1fm0D 46 :LEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTG Number of specific fragments extracted= 3 number of extra gaps= 0 total=267 Number of alignments=57 # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1fm0D)M1 T0363 13 :INIEI 1fm0D 2 :IKVLF T0363 22 :PERYY 1fm0D 15 :GTDAT T0363 31 :QVDEGI 1fm0D 20 :EVAADF T0363 37 :TVQTAITQS 1fm0D 27 :TVEALRQHM T0363 54 :IDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLL 1fm0D 46 :LEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVT Number of specific fragments extracted= 5 number of extra gaps= 0 total=272 Number of alignments=58 # 1fm0D read from 1fm0D/merged-good-all-a2m # found chain 1fm0D in training set T0363 29 :SFQVDEGI 1fm0D 18 :ATEVAADF T0363 37 :TVQTAITQSGILSQ 1fm0D 27 :TVEALRQHMAAQSD T0363 55 :DLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1fm0D 47 :EDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPVTG Number of specific fragments extracted= 3 number of extra gaps= 0 total=275 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bt0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bt0A expands to /projects/compbio/data/pdb/1bt0.pdb.gz 1bt0A:# T0363 read from 1bt0A/merged-good-all-a2m # 1bt0A read from 1bt0A/merged-good-all-a2m # adding 1bt0A to template set # found chain 1bt0A in template set Warning: unaligning (T0363)N11 because first residue in template chain is (1bt0A)M1 T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1bt0A 7 :TLTGKEIEIDIEPTDTIDRIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEIY 1bt0A 61 :IEGGSVLHLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=279 Number of alignments=60 # 1bt0A read from 1bt0A/merged-good-all-a2m # found chain 1bt0A in template set Warning: unaligning (T0363)L86 because last residue in template chain is (1bt0A)L73 T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGILS 1bt0A 7 :TLTGKEIEIDIEPTDTIDRIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEIYRP 1bt0A 61 :IEGGSVLHLVLA Number of specific fragments extracted= 4 number of extra gaps= 0 total=283 Number of alignments=61 # 1bt0A read from 1bt0A/merged-good-all-a2m # found chain 1bt0A in template set T0363 12 :QINIE 1bt0A 2 :LIKVK T0363 21 :FPER 1bt0A 8 :LTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 1bt0A 12 :EIEIDIEPTDTIDRIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1bt0A 35 :GIPPVQQRLIYAGKQLADDKT T0363 74 :LKEGDRIEI 1bt0A 61 :IEGGSVLHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=288 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yj1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yj1A expands to /projects/compbio/data/pdb/1yj1.pdb.gz 1yj1A:Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1yj1A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1yj1A # T0363 read from 1yj1A/merged-good-all-a2m # 1yj1A read from 1yj1A/merged-good-all-a2m # adding 1yj1A to template set # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 7 :TLTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1yj1A 61 :IQKESTLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=292 Number of alignments=63 # 1yj1A read from 1yj1A/merged-good-all-a2m # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 22 :PERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 7 :TLTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGDRIEI 1yj1A 61 :IQKESTLHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=296 Number of alignments=64 # 1yj1A read from 1yj1A/merged-good-all-a2m # found chain 1yj1A in template set Warning: unaligning (T0363)S49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yj1A)I36 Warning: unaligning (T0363)I54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yj1A)I36 T0363 12 :QINIE 1yj1A 2 :QIFVK T0363 21 :F 1yj1A 7 :T T0363 23 :ERYYLKSFQVDEGITVQTAITQSGIL 1yj1A 8 :LTGKTITLEVEPSDTIENVKAKIQDK T0363 55 :DLSTNKIGIFSRPIKLTDV 1yj1A 37 :PPDQQRLIFAGKQLEDGRT T0363 74 :LKEGD 1yj1A 61 :IQKES Number of specific fragments extracted= 5 number of extra gaps= 0 total=301 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xlqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xlqA expands to /projects/compbio/data/pdb/1xlq.pdb.gz 1xlqA:# T0363 read from 1xlqA/merged-good-all-a2m # 1xlqA read from 1xlqA/merged-good-all-a2m # adding 1xlqA to template set # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPE 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGD T0363 54 :IDLSTNKIGI 1xlqA 43 :ASCATCHVYV Number of specific fragments extracted= 3 number of extra gaps= 0 total=304 Number of alignments=66 # 1xlqA read from 1xlqA/merged-good-all-a2m # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQFPE 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIVGD T0363 54 :IDLSTNKIGIF 1xlqA 41 :GSASCATCHVY Number of specific fragments extracted= 3 number of extra gaps= 0 total=307 Number of alignments=67 # 1xlqA read from 1xlqA/merged-good-all-a2m # found chain 1xlqA in template set T0363 17 :IAYAFPERY 1xlqA 3 :VVYVSHDGT T0363 27 :LKSFQVDEGITVQTAITQSGILSQF 1xlqA 12 :RRELDVADGVSLMQAAVSNGIYDIV T0363 52 :PEIDLSTNKIGIFS 1xlqA 39 :CGGSASCATCHVYV Number of specific fragments extracted= 3 number of extra gaps= 0 total=310 Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ryjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ryjA expands to /projects/compbio/data/pdb/1ryj.pdb.gz 1ryjA:# T0363 read from 1ryjA/merged-good-all-a2m # 1ryjA read from 1ryjA/merged-good-all-a2m # adding 1ryjA to template set # found chain 1ryjA in template set Warning: unaligning (T0363)H7 because first residue in template chain is (1ryjA)M4 T0363 8 :HSLNQINIE 1ryjA 5 :VIGMKFTVI T0363 21 :FPERYYLKSF 1ryjA 14 :TDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLLA 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRVIYG Number of specific fragments extracted= 4 number of extra gaps= 0 total=314 Number of alignments=69 # 1ryjA read from 1ryjA/merged-good-all-a2m # found chain 1ryjA in template set Warning: unaligning (T0363)H7 because first residue in template chain is (1ryjA)M4 T0363 8 :HSLNQINIE 1ryjA 5 :VIGMKFTVI T0363 21 :FPERYYLKSF 1ryjA 14 :TDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRPLL 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRVIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=318 Number of alignments=70 # 1ryjA read from 1ryjA/merged-good-all-a2m # found chain 1ryjA in template set T0363 13 :INIEI 1ryjA 8 :MKFTV T0363 20 :AFPERYYLKSF 1ryjA 13 :ITDDGKKILES T0363 33 :DEGITVQTAITQS 1ryjA 24 :GAPRRIKDVLGEL T0363 53 :EIDLSTNKIGIFSRPIKLTDVLKEGDRIEIYRP 1ryjA 37 :EIPIETVVVKKNGQIVIDEEEIFDGDIIEVIRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=322 Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cu3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cu3A expands to /projects/compbio/data/pdb/2cu3.pdb.gz 2cu3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0363 read from 2cu3A/merged-good-all-a2m # 2cu3A read from 2cu3A/merged-good-all-a2m # adding 2cu3A to template set # found chain 2cu3A in template set T0363 16 :EI 2cu3A 3 :WL T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIKL 2cu3A 25 :VELKGVAVLLNEEAFLG T0363 71 :TDVLKEGDRIEI 2cu3A 46 :DRPLRDGDVVEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=327 Number of alignments=72 # 2cu3A read from 2cu3A/merged-good-all-a2m # found chain 2cu3A in template set T0363 16 :EI 2cu3A 3 :WL T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIKL 2cu3A 25 :VELKGVAVLLNEEAFLG T0363 71 :TDVLKEGDRIEI 2cu3A 46 :DRPLRDGDVVEV Number of specific fragments extracted= 5 number of extra gaps= 0 total=332 Number of alignments=73 # 2cu3A read from 2cu3A/merged-good-all-a2m # found chain 2cu3A in template set T0363 22 :PERYY 2cu3A 5 :NGEPR T0363 34 :EGITVQTAITQSG 2cu3A 12 :EGKTLKEVLEEMG T0363 54 :IDLSTNKIGIFSRPIK 2cu3A 25 :VELKGVAVLLNEEAFL T0363 70 :LTDVLKEGDRIEIY 2cu3A 45 :PDRPLRDGDVVEVV Number of specific fragments extracted= 4 number of extra gaps= 0 total=336 Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bwfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bwfA expands to /projects/compbio/data/pdb/2bwf.pdb.gz 2bwfA:# T0363 read from 2bwfA/merged-good-all-a2m # 2bwfA read from 2bwfA/merged-good-all-a2m # adding 2bwfA to template set # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 24 :RYYLKSFQVDEGITVQTAITQSGILS 2bwfA 10 :GQDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=340 Number of alignments=75 # 2bwfA read from 2bwfA/merged-good-all-a2m # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 24 :RYYLKSFQVDEGITVQTAITQSGILS 2bwfA 10 :GQDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=344 Number of alignments=76 # 2bwfA read from 2bwfA/merged-good-all-a2m # found chain 2bwfA in template set T0363 12 :QINIEIAY 2bwfA 2 :SLNIHIKS T0363 22 :P 2bwfA 10 :G T0363 25 :YYLKSFQVDEGITVQTAITQSGILS 2bwfA 11 :QDKWEVNVAPESTVLQFKEAINKAN T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bwfA 36 :GIPVANQRLIYSGKILKDDQT T0363 74 :LKEGDRIEIYR 2bwfA 62 :IQDGHSVHLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=349 Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1frrA expands to /projects/compbio/data/pdb/1frr.pdb.gz 1frrA:# T0363 read from 1frrA/merged-good-all-a2m # 1frrA read from 1frrA/merged-good-all-a2m # adding 1frrA to template set # found chain 1frrA in template set T0363 13 :INIE 1frrA 4 :TVLK T0363 21 :FPERY 1frrA 8 :TPSGE T0363 28 :KSFQVDEGITVQTAITQSGI 1frrA 13 :FTLDVPEGTTILDAAEEAGY T0363 53 :EIDLSTN 1frrA 33 :DLPFSCR Number of specific fragments extracted= 4 number of extra gaps= 0 total=353 Number of alignments=78 # 1frrA read from 1frrA/merged-good-all-a2m # found chain 1frrA in template set T0363 17 :IAYAFPERYY 1frrA 4 :TVLKTPSGEF T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDL 1frrA 14 :TLDVPEGTTILDAAEEAGYDLPFSCRAG T0363 57 :STNKIGIFSRPIKLTDV 1frrA 44 :SSCLGKVVSGSVDESEG T0363 86 :LLADPKEIR 1frrA 61 :SFLDDGQME Number of specific fragments extracted= 4 number of extra gaps= 0 total=357 Number of alignments=79 # 1frrA read from 1frrA/merged-good-all-a2m # found chain 1frrA in template set T0363 17 :IAYAFPERYY 1frrA 4 :TVLKTPSGEF T0363 29 :SFQVDEGITVQTAITQSGILSQFPEIDLSTNK 1frrA 14 :TLDVPEGTTILDAAEEAGYDLPFSCRAGACSS T0363 63 :IFSRPIKLT 1frrA 46 :CLGKVVSGS Number of specific fragments extracted= 3 number of extra gaps= 0 total=360 Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bkrB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bkrB expands to /projects/compbio/data/pdb/2bkr.pdb.gz 2bkrB:# T0363 read from 2bkrB/merged-good-all-a2m # 2bkrB read from 2bkrB/merged-good-all-a2m # adding 2bkrB to template set # found chain 2bkrB in template set Warning: unaligning (T0363)D89 because last residue in template chain is (2bkrB)G76 T0363 11 :NQINIEI 2bkrB 1 :MLIKVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQS 2bkrB 8 :LTGKEIEIDIEPTDKVERIKERV T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLLA 2bkrB 61 :ILGGSVLHLVLALRG Number of specific fragments extracted= 4 number of extra gaps= 0 total=364 Number of alignments=81 # 2bkrB read from 2bkrB/merged-good-all-a2m # found chain 2bkrB in template set T0363 12 :QINIEI 2bkrB 2 :LIKVKT T0363 23 :ERYYLKSFQVDEGITVQTAITQSGILS 2bkrB 8 :LTGKEIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLLA 2bkrB 61 :ILGGSVLHLVLALRG Number of specific fragments extracted= 4 number of extra gaps= 0 total=368 Number of alignments=82 # 2bkrB read from 2bkrB/merged-good-all-a2m # found chain 2bkrB in template set T0363 13 :INIEIAY 2bkrB 1 :MLIKVKT T0363 21 :FPER 2bkrB 8 :LTGK T0363 27 :LKSFQVDEGITVQTAITQSGILS 2bkrB 12 :EIEIDIEPTDKVERIKERVEEKE T0363 53 :EIDLSTNKIGIFSRPIKLTDV 2bkrB 35 :GIPPQQQRLIYSGKQMNDEKT T0363 74 :LKEGDRIEIYRPLL 2bkrB 61 :ILGGSVLHLVLALR Number of specific fragments extracted= 5 number of extra gaps= 0 total=373 Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wm3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1wm3A/merged-good-all-a2m # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1wm3A 24 :GQDGSVVQFKIKRHTPLSKLMKAY T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=377 Number of alignments=84 # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 22 :PERYYLKSFQVDEGITVQTAITQS 1wm3A 24 :GQDGSVVQFKIKRHTPLSKLMKAY T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=381 Number of alignments=85 # 1wm3A read from 1wm3A/merged-good-all-a2m # found chain 1wm3A in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1wm3A)H17 T0363 13 :INIEIA 1wm3A 18 :INLKVA T0363 21 :F 1wm3A 24 :G T0363 23 :ERYYLKSFQVDEGITVQTAITQSG 1wm3A 25 :QDGSVVQFKIKRHTPLSKLMKAYC T0363 49 :SQF 1wm3A 49 :ERQ T0363 53 :EIDLSTNKIGIFSRPIKLTDV 1wm3A 52 :GLSMRQIRFRFDGQPINETDT T0363 74 :LKEGDRIEIY 1wm3A 78 :MEDEDTIDVF Number of specific fragments extracted= 6 number of extra gaps= 0 total=387 Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0363 read from 1vjkA/merged-good-all-a2m # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAY 1vjkA 2 :VKVKVKY T0363 24 :RYYLKSFQVDEGITVQTAITQS 1vjkA 17 :GVDEEEIELPEGARVRDLIEEI T0363 48 :LSQFPEIDL 1vjkA 39 :KKRHEKFKE T0363 57 :STNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 58 :ADVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 4 number of extra gaps= 1 total=391 Number of alignments=87 # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAY 1vjkA 2 :VKVKVKY T0363 24 :RYYLKSFQVDEGITVQTAITQS 1vjkA 17 :GVDEEEIELPEGARVRDLIEEI T0363 48 :LSQFPEIDL 1vjkA 42 :HEKFKEEVF T0363 57 :STNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 58 :ADVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 4 number of extra gaps= 1 total=395 Number of alignments=88 # 1vjkA read from 1vjkA/merged-good-all-a2m # found chain 1vjkA in training set Warning: unaligning (T0363)Q12 because first residue in template chain is (1vjkA)S1 Warning: unaligning (T0363)L86 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjkA)S88 T0363 13 :INIEIAYAF 1vjkA 2 :VKVKVKYFA T0363 27 :LKSFQVDEGITVQTAITQSG 1vjkA 20 :EEEIELPEGARVRDLIEEIK T0363 47 :ILSQFPEID 1vjkA 41 :RHEKFKEEV T0363 56 :L 1vjkA 57 :D T0363 58 :TNKIGIFSRPIKLTDVLKEGDRIEIYRP 1vjkA 59 :DVNIAVNGRYVSWDEELKDGDVVGVFPP Number of specific fragments extracted= 5 number of extra gaps= 1 total=400 Number of alignments=89 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/T0363/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0363//projects/compbio/experiments/protein-predict/casp7/T0363/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0363/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0363/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((T0363)V32.CB, (T0363)A41.CB) [> 3.2691 = 5.4485 < 7.0831] w=1.0000 to align # Constraint # added constraint: constraint((T0363)F30.CB, (T0363)A41.CB) [> 3.6608 = 6.1013 < 7.9316] w=0.9928 to align # Constraint # added constraint: constraint((T0363)F30.CB, (T0363)S45.CB) [> 3.5531 = 5.9218 < 7.6983] w=0.8296 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)I61.CB) [> 3.8321 = 6.3868 < 8.3028] w=0.8070 to align # Constraint # added constraint: constraint((T0363)I42.CB, (T0363)I61.CB) [> 4.2333 = 7.0555 < 9.1722] w=0.7939 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)F30.CB) [> 3.4901 = 5.8169 < 7.5619] w=0.7537 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)S29.CB) [> 3.5938 = 5.9897 < 7.7866] w=0.7537 to align # Constraint # added constraint: constraint((T0363)I42.CB, (T0363)L56.CB) [> 3.2980 = 5.4966 < 7.1456] w=0.7231 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)I68.CB) [> 3.4263 = 5.7106 < 7.4237] w=0.7105 to align # Constraint # added constraint: constraint((T0363)K28.CB, (T0363)S45.CB) [> 4.1761 = 6.9601 < 9.0482] w=0.7030 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)S29.CB) [> 4.4846 = 7.4743 < 9.7166] w=0.6913 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)D78.CB) [> 3.7557 = 6.2594 < 8.1373] w=0.6878 to align # Constraint # added constraint: constraint((T0363)I61.CB, (T0363)I82.CB) [> 3.4704 = 5.7840 < 7.5192] w=0.6865 to align # Constraint # added constraint: constraint((T0363)I36.CB, (T0363)V73.CB) [> 4.1426 = 6.9043 < 8.9755] w=0.6768 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)F30.CB) [> 4.4337 = 7.3894 < 9.6062] w=0.6565 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)I80.CB) [> 3.1480 = 5.2467 < 6.8207] w=0.6470 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)I80.CB) [> 3.6058 = 6.0096 < 7.8125] w=0.6470 to align # Constraint # added constraint: constraint((T0363)I61.CB, (T0363)I80.CB) [> 3.4182 = 5.6970 < 7.4062] w=0.6470 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)F30.CB) [> 3.6039 = 6.0064 < 7.8084] w=0.6469 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)E81.CB) [> 2.9176 = 4.8627 < 6.3215] w=0.6414 to align # Constraint # added constraint: constraint((T0363)I61.CB, (T0363)E81.CB) [> 4.1106 = 6.8509 < 8.9062] w=0.6414 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)V32.CB) [> 3.5062 = 5.8437 < 7.5968] w=0.6394 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)L27.CB) [> 3.5376 = 5.8960 < 7.6648] w=0.6310 to align # Constraint # added constraint: constraint((T0363)T37.CB, (T0363)T71.CB) [> 3.7215 = 6.2025 < 8.0632] w=0.6189 to align # Constraint # added constraint: constraint((T0363)K60.CB, (T0363)I82.CB) [> 4.3407 = 7.2345 < 9.4049] w=0.6171 to align # Constraint # added constraint: constraint((T0363)Q39.CB, (T0363)L56.CB) [> 3.9007 = 6.5012 < 8.4516] w=0.6138 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)S29.CB) [> 4.5380 = 7.5634 < 9.8324] w=0.6044 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)I82.CB) [> 4.5560 = 7.5933 < 9.8713] w=0.5891 to align # Constraint # added constraint: constraint((T0363)Q39.CB, (T0363)L70.CB) [> 2.6420 = 4.4033 < 5.7244] w=0.5868 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)L74.CB) [> 3.8807 = 6.4678 < 8.4081] w=0.5727 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)L70.CB) [> 3.2016 = 5.3360 < 6.9368] w=0.5682 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)K28.CB) [> 3.4072 = 5.6786 < 7.3822] w=0.5679 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)I80.CB) [> 4.2048 = 7.0080 < 9.1104] w=0.5653 to align # Constraint # added constraint: constraint((T0363)N59.CB, (T0363)I82.CB) [> 3.3883 = 5.6471 < 7.3412] w=0.5625 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)L74.CB) [> 3.8841 = 6.4735 < 8.4155] w=0.5550 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)R79.CB) [> 4.1470 = 6.9117 < 8.9852] w=0.5550 to align # Constraint # added constraint: constraint((T0363)T43.CB, (T0363)L56.CB) [> 3.6414 = 6.0691 < 7.8898] w=0.5530 to align # Constraint # added constraint: constraint((T0363)F30.CB, (T0363)Q44.CB) [> 3.4483 = 5.7472 < 7.4714] w=0.5495 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)L27.CB) [> 3.1824 = 5.3040 < 6.8952] w=0.5444 to align # Constraint # added constraint: constraint((T0363)I42.CB, (T0363)L70.CB) [> 4.1364 = 6.8939 < 8.9621] w=0.5392 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)E81.CB) [> 4.2851 = 7.1418 < 9.2843] w=0.5375 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)I80.CB) [> 3.2157 = 5.3596 < 6.9674] w=0.5348 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)G77.CA) [> 3.8606 = 6.4344 < 8.3647] w=0.5287 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)D78.CB) [> 3.8836 = 6.4727 < 8.4145] w=0.5247 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)K28.CB) [> 4.4822 = 7.4704 < 9.7115] w=0.5245 to align # Constraint # added constraint: constraint((T0363)V32.CB, (T0363)Q44.CB) [> 4.1768 = 6.9613 < 9.0497] w=0.5241 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)A41.CB) [> 4.1348 = 6.8913 < 8.9587] w=0.5236 to align # Constraint # added constraint: constraint((T0363)Q12.CB, (T0363)Q31.CB) [> 3.3830 = 5.6383 < 7.3298] w=0.5200 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)Q31.CB) [> 4.3689 = 7.2814 < 9.4658] w=0.4983 to align # Constraint # added constraint: constraint((T0363)A41.CB, (T0363)I80.CB) [> 4.3351 = 7.2252 < 9.3928] w=0.4938 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)S29.CB) [> 3.4336 = 5.7226 < 7.4394] w=0.4873 to align # Constraint # added constraint: constraint((T0363)Q12.CB, (T0363)V32.CB) [> 4.2648 = 7.1080 < 9.2404] w=0.4711 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)A41.CB) [> 4.0007 = 6.6679 < 8.6682] w=0.4697 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)L27.CB) [> 4.1923 = 6.9872 < 9.0833] w=0.4686 to align # Constraint # added constraint: constraint((T0363)K60.CB, (T0363)Y83.CB) [> 3.0826 = 5.1377 < 6.6790] w=0.4567 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)V32.CB) [> 3.7129 = 6.1881 < 8.0445] w=0.4546 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)Q31.CB) [> 3.2123 = 5.3539 < 6.9601] w=0.4546 to align # Constraint # added constraint: constraint((T0363)I42.CB, (T0363)N59.CB) [> 3.5420 = 5.9033 < 7.6743] w=0.4422 to align # Constraint # added constraint: constraint((T0363)A41.CB, (T0363)I61.CB) [> 4.2086 = 7.0143 < 9.1186] w=0.4256 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)K75.CB) [> 4.0732 = 6.7886 < 8.8252] w=0.4190 to align # Constraint # added constraint: constraint((T0363)E34.CB, (T0363)L74.CB) [> 4.2397 = 7.0661 < 9.1860] w=0.4133 to align # Constraint # added constraint: constraint((T0363)N59.CB, (T0363)Y83.CB) [> 4.2989 = 7.1648 < 9.3142] w=0.3985 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)E34.CB) [> 3.4524 = 5.7540 < 7.4802] w=0.3972 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)D33.CB) [> 4.6054 = 7.6757 < 9.9784] w=0.3699 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)D78.CB) [> 4.2768 = 7.1280 < 9.2664] w=0.3685 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)I80.CB) [> 3.0873 = 5.1455 < 6.6892] w=0.3685 to align # Constraint # added constraint: constraint((T0363)I54.CB, (T0363)I82.CB) [> 4.1802 = 6.9669 < 9.0570] w=0.3594 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)Y25.CB) [> 3.5267 = 5.8779 < 7.6412] w=0.3566 to align # Constraint # added constraint: constraint((T0363)I13.CB, (T0363)S29.CB) [> 4.4481 = 7.4135 < 9.6376] w=0.3458 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)K28.CB) [> 4.3880 = 7.3133 < 9.5073] w=0.3458 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)K28.CB) [> 3.2336 = 5.3894 < 7.0062] w=0.3458 to align # Constraint # added constraint: constraint((T0363)G46.CA, (T0363)D55.CB) [> 4.3938 = 7.3230 < 9.5199] w=0.3404 to align # Constraint # added constraint: constraint((T0363)F64.CB, (T0363)D78.CB) [> 3.9700 = 6.6166 < 8.6016] w=0.3403 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)L74.CB) [> 3.6800 = 6.1334 < 7.9734] w=0.3379 to align # Constraint # added constraint: constraint((T0363)I42.CB, (T0363)I54.CB) [> 2.9892 = 4.9820 < 6.4767] w=0.3359 to align # Constraint # added constraint: constraint((T0363)K60.CB, (T0363)P85.CB) [> 3.6632 = 6.1053 < 7.9369] w=0.3299 to align # Constraint # added constraint: constraint((T0363)T58.CB, (T0363)P85.CB) [> 3.6342 = 6.0570 < 7.8741] w=0.3299 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)Y26.CB) [> 4.2535 = 7.0891 < 9.2159] w=0.3210 to align # Constraint # added constraint: constraint((T0363)I68.CB, (T0363)I80.CB) [> 4.3632 = 7.2720 < 9.4536] w=0.3116 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)Y83.CB) [> 4.4210 = 7.3683 < 9.5788] w=0.3107 to align # Constraint # added constraint: constraint((T0363)Q12.CB, (T0363)F30.CB) [> 4.2517 = 7.0862 < 9.2121] w=0.3009 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)I63.CB) [> 4.3643 = 7.2739 < 9.4561] w=0.3006 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)K28.CB) [> 4.4245 = 7.3742 < 9.5865] w=0.2968 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)R79.CB) [> 3.4534 = 5.7556 < 7.4823] w=0.2941 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)I80.CB) [> 4.2646 = 7.1077 < 9.2400] w=0.2941 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)E81.CB) [> 3.2302 = 5.3837 < 6.9989] w=0.2941 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)I82.CB) [> 4.1412 = 6.9020 < 8.9726] w=0.2941 to align # Constraint # added constraint: constraint((T0363)K28.CB, (T0363)I47.CB) [> 3.6366 = 6.0609 < 7.8792] w=0.2796 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)Y26.CB) [> 3.3957 = 5.6595 < 7.3573] w=0.2792 to align # Constraint # added constraint: constraint((T0363)I61.CB, (T0363)L70.CB) [> 3.9802 = 6.6337 < 8.6237] w=0.2769 to align # Constraint # added constraint: constraint((T0363)P22.CB, (T0363)I82.CB) [> 3.7404 = 6.2340 < 8.1041] w=0.2723 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)F30.CB) [> 4.5931 = 7.6551 < 9.9517] w=0.2659 to align # Constraint # added constraint: constraint((T0363)N59.CB, (T0363)P85.CB) [> 4.4187 = 7.3645 < 9.5739] w=0.2590 to align # Constraint # added constraint: constraint((T0363)F30.CB, (T0363)I47.CB) [> 4.2634 = 7.1056 < 9.2373] w=0.2575 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)E81.CB) [> 4.6082 = 7.6804 < 9.9845] w=0.2534 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)L27.CB) [> 3.3799 = 5.6332 < 7.3232] w=0.2516 to align # Constraint # added constraint: constraint((T0363)K28.CB, (T0363)L48.CB) [> 3.2798 = 5.4664 < 7.1062] w=0.2385 to align # Constraint # added constraint: constraint((T0363)I61.CB, (T0363)Y83.CB) [> 4.5513 = 7.5855 < 9.8612] w=0.2369 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)L27.CB) [> 4.2667 = 7.1112 < 9.2445] w=0.2206 to align # Constraint # added constraint: constraint((T0363)S65.CB, (T0363)E81.CB) [> 4.4286 = 7.3809 < 9.5952] w=0.2181 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)K28.CB) [> 3.3438 = 5.5730 < 7.2449] w=0.2161 to align # Constraint # added constraint: constraint((T0363)F30.CB, (T0363)L48.CB) [> 4.0451 = 6.7418 < 8.7644] w=0.2161 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)I61.CB) [> 4.5595 = 7.5992 < 9.8790] w=0.2141 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)I42.CB) [> 3.8616 = 6.4360 < 8.3669] w=0.2079 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)F30.CB) [> 4.2472 = 7.0786 < 9.2022] w=0.2079 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)S29.CB) [> 3.0656 = 5.1093 < 6.6421] w=0.2079 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)V32.CB) [> 2.9282 = 4.8803 < 6.3444] w=0.2079 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)I82.CB) [> 3.4345 = 5.7241 < 7.4413] w=0.2029 to align # Constraint # added constraint: constraint((T0363)N11.CB, (T0363)E34.CB) [> 3.2907 = 5.4845 < 7.1299] w=0.1998 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)V32.CB) [> 4.5547 = 7.5912 < 9.8685] w=0.1993 to align # Constraint # added constraint: constraint((T0363)V32.CB, (T0363)L74.CB) [> 3.9254 = 6.5423 < 8.5050] w=0.1989 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)I82.CB) [> 3.0117 = 5.0195 < 6.5254] w=0.1967 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)F30.CB) [> 4.6217 = 7.7028 < 10.0137] w=0.1940 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)I47.CB) [> 3.3650 = 5.6083 < 7.2908] w=0.1921 to align # Constraint # added constraint: constraint((T0363)S65.CB, (T0363)R79.CB) [> 4.1882 = 6.9803 < 9.0744] w=0.1787 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)S29.CB) [> 4.6478 = 7.7463 < 10.0702] w=0.1725 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)I61.CB) [> 4.5005 = 7.5008 < 9.7510] w=0.1719 to align # Constraint # added constraint: constraint((T0363)T40.CB, (T0363)L74.CB) [> 4.5976 = 7.6627 < 9.9615] w=0.1703 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)I82.CB) [> 4.2134 = 7.0224 < 9.1291] w=0.1609 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)Y83.CB) [> 4.1830 = 6.9717 < 9.0632] w=0.1588 to align # Constraint # added constraint: constraint((T0363)L10.CB, (T0363)D33.CB) [> 2.7714 = 4.6191 < 6.0048] w=0.1474 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)E81.CB) [> 3.5875 = 5.9791 < 7.7729] w=0.1419 to align # Constraint # added constraint: constraint((T0363)P22.CB, (T0363)E81.CB) [> 3.7763 = 6.2938 < 8.1819] w=0.1365 to align # Constraint # added constraint: constraint((T0363)F51.CB, (T0363)I63.CB) [> 3.7866 = 6.3111 < 8.2044] w=0.1282 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)Y83.CB) [> 4.3035 = 7.1726 < 9.3244] w=0.1279 to align # Constraint # added constraint: constraint((T0363)E23.CB, (T0363)Y83.CB) [> 3.9533 = 6.5888 < 8.5654] w=0.1217 to align # Constraint # added constraint: constraint((T0363)L27.CB, (T0363)R79.CB) [> 4.3413 = 7.2355 < 9.4061] w=0.1162 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)I47.CB) [> 3.5180 = 5.8633 < 7.6222] w=0.1159 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)I63.CB) [> 4.3287 = 7.2145 < 9.3789] w=0.1158 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)E81.CB) [> 4.3339 = 7.2232 < 9.3901] w=0.1013 to align # Constraint # added constraint: constraint((T0363)N14.CB, (T0363)Y25.CB) [> 3.3290 = 5.5484 < 7.2129] w=0.0986 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)Y25.CB) [> 4.2647 = 7.1078 < 9.2401] w=0.0986 to align # Constraint # added constraint: constraint((T0363)E23.CB, (T0363)R84.CB) [> 4.0433 = 6.7389 < 8.7605] w=0.0978 to align # Constraint # added constraint: constraint((T0363)I63.CB, (T0363)D72.CB) [> 4.0562 = 6.7603 < 8.7884] w=0.0936 to align # Constraint # added constraint: constraint((T0363)F64.CB, (T0363)E81.CB) [> 3.9263 = 6.5438 < 8.5069] w=0.0905 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)I47.CB) [> 4.6569 = 7.7615 < 10.0900] w=0.0900 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)L48.CB) [> 4.2440 = 7.0733 < 9.1952] w=0.0877 to align # Constraint # added constraint: constraint((T0363)L10.CB, (T0363)G35.CA) [> 3.2620 = 5.4366 < 7.0676] w=0.0850 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)S45.CB) [> 4.0375 = 6.7292 < 8.7480] w=0.0823 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)E81.CB) [> 4.3582 = 7.2636 < 9.4427] w=0.0806 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)L74.CB) [> 3.7887 = 6.3145 < 8.2089] w=0.0758 to align # Constraint # added constraint: constraint((T0363)R24.CB, (T0363)F51.CB) [> 3.6467 = 6.0778 < 7.9011] w=0.0757 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)R84.CB) [> 4.3250 = 7.2083 < 9.3708] w=0.0756 to align # Constraint # added constraint: constraint((T0363)F51.CB, (T0363)I61.CB) [> 3.8654 = 6.4422 < 8.3749] w=0.0676 to align # Constraint # added constraint: constraint((T0363)K60.CB, (T0363)L86.CB) [> 4.5881 = 7.6469 < 9.9410] w=0.0644 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)Y83.CB) [> 3.0891 = 5.1485 < 6.6931] w=0.0638 to align # Constraint # added constraint: constraint((T0363)L56.CB, (T0363)R84.CB) [> 4.2885 = 7.1474 < 9.2917] w=0.0588 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)F64.CB) [> 4.5680 = 7.6134 < 9.8974] w=0.0515 to align # Constraint # added constraint: constraint((T0363)T58.CB, (T0363)L87.CB) [> 3.6370 = 6.0617 < 7.8802] w=0.0512 to align # Constraint # added constraint: constraint((T0363)N11.CB, (T0363)L74.CB) [> 3.9245 = 6.5408 < 8.5031] w=0.0510 to align # Constraint # added constraint: constraint((T0363)S57.CB, (T0363)P85.CB) [> 3.7838 = 6.3063 < 8.1981] w=0.0497 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)F64.CB) [> 3.5981 = 5.9968 < 7.7959] w=0.0482 to align # Constraint # added constraint: constraint((T0363)Y26.CB, (T0363)F64.CB) [> 3.5019 = 5.8365 < 7.5874] w=0.0482 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)R84.CB) [> 4.3348 = 7.2246 < 9.3920] w=0.0473 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)G62.CA) [> 4.5641 = 7.6069 < 9.8890] w=0.0470 to align # Constraint # added constraint: constraint((T0363)L10.CB, (T0363)I36.CB) [> 4.6244 = 7.7073 < 10.0196] w=0.0469 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)Q44.CB) [> 4.6453 = 7.7422 < 10.0649] w=0.0469 to align # Constraint # added constraint: constraint((T0363)P22.CB, (T0363)R84.CB) [> 4.3064 = 7.1773 < 9.3305] w=0.0466 to align # Constraint # added constraint: constraint((T0363)V73.CB, (T0363)A88.CB) [> 3.4367 = 5.7278 < 7.4461] w=0.0452 to align # Constraint # added constraint: constraint((T0363)V73.CB, (T0363)L87.CB) [> 3.7078 = 6.1796 < 8.0335] w=0.0452 to align # Constraint # added constraint: constraint((T0363)L70.CB, (T0363)I93.CB) [> 4.4235 = 7.3726 < 9.5843] w=0.0452 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)F64.CB) [> 4.3444 = 7.2407 < 9.4129] w=0.0447 to align # Constraint # added constraint: constraint((T0363)I54.CB, (T0363)I63.CB) [> 4.4182 = 7.3637 < 9.5728] w=0.0446 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)R79.CB) [> 3.7387 = 6.2313 < 8.1006] w=0.0438 to align # Constraint # added constraint: constraint((T0363)L56.CB, (T0363)P85.CB) [> 3.6185 = 6.0308 < 7.8400] w=0.0425 to align # Constraint # added constraint: constraint((T0363)P22.CB, (T0363)I54.CB) [> 4.0150 = 6.6917 < 8.6992] w=0.0424 to align # Constraint # added constraint: constraint((T0363)F21.CB, (T0363)N59.CB) [> 4.7451 = 7.9085 < 10.2810] w=0.0410 to align # Constraint # added constraint: constraint((T0363)Y26.CB, (T0363)Q44.CB) [> 4.2656 = 7.1094 < 9.2422] w=0.0410 to align # Constraint # added constraint: constraint((T0363)G62.CA, (T0363)V73.CB) [> 3.4894 = 5.8157 < 7.5603] w=0.0404 to align # Constraint # added constraint: constraint((T0363)P67.CB, (T0363)G77.CA) [> 4.2132 = 7.0220 < 9.1287] w=0.0354 to align # Constraint # added constraint: constraint((T0363)Q50.CB, (T0363)G62.CA) [> 4.5825 = 7.6376 < 9.9288] w=0.0322 to align # Constraint # added constraint: constraint((T0363)P22.CB, (T0363)L56.CB) [> 4.6381 = 7.7301 < 10.0492] w=0.0313 to align # Constraint # added constraint: constraint((T0363)N11.CB, (T0363)S29.CB) [> 3.8493 = 6.4155 < 8.3401] w=0.0311 to align # Constraint # added constraint: constraint((T0363)Q12.CB, (T0363)L27.CB) [> 4.1993 = 6.9987 < 9.0984] w=0.0311 to align # Constraint # added constraint: constraint((T0363)L56.CB, (T0363)L86.CB) [> 3.1152 = 5.1920 < 6.7497] w=0.0306 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)S65.CB) [> 4.3323 = 7.2206 < 9.3867] w=0.0306 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)I68.CB) [> 4.5712 = 7.6186 < 9.9042] w=0.0300 to align # Constraint # added constraint: constraint((T0363)I15.CB, (T0363)R66.CB) [> 4.5792 = 7.6319 < 9.9215] w=0.0291 to align # Constraint # added constraint: constraint((T0363)I54.CB, (T0363)L86.CB) [> 2.9419 = 4.9031 < 6.3741] w=0.0291 to align # Constraint # added constraint: constraint((T0363)K60.CB, (T0363)A88.CB) [> 4.7813 = 7.9689 < 10.3595] w=0.0291 to align # Constraint # added constraint: constraint((T0363)E16.CB, (T0363)F64.CB) [> 4.7305 = 7.8842 < 10.2495] w=0.0282 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)S49.CB) [> 4.2438 = 7.0730 < 9.1949] w=0.0204 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)R84.CB) [> 4.7846 = 7.9743 < 10.3666] w=0.0198 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)R84.CB) [> 4.1361 = 6.8935 < 8.9616] w=0.0161 to align # Constraint # added constraint: constraint((T0363)Q50.CB, (T0363)F64.CB) [> 4.7527 = 7.9212 < 10.2975] w=0.0160 to align # Constraint # added constraint: constraint((T0363)I17.CB, (T0363)R66.CB) [> 4.6777 = 7.7961 < 10.1350] w=0.0160 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)I68.CB) [> 4.5023 = 7.5039 < 9.7550] w=0.0146 to align # Constraint # added constraint: constraint((T0363)F64.CB, (T0363)A88.CB) [> 4.6123 = 7.6873 < 9.9934] w=0.0146 to align # Constraint # added constraint: constraint((T0363)L74.CB, (T0363)P85.CB) [> 2.9376 = 4.8960 < 6.3648] w=0.0146 to align # Constraint # added constraint: constraint((T0363)L74.CB, (T0363)A88.CB) [> 4.7709 = 7.9514 < 10.3369] w=0.0146 to align # Constraint # added constraint: constraint((T0363)L74.CB, (T0363)I93.CB) [> 4.4001 = 7.3335 < 9.5336] w=0.0146 to align # Constraint # added constraint: constraint((T0363)S65.CB, (T0363)L74.CB) [> 3.2805 = 5.4675 < 7.1078] w=0.0141 to align # Constraint # added constraint: constraint((T0363)F64.CB, (T0363)L74.CB) [> 3.9049 = 6.5081 < 8.4605] w=0.0141 to align # Constraint # added constraint: constraint((T0363)Y19.CB, (T0363)S65.CB) [> 4.4890 = 7.4816 < 9.7261] w=0.0140 to align # Constraint # added constraint: constraint((T0363)A18.CB, (T0363)K69.CB) [> 4.6757 = 7.7928 < 10.1307] w=0.0140 to align # Constraint # added constraint: constraint((T0363)R24.CB, (T0363)S45.CB) [> 4.7519 = 7.9198 < 10.2957] w=0.0137 to align # Constraint # added constraint: constraint((T0363)A20.CB, (T0363)F51.CB) [> 3.3294 = 5.5490 < 7.2137] w=0.0119 to align # Constraint # added constraint: constraint((T0363)T37.CB, (T0363)L86.CB) [> 3.7061 = 6.1768 < 8.0299] w=0.0118 to align # Constraint # added constraint: constraint((T0363)T37.CB, (T0363)P85.CB) [> 4.5335 = 7.5558 < 9.8225] w=0.0118 to align # Constraint # added constraint: constraint((T0363)I36.CB, (T0363)L87.CB) [> 3.7113 = 6.1854 < 8.0410] w=0.0118 to align # Constraint # added constraint: constraint((T0363)G35.CA, (T0363)D89.CB) [> 3.3509 = 5.5848 < 7.2602] w=0.0118 to align # Constraint # added constraint: constraint((T0363)V32.CB, (T0363)A88.CB) [> 2.1172 = 3.5287 < 4.5873] w=0.0118 to align # Constraint # added constraint: constraint((T0363)S65.CB, (T0363)L86.CB) [> 4.6679 = 7.7799 < 10.1138] w=0.0118 to align # Constraint # added constraint: constraint((T0363)V38.CB, (T0363)L86.CB) [> 3.8802 = 6.4669 < 8.4070] w=0.0118 to align # Constraint # added constraint: constraint((T0363)T37.CB, (T0363)L87.CB) [> 3.0315 = 5.0525 < 6.5682] w=0.0118 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0363/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0363/decoys/ # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model10.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model6.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model7.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model8.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model9.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 # Found a chain break before 79 # copying to AlignedFragments data structure # 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 T0363 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 T0363 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 T0363 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 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 72 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 38 # 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 83 # 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 83 # 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 84 # 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 87 # 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 68 # 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 83 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # 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 85 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 89 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 96 # 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 84 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 85 # 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 47 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # 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 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 27, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 57, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 187, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 can't currently be optimized by undertaker # 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 84 # 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 62 # 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 94 # 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 83 # 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 # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # 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 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # 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 46 # 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 # 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 87 # 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 89 # 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 88 # 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 95 # 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 84 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 75 # 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 38 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # 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 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # 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 66 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # 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 T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 43 # 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 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # 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 67 # 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 65 # 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 51 # 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 89 # 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 94 # 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 92 # 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 89 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 20 # 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 19 # 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 85 # 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 59 # 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 25 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 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 88 # 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 T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 67 # 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 46 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 65 # 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 20 # 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 60 # 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 84 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 73 # 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 T0363 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 T0363 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 T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 89 # 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 86 # 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 82 # 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 95 # 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 93 # 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 96 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 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 T0363 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 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # 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 # Found a chain break before 94 # 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 WARNING: atoms too close: (T0363)N11.O and (T0363)Q12.N only 0.000 apart, marking (T0363)Q12.N as missing # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # 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 WARNING: atoms too close: (T0363)E34.O and (T0363)G35.N only 0.000 apart, marking (T0363)G35.N as missing # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # 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 WARNING: atoms too close: (T0363)N11.O and (T0363)Q12.N only 0.000 apart, marking (T0363)Q12.N as missing WARNING: atoms too close: (T0363)N14.O and (T0363)I15.N only 0.000 apart, marking (T0363)I15.N as missing WARNING: atoms too close: (T0363)R79.O and (T0363)I80.N only 0.000 apart, marking (T0363)I80.N as missing # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # 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 # Found a chain break before 94 # 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 T0363 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 T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0363 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 T0363 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 T0363 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0363)Y19.N and (T0363)A20.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)A20.CA only 0.000 apart, marking (T0363)A20.CA as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)A20.CB only 0.000 apart, marking (T0363)A20.CB as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)A20.O only 0.000 apart, marking (T0363)A20.O as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)A20.C only 0.000 apart, marking (T0363)A20.C as missing WARNING: atoms too close: (T0363)A20.N and (T0363)F21.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)F21.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)F21.CA only 0.000 apart, marking (T0363)F21.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)F21.CA only 0.000 apart, marking (T0363)F21.CA as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)F21.CB only 0.000 apart, marking (T0363)F21.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)F21.CB only 0.000 apart, marking (T0363)F21.CB as missing WARNING: atoms too close: (T0363)A20.O and (T0363)F21.O only 0.000 apart, marking (T0363)F21.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)F21.O only 0.000 apart, marking (T0363)F21.O as missing WARNING: atoms too close: (T0363)A20.C and (T0363)F21.C only 0.000 apart, marking (T0363)F21.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)F21.C only 0.000 apart, marking (T0363)F21.C as missing WARNING: atoms too close: (T0363)F21.N and (T0363)P22.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)P22.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)P22.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)P22.CA only 0.000 apart, marking (T0363)P22.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)P22.CA only 0.000 apart, marking (T0363)P22.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)P22.CA only 0.000 apart, marking (T0363)P22.CA as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)P22.CB only 0.000 apart, marking (T0363)P22.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)P22.CB only 0.000 apart, marking (T0363)P22.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)P22.CB only 0.000 apart, marking (T0363)P22.CB as missing WARNING: atoms too close: (T0363)F21.O and (T0363)P22.O only 0.000 apart, marking (T0363)P22.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)P22.O only 0.000 apart, marking (T0363)P22.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)P22.O only 0.000 apart, marking (T0363)P22.O as missing WARNING: atoms too close: (T0363)F21.C and (T0363)P22.C only 0.000 apart, marking (T0363)P22.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)P22.C only 0.000 apart, marking (T0363)P22.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)P22.C only 0.000 apart, marking (T0363)P22.C as missing WARNING: atoms too close: (T0363)P22.N and (T0363)F51.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)F51.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)F51.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)F51.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)F51.CA only 0.000 apart, marking (T0363)F51.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)F51.CA only 0.000 apart, marking (T0363)F51.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)F51.CA only 0.000 apart, marking (T0363)F51.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)F51.CA only 0.000 apart, marking (T0363)F51.CA as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)F51.CB only 0.000 apart, marking (T0363)F51.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)F51.CB only 0.000 apart, marking (T0363)F51.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)F51.CB only 0.000 apart, marking (T0363)F51.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)F51.CB only 0.000 apart, marking (T0363)F51.CB as missing WARNING: atoms too close: (T0363)P22.O and (T0363)F51.O only 0.000 apart, marking (T0363)F51.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)F51.O only 0.000 apart, marking (T0363)F51.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)F51.O only 0.000 apart, marking (T0363)F51.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)F51.O only 0.000 apart, marking (T0363)F51.O as missing WARNING: atoms too close: (T0363)P22.C and (T0363)F51.C only 0.000 apart, marking (T0363)F51.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)F51.C only 0.000 apart, marking (T0363)F51.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)F51.C only 0.000 apart, marking (T0363)F51.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)F51.C only 0.000 apart, marking (T0363)F51.C as missing WARNING: atoms too close: (T0363)F51.N and (T0363)P52.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)P52.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)P52.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)P52.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)P52.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)P52.CA only 0.000 apart, marking (T0363)P52.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)P52.CA only 0.000 apart, marking (T0363)P52.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)P52.CA only 0.000 apart, marking (T0363)P52.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)P52.CA only 0.000 apart, marking (T0363)P52.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)P52.CA only 0.000 apart, marking (T0363)P52.CA as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)P52.CB only 0.000 apart, marking (T0363)P52.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)P52.CB only 0.000 apart, marking (T0363)P52.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)P52.CB only 0.000 apart, marking (T0363)P52.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)P52.CB only 0.000 apart, marking (T0363)P52.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)P52.CB only 0.000 apart, marking (T0363)P52.CB as missing WARNING: atoms too close: (T0363)F51.O and (T0363)P52.O only 0.000 apart, marking (T0363)P52.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)P52.O only 0.000 apart, marking (T0363)P52.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)P52.O only 0.000 apart, marking (T0363)P52.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)P52.O only 0.000 apart, marking (T0363)P52.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)P52.O only 0.000 apart, marking (T0363)P52.O as missing WARNING: atoms too close: (T0363)F51.C and (T0363)P52.C only 0.000 apart, marking (T0363)P52.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)P52.C only 0.000 apart, marking (T0363)P52.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)P52.C only 0.000 apart, marking (T0363)P52.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)P52.C only 0.000 apart, marking (T0363)P52.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)P52.C only 0.000 apart, marking (T0363)P52.C as missing WARNING: atoms too close: (T0363)P52.N and (T0363)E53.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.N and (T0363)E53.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)E53.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)E53.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)E53.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)E53.N only 0.000 apart, marking (T0363)E53.N as missing WARNING: atoms too close: (T0363)P52.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)E53.CA only 0.000 apart, marking (T0363)E53.CA as missing WARNING: atoms too close: (T0363)P52.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)E53.CB only 0.000 apart, marking (T0363)E53.CB as missing WARNING: atoms too close: (T0363)P52.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)F51.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)E53.O only 0.000 apart, marking (T0363)E53.O as missing WARNING: atoms too close: (T0363)P52.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)F51.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)E53.C only 0.000 apart, marking (T0363)E53.C as missing WARNING: atoms too close: (T0363)E53.N and (T0363)I54.N only 0.000 apart, marking (T0363)E53.N as missing WARNING: atoms too close: (T0363)P52.N and (T0363)I54.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.N and (T0363)I54.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)I54.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)I54.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)I54.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)I54.N only 0.000 apart, marking (T0363)I54.N as missing WARNING: atoms too close: (T0363)E53.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)P52.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)I54.CA only 0.000 apart, marking (T0363)I54.CA as missing WARNING: atoms too close: (T0363)E53.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)P52.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)I54.CB only 0.000 apart, marking (T0363)I54.CB as missing WARNING: atoms too close: (T0363)E53.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)P52.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)F51.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)I54.O only 0.000 apart, marking (T0363)I54.O as missing WARNING: atoms too close: (T0363)E53.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)P52.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)F51.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)I54.C only 0.000 apart, marking (T0363)I54.C as missing WARNING: atoms too close: (T0363)I54.N and (T0363)D55.N only 0.000 apart, marking (T0363)I54.N as missing WARNING: atoms too close: (T0363)E53.N and (T0363)D55.N only 0.000 apart, marking (T0363)E53.N as missing WARNING: atoms too close: (T0363)P52.N and (T0363)D55.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.N and (T0363)D55.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)D55.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)D55.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)D55.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)D55.N only 0.000 apart, marking (T0363)D55.N as missing WARNING: atoms too close: (T0363)I54.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)E53.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)P52.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)D55.CA only 0.000 apart, marking (T0363)D55.CA as missing WARNING: atoms too close: (T0363)I54.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)E53.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)P52.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)D55.CB only 0.000 apart, marking (T0363)D55.CB as missing WARNING: atoms too close: (T0363)I54.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)E53.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)P52.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)F51.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)D55.O only 0.000 apart, marking (T0363)D55.O as missing WARNING: atoms too close: (T0363)I54.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)E53.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)P52.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)F51.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)D55.C only 0.000 apart, marking (T0363)D55.C as missing WARNING: atoms too close: (T0363)D55.N and (T0363)I63.N only 0.000 apart, marking (T0363)D55.N as missing WARNING: atoms too close: (T0363)I54.N and (T0363)I63.N only 0.000 apart, marking (T0363)I54.N as missing WARNING: atoms too close: (T0363)E53.N and (T0363)I63.N only 0.000 apart, marking (T0363)E53.N as missing WARNING: atoms too close: (T0363)P52.N and (T0363)I63.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.N and (T0363)I63.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)I63.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)I63.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)I63.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)I63.N only 0.000 apart, marking (T0363)I63.N as missing WARNING: atoms too close: (T0363)D55.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)I54.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)E53.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)P52.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)I63.CA only 0.000 apart, marking (T0363)I63.CA as missing WARNING: atoms too close: (T0363)D55.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)I54.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)E53.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)P52.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)I63.CB only 0.000 apart, marking (T0363)I63.CB as missing WARNING: atoms too close: (T0363)D55.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)I54.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)E53.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)P52.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)F51.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)I63.O only 0.000 apart, marking (T0363)I63.O as missing WARNING: atoms too close: (T0363)D55.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)I54.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)E53.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)P52.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)F51.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)I63.C only 0.000 apart, marking (T0363)I63.C as missing WARNING: atoms too close: (T0363)I63.N and (T0363)F64.N only 0.000 apart, marking (T0363)I63.N as missing WARNING: atoms too close: (T0363)D55.N and (T0363)F64.N only 0.000 apart, marking (T0363)D55.N as missing WARNING: atoms too close: (T0363)I54.N and (T0363)F64.N only 0.000 apart, marking (T0363)I54.N as missing WARNING: atoms too close: (T0363)E53.N and (T0363)F64.N only 0.000 apart, marking (T0363)E53.N as missing WARNING: atoms too close: (T0363)P52.N and (T0363)F64.N only 0.000 apart, marking (T0363)P52.N as missing WARNING: atoms too close: (T0363)F51.N and (T0363)F64.N only 0.000 apart, marking (T0363)F51.N as missing WARNING: atoms too close: (T0363)P22.N and (T0363)F64.N only 0.000 apart, marking (T0363)P22.N as missing WARNING: atoms too close: (T0363)F21.N and (T0363)F64.N only 0.000 apart, marking (T0363)F21.N as missing WARNING: atoms too close: (T0363)A20.N and (T0363)F64.N only 0.000 apart, marking (T0363)A20.N as missing WARNING: atoms too close: (T0363)Y19.N and (T0363)F64.N only 0.000 apart, marking (T0363)F64.N as missing WARNING: atoms too close: (T0363)I63.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)D55.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)I54.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)E53.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)P52.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)F51.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)P22.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)F21.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)A20.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)Y19.CA and (T0363)F64.CA only 0.000 apart, marking (T0363)F64.CA as missing WARNING: atoms too close: (T0363)I63.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)D55.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)I54.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)E53.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)P52.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)F51.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)P22.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)F21.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)A20.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)Y19.CB and (T0363)F64.CB only 0.000 apart, marking (T0363)F64.CB as missing WARNING: atoms too close: (T0363)I63.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)D55.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)I54.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)E53.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)P52.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)F51.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)P22.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)F21.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)A20.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)Y19.O and (T0363)F64.O only 0.000 apart, marking (T0363)F64.O as missing WARNING: atoms too close: (T0363)I63.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)D55.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)I54.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)E53.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)P52.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)F51.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)P22.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)F21.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)A20.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing WARNING: atoms too close: (T0363)Y19.C and (T0363)F64.C only 0.000 apart, marking (T0363)F64.C as missing # WARNING: incomplete conformation T0363 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 T0363 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.2393 model score 0.7487 model score 0.6569 model score -0.2627 model score 0.9107 model score 0.0728 model score 0.7480 model score -0.2414 model score 0.8287 model score -0.2460 model score 1.1055 model score 1.2699 model score 1.1810 model score 1.0910 model score 1.4214 model score 0.9472 model score 0.6411 model score 1.0024 model score 0.9683 model score 0.9547 model score 1.3779 model score 1.7433 model score 1.3180 model score 0.6411 model score 0.9090 model score -0.1516 model score 1.6004 model score 0.4864 model score 0.6372 model score 1.1782 model score 0.6372 model score 0.8113 model score 0.9199 model score 0.4561 model score 1.2090 model score -0.1951 model score -0.0005 model score 0.0366 model score 0.0395 model score 0.2720 model score -0.0191 model score 1.1303 model score -0.0767 model score 0.3317 model score 1.3516 model score 0.2654 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.0127 model score 0.0376 model score -0.0528 model score -0.0356 model score -0.1531 model score 0.0469 model score -0.0005 model score 0.2619 model score -0.0528 model score 0.0366 model score -0.2262 model score 1.5741 model score -0.1516 model score 1.0112 model score 0.1471 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.9137 model score 1.8921 model score 1.9683 model score 1.9110 model score 1.9975 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.0136 model score 0.0350 model score 0.2619 model score 0.5148 model score -0.1139 model score 1.6266 model score 1.6051 model score 1.4748 model score 0.2015 model score -0.0888 model score 0.7760 model score 0.3230 model score 0.1553 model score -0.2764 model score -0.1977 model score -0.2722 model score 1.5769 model score 1.5517 model score 1.1456 model score 1.2776 model score 1.4041 model score 0.2888 model score -0.2449 model score 1.8901 model score 0.4664 model score 1.1503 model score -0.0638 model score -0.1650 model score 1.6619 model score -0.0034 model score 0.3274 model score -0.1339 model score -0.1542 model score 0.4664 model score -0.0034 model score 0.3274 model score -0.3877 model score -0.4024 model score -0.3339 model score -0.3953 model score -0.3851 model score 2.1382 model score 2.2362 model score 2.1604 model score 1.7351 model score 1.7823 model score 1.0553 model score 1.0525 model score 1.0531 model score 0.9290 model score 0.9282 model score 1.0500 model score 0.9241 model score 0.9270 model score 0.9563 model score 0.9266 model score -0.2447 model score -0.0351 model score -0.0308 model score -0.2393 model score -0.2850 model score -0.1121 model score 0.1330 model score -0.1003 model score -0.0467 model score -0.0630 model score -0.0578 model score -0.2393 model score -0.2850 model score -0.2414 model score 0.0140 model score -0.2460 model score -0.3403 model score 0.3494 model score -0.2607 model score 0.0181 model score 0.2099 model score -0.0545 model score -0.1139 model score -0.1649 model score -0.0794 model score -0.1581 model score -0.1554 model score -0.1065 model score -0.1757 model score -0.1630 model score -0.1133 model score -0.2393 model score 0.6569 model score -0.2627 model score 0.9107 model score 0.0728 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3824 model score -0.2180 model score 0.9011 model score 0.8917 model score 0.2475 model score 0.0181 model score -0.0928 model score 0.1194 model score 0.0423 model score -0.2607 model score -0.0753 model score -0.1795 model score 0.1788 model score 0.7847 model score -0.0030 model score -0.1963 model score 0.1579 model score 0.3544 model score 0.0617 model score 0.0021 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.1728 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3751 model score -0.3857 model score -0.3516 model score -0.3577 model score -0.3929 model score -0.3833 model score 0.0937 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.3171 model score 0.2563 model score 0.2174 model score 0.3288 model score 0.4517 model score 1.6363 model score 1.8163 model score 1.4856 model score 1.0396 model score 1.0794 model score 0.0858 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0.7546 cost: 0.3171 min: -0.4024 max: 2.2362 USE_META, weight: 0.7753 cost: 0.2563 min: -0.4024 max: 2.2362 USE_META, weight: 0.7886 cost: 0.2174 min: -0.4024 max: 2.2362 USE_META, weight: 0.7506 cost: 0.3288 min: -0.4024 max: 2.2362 USE_META, weight: 0.7087 cost: 0.4517 min: -0.4024 max: 2.2362 USE_META, weight: 0.3046 cost: 1.6363 min: -0.4024 max: 2.2362 USE_META, weight: 0.2432 cost: 1.8163 min: -0.4024 max: 2.2362 USE_META, weight: 0.3560 cost: 1.4856 min: -0.4024 max: 2.2362 USE_META, weight: 0.5082 cost: 1.0396 min: -0.4024 max: 2.2362 USE_META, weight: 0.4946 cost: 1.0794 min: -0.4024 max: 2.2362 USE_META, weight: 0.8335 cost: 0.0858 min: -0.4024 max: 2.2362 USE_META, weight: 0.7973 cost: 0.1918 min: -0.4024 max: 2.2362 USE_META, weight: 0.7280 cost: 0.3951 min: -0.4024 max: 2.2362 USE_META, weight: 0.6988 cost: 0.4807 min: -0.4024 max: 2.2362 USE_META, weight: 0.7494 cost: 0.3322 min: -0.4024 max: 2.2362 USE_META, weight: 0.7992 cost: 0.1862 min: -0.4024 max: 2.2362 USE_META, weight: 0.7739 cost: 0.2604 min: -0.4024 max: 2.2362 USE_META, weight: 0.8014 cost: 0.1799 min: -0.4024 max: 2.2362 USE_META, weight: 0.8161 cost: 0.1366 min: -0.4024 max: 2.2362 USE_META, weight: 0.7297 cost: 0.3902 min: -0.4024 max: 2.2362 USE_META, weight: 0.8243 cost: 0.1128 min: -0.4024 max: 2.2362 USE_META, weight: 0.3419 cost: 1.5271 min: -0.4024 max: 2.2362 USE_META, weight: 0.3653 cost: 1.4584 min: -0.4024 max: 2.2362 USE_META, weight: 0.7499 cost: 0.3307 min: -0.4024 max: 2.2362 USE_META, weight: 0.3956 cost: 1.3695 min: -0.4024 max: 2.2362 USE_META, weight: 0.7931 cost: 0.2041 min: -0.4024 max: 2.2362 USE_META, weight: 0.6096 cost: 0.7420 min: -0.4024 max: 2.2362 USE_META, weight: 0.9759 cost: -0.3317 min: -0.4024 max: 2.2362 USE_EVALUE, weight: 0.9045 eval: 1.1743 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9045 eval: 1.1743 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9045 eval: 1.1743 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9815 eval: 0.2282 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9815 eval: 0.2282 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9815 eval: 0.2282 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8634 eval: 1.6809 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8634 eval: 1.6809 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8634 eval: 1.6809 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.4378 eval: 6.9155 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.4378 eval: 6.9155 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.4378 eval: 6.9155 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8276 eval: 2.1212 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8276 eval: 2.1212 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8276 eval: 2.1212 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9011 eval: 1.2172 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9011 eval: 1.2172 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9011 eval: 1.2172 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8641 eval: 1.6715 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8641 eval: 1.6715 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8641 eval: 1.6715 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9223 eval: 0.9558 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9223 eval: 0.9558 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8746 eval: 1.5422 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8746 eval: 1.5422 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8746 eval: 1.5422 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9677 eval: 0.3978 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9677 eval: 0.3978 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9677 eval: 0.3978 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7309 eval: 3.3100 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7309 eval: 3.3100 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7309 eval: 3.3100 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1572 eval: 10.3670 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1572 eval: 10.3670 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1572 eval: 10.3670 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8329 eval: 2.0550 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8329 eval: 2.0550 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8329 eval: 2.0550 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9877 eval: 0.1511 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9877 eval: 0.1511 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9877 eval: 0.1511 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6125 eval: 4.7661 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6125 eval: 4.7661 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6125 eval: 4.7661 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9979 eval: 0.0267 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9979 eval: 0.0267 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9979 eval: 0.0267 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8455 eval: 1.9007 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8455 eval: 1.9007 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8455 eval: 1.9007 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9949 eval: 0.0627 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9949 eval: 0.0627 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9949 eval: 0.0627 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7393 eval: 3.2067 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7393 eval: 3.2067 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.7393 eval: 3.2067 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9696 eval: 0.3747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9696 eval: 0.3747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9696 eval: 0.3747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1000 eval: 11.0700 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1000 eval: 11.0700 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.1000 eval: 11.0700 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8688 eval: 1.6136 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8688 eval: 1.6136 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.8688 eval: 1.6136 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9977 eval: 0.0287 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9977 eval: 0.0287 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9977 eval: 0.0287 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9622 eval: 0.4655 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9622 eval: 0.4655 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9622 eval: 0.4655 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9460 eval: 0.6640 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9460 eval: 0.6640 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9460 eval: 0.6640 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9770 eval: 0.2826 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9770 eval: 0.2826 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9770 eval: 0.2826 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9939 eval: 0.0754 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9939 eval: 0.0754 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.9939 eval: 0.0754 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.3598 eval: 7.8747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.3598 eval: 7.8747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.3598 eval: 7.8747 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6994 eval: 3.6975 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6994 eval: 3.6975 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 0.6994 eval: 3.6975 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0002 max: 11.0700 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0002 max: 11.0700 Number of contacts in models: 259 Number of contacts in alignments: 89 NUMB_ALIGNS: 89 Adding 2992 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: -180.9786, CN propb: -180.9786 weights: 0.2948 constraints: 270 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 270 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 270 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2722 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2722 # 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 2992 # command: