# command:# Seed set to 1041514401 # command:# Prefix for input files set to # command:# reading script from file define-score.under # Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ # reading monomeric-50pc.atoms # After reading monomeric-50pc.atoms have 448 chains in training database # 111547 residues have no bad marker # 670 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 28 # Note: may sum to more than number of residues, # because one residue may have multiple problems # Reading rotamer library from monomeric-50pc.rot # Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/spots/ # ReadAtomType pdb-name.types Read AtomType pdb-name with 37 types. # ReadClashTable pdb-atom-name.clash # Read ClashTable pdb-atom-name Reading spots from monomeric-50pc-dry-5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 Reading spots from monomeric-50pc-wet-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 Reading spots from monomeric-50pc-dry-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 Reading spots from monomeric-50pc-generic-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 Reading spots from monomeric-50pc-dry-8.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 Reading spots from monomeric-50pc-dry-10.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 Reading spots from monomeric-50pc-dry-12.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 # reading histogram from monomeric-smoothed-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # reading histogram from monomeric-smoothed-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins CPU_time= 10520 msec, elapsed time= 10522.6 msec) # Prefix for input files set to Created new target YGR008C from YGR008C.a2m # Prefix for input files set to /projects/compbio/lib/alphabet/ # Read 3 alphabets from alpha.alphabet # Prefix for input files set to # reading predictions from YGR008C.t2k.alpha.rdb # created predicted alpha cost function pred_alpha2 with 360 bins # SetCost created cost = # ( 0.2 * gen6.5(6.5) + 0.5 * wet6.5(6.5, /log(length)) + 2 * dry5(5) + 8 * dry6.5(6.5) + 4 * dry8(8) + 1 * dry12(12) + 0.5 * phobic_fit + 0.2 * sidechain + 1 * clashes + -0.2 * sidechain_clashes + 0.5 * backbone_clashes + 10 * break + 1 * pred_alpha2 + 0.05 * constraints + 1 * contact_order ) # command:# No conformations to remove in PopConform # command:CPU_time= 17900 msec, elapsed time= 17930.6 msec) # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 407 20 (100%) # n-terminus 2 408 196 (49%) # middle 1 109496 20 (100%) # middle 2 108592 400 (100%) # middle 3 107719 7822 (97.775%) # middle 4 106865 64233 (40.1456%) # c-terminus 1 408 20 (100%) # c-terminus 2 406 227 (56.75%) # ss-bonds 409 # command:CPU_time= 22630 msec, elapsed time= 22668.2 msec) # command:# Prefix for input files set to # command:# reading script from file YGR008C.t2k.undertaker-align.under # Reading fragments from alignment file # YGR008C read from 1qg1E/YGR008C-1qg1E-global-adpstyle5.a2m # 1qg1E read from 1qg1E/YGR008C-1qg1E-global-adpstyle5.a2m # adding 1qg1E to template set 1qg1E:# found chain 1qg1E in template set YGR008C 1 :MTRT 1qg1E 1 :GSHP Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues YGR008C 5 :NKWTEREGKADPKYFSHTGNYGESPNHIKKQGSGKGN 1qg1E 26 :GAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGK Fragment has 33 clashes (null) has 33 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 39 residues other bump:2.23794 Ang S34.OG and N38.ND2 other bump:2.81286 Ang S34.OG and N38.CG other bump:2.5729 Ang S34.OG and N38.CB other bump:2.11972 Ang E6.CD and K31.NZ other bump:1.19666 Ang E6.OE2 and K31.NZ other bump:3.18227 Ang F16.C and K31.CB other bump:2.94836 Ang F16.CB and K31.CB other bump:3.15738 Ang H18.CD2 and I29.CB other bump:2.81406 Ang T19.CG2 and H28.CD2 other bump:2.58933 Ang H18.O and H28.CB other bump:2.59124 Ang H18.O and H28.CA other bump:2.74364 Ang Y22.CE2 and N27.OD1 other bump:2.79968 Ang Y22.CD2 and N27.CB other bump:3.00346 Ang Y22.CE2 and N27.CB neighbor-bump: 2.79409 Ang S25.C and P26.CG other bump:2.73355 Ang N21.OD1 and E24.C neighbor-bump: 2.67907 Ang G23.C and E24.CB other bump:2.67431 Ang N21.OD1 and E24.CA other bump:2.75437 Ang T5.CG2 and T19.OG1 other bump:3.31525 Ang R7.CD and T19.CG2 neighbor-bump: 2.65847 Ang F16.C and S17.OG other bump:2.47284 Ang G9.N and Y15.O other bump:2.50404 Ang P13.CD and Y15.CE1 other bump:2.37822 Ang D12.CB and Y15.CD1 other bump:2.68481 Ang D12.CG and Y15.CD1 neighbor-bump: 2.33527 Ang P13.C and K14.CG neighbor-bump: 1.30189 Ang P13.O and K14.CG neighbor-bump: 2.45515 Ang P13.C and K14.CB neighbor-bump: 2.10117 Ang P13.O and K14.CB other bump:2.2531 Ang N2.O and W4.CE3 other bump:3.21647 Ang N2.C and W4.CE3 neighbor-bump: 2.18978 Ang G1.O and N2.CG self-bump: 1.37059 Ang N2.CA and N2.CB YGR008C 42 :WGKPGDEIDDLIDNGEIPPV 1qg1E 66 :WVVKFNSLNELVDYHRSTSV Fragment has 10 clashes (null) has 10 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 22 residues neighbor-bump: 2.67216 Ang P19.C and P20.O neighbor-bump: 2.65841 Ang I18.N and P19.CD other bump:1.52803 Ang N15.O and P19.CD other bump:2.73748 Ang N15.C and P19.CD other bump:1.90283 Ang N15.O and P19.CG other bump:2.80214 Ang N15.C and P19.CG other bump:3.25994 Ang I13.C and E17.CG other bump:2.81651 Ang E8.CG and D11.OD2 other bump:2.8199 Ang E8.CB and D11.CG self-bump: 3.04691 Ang W2.CA and W2.CE3 YGR008C 68 :GSNLQSHEQKFENVQK 1qg1E 86 :SRNQQIFLRDIEQVPQ Fragment has 6 clashes (null) has 6 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues neighbor-bump: 2.19194 Ang N14.O and V15.O neighbor-bump: 2.56924 Ang N14.C and V15.O neighbor-bump: 2.51288 Ang N14.O and V15.CG2 neighbor-bump: 2.87004 Ang N14.C and V15.CG2 neighbor-bump: 2.65492 Ang F12.C and E13.O neighbor-bump: 2.24936 Ang F12.O and E13.O Number of specific fragments= 4 total=4 Number of alignments=1 # Reading fragments from alignment file # YGR008C read from 1outA/1abwA-YGR008C-fssp-global-adpstyle5.a2m # 1outA read from 1outA/1abwA-YGR008C-fssp-global-adpstyle5.a2m # adding 1outA to template set 1outA:Skipped atom 107, because occupancy 0.5 <= existing 0.500001 Skipped atom 109, because occupancy 0.5 <= existing 0.500001 Skipped atom 111, because occupancy 0.5 <= existing 0.500001 Skipped atom 113, because occupancy 0.5 <= existing 0.500001 Skipped atom 115, because occupancy 0.5 <= existing 0.500001 Skipped atom 117, because occupancy 0.5 <= existing 0.500001 Skipped atom 119, because occupancy 0.5 <= existing 0.500001 Skipped atom 121, because occupancy 0.5 <= existing 0.500001 Skipped atom 123, because occupancy 0.5 <= existing 0.500001 Skipped atom 351, because occupancy 0.5 <= existing 0.500001 Skipped atom 353, because occupancy 0.5 <= existing 0.500001 Skipped atom 355, because occupancy 0.5 <= existing 0.500001 Skipped atom 357, because occupancy 0.5 <= existing 0.500001 Skipped atom 359, because occupancy 0.5 <= existing 0.500001 # found chain 1outA in template set YGR008C 7 :WTEREGK 1outA 2 :LTAKDKS Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 9 residues other bump:1.89962 Ang W2.CE3 and E6.OE1 other bump:2.64031 Ang W2.CZ3 and E6.OE1 other bump:2.90646 Ang W2.CE3 and E6.CD other bump:2.99959 Ang W2.CE3 and E6.CB YGR008C 14 :ADPKYFSHT 1outA 38 :QTKTYFSHW Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues YGR008C 23 :GNYGES 1outA 48 :DLSPGS Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 8 residues YGR008C 29 :PNHIKKQGSGKGNWGKPGDEIDDLIDNGE 1outA 86 :DLHAFKLRVDPGNFKILSHNILVTLAIHF Fragment has 6 clashes (null) has 6 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 31 residues other bump:1.64019 Ang N14.O and P18.CD other bump:2.85412 Ang N14.C and P18.CD other bump:3.10796 Ang W15.C and P18.CD other bump:2.47221 Ang N14.O and P18.CG other bump:3.00307 Ang K12.CG and W15.CH2 other bump:3.06478 Ang K12.CG and W15.CZ3 YGR008C 58 :IPPVFKKDR 1outA 133 :VSAALADKY Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues other bump:2.60163 Ang I2.O and F6.CD1 other bump:3.03274 Ang G1.C and P4.CD neighbor-bump: 2.95043 Ang P3.CD and P4.CD Number of specific fragments= 5 total=9 Number of alignments=2 # Reading fragments from alignment file # YGR008C read from 1jyrA/YGR008C-1jyrA-local-str-0.3-adpstyle5.a2m # 1jyrA read from 1jyrA/YGR008C-1jyrA-local-str-0.3-adpstyle5.a2m # adding 1jyrA to template set 1jyrA:Skipped atom 79, because occupancy 0.5 <= existing 0.500001 Skipped atom 81, because occupancy 0.5 <= existing 0.500001 Skipped atom 83, because occupancy 0.5 <= existing 0.500001 Skipped atom 113, because occupancy 0.5 <= existing 0.500001 Skipped atom 115, because occupancy 0.5 <= existing 0.500001 Skipped atom 117, because occupancy 0.5 <= existing 0.500001 Skipped atom 119, because occupancy 0.5 <= existing 0.500001 Skipped atom 149, because occupancy 0.5 <= existing 0.500001 Skipped atom 151, because occupancy 0.5 <= existing 0.500001 Skipped atom 153, because occupancy 0.5 <= existing 0.500001 Skipped atom 168, because occupancy 0.5 <= existing 0.500001 Skipped atom 204, because occupancy 0.5 <= existing 0.500001 Skipped atom 206, because occupancy 0.5 <= existing 0.500001 Skipped atom 208, because occupancy 0.5 <= existing 0.500001 Skipped atom 210, because occupancy 0.5 <= existing 0.500001 Skipped atom 212, because occupancy 0.5 <= existing 0.500001 Skipped atom 288, because occupancy 0.5 <= existing 0.500001 Skipped atom 290, because occupancy 0.5 <= existing 0.500001 Skipped atom 292, because occupancy 0.5 <= existing 0.500001 Skipped atom 294, because occupancy 0.5 <= existing 0.500001 Skipped atom 296, because occupancy 0.5 <= existing 0.500001 Skipped atom 351, because occupancy 0.5 <= existing 0.500001 Skipped atom 353, because occupancy 0.5 <= existing 0.500001 Skipped atom 366, because occupancy 0.5 <= existing 0.500001 Skipped atom 368, because occupancy 0.5 <= existing 0.500001 Skipped atom 400, because occupancy 0.5 <= existing 0.500001 Skipped atom 402, because occupancy 0.5 <= existing 0.500001 Skipped atom 408, because occupancy 0.5 <= existing 0.500001 Skipped atom 410, because occupancy 0.5 <= existing 0.500001 Skipped atom 412, because occupancy 0.5 <= existing 0.500001 Skipped atom 414, because occupancy 0.5 <= existing 0.500001 Skipped atom 481, because occupancy 0.5 <= existing 0.500001 Skipped atom 483, because occupancy 0.5 <= existing 0.500001 Skipped atom 485, because occupancy 0.5 <= existing 0.500001 Skipped atom 487, because occupancy 0.5 <= existing 0.500001 Skipped atom 489, because occupancy 0.5 <= existing 0.500001 Skipped atom 491, because occupancy 0.5 <= existing 0.500001 Skipped atom 493, because occupancy 0.5 <= existing 0.500001 Skipped atom 575, because occupancy 0.5 <= existing 0.500001 Skipped atom 577, because occupancy 0.5 <= existing 0.500001 Skipped atom 651, because occupancy 0.5 <= existing 0.500001 Skipped atom 653, because occupancy 0.5 <= existing 0.500001 Skipped atom 752, because occupancy 0.5 <= existing 0.500001 Skipped atom 754, because occupancy 0.5 <= existing 0.500001 Skipped atom 761, because occupancy 0.5 <= existing 0.500001 Skipped atom 763, because occupancy 0.5 <= existing 0.500001 Skipped atom 765, because occupancy 0.5 <= existing 0.500001 Skipped atom 767, because occupancy 0.5 <= existing 0.500001 # found chain 1jyrA in template set YGR008C 5 :NKWTEREGKADPKYFSHTG 1jyrA 81 :GAFLIRESESAPGDFSLSV Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 21 residues other bump:2.71113 Ang D12.CG and Y15.CE2 other bump:2.37649 Ang D12.OD2 and Y15.CE2 other bump:2.42746 Ang D12.OD1 and Y15.CE2 other bump:2.08071 Ang D12.CG and Y15.CD2 other bump:1.63927 Ang D12.OD2 and Y15.CD2 other bump:2.31729 Ang D12.OD1 and Y15.CD2 other bump:2.27329 Ang D12.OD2 and Y15.CG other bump:2.37447 Ang N2.O and W4.CZ3 other bump:3.29295 Ang N2.C and W4.CZ3 other bump:1.57438 Ang N2.O and W4.CE3 other bump:2.79869 Ang N2.C and W4.CE3 self-bump: 1.39622 Ang N2.CA and N2.CB YGR008C 26 :GESPNHIKKQGSGKGN 1jyrA 102 :GNDVQHFKVLRDGAGK Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues neighbor-bump: 2.06427 Ang S4.C and P5.CD YGR008C 42 :WGKPGDEIDDLIDN 1jyrA 121 :WVVKFNSLNELVDY Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues Number of specific fragments= 3 total=12 Number of alignments=3 # command:superimposing iter= 0 total_weight= 610 weighted rmsd= 0 superimposing iter= 1 total_weight= 6100 weighted rmsd= 0 superimposing iter= 2 total_weight= 6100 weighted rmsd= 0 superimposing iter= 3 total_weight= 6100 weighted rmsd= 0 superimposing iter= 4 total_weight= 6100 weighted rmsd= 0 superimposing iter= 5 total_weight= 6100 weighted rmsd= 0 superimposing iter= 0 total_weight= 429 weighted rmsd= 15.1452 superimposing iter= 1 total_weight= 851.282 weighted rmsd= 10.4719 superimposing iter= 2 total_weight= 525.316 weighted rmsd= 9.36265 superimposing iter= 3 total_weight= 482.851 weighted rmsd= 8.76421 superimposing iter= 4 total_weight= 461.305 weighted rmsd= 8.41838 superimposing iter= 5 total_weight= 442.535 weighted rmsd= 8.2734 superimposing iter= 0 total_weight= 384 weighted rmsd= 1.85403 superimposing iter= 1 total_weight= 1174.33 weighted rmsd= 1.02926 superimposing iter= 2 total_weight= 501.222 weighted rmsd= 0.892868 superimposing iter= 3 total_weight= 414.543 weighted rmsd= 0.856079 superimposing iter= 4 total_weight= 391.651 weighted rmsd= 0.845485 superimposing iter= 5 total_weight= 387.975 weighted rmsd= 0.839318 # command: