# 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/T0349/ # command:# Making conformation for sequence T0349 numbered 1 through 75 Created new target T0349 from T0349.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0349/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f06A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f06A expands to /projects/compbio/data/pdb/2f06.pdb.gz 2f06A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 22, because occupancy 0.5 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 850, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 854, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2f06A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1057, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f06A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f06A # T0349 read from 2f06A/merged-good-all-a2m # 2f06A read from 2f06A/merged-good-all-a2m # adding 2f06A to template set # found chain 2f06A in template set Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 13 :LSAVGALLDGADIGHLVLD 2f06A 17 :LTEVTEVLAKENINLSALC # choosing archetypes in rotamer library T0349 43 :VIP 2f06A 36 :IAE T0349 46 :R 2f06A 45 :L T0349 49 :LVH 2f06A 48 :IVS T0349 54 :DLAGARRLLTDAGLA 2f06A 51 :DPDKAYKALKDNHFA Number of specific fragments extracted= 5 number of extra gaps= 1 total=5 Number of alignments=1 # 2f06A read from 2f06A/merged-good-all-a2m # found chain 2f06A in template set Warning: unaligning (T0349)L12 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)R16 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE in next template residue (2f06A)I44 Warning: unaligning (T0349)I36 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)I44 Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 13 :LSAVGALLDGADIGHLVLD 2f06A 17 :LTEVTEVLAKENINLSALC T0349 32 :QNM 2f06A 40 :ADF T0349 37 :L 2f06A 45 :L T0349 49 :LVH 2f06A 48 :IVS T0349 54 :DLAGARRLLTDAGLAHE 2f06A 51 :DPDKAYKALKDNHFAVN Number of specific fragments extracted= 5 number of extra gaps= 3 total=10 Number of alignments=2 # 2f06A read from 2f06A/merged-good-all-a2m # found chain 2f06A in template set Warning: unaligning (T0349)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)S14 Warning: unaligning (T0349)A10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)S14 Warning: unaligning (T0349)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G15 Warning: unaligning (T0349)L12 because of BadResidue code BAD_PEPTIDE at template residue (2f06A)R16 Warning: unaligning (T0349)R47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f06A)G47 Warning: unaligning (T0349)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f06A)G47 T0349 8 :N 2f06A 12 :N T0349 13 :LSAVGALLDGADIGH 2f06A 17 :LTEVTEVLAKENINL T0349 32 :QNMSILEGSL 2f06A 32 :SALCIAENAD T0349 46 :R 2f06A 45 :L T0349 49 :LVHE 2f06A 48 :IVSD T0349 55 :LAGARRLLTDAGLA 2f06A 52 :PDKAYKALKDNHFA Number of specific fragments extracted= 6 number of extra gaps= 2 total=16 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ve1A expands to /projects/compbio/data/pdb/1ve1.pdb.gz 1ve1A:# T0349 read from 1ve1A/merged-good-all-a2m # 1ve1A read from 1ve1A/merged-good-all-a2m # adding 1ve1A to template set # found chain 1ve1A in template set T0349 9 :DAVLLSAVGALLDG 1ve1A 177 :GGTITGVGRYLKER T0349 23 :ADIGHLVLD 1ve1A 192 :PHVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=21 Number of alignments=4 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0349 8 :NDAVLLSAVGALLDG 1ve1A 176 :TGGTITGVGRYLKER T0349 23 :ADIGHLVLD 1ve1A 192 :PHVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=26 Number of alignments=5 # 1ve1A read from 1ve1A/merged-good-all-a2m # found chain 1ve1A in template set T0349 7 :TNDAVLLSAVGALLDGA 1ve1A 174 :SGTGGTITGVGRYLKER T0349 24 :DIGHLVLD 1ve1A 193 :HVKVIAVE T0349 32 :QNMSILEGS 1ve1A 202 :ARSNVLSGG T0349 41 :LGVIPRRVLVHEDD 1ve1A 231 :LSLLDGVIQVWEED T0349 55 :LAGARRLLTDAGLA 1ve1A 246 :FPLARRLAREEGLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=31 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gt1A expands to /projects/compbio/data/pdb/1gt1.pdb.gz 1gt1A:# T0349 read from 1gt1A/merged-good-all-a2m # 1gt1A read from 1gt1A/merged-good-all-a2m # adding 1gt1A to template set # found chain 1gt1A in template set T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1gt1A 124 :VEDEDLEKFWKLTEDKGIDKKN Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 Number of alignments=7 # 1gt1A read from 1gt1A/merged-good-all-a2m # found chain 1gt1A in template set T0349 31 :DQNMSILEGSLGV 1gt1A 107 :DKHGQTTELTELF T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1gt1A 120 :VKLNVEDEDLEKFWKLTEDKGIDKKN Number of specific fragments extracted= 2 number of extra gaps= 0 total=34 Number of alignments=8 # 1gt1A read from 1gt1A/merged-good-all-a2m # found chain 1gt1A in template set T0349 50 :VHEDDLAGARRLLTDAGLAHE 1gt1A 124 :VEDEDLEKFWKLTEDKGIDKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=35 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gnkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gnkA expands to /projects/compbio/data/pdb/1gnk.pdb.gz 1gnkA:# T0349 read from 1gnkA/merged-good-all-a2m # 1gnkA read from 1gnkA/merged-good-all-a2m # adding 1gnkA to template set # found chain 1gnkA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLA 1gnkA 6 :VIIKPFKLEDVREALSSIGIQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=36 Number of alignments=10 # 1gnkA read from 1gnkA/merged-good-all-a2m # found chain 1gnkA in template set Warning: unaligning (T0349)L41 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gnkA)V53 T0349 16 :VGALLDGADIGHLVLD 1gnkA 16 :VREALSSIGIQGLTVT T0349 42 :GVIPR 1gnkA 54 :NFLPK T0349 47 :RVLVHEDDLAGARRLLTDAG 1gnkA 62 :DVAIADDQLDEVIDIVSKAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Number of alignments=11 # 1gnkA read from 1gnkA/merged-good-all-a2m # found chain 1gnkA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLAH 1gnkA 6 :VIIKPFKLEDVREALSSIGIQG Number of specific fragments extracted= 1 number of extra gaps= 0 total=40 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yj7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yj7A expands to /projects/compbio/data/pdb/1yj7.pdb.gz 1yj7A:Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 1yj7A Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1yj7A # T0349 read from 1yj7A/merged-good-all-a2m # 1yj7A read from 1yj7A/merged-good-all-a2m # adding 1yj7A to template set # found chain 1yj7A in template set T0349 13 :LSAVGALLDGADIGH 1yj7A 33 :ANQMQALLLSNDVNV T0349 28 :LVLDQNMS 1yj7A 49 :KEMDKSGN T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1yj7A 57 :MTLSVAAADFVRAITILNNNGFPKKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=43 Number of alignments=13 # 1yj7A read from 1yj7A/merged-good-all-a2m # found chain 1yj7A in template set T0349 10 :AVLLSAVGALLDGADIGHL 1yj7A 30 :EKEANQMQALLLSNDVNVS T0349 29 :VLDQNMS 1yj7A 50 :EMDKSGN T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHEL 1yj7A 57 :MTLSVAAADFVRAITILNNNGFPKKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=46 Number of alignments=14 # 1yj7A read from 1yj7A/merged-good-all-a2m # found chain 1yj7A in template set T0349 1 :MRELLRTN 1yj7A 20 :MKEQLYTG T0349 9 :DAVLLSAVGALLDGADIG 1yj7A 29 :TEKEANQMQALLLSNDVN T0349 30 :LDQN 1yj7A 51 :MDKS T0349 39 :G 1yj7A 55 :G T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1yj7A 56 :NMTLSVAAADFVRAITILNNNGFPKK T0349 74 :D 1yj7A 82 :K Number of specific fragments extracted= 6 number of extra gaps= 0 total=52 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nm2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nm2A expands to /projects/compbio/data/pdb/1nm2.pdb.gz 1nm2A:# T0349 read from 1nm2A/merged-good-all-a2m # 1nm2A read from 1nm2A/merged-good-all-a2m # adding 1nm2A to template set # found chain 1nm2A in template set T0349 13 :LSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 257 :WDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=54 Number of alignments=16 # 1nm2A read from 1nm2A/merged-good-all-a2m # found chain 1nm2A in template set T0349 13 :LSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 257 :WDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=56 Number of alignments=17 # 1nm2A read from 1nm2A/merged-good-all-a2m # found chain 1nm2A in template set T0349 8 :NDAVLLSAVGALLDGADIGHLVLDQNMSILEG 1nm2A 252 :ANPVRWDLCMETFKELGVTAIIEVCPGGTLTG T0349 40 :SLGVIPRRVLVHEDDLAGARRLLTDA 1nm2A 288 :ALPGVKTLALKTPDDLDAARELVAEH Number of specific fragments extracted= 2 number of extra gaps= 0 total=58 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ipd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ipd expands to /projects/compbio/data/pdb/1ipd.pdb.gz 1ipd:Warning: there is no chain 1ipd will retry with 1ipdA # T0349 read from 1ipd/merged-good-all-a2m # 1ipd read from 1ipd/merged-good-all-a2m # adding 1ipd to template set # found chain 1ipd in template set T0349 11 :VLLSAVGALLDGADIGHLVLDQNMS 1ipd 164 :RVARVAFEAARKRRKHVVSVDKANV T0349 52 :EDDLAGARRLLTDA 1ipd 189 :LEVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=60 Number of alignments=19 # 1ipd read from 1ipd/merged-good-all-a2m # found chain 1ipd in template set T0349 11 :VLLSAVGALLDGADIGHLVLDQNMSI 1ipd 164 :RVARVAFEAARKRRKHVVSVDKANVL T0349 53 :DDLAGARRLLTDA 1ipd 190 :EVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=62 Number of alignments=20 # 1ipd read from 1ipd/merged-good-all-a2m # found chain 1ipd in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNMS 1ipd 165 :VARVAFEAARKRRKHVVSVDKANV T0349 52 :EDDLAGARRLLTDA 1ipd 189 :LEVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=64 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a3yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a3yA expands to /projects/compbio/data/pdb/1a3y.pdb.gz 1a3yA:# T0349 read from 1a3yA/merged-good-all-a2m # 1a3yA read from 1a3yA/merged-good-all-a2m # adding 1a3yA to template set # found chain 1a3yA in template set T0349 44 :IPRRVL 1a3yA 114 :MTGLLG T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1a3yA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=66 Number of alignments=22 # 1a3yA read from 1a3yA/merged-good-all-a2m # found chain 1a3yA in template set T0349 35 :SILEGSLGV 1a3yA 112 :TIMTGLLGK T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1a3yA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Number of alignments=23 # 1a3yA read from 1a3yA/merged-good-all-a2m # found chain 1a3yA in template set T0349 50 :VHEDDLAGARRLLTDAGLAHE 1a3yA 124 :IEDQDLEKFKEVTRENGIPEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=69 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qd9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qd9A expands to /projects/compbio/data/pdb/1qd9.pdb.gz 1qd9A:Skipped atom 598, because occupancy 0.230 <= existing 0.770 in 1qd9A Skipped atom 600, because occupancy 0.230 <= existing 0.770 in 1qd9A Skipped atom 602, because occupancy 0.230 <= existing 0.770 in 1qd9A # T0349 read from 1qd9A/merged-good-all-a2m # 1qd9A read from 1qd9A/merged-good-all-a2m # adding 1qd9A to template set # found chain 1qd9A in template set T0349 6 :RTNDAVLLSAVGALLDGADIGH 1qd9A 47 :KEQTHQVFSNLKAVLEEAGASF T0349 42 :GVIPRRVLV 1qd9A 70 :TVVKATVFI T0349 51 :HEDDLAGARRLLTDA 1qd9A 80 :DMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 Number of alignments=25 # 1qd9A read from 1qd9A/merged-good-all-a2m # found chain 1qd9A in template set T0349 9 :DAVLLSAVGALLDGADIGHL 1qd9A 50 :THQVFSNLKAVLEEAGASFE T0349 35 :SILEG 1qd9A 70 :TVVKA T0349 46 :RRVLVHEDDLAGARRLLTDA 1qd9A 75 :TVFIADMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=75 Number of alignments=26 # 1qd9A read from 1qd9A/merged-good-all-a2m # found chain 1qd9A in template set T0349 11 :VLLSAVGALLDGADIG 1qd9A 52 :QVFSNLKAVLEEAGAS T0349 37 :LEGSLGV 1qd9A 68 :FETVVKA T0349 46 :RRVLVHEDDLAGARRLLTDA 1qd9A 75 :TVFIADMEQFAEVNEVYGQY Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oo0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oo0A expands to /projects/compbio/data/pdb/1oo0.pdb.gz 1oo0A:# T0349 read from 1oo0A/merged-good-all-a2m # 1oo0A read from 1oo0A/merged-good-all-a2m # adding 1oo0A to template set # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=79 Number of alignments=28 # 1oo0A read from 1oo0A/merged-good-all-a2m # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 Number of alignments=29 # 1oo0A read from 1oo0A/merged-good-all-a2m # found chain 1oo0A in template set T0349 43 :VIPRRVLVHEDDLAGARRLLTDAGLAHE 1oo0A 46 :MIRKEAFVHQSVMEELKRIIIDSEIMQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwmA expands to /projects/compbio/data/pdb/1kwm.pdb.gz 1kwmA:Skipped atom 268, because occupancy 0.470 <= existing 0.530 in 1kwmA Skipped atom 270, because occupancy 0.470 <= existing 0.530 in 1kwmA Skipped atom 272, because occupancy 0.470 <= existing 0.530 in 1kwmA WARNING: atom 790 has residue number 4 < previous residue 95A in 1kwmA Skipped atom 1086, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1088, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1090, because occupancy 0.330 <= existing 0.670 in 1kwmA Skipped atom 1311, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1313, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1315, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1317, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1319, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1321, because occupancy 0.470 <= existing 0.520 in 1kwmA Skipped atom 1961, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1963, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1965, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1967, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1969, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1971, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 1973, because occupancy 0.430 <= existing 0.570 in 1kwmA Skipped atom 2225, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2227, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2229, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2231, because occupancy 0.350 <= existing 0.650 in 1kwmA Skipped atom 2315, because occupancy 0.340 <= existing 0.660 in 1kwmA Skipped atom 2317, because occupancy 0.340 <= existing 0.660 in 1kwmA # T0349 read from 1kwmA/merged-good-all-a2m # 1kwmA read from 1kwmA/merged-good-all-a2m # adding 1kwmA to template set # found chain 1kwmA in template set T0349 9 :DAVLLSAVGALLDGADIGHLVLDQNMSI 1kwmA 19A:DENHINIIRELASTTQIDFWKPDSVTQI T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLA 1kwmA 47A:KPHSTVDFRVKAEDTVTVENVLKQNELQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=83 Number of alignments=31 # 1kwmA read from 1kwmA/merged-good-all-a2m # found chain 1kwmA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGHLVLDQNMSI 1kwmA 15A:VNVEDENHINIIRELASTTQIDFWKPDSVTQI T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLAHE 1kwmA 47A:KPHSTVDFRVKAEDTVTVENVLKQNELQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=85 Number of alignments=32 # 1kwmA read from 1kwmA/merged-good-all-a2m # found chain 1kwmA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGHLV 1kwmA 15A:VNVEDENHINIIRELASTTQIDFWK T0349 34 :MSILEGSLGVIPRRVLVHEDDLAGARRLLTDAGLA 1kwmA 40A:PDSVTQIKPHSTVDFRVKAEDTVTVENVLKQNELQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=87 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cvlA expands to /projects/compbio/data/pdb/2cvl.pdb.gz 2cvlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0349 read from 2cvlA/merged-good-all-a2m # 2cvlA read from 2cvlA/merged-good-all-a2m # adding 2cvlA to template set # found chain 2cvlA in template set T0349 5 :LRTNDAVLLSAVGALLDGADIGH 2cvlA 45 :IRVQTERVMENLKAVLEAAGSGL T0349 42 :GVIP 2cvlA 69 :RVVQ T0349 46 :RRVLVHEDDLAGARRLLTDA 2cvlA 74 :TCFLADMEDFPGFNEVYARY T0349 67 :LAHE 2cvlA 94 :FTPP Number of specific fragments extracted= 4 number of extra gaps= 0 total=91 Number of alignments=34 # 2cvlA read from 2cvlA/merged-good-all-a2m # found chain 2cvlA in template set T0349 6 :RTNDAVLLSAVGALLDGADIGH 2cvlA 46 :RVQTERVMENLKAVLEAAGSGL T0349 28 :LVLD 2cvlA 70 :VVQT T0349 46 :RRVLVHEDDLAGARRLLTDA 2cvlA 74 :TCFLADMEDFPGFNEVYARY T0349 67 :LAH 2cvlA 94 :FTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=95 Number of alignments=35 # 2cvlA read from 2cvlA/merged-good-all-a2m # found chain 2cvlA in template set T0349 11 :VLLSAVGALLDGADIG 2cvlA 51 :RVMENLKAVLEAAGSG T0349 37 :LEGSLG 2cvlA 67 :LSRVVQ T0349 45 :PRRVLVHEDDLAGARRLLTDA 2cvlA 73 :TTCFLADMEDFPGFNEVYARY Number of specific fragments extracted= 3 number of extra gaps= 0 total=98 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0349 read from 1g61A/merged-good-all-a2m # 1g61A read from 1g61A/merged-good-all-a2m # found chain 1g61A in training set Warning: unaligning (T0349)N33 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 13 :LSAVGALLD 1g61A 2037 :VNEVSEVLE T0349 25 :IGHLVLD 1g61A 2046 :TKCLQTN T0349 32 :Q 1g61A 2054 :G T0349 35 :SILEGSLGVIPRRVL 1g61A 2057 :SLVGSLSVANKYGLL T0349 50 :VHEDDLAGARRLLTDAGLAH 1g61A 2076 :VEDEELDRIKNFLKENNLDL Number of specific fragments extracted= 5 number of extra gaps= 1 total=103 Number of alignments=37 # 1g61A read from 1g61A/merged-good-all-a2m # found chain 1g61A in training set Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 9 :DAVLLSAVGALLD 1g61A 2033 :DKDDVNEVSEVLE T0349 25 :IGHLVLDQN 1g61A 2046 :TKCLQTNIG T0349 36 :ILEGSLGVI 1g61A 2057 :SLVGSLSVA T0349 45 :PRRVL 1g61A 2067 :KYGLL T0349 50 :VHEDDLAGARRLLTDAGLAHE 1g61A 2076 :VEDEELDRIKNFLKENNLDLN Number of specific fragments extracted= 5 number of extra gaps= 1 total=108 Number of alignments=38 # 1g61A read from 1g61A/merged-good-all-a2m # found chain 1g61A in training set Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE in next template residue (1g61A)S2056 Warning: unaligning (T0349)S35 because of BadResidue code BAD_PEPTIDE at template residue (1g61A)S2056 T0349 12 :LLSAVGALLD 1g61A 2036 :DVNEVSEVLE T0349 25 :IGHLVLDQN 1g61A 2046 :TKCLQTNIG T0349 36 :ILEGSLG 1g61A 2057 :SLVGSLS T0349 43 :VIPRRVL 1g61A 2065 :ANKYGLL T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1g61A 2076 :VEDEELDRIKNFLKENNLDLNV Number of specific fragments extracted= 5 number of extra gaps= 1 total=113 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjqA expands to /projects/compbio/data/pdb/1vjq.pdb.gz 1vjqA:Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 1vjqA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 1vjqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0349 read from 1vjqA/merged-good-all-a2m # 1vjqA read from 1vjqA/merged-good-all-a2m # adding 1vjqA to template set # found chain 1vjqA in template set Warning: unaligning (T0349)G26 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)L28 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 9 :DAVLLSAVGALLDGADI 1vjqA 10 :NEEQVAFLEALAKQDEL T0349 30 :LDQNMS 1vjqA 30 :WQNPPT T0349 38 :EGS 1vjqA 37 :PGQ T0349 45 :PRRVLVHEDDLAGARRLLTDAGLA 1vjqA 40 :PVVILIPSDMVEWFLEMLKAKGIP Number of specific fragments extracted= 4 number of extra gaps= 1 total=117 Number of alignments=40 # 1vjqA read from 1vjqA/merged-good-all-a2m # found chain 1vjqA in template set Warning: unaligning (T0349)G26 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)H27 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)L28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 5 :LRTNDAVLLSAVGALLDGADI 1vjqA 6 :IVPTNEEQVAFLEALAKQDEL T0349 30 :L 1vjqA 30 :W T0349 32 :QNMSILEGS 1vjqA 31 :QNPPTEPGQ T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1vjqA 40 :PVVILIPSDMVEWFLEMLKAKGIPFT Number of specific fragments extracted= 4 number of extra gaps= 1 total=121 Number of alignments=41 # 1vjqA read from 1vjqA/merged-good-all-a2m # found chain 1vjqA in template set Warning: unaligning (T0349)N33 because of BadResidue code BAD_PEPTIDE in next template residue (1vjqA)F28 Warning: unaligning (T0349)M34 because of BadResidue code BAD_PEPTIDE at template residue (1vjqA)F28 Warning: unaligning (T0349)S35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjqA)D29 T0349 4 :LLRTNDAVLLSAVGALLDGAD 1vjqA 5 :VIVPTNEEQVAFLEALAKQDE T0349 32 :Q 1vjqA 26 :L T0349 36 :ILEGS 1vjqA 30 :WQNPP T0349 41 :LGVIPRRVLVHEDDLAGARRLLTDAGLA 1vjqA 36 :EPGQPVVILIPSDMVEWFLEMLKAKGIP Number of specific fragments extracted= 4 number of extra gaps= 1 total=125 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pba/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pba expands to /projects/compbio/data/pdb/1pba.pdb.gz 1pba:Warning: there is no chain 1pba will retry with 1pbaA # T0349 read from 1pba/merged-good-all-a2m # 1pba read from 1pba/merged-good-all-a2m # adding 1pba to template set # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 9 :DAVLLSAVGALLDGADIGH 1pba 19 :DENDISELHELASTRQIDF T0349 31 :D 1pba 38 :W T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GS 1pba 49 :HS T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 1pba 51 :TVDFRVKAEDILAVEDFLEQNELQYE Number of specific fragments extracted= 5 number of extra gaps= 1 total=130 Number of alignments=43 # 1pba read from 1pba/merged-good-all-a2m # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 5 :LRTNDAVLLSAVGALLDGADIGHL 1pba 15 :VNVEDENDISELHELASTRQIDFW T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GS 1pba 49 :HS T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHELR 1pba 51 :TVDFRVKAEDILAVEDFLEQNELQYEVL Number of specific fragments extracted= 4 number of extra gaps= 1 total=134 Number of alignments=44 # 1pba read from 1pba/merged-good-all-a2m # found chain 1pba in template set Warning: unaligning (T0349)Q32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pba)P40 Warning: unaligning (T0349)N33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pba)P40 T0349 5 :LRTNDAVLLSAVGALLDGADIG 1pba 15 :VNVEDENDISELHELASTRQID T0349 30 :LD 1pba 37 :FW T0349 34 :MSILE 1pba 41 :DSVTQ T0349 39 :GSL 1pba 49 :HST T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHE 1pba 52 :VDFRVKAEDILAVEDFLEQNELQYE Number of specific fragments extracted= 5 number of extra gaps= 1 total=139 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gukA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gukA expands to /projects/compbio/data/pdb/2guk.pdb.gz 2gukA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 271, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 273, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 275, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 277, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 279, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 2gukA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2gukA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2gukA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 2gukA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2gukA # T0349 read from 2gukA/merged-good-all-a2m # 2gukA read from 2gukA/merged-good-all-a2m # adding 2gukA to template set # found chain 2gukA in template set T0349 10 :AVLLSAVGALLDGAD 2gukA 11 :RVFMHHIYEFEKGVR T0349 40 :SL 2gukA 26 :SM T0349 46 :RRVLVHEDDLAGARRLLTDAGLA 2gukA 28 :VLATLANDDIPYAEERLRSRQIP Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=46 # 2gukA read from 2gukA/merged-good-all-a2m # found chain 2gukA in template set T0349 9 :DAVLLSAVGALLDGAD 2gukA 10 :LRVFMHHIYEFEKGVR T0349 40 :S 2gukA 26 :S T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHE 2gukA 27 :MVLATLANDDIPYAEERLRSRQIPYF Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 Number of alignments=47 # 2gukA read from 2gukA/merged-good-all-a2m # found chain 2gukA in template set T0349 48 :VLVHEDDLAGARRLLTDAGLA 2gukA 30 :ATLANDDIPYAEERLRSRQIP Number of specific fragments extracted= 1 number of extra gaps= 0 total=146 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zvpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zvpA expands to /projects/compbio/data/pdb/1zvp.pdb.gz 1zvpA:# T0349 read from 1zvpA/merged-good-all-a2m # 1zvpA read from 1zvpA/merged-good-all-a2m # adding 1zvpA to template set # found chain 1zvpA in template set T0349 15 :AVGALLDGADIGH 1zvpA 89 :AFATKLAEHGISA T0349 35 :SILEG 1zvpA 102 :NVIAG T0349 43 :VIPRRVLVHEDDLAGARRLLTD 1zvpA 107 :YYHDHIFVQKEKAQQALQALGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=149 Number of alignments=49 # 1zvpA read from 1zvpA/merged-good-all-a2m # found chain 1zvpA in template set T0349 13 :LSAVGALLDGADIGHLVL 1zvpA 87 :TAAFATKLAEHGISANVI T0349 38 :E 1zvpA 105 :A T0349 42 :GVIPRRVLVHEDDLAGARRLLT 1zvpA 106 :GYYHDHIFVQKEKAQQALQALG Number of specific fragments extracted= 3 number of extra gaps= 0 total=152 Number of alignments=50 # 1zvpA read from 1zvpA/merged-good-all-a2m # found chain 1zvpA in template set T0349 14 :SAVGALLDGADIG 1zvpA 88 :AAFATKLAEHGIS T0349 34 :MSILEG 1zvpA 101 :ANVIAG T0349 43 :VIPRRVLVHEDDLAGARRLLT 1zvpA 107 :YYHDHIFVQKEKAQQALQALG Number of specific fragments extracted= 3 number of extra gaps= 0 total=155 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0349 read from 1v6sA/merged-good-all-a2m # 1v6sA read from 1v6sA/merged-good-all-a2m # found chain 1v6sA in training set T0349 13 :LSAVGALLD 1v6sA 199 :IGVIESLLP T0349 24 :DIGHLVLDQNMS 1v6sA 208 :RIDRLLIGGAMA T0349 36 :ILEGSLGVI 1v6sA 225 :ALGGEVGRS T0349 49 :LVHEDDLAGARRLLTDA 1v6sA 234 :LVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=159 Number of alignments=52 # 1v6sA read from 1v6sA/merged-good-all-a2m # found chain 1v6sA in training set T0349 13 :LSAVGALL 1v6sA 199 :IGVIESLL T0349 23 :ADIGHLVLDQNMS 1v6sA 207 :PRIDRLLIGGAMA T0349 36 :ILEGSLGVI 1v6sA 225 :ALGGEVGRS T0349 49 :LVHEDDLAGARRLLTDA 1v6sA 234 :LVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=163 Number of alignments=53 # 1v6sA read from 1v6sA/merged-good-all-a2m # found chain 1v6sA in training set T0349 13 :LSAVGALLD 1v6sA 199 :IGVIESLLP T0349 24 :DIGHLVLDQNMS 1v6sA 208 :RIDRLLIGGAMA T0349 36 :ILEGSLG 1v6sA 225 :ALGGEVG T0349 47 :RVLVHEDDLAGARRLLTDA 1v6sA 232 :RSLVEEDRLDLAKDLLGRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=167 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0349 read from 1hdoA/merged-good-all-a2m # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0349)V50 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0349)A65 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0349)G66 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0349 11 :VLLSAVGALLDGADIGHLVLDQNMSILEGSL 1hdoA 89 :EGARNIVAAMKAHGVDKVVACTSAFLLWDPT T0349 51 :HEDDLA 1hdoA 122 :PPRLQA T0349 57 :GARRLLTD 1hdoA 134 :RMHKVLRE T0349 67 :L 1hdoA 144 :L Number of specific fragments extracted= 4 number of extra gaps= 2 total=171 Number of alignments=55 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set T0349 4 :LLRTNDAVLLSAVGALLD 1hdoA 8 :IFGATGQTGLTTLAQAVQ T0349 23 :ADIGHLVLDQNMSILEGSL 1hdoA 26 :AGYEVTVLVRDSSRLPSEG T0349 43 :VIPRRVLVHE 1hdoA 45 :PRPAHVVVGD T0349 53 :DDLAGARRLL 1hdoA 56 :LQAADVDKTV Number of specific fragments extracted= 4 number of extra gaps= 0 total=175 Number of alignments=56 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0349)V43 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0349)A65 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0349)G66 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0349 12 :LLSAVGALLDGADIGHLVLDQNMSILEGSL 1hdoA 90 :GARNIVAAMKAHGVDKVVACTSAFLLWDPT T0349 44 :IPRR 1hdoA 122 :PPRL T0349 49 :LVHEDDLAGARRLLTD 1hdoA 126 :QAVTDDHIRMHKVLRE T0349 67 :LA 1hdoA 144 :LK Number of specific fragments extracted= 4 number of extra gaps= 2 total=179 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dzkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0349 read from 1dzkA/merged-good-all-a2m # 1dzkA read from 1dzkA/merged-good-all-a2m # found chain 1dzkA in training set T0349 42 :GVIPRRVL 1dzkA 112 :TIMTGLLG T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1dzkA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=181 Number of alignments=58 # 1dzkA read from 1dzkA/merged-good-all-a2m # found chain 1dzkA in training set T0349 35 :SILEGSLGV 1dzkA 112 :TIMTGLLGK T0349 50 :VHEDDLAGARRLLTDAGLAHEL 1dzkA 124 :IEDQDLEKFKEVTRENGIPEEN Number of specific fragments extracted= 2 number of extra gaps= 0 total=183 Number of alignments=59 # 1dzkA read from 1dzkA/merged-good-all-a2m # found chain 1dzkA in training set T0349 50 :VHEDDLAGARRLLTDAGLAHE 1dzkA 124 :IEDQDLEKFKEVTRENGIPEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=184 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zhvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zhvA expands to /projects/compbio/data/pdb/1zhv.pdb.gz 1zhvA:# T0349 read from 1zhvA/merged-good-all-a2m # 1zhvA read from 1zhvA/merged-good-all-a2m # adding 1zhvA to template set # found chain 1zhvA in template set T0349 13 :LSAVGALLDGADIGHLVLDQNM 1zhvA 80 :VLSVISPLSTNGIGIFVVSTFD T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAH 1zhvA 102 :GDHLLVRSNDLEKTADLLANAGHSL Number of specific fragments extracted= 2 number of extra gaps= 0 total=186 Number of alignments=61 # 1zhvA read from 1zhvA/merged-good-all-a2m # found chain 1zhvA in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNM 1zhvA 79 :IVLSVISPLSTNGIGIFVVSTFD T0349 45 :PRRVLVHEDDLAGARRLLTDAGLAHELRSD 1zhvA 102 :GDHLLVRSNDLEKTADLLANAGHSLLLEHH Number of specific fragments extracted= 2 number of extra gaps= 0 total=188 Number of alignments=62 # 1zhvA read from 1zhvA/merged-good-all-a2m # found chain 1zhvA in template set T0349 9 :DAVLLSAVGALLDGADIGHLVLDQ 1zhvA 76 :ETGIVLSVISPLSTNGIGIFVVST T0349 37 :LEG 1zhvA 100 :FDG T0349 46 :RRVLVHEDDLAGARRLLTDAGLAHELRS 1zhvA 103 :DHLLVRSNDLEKTADLLANAGHSLLLEH Number of specific fragments extracted= 3 number of extra gaps= 0 total=191 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xaa/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xaa expands to /projects/compbio/data/pdb/1xaa.pdb.gz 1xaa:Warning: there is no chain 1xaa will retry with 1xaaA # T0349 read from 1xaa/merged-good-all-a2m # 1xaa read from 1xaa/merged-good-all-a2m # adding 1xaa to template set # found chain 1xaa in template set T0349 10 :AVLLSAVGALLDGADIGHLVLDQNMS 1xaa 17 :EAALKVLRALDEAEGLGLAYEVFPFG T0349 36 :ILEGSLGVI 1xaa 45 :AIDAFGEPF T0349 55 :LAGARRLLTD 1xaa 54 :PEPTRKGVEE T0349 65 :AGLAHELR 1xaa 78 :DGLPRKIR Number of specific fragments extracted= 4 number of extra gaps= 0 total=195 Number of alignments=64 # 1xaa read from 1xaa/merged-good-all-a2m # found chain 1xaa in template set T0349 11 :VLLSAVGALLD 1xaa 18 :AALKVLRALDE T0349 22 :GADIGHLVLDQNMSILEGSLGVI 1xaa 31 :GLGLAYEVFPFGGAAIDAFGEPF T0349 51 :HEDDLAGARR 1xaa 54 :PEPTRKGVEE T0349 65 :AGLAHELR 1xaa 78 :DGLPRKIR Number of specific fragments extracted= 4 number of extra gaps= 0 total=199 Number of alignments=65 # 1xaa read from 1xaa/merged-good-all-a2m # found chain 1xaa in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNMS 1xaa 165 :VARVAFEAARKRRKHVVSVDKANV T0349 52 :EDDLAGARRLLTDA 1xaa 189 :LEVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=201 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jbeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0349 read from 1jbeA/merged-good-all-a2m # 1jbeA read from 1jbeA/merged-good-all-a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 16 :VGALLDGADIGHLVLDQNMS 1jbeA 42 :ALNKLQAGGYGFVISDWNMP T0349 43 :VIPRRVLV 1jbeA 80 :ALPVLMVT T0349 51 :HEDDLAGARR 1jbeA 91 :KKENIIAAAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=204 Number of alignments=67 # 1jbeA read from 1jbeA/merged-good-all-a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 5 :LRTNDAV 1jbeA 34 :EEAEDGV T0349 15 :AVGALLDGADIGHLVLDQNMS 1jbeA 41 :DALNKLQAGGYGFVISDWNMP T0349 43 :VIPRRVLV 1jbeA 80 :ALPVLMVT T0349 51 :HEDDLAGARR 1jbeA 91 :KKENIIAAAQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=208 Number of alignments=68 # 1jbeA read from 1jbeA/merged-good-all-a2m # found chain 1jbeA in training set Warning: unaligning (T0349)S40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jbeA)A77 Warning: unaligning (T0349)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1jbeA)S79 Warning: unaligning (T0349)G42 because of BadResidue code BAD_PEPTIDE at template residue (1jbeA)S79 T0349 16 :VGALLDGADIGHLVLDQNMSIL 1jbeA 42 :ALNKLQAGGYGFVISDWNMPNM T0349 43 :VIPRRVLVH 1jbeA 80 :ALPVLMVTA T0349 52 :EDDLAGARR 1jbeA 92 :KENIIAAAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=211 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1idm/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1idm expands to /projects/compbio/data/pdb/1idm.pdb.gz 1idm:Warning: there is no chain 1idm will retry with 1idmA # T0349 read from 1idm/merged-good-all-a2m # 1idm read from 1idm/merged-good-all-a2m # adding 1idm to template set # found chain 1idm in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNMS 1idm 163 :VARVAFEAARKRRKHVVSVDKANV T0349 52 :EDDLAGARRLLTDA 1idm 187 :LEVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=213 Number of alignments=70 # 1idm read from 1idm/merged-good-all-a2m # found chain 1idm in template set T0349 11 :VLLSAVGALLDGADIGHLVLDQNMSI 1idm 162 :RVARVAFEAARKRRKHVVSVDKANVL T0349 53 :DDLAGARRLLTDA 1idm 188 :EVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=215 Number of alignments=71 # 1idm read from 1idm/merged-good-all-a2m # found chain 1idm in template set T0349 12 :LLSAVGALLDGADIGHLVLDQNMS 1idm 163 :VARVAFEAARKRRKHVVSVDKANV T0349 52 :EDDLAGARRLLTDA 1idm 187 :LEVGEFWRKTVEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=217 Number of alignments=72 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0349//projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0349/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0349/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((T0349)G17.CA, (T0349)H27.CB) [> 3.5414 = 5.9023 < 7.6730] w=1.0000 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)H27.CB) [> 3.7183 = 6.1972 < 8.0564] w=0.8185 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)R46.CB) [> 4.0889 = 6.8148 < 8.8593] w=0.7176 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)R47.CB) [> 3.3590 = 5.5983 < 7.2778] w=0.7158 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L61.CB) [> 4.0370 = 6.7283 < 8.7468] w=0.7042 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)A58.CB) [> 3.4836 = 5.8060 < 7.5478] w=0.6821 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L61.CB) [> 3.3579 = 5.5965 < 7.2755] w=0.6821 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)R47.CB) [> 4.1664 = 6.9439 < 9.0271] w=0.6800 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)R46.CB) [> 4.2531 = 7.0885 < 9.2150] w=0.6451 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)L67.CB) [> 3.8496 = 6.4160 < 8.3408] w=0.6091 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)V50.CB) [> 3.5717 = 5.9529 < 7.7387] w=0.5778 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L61.CB) [> 3.9624 = 6.6040 < 8.5852] w=0.5752 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)V29.CB) [> 4.1312 = 6.8853 < 8.9508] w=0.5743 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)R47.CB) [> 3.7685 = 6.2809 < 8.1652] w=0.5692 to align # Constraint # added constraint: constraint((T0349)V48.CB, (T0349)A58.CB) [> 4.0251 = 6.7086 < 8.7211] w=0.5661 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)V50.CB) [> 3.8662 = 6.4436 < 8.3767] w=0.5425 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)L67.CB) [> 4.1636 = 6.9393 < 9.0211] w=0.5407 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)A65.CB) [> 3.9622 = 6.6036 < 8.5847] w=0.5397 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)L62.CB) [> 3.9759 = 6.6264 < 8.6143] w=0.5381 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)V48.CB) [> 3.8027 = 6.3378 < 8.2392] w=0.5380 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)H51.CB) [> 3.9488 = 6.5813 < 8.5558] w=0.5380 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)L49.CB) [> 4.0512 = 6.7519 < 8.7775] w=0.5379 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)V48.CB) [> 3.6073 = 6.0122 < 7.8158] w=0.5352 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L62.CB) [> 3.5658 = 5.9431 < 7.7260] w=0.5285 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)L49.CB) [> 4.5167 = 7.5279 < 9.7862] w=0.5057 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)D54.CB) [> 4.1551 = 6.9252 < 9.0028] w=0.4997 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)V50.CB) [> 3.4871 = 5.8119 < 7.5554] w=0.4989 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L49.CB) [> 3.1529 = 5.2548 < 6.8312] w=0.4690 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)L61.CB) [> 3.1349 = 5.2248 < 6.7922] w=0.4688 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)A58.CB) [> 3.6287 = 6.0478 < 7.8622] w=0.4688 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L62.CB) [> 3.8683 = 6.4472 < 8.3813] w=0.4688 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)V48.CB) [> 3.5715 = 5.9526 < 7.7384] w=0.4672 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)R46.CB) [> 4.0202 = 6.7004 < 8.7105] w=0.4666 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)L49.CB) [> 4.0844 = 6.8073 < 8.8495] w=0.4653 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)L49.CB) [> 3.5160 = 5.8600 < 7.6180] w=0.4599 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)G26.CA) [> 4.1165 = 6.8608 < 8.9191] w=0.4595 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)V50.CB) [> 4.1459 = 6.9099 < 8.9829] w=0.4336 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)H51.CB) [> 4.0315 = 6.7191 < 8.7348] w=0.4290 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)V48.CB) [> 4.0623 = 6.7706 < 8.8017] w=0.4286 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)R47.CB) [> 4.5089 = 7.5148 < 9.7693] w=0.4267 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)R46.CB) [> 3.1377 = 5.2295 < 6.7984] w=0.4251 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)A65.CB) [> 4.4190 = 7.3650 < 9.5745] w=0.4219 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)L67.CB) [> 3.6755 = 6.1259 < 7.9636] w=0.3950 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)L49.CB) [> 3.1092 = 5.1821 < 6.7367] w=0.3908 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)R47.CB) [> 3.4694 = 5.7822 < 7.5169] w=0.3907 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)A65.CB) [> 2.9040 = 4.8400 < 6.2920] w=0.3616 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)V50.CB) [> 3.6115 = 6.0192 < 7.8249] w=0.3615 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)A58.CB) [> 4.1132 = 6.8554 < 8.9120] w=0.3595 to align # Constraint # added constraint: constraint((T0349)A23.CB, (T0349)G57.CA) [> 4.1296 = 6.8826 < 8.9474] w=0.3595 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)R46.CB) [> 4.0178 = 6.6963 < 8.7052] w=0.3587 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)A58.CB) [> 4.0670 = 6.7783 < 8.8118] w=0.3564 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)R47.CB) [> 3.8982 = 6.4970 < 8.4461] w=0.3564 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)H51.CB) [> 3.9952 = 6.6586 < 8.6562] w=0.3558 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)P45.CB) [> 3.5760 = 5.9601 < 7.7481] w=0.3539 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)P45.CB) [> 2.8698 = 4.7829 < 6.2178] w=0.3539 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)P45.CB) [> 3.9805 = 6.6341 < 8.6244] w=0.3539 to align # Constraint # added constraint: constraint((T0349)R59.CB, (T0349)H69.CB) [> 3.8920 = 6.4867 < 8.4327] w=0.3362 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)R46.CB) [> 3.2510 = 5.4183 < 7.0437] w=0.3261 to align # Constraint # added constraint: constraint((T0349)V16.CB, (T0349)V48.CB) [> 3.9062 = 6.5103 < 8.4634] w=0.3256 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)R46.CB) [> 4.0616 = 6.7693 < 8.8001] w=0.3210 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)V50.CB) [> 4.1652 = 6.9420 < 9.0246] w=0.3208 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)L55.CB) [> 2.6259 = 4.3765 < 5.6895] w=0.3206 to align # Constraint # added constraint: constraint((T0349)R47.CB, (T0349)A58.CB) [> 3.7575 = 6.2625 < 8.1412] w=0.3204 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)I44.CB) [> 3.7890 = 6.3149 < 8.2094] w=0.3184 to align # Constraint # added constraint: constraint((T0349)H27.CB, (T0349)I44.CB) [> 3.8518 = 6.4197 < 8.3456] w=0.3184 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)L67.CB) [> 4.2102 = 7.0170 < 9.1220] w=0.2863 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)A58.CB) [> 4.1620 = 6.9367 < 9.0177] w=0.2851 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)L55.CB) [> 4.0982 = 6.8304 < 8.8795] w=0.2850 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)L55.CB) [> 2.3947 = 3.9912 < 5.1885] w=0.2850 to align # Constraint # added constraint: constraint((T0349)L49.CB, (T0349)A58.CB) [> 3.6379 = 6.0632 < 7.8821] w=0.2804 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)V50.CB) [> 4.1950 = 6.9916 < 9.0891] w=0.2534 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)V48.CB) [> 4.5425 = 7.5708 < 9.8421] w=0.2515 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)A68.CB) [> 2.9067 = 4.8445 < 6.2979] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)V48.CB) [> 4.2755 = 7.1258 < 9.2635] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)V16.CB) [> 4.0936 = 6.8227 < 8.8695] w=0.2513 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)A58.CB) [> 3.9724 = 6.6207 < 8.6069] w=0.2512 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L37.CB) [> 4.5159 = 7.5264 < 9.7844] w=0.2504 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)A65.CB) [> 3.8438 = 6.4063 < 8.3282] w=0.2494 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)L55.CB) [> 2.4011 = 4.0018 < 5.2024] w=0.2494 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)G57.CA) [> 4.5097 = 7.5162 < 9.7711] w=0.2494 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)R46.CB) [> 3.3977 = 5.6628 < 7.3616] w=0.2494 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)I44.CB) [> 4.4745 = 7.4575 < 9.6948] w=0.2482 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)V48.CB) [> 4.1496 = 6.9160 < 8.9909] w=0.2183 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R46.CB) [> 3.5360 = 5.8934 < 7.6613] w=0.2165 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)A68.CB) [> 4.1577 = 6.9295 < 9.0084] w=0.2149 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)R46.CB) [> 2.9759 = 4.9599 < 6.4478] w=0.2149 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)R47.CB) [> 4.3252 = 7.2086 < 9.3712] w=0.2139 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)E52.CB) [> 2.9571 = 4.9284 < 6.4069] w=0.2137 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)E52.CB) [> 3.0183 = 5.0304 < 6.5396] w=0.2137 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)H51.CB) [> 4.2547 = 7.0911 < 9.2184] w=0.2136 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)R47.CB) [> 2.9464 = 4.9107 < 6.3839] w=0.2136 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)A58.CB) [> 4.2812 = 7.1353 < 9.2759] w=0.2133 to align # Constraint # added constraint: constraint((T0349)Q32.CB, (T0349)A58.CB) [> 4.1086 = 6.8477 < 8.9020] w=0.2123 to align # Constraint # added constraint: constraint((T0349)L19.CB, (T0349)D64.CB) [> 4.2569 = 7.0948 < 9.2233] w=0.1803 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)P45.CB) [> 3.1467 = 5.2445 < 6.8179] w=0.1801 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)L61.CB) [> 3.9714 = 6.6190 < 8.6047] w=0.1801 to align # Constraint # added constraint: constraint((T0349)L41.CB, (T0349)V50.CB) [> 4.1263 = 6.8771 < 8.9403] w=0.1790 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)V48.CB) [> 4.4217 = 7.3696 < 9.5805] w=0.1789 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)L49.CB) [> 3.4845 = 5.8075 < 7.5498] w=0.1788 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)S40.CB) [> 3.5147 = 5.8579 < 7.6153] w=0.1786 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)V50.CB) [> 4.2332 = 7.0554 < 9.1720] w=0.1785 to align # Constraint # added constraint: constraint((T0349)S35.CB, (T0349)V48.CB) [> 3.4317 = 5.7195 < 7.4354] w=0.1785 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V50.CB) [> 3.3245 = 5.5409 < 7.2032] w=0.1783 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V48.CB) [> 2.2562 = 3.7603 < 4.8884] w=0.1783 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R59.CB) [> 3.0901 = 5.1502 < 6.6953] w=0.1774 to align # Constraint # added constraint: constraint((T0349)G17.CA, (T0349)L61.CB) [> 4.3884 = 7.3140 < 9.5082] w=0.1774 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)A58.CB) [> 3.3472 = 5.5788 < 7.2524] w=0.1733 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)L61.CB) [> 3.7511 = 6.2519 < 8.1275] w=0.1470 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)P45.CB) [> 4.2026 = 7.0043 < 9.1056] w=0.1456 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)R46.CB) [> 4.5182 = 7.5303 < 9.7894] w=0.1455 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)G42.CA) [> 3.8925 = 6.4875 < 8.4338] w=0.1453 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)G42.CA) [> 4.5555 = 7.5925 < 9.8702] w=0.1453 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)G42.CA) [> 4.3488 = 7.2480 < 9.4224] w=0.1453 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L61.CB) [> 2.9088 = 4.8480 < 6.3024] w=0.1445 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)S40.CB) [> 4.5130 = 7.5217 < 9.7782] w=0.1434 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L41.CB) [> 4.1800 = 6.9667 < 9.0567] w=0.1425 to align # Constraint # added constraint: constraint((T0349)D21.CB, (T0349)L41.CB) [> 4.2182 = 7.0303 < 9.1393] w=0.1425 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)L61.CB) [> 3.9689 = 6.6148 < 8.5992] w=0.1425 to align # Constraint # added constraint: constraint((T0349)R6.CB, (T0349)H69.CB) [> 4.3052 = 7.1754 < 9.3279] w=0.1422 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)A58.CB) [> 3.0317 = 5.0529 < 6.5688] w=0.1420 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L61.CB) [> 3.4190 = 5.6984 < 7.4079] w=0.1387 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)P45.CB) [> 3.9593 = 6.5988 < 8.5784] w=0.1092 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)G66.CA) [> 4.6536 = 7.7559 < 10.0827] w=0.1091 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)G42.CA) [> 3.3489 = 5.5815 < 7.2560] w=0.1090 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)V43.CB) [> 4.5684 = 7.6140 < 9.8982] w=0.1090 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)I44.CB) [> 3.6697 = 6.1161 < 7.9509] w=0.1090 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)G42.CA) [> 3.8100 = 6.3500 < 8.2549] w=0.1090 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)V43.CB) [> 3.6838 = 6.1397 < 7.9816] w=0.1090 to align # Constraint # added constraint: constraint((T0349)I44.CB, (T0349)H69.CB) [> 4.4895 = 7.4824 < 9.7272] w=0.1090 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)A58.CB) [> 4.0846 = 6.8077 < 8.8499] w=0.1090 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)V43.CB) [> 4.7220 = 7.8701 < 10.2311] w=0.1089 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)L61.CB) [> 4.0662 = 6.7771 < 8.8102] w=0.1089 to align # Constraint # added constraint: constraint((T0349)D24.CB, (T0349)H51.CB) [> 3.4114 = 5.6857 < 7.3914] w=0.1089 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)M34.CB) [> 3.4260 = 5.7101 < 7.4231] w=0.1085 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)R47.CB) [> 4.3534 = 7.2557 < 9.4324] w=0.1079 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)V48.CB) [> 3.2493 = 5.4155 < 7.0401] w=0.1079 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L49.CB) [> 4.2252 = 7.0420 < 9.1546] w=0.1079 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L67.CB) [> 4.3922 = 7.3204 < 9.5165] w=0.1075 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)L41.CB) [> 4.0116 = 6.6859 < 8.6917] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L37.CB) [> 4.6413 = 7.7355 < 10.0562] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)E38.CB) [> 4.2996 = 7.1660 < 9.3158] w=0.1070 to align # Constraint # added constraint: constraint((T0349)L28.CB, (T0349)L41.CB) [> 4.2811 = 7.1351 < 9.2757] w=0.1070 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)R47.CB) [> 4.5219 = 7.5365 < 9.7974] w=0.1070 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)V48.CB) [> 2.4730 = 4.1217 < 5.3583] w=0.1070 to align # Constraint # added constraint: constraint((T0349)G39.CA, (T0349)V48.CB) [> 4.7785 = 7.9641 < 10.3534] w=0.1070 to align # Constraint # added constraint: constraint((T0349)R47.CB, (T0349)L61.CB) [> 3.2738 = 5.4564 < 7.0933] w=0.1070 to align # Constraint # added constraint: constraint((T0349)N33.CB, (T0349)I44.CB) [> 4.3232 = 7.2053 < 9.3669] w=0.1065 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)L62.CB) [> 4.7728 = 7.9546 < 10.3410] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)R59.CB) [> 4.3404 = 7.2340 < 9.4042] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L62.CB) [> 4.5981 = 7.6636 < 9.9627] w=0.1064 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)V29.CB) [> 4.0055 = 6.6758 < 8.6786] w=0.1060 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)G39.CA) [> 3.3340 = 5.5566 < 7.2236] w=0.1059 to align # Constraint # added constraint: constraint((T0349)V29.CB, (T0349)I44.CB) [> 3.1225 = 5.2042 < 6.7654] w=0.1058 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)S40.CB) [> 4.1186 = 6.8644 < 8.9237] w=0.1057 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L37.CB) [> 3.5633 = 5.9388 < 7.7204] w=0.1057 to align # Constraint # added constraint: constraint((T0349)D9.CB, (T0349)G39.CA) [> 4.1981 = 6.9968 < 9.0958] w=0.1044 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)E38.CB) [> 4.0540 = 6.7567 < 8.7838] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)L30.CB) [> 2.9340 = 4.8900 < 6.3570] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)R47.CB) [> 3.6117 = 6.0195 < 7.8254] w=0.0727 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)S40.CB) [> 3.0361 = 5.0602 < 6.5782] w=0.0727 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)R46.CB) [> 3.4982 = 5.8304 < 7.5795] w=0.0727 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)L49.CB) [> 4.6492 = 7.7487 < 10.0733] w=0.0715 to align # Constraint # added constraint: constraint((T0349)I36.CB, (T0349)D53.CB) [> 3.3241 = 5.5402 < 7.2022] w=0.0713 to align # Constraint # added constraint: constraint((T0349)V43.CB, (T0349)L71.CB) [> 3.9064 = 6.5107 < 8.4639] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L41.CB, (T0349)L71.CB) [> 4.7035 = 7.8392 < 10.1910] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L37.CB, (T0349)L71.CB) [> 3.7103 = 6.1839 < 8.0391] w=0.0712 to align # Constraint # added constraint: constraint((T0349)M34.CB, (T0349)V43.CB) [> 4.1676 = 6.9461 < 9.0299] w=0.0712 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)G39.CA) [> 4.0012 = 6.6686 < 8.6692] w=0.0711 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)L61.CB) [> 3.2244 = 5.3740 < 6.9862] w=0.0711 to align # Constraint # added constraint: constraint((T0349)A18.CB, (T0349)V43.CB) [> 4.2759 = 7.1265 < 9.2644] w=0.0708 to align # Constraint # added constraint: constraint((T0349)L12.CB, (T0349)V43.CB) [> 4.2450 = 7.0750 < 9.1975] w=0.0705 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)S40.CB) [> 4.7346 = 7.8910 < 10.2583] w=0.0696 to align # Constraint # added constraint: constraint((T0349)I25.CB, (T0349)G39.CA) [> 3.6470 = 6.0783 < 7.9017] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)L37.CB) [> 2.9155 = 4.8592 < 6.3170] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G26.CA, (T0349)G39.CA) [> 3.2200 = 5.3667 < 6.9767] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)R46.CB) [> 2.5539 = 4.2565 < 5.5335] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A15.CB, (T0349)V48.CB) [> 3.7338 = 6.2230 < 8.0899] w=0.0693 to align # Constraint # added constraint: constraint((T0349)A18.CB, (T0349)R46.CB) [> 4.0776 = 6.7961 < 8.8349] w=0.0693 to align # Constraint # added constraint: constraint((T0349)G22.CA, (T0349)S40.CB) [> 4.6508 = 7.7513 < 10.0767] w=0.0693 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)A58.CB) [> 3.9779 = 6.6298 < 8.6187] w=0.0399 to align # Constraint # added constraint: constraint((T0349)E38.CB, (T0349)L61.CB) [> 3.3762 = 5.6270 < 7.3151] w=0.0399 to align # Constraint # added constraint: constraint((T0349)G39.CA, (T0349)A58.CB) [> 4.0175 = 6.6958 < 8.7046] w=0.0399 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)A58.CB) [> 4.0631 = 6.7719 < 8.8034] w=0.0399 to align # Constraint # added constraint: constraint((T0349)P45.CB, (T0349)L62.CB) [> 2.7375 = 4.5625 < 5.9313] w=0.0399 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L41.CB) [> 4.6659 = 7.7765 < 10.1095] w=0.0364 to align # Constraint # added constraint: constraint((T0349)A10.CB, (T0349)L37.CB) [> 4.6986 = 7.8310 < 10.1803] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)R46.CB) [> 4.3854 = 7.3090 < 9.5016] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)P45.CB) [> 3.1994 = 5.3323 < 6.9320] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L13.CB, (T0349)L41.CB) [> 3.8691 = 6.4484 < 8.3829] w=0.0364 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)M34.CB) [> 4.7072 = 7.8454 < 10.1990] w=0.0364 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)S35.CB) [> 4.7838 = 7.9730 < 10.3649] w=0.0364 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)L49.CB) [> 3.1598 = 5.2663 < 6.8463] w=0.0363 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)V48.CB) [> 4.6687 = 7.7812 < 10.1156] w=0.0363 to align # Constraint # added constraint: constraint((T0349)R2.CB, (T0349)H51.CB) [> 3.8890 = 6.4816 < 8.4261] w=0.0363 to align # Constraint # added constraint: constraint((T0349)R2.CB, (T0349)L49.CB) [> 2.9534 = 4.9223 < 6.3990] w=0.0363 to align # Constraint # added constraint: constraint((T0349)M1.CB, (T0349)E52.CB) [> 2.4749 = 4.1248 < 5.3622] w=0.0363 to align # Constraint # added constraint: constraint((T0349)M1.CB, (T0349)H51.CB) [> 4.3668 = 7.2780 < 9.4614] w=0.0363 to align # Constraint # added constraint: constraint((T0349)L30.CB, (T0349)G39.CA) [> 3.1554 = 5.2590 < 6.8367] w=0.0363 to align # Constraint # added constraint: constraint((T0349)N8.CB, (T0349)R47.CB) [> 4.6977 = 7.8294 < 10.1783] w=0.0363 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)I44.CB) [> 4.0093 = 6.6821 < 8.6868] w=0.0360 to align # Constraint # added constraint: constraint((T0349)D31.CB, (T0349)V43.CB) [> 3.5015 = 5.8359 < 7.5867] w=0.0360 to align # Constraint # added constraint: constraint((T0349)I44.CB, (T0349)A58.CB) [> 3.2181 = 5.3634 < 6.9725] w=0.0356 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)L30.CB) [> 4.7972 = 7.9953 < 10.3938] w=0.0355 to align # Constraint # added constraint: constraint((T0349)L4.CB, (T0349)A15.CB) [> 3.7346 = 6.2243 < 8.0917] w=0.0355 to align # Constraint # added constraint: constraint((T0349)H51.CB, (T0349)R60.CB) [> 4.1973 = 6.9955 < 9.0942] w=0.0355 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)R46.CB) [> 4.5731 = 7.6218 < 9.9083] w=0.0355 to align # Constraint # added constraint: constraint((T0349)S14.CB, (T0349)V43.CB) [> 3.6430 = 6.0716 < 7.8931] w=0.0353 to align # Constraint # added constraint: constraint((T0349)T7.CB, (T0349)A18.CB) [> 4.6184 = 7.6972 < 10.0064] w=0.0352 to align # Constraint # added constraint: constraint((T0349)L5.CB, (T0349)L41.CB) [> 4.2968 = 7.1614 < 9.3098] w=0.0348 to align # Constraint # added constraint: constraint((T0349)L20.CB, (T0349)G42.CA) [> 4.5832 = 7.6386 < 9.9302] w=0.0347 to align # Constraint # added constraint: constraint((T0349)R46.CB, (T0349)A58.CB) [> 4.7732 = 7.9554 < 10.3420] w=0.0036 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0349/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0349/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # 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 T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 62 # 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 54 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # 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 54 # 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 49 # 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 3 # 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 48 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # 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 67 # 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 66 # 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 44 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 72 # 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 74 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # 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 50 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 44 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # 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 # 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 T0349 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 T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 73 # 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 73 # 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 16 # 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 11 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 33 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 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 42 # 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 # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 46 # 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 67 # 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 # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # 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 72 # 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 73 # 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 70 # 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 71 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # 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 10 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 69 # 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 70 # 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 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 35 # 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 # Found a chain break before 32 # 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 # Found a chain break before 8 # 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 67 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 24 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 29 # 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 29 # 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 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # 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 44 # 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 5 # 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 72 # 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 16 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 24 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # 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 46 # 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 72 # 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 T0349 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 T0349 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 T0349 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 T0349 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 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 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 43 # 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 69 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 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 119, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 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 45 # 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 39 # 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 70 # 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 69 # 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 46 # 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 74 # 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 T0349 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 T0349 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 Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz # WARNING: incomplete conformation T0349 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 Skipped atom 154, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 156, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 166, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 168, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 172, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 174, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 176, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0349 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 T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 47 # 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 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0349)L41.O and (T0349)G42.N only 0.000 apart, marking (T0349)G42.N as missing # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 74 # 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: (T0349)V43.O and (T0349)I44.N only 0.000 apart, marking (T0349)I44.N as missing # WARNING: incomplete conformation T0349 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 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0349)L4.O and (T0349)L5.N only 0.000 apart, marking (T0349)L5.N as missing # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # 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 T0349 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 T0349 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 T0349 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 T0349 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 T0349 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0349 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 2.5950 model score 2.3789 model score 1.4581 model score 1.3090 model score 2.2559 model score 1.2418 model score 1.1791 model score 1.1761 model score 1.4065 model score 1.1791 model score 1.1164 model score 1.6934 model score 1.7141 model score 1.8297 model score 1.9950 model score 0.9198 model score 1.5635 model score 0.6842 model score 1.3248 model score 0.9025 model score 0.9198 model score 0.6842 model score 1.2494 model score 0.7606 model score 0.9370 model score 0.3822 model score 1.0871 model score 0.5739 model score 1.1234 model score 1.1510 model score 1.1750 model score 0.4641 model score 0.5459 model score 0.8387 model score 0.6506 model score 0.4784 model score 1.8478 model score 1.2063 model score 1.2724 model score 1.3961 model score 1.4660 model score 1.2625 model score 1.2727 model score 1.2635 model score 1.2724 model score 1.2742 model score 0.7663 model score 1.0527 model score 0.7931 model score 0.9591 model score 0.9881 model score 0.5609 model score 0.4784 model score 0.8387 model score 0.7682 model score 0.6506 model score 1.3248 model score 1.6822 model score 2.6030 model score 1.5635 model score 1.3248 model score 1.2772 model score 1.2723 model score 1.2733 model score 1.2697 model score 1.2675 model score 1.2723 model score 1.2787 model score 1.2733 model score 1.2697 model score 1.2879 model score 2.1006 model score 1.9695 model score 1.7099 model score 1.5387 model score 1.9473 model score 0.7749 model score 1.7949 model score 0.5673 model score 1.3474 model score 0.9068 model score 1.2758 model score 1.2654 model score 1.2655 model score 1.2603 model score 1.2768 model score 0.9731 model score 1.2289 model score 0.9335 model score 0.6463 model score 1.2374 model score 1.5030 model score 1.4727 model score 0.5809 model score 0.5051 model score 0.6044 model score 0.5216 model score 0.7005 model score 0.5556 model score 0.5556 model score 0.6136 model score 1.1727 model score 1.2391 model score 1.3572 model score 1.6440 model score 0.6855 model score 1.5515 model score 0.7955 model score 1.1233 model score 1.2012 model score 1.1741 model score 1.2756 model score 0.6300 model score 1.6413 model score 0.7074 model score 0.9406 model score 0.8671 model score 1.2174 model score 0.9406 model score 0.8671 model score 0.8171 model score 1.6735 model score 0.4691 model score 0.4752 model score 0.4411 model score 0.4895 model score 0.3924 model score 1.2758 model score 1.6688 model score 2.0995 model score 1.5132 model score 2.1480 model score 1.6779 model score 1.3061 model score 1.3052 model score 1.3213 model score 1.3112 model score 1.3213 model score 1.3087 model score 0.8504 model score 0.9063 model score 1.2948 model score 0.6397 model score 0.6201 model score 0.6201 model score 0.6201 model score 0.5201 model score 0.6157 model score 1.0581 model score 1.5906 model score 1.5651 model score 1.5514 model score 1.7668 model score 1.3497 model score 0.5742 model score 0.6258 model score 0.5381 model score 0.6911 model score 0.6157 model score 0.7196 model score 0.5848 model score 0.5928 model score 0.7756 model score 0.7756 model score 1.3174 model score 1.0582 model score 0.8596 model score 0.8976 model score 0.6823 model score 1.0171 model score 1.3128 model score 0.8379 model score 0.7816 model score 0.6956 model score 0.5381 model score 1.4023 model score 0.5742 model score 1.5077 model score 0.6258 model score 1.2638 model score 1.2676 model score 1.2661 model score 1.2707 model score 1.2761 model score 1.2835 model score 1.2741 model score 1.2637 model score 1.2588 model score 1.2672 model score 0.7466 model score 0.4513 model score 0.7748 model score 1.0580 model score 1.3690 model score 0.4520 model score 0.9247 model score 1.0102 model score 1.3112 model score 0.6758 model score 0.4520 model score 1.0732 model score 1.5951 model score 1.1631 model score 1.1961 model score 1.0122 model score 0.8352 model score 1.8718 model score 1.9104 model score 1.6093 model score 1.2657 model score 1.2750 model score 1.2737 model score 1.2675 model score 1.2623 model score 0.4317 model score 1.2657 model score 1.2771 model score 1.2750 model score 1.2697 model score 1.2641 model score 0.4765 model score 0.4257 model score 0.4189 model score 0.4010 model score 0.5059 model score 0.4806 model score 0.7504 model score 1.2714 model score 1.2594 model score 1.2749 model score 1.2755 model score 1.2692 model score 1.5496 model score 1.6301 model score 1.7306 model score 1.6310 model score 2.0921 model score 1.6858 model score 1.7691 model score 1.8303 model score 1.5820 model score 1.3823 model score 0.8133 model score 0.6226 model score 0.7173 model score 0.7942 model score 1.2769 model score 1.3137 model score 2.1035 model score 2.0402 model score 1.2010 model score 0.4800 model score 0.4865 model score 1.4275 model score 1.3578 model score 1.3883 model score 1.6910 model score 0.8560 USE_META, weight: 0.1033 cost: 2.5950 min: 0.3822 max: 2.6030 USE_META, weight: 0.1908 cost: 2.3789 min: 0.3822 max: 2.6030 USE_META, weight: 0.5640 cost: 1.4581 min: 0.3822 max: 2.6030 USE_META, weight: 0.6244 cost: 1.3090 min: 0.3822 max: 2.6030 USE_META, weight: 0.2407 cost: 2.2559 min: 0.3822 max: 2.6030 USE_META, weight: 0.6517 cost: 1.2418 min: 0.3822 max: 2.6030 USE_META, weight: 0.6771 cost: 1.1791 min: 0.3822 max: 2.6030 USE_META, weight: 0.6783 cost: 1.1761 min: 0.3822 max: 2.6030 USE_META, weight: 0.5849 cost: 1.4065 min: 0.3822 max: 2.6030 USE_META, weight: 0.6771 cost: 1.1791 min: 0.3822 max: 2.6030 USE_META, weight: 0.7025 cost: 1.1164 min: 0.3822 max: 2.6030 USE_META, weight: 0.4686 cost: 1.6934 min: 0.3822 max: 2.6030 USE_META, weight: 0.4602 cost: 1.7141 min: 0.3822 max: 2.6030 USE_META, weight: 0.4134 cost: 1.8297 min: 0.3822 max: 2.6030 USE_META, weight: 0.3464 cost: 1.9950 min: 0.3822 max: 2.6030 USE_META, weight: 0.7821 cost: 0.9198 min: 0.3822 max: 2.6030 USE_META, weight: 0.5213 cost: 1.5635 min: 0.3822 max: 2.6030 USE_META, weight: 0.8776 cost: 0.6842 min: 0.3822 max: 2.6030 USE_META, weight: 0.6180 cost: 1.3248 min: 0.3822 max: 2.6030 USE_META, weight: 0.7891 cost: 0.9025 min: 0.3822 max: 2.6030 USE_META, weight: 0.7821 cost: 0.9198 min: 0.3822 max: 2.6030 USE_META, weight: 0.8776 cost: 0.6842 min: 0.3822 max: 2.6030 USE_META, weight: 0.6485 cost: 1.2494 min: 0.3822 max: 2.6030 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66.7000 USE_EVALUE, weight: 0.9674 eval: 2.4278 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9528 eval: 3.5066 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9528 eval: 3.5066 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9528 eval: 3.5066 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9672 eval: 2.4397 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9672 eval: 2.4397 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9672 eval: 2.4397 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9971 eval: 0.2267 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9971 eval: 0.2267 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9971 eval: 0.2267 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9789 eval: 1.5778 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9789 eval: 1.5778 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9789 eval: 1.5778 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.1000 eval: 66.7000 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.1000 eval: 66.7000 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.1000 eval: 66.7000 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9495 eval: 3.7561 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9495 eval: 3.7561 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9495 eval: 3.7561 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9440 eval: 4.1579 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9440 eval: 4.1579 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9440 eval: 4.1579 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9965 eval: 0.2685 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9965 eval: 0.2685 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9965 eval: 0.2685 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9536 eval: 3.4511 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9536 eval: 3.4511 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9536 eval: 3.4511 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9969 eval: 0.2452 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9969 eval: 0.2452 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9969 eval: 0.2452 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9978 eval: 0.1717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9978 eval: 0.1717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9978 eval: 0.1717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9547 eval: 3.3717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9547 eval: 3.3717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9547 eval: 3.3717 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9506 eval: 3.6706 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9506 eval: 3.6706 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9506 eval: 3.6706 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9810 eval: 1.4213 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9810 eval: 1.4213 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9810 eval: 1.4213 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9730 eval: 2.0152 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9730 eval: 2.0152 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9730 eval: 2.0152 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9749 eval: 1.8689 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9749 eval: 1.8689 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9749 eval: 1.8689 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9962 eval: 0.2922 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9962 eval: 0.2922 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9962 eval: 0.2922 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 1.0000 eval: 0.0121 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 1.0000 eval: 0.0121 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 1.0000 eval: 0.0121 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9776 eval: 1.6700 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9665 eval: 2.4979 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9665 eval: 2.4979 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9665 eval: 2.4979 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9783 eval: 1.6200 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9783 eval: 1.6200 min: 0.0121 max: 66.7000 USE_EVALUE, weight: 0.9783 eval: 1.6200 min: 0.0121 max: 66.7000 Number of contacts in models: 258 Number of contacts in alignments: 72 NUMB_ALIGNS: 72 Adding 1984 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: -133.7950, CN propb: -133.7950 weights: 0.3137 constraints: 198 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 198 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 198 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 1786 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 1786 # 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 1984 # command: