# command:# Seed set to 1041597583 # 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= 10531.4 msec) # Prefix for input files set to Created new target YGR022C from YGR022C.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 YGR022C.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= 18630 msec, elapsed time= 18681.1 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= 23370 msec, elapsed time= 23425.6 msec) # command:# Prefix for input files set to # command:# reading script from file YGR022C.t2k.undertaker-align.under # Reading fragments from alignment file # YGR022C read from 1in6A/YGR022C-1in6A-local-str-0.3-adpstyle5.a2m # 1in6A read from 1in6A/YGR022C-1in6A-local-str-0.3-adpstyle5.a2m # adding 1in6A to template set 1in6A:Skipped atom 153, because occupancy 0.5 <= existing 0.500001 Skipped atom 155, because occupancy 0.5 <= existing 0.500001 Skipped atom 157, because occupancy 0.5 <= existing 0.500001 Skipped atom 159, because occupancy 0.5 <= existing 0.500001 Skipped atom 161, because occupancy 0.5 <= existing 0.500001 Skipped atom 163, because occupancy 0.5 <= existing 0.500001 Skipped atom 165, because occupancy 0.5 <= existing 0.500001 Skipped atom 167, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 1005, because occupancy 0.33 <= existing 0.670001 Skipped atom 1007, because occupancy 0.33 <= existing 0.670001 Skipped atom 1009, because occupancy 0.33 <= existing 0.670001 Skipped atom 1011, because occupancy 0.33 <= existing 0.670001 Skipped atom 1013, because occupancy 0.33 <= existing 0.670001 Skipped atom 1015, because occupancy 0.33 <= existing 0.670001 Skipped atom 1017, because occupancy 0.33 <= existing 0.670001 Skipped atom 1019, because occupancy 0.33 <= existing 0.670001 Skipped atom 1021, because occupancy 0.33 <= existing 0.670001 Skipped atom 1023, because occupancy 0.33 <= existing 0.670001 Skipped atom 1025, because occupancy 0.33 <= existing 0.670001 Skipped atom 2008, because occupancy 0.25 <= existing 0.750001 Skipped atom 2010, because occupancy 0.25 <= existing 0.750001 Skipped atom 2012, because occupancy 0.25 <= existing 0.750001 Skipped atom 2014, because occupancy 0.25 <= existing 0.750001 Skipped atom 2016, because occupancy 0.25 <= existing 0.750001 Skipped atom 2018, because occupancy 0.25 <= existing 0.750001 # found chain 1in6A in template set YGR022C 16 :SSEELCGKEVKDT 1in6A 23 :SLDEFIGQENVKK Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues YGR022C 36 :KLAL 1in6A 36 :KLSL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR022C 51 :TAESEVMEGAVLDVVLLAGTNSCERTLSGSV 1in6A 40 :ALEAAKMRGEVLDHVLLAGPPGLGRTTLAHI Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 33 residues neighbor-bump: 2.45708 Ang C24.O and E25.CG neighbor-bump: 2.82283 Ang C24.C and E25.CG neighbor-bump: 2.19661 Ang N22.O and S23.CB neighbor-bump: 2.46921 Ang N22.C and S23.CB other bump:2.71931 Ang T2.CG2 and L13.CD1 other bump:2.88826 Ang E6.OE2 and V12.CA other bump:3.17713 Ang E6.CG and A11.C other bump:3.0454 Ang E6.CD and A11.C other bump:2.30218 Ang E6.OE2 and A11.C other bump:2.36107 Ang E6.CG and A11.O other bump:1.85618 Ang E6.CD and A11.O other bump:1.19043 Ang E6.OE2 and A11.O Number of specific fragments= 3 total=3 Number of alignments=1 # Reading fragments from alignment file # YGR022C read from 1faaA/YGR022C-1faaA-local-str-0.3-adpstyle5.a2m # 1faaA read from 1faaA/YGR022C-1faaA-local-str-0.3-adpstyle5.a2m # adding 1faaA to template set 1faaA:# found chain 1faaA in template set YGR022C 29 :EAILGVDKLALLVASVLDVNDSTAESEVMEGAVLDVVLLAGTNSCER 1faaA 2 :ELALGTQEMEAIVGKVTEVNKDTFWPIVKAAGDKPVVLDMFTQWCGP Fragment has 13 clashes (null) has 13 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 49 residues self-bump: 1.25714 Ang A33.CA and A33.CB other bump:2.43378 Ang L10.CD1 and E31.O other bump:1.76768 Ang L5.O and E31.OE1 other bump:2.63162 Ang L5.C and E31.OE1 other bump:2.31541 Ang L5.O and E31.CD other bump:3.00429 Ang L5.C and E31.CD other bump:2.64328 Ang L5.CB and E31.CG other bump:2.70287 Ang L13.CB and L18.CD1 other bump:2.18941 Ang L13.CD2 and L18.CD1 other bump:2.55337 Ang L13.CG and L18.CD1 other bump:2.64812 Ang L13.CD1 and L18.CD1 neighbor-bump: 2.23379 Ang V14.O and A15.CB neighbor-bump: 2.56138 Ang V14.C and A15.CB Number of specific fragments= 1 total=4 Number of alignments=2 # Reading fragments from alignment file # YGR022C read from 1grj/YGR022C-1grj-local-str-0.3-adpstyle5.a2m # 1grj read from 1grj/YGR022C-1grj-local-str-0.3-adpstyle5.a2m # adding 1grj to template set 1grj:# found chain 1grj in template set YGR022C 14 :RVSSEELCGKEVKDTEAIL 1grj 51 :AREQQGFCEGRIKDIEAKL Fragment has 10 clashes (null) has 10 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 21 residues other bump:3.26196 Ang A18.C and G21.N other bump:2.36317 Ang D15.OD1 and I19.CD1 other bump:1.99895 Ang E7.OE2 and K11.NZ other bump:2.55217 Ang E7.CD and K11.CE other bump:1.36317 Ang E7.OE2 and K11.CE other bump:3.02125 Ang E7.CD and K11.CD other bump:2.24776 Ang E7.OE2 and K11.CD other bump:3.13324 Ang S4.C and L8.CD2 other bump:3.23067 Ang S5.CA and L8.CD2 self-bump: 1.39805 Ang S4.CA and S4.CB YGR022C 40 :LVASVLDVNDSTAESEVMEGAVLDVVLLAGT 1grj 70 :SNAQVIDVTKMPNNGRVIFGATVTVLNLDSD Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 33 residues other bump:2.72105 Ang V18.CG2 and L24.CD1 other bump:3.00428 Ang V18.CB and L24.CD1 other bump:2.31415 Ang V18.CG1 and L24.CD1 Number of specific fragments= 2 total=6 Number of alignments=3 # Reading fragments from alignment file # YGR022C read from 1c0pA/YGR022C-1c0pA-global-str-1.5-adpstyle5.a2m # 1c0pA read from 1c0pA/YGR022C-1c0pA-global-str-1.5-adpstyle5.a2m # adding 1c0pA to template set 1c0pA:Skipped atom 75, because occupancy 0.38 <= existing 0.620001 Skipped atom 77, because occupancy 0.38 <= existing 0.620001 Skipped atom 79, because occupancy 0.38 <= existing 0.620001 Skipped atom 1361, because occupancy 0.34 <= existing 0.660001 Skipped atom 1363, because occupancy 0.34 <= existing 0.660001 Skipped atom 1365, because occupancy 0.34 <= existing 0.660001 Skipped atom 1367, because occupancy 0.34 <= existing 0.660001 Skipped atom 1682, because occupancy 0.42 <= existing 0.580001 Skipped atom 1684, because occupancy 0.42 <= existing 0.580001 Skipped atom 1804, because occupancy 0.22 <= existing 0.780001 Skipped atom 1806, because occupancy 0.22 <= existing 0.780001 Skipped atom 1808, because occupancy 0.22 <= existing 0.780001 # found chain 1c0pA in template set YGR022C 1 :MDEEESS 1c0pA 999 :LMMHSQK Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 8 residues YGR022C 8 :EDNVDERVSSEELCGKEVKDTEAILGVDKLALLVASVL 1c0pA 1038 :PEDVSSQTFASPWAGANWTPFMTLTDGPRQAKWEESTF Fragment has 21 clashes (null) has 21 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 40 residues other bump:2.59968 Ang D21.OD1 and V35.CG1 other bump:3.01463 Ang V28.CB and L31.CD1 other bump:2.25169 Ang V28.CG1 and L31.CD1 other bump:2.99377 Ang E23.CD and L31.CD1 other bump:2.30331 Ang E23.OE2 and L31.CD1 other bump:2.2806 Ang V28.CG1 and L31.CG other bump:2.73001 Ang V28.CG1 and L31.CB other bump:0.438946 Ang E23.OE1 and V28.CG2 other bump:2.67053 Ang E23.CG and V28.CG2 other bump:1.35388 Ang E23.CD and V28.CG2 other bump:2.06719 Ang E23.OE2 and V28.CG2 other bump:3.166 Ang E23.CD and V28.CG1 other bump:3.09776 Ang E23.OE2 and V28.CG1 other bump:1.71259 Ang E23.OE1 and V28.CB other bump:2.37968 Ang E23.CD and V28.CB other bump:2.58771 Ang E23.OE1 and V28.CA other bump:2.87884 Ang E23.OE1 and G27.C other bump:2.83782 Ang C15.SG and K17.CE other bump:3.27401 Ang E7.CD and V9.CG2 other bump:2.38493 Ang E7.OE1 and V9.CG2 other bump:2.7476 Ang E7.OE1 and V9.CB YGR022C 51 :TAESEVMEG 1c0pA 1076 :KKWVELVPT Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues YGR022C 60 :AVLDVVLLAGTNSC 1c0pA 1089 :WLKGTRRFAQNEDG Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues other bump:2.94139 Ang A10.CB and C15.CB YGR022C 75 :RTL 1c0pA 1116 :RPL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues YGR022C 78 :SGSV 1c0pA 1125 :PGAI Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues other bump:2.18098 Ang G1.O and S4.OG YGR022C 82 :VNAMRIVLHIDRLEAELFFLV 1c0pA 1130 :VTYDTLSVHAPKYCQYLAREL Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues other bump:2.37023 Ang H10.CE1 and D12.OD1 YGR022C 103 :GLQ 1c0pA 1154 :GAT Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues Number of specific fragments= 8 total=14 Number of alignments=4 # Reading fragments from alignment file # YGR022C read from 1c7nA/YGR022C-1c7nA-global-str-1.5-adpstyle5.a2m # 1c7nA read from 1c7nA/YGR022C-1c7nA-global-str-1.5-adpstyle5.a2m # adding 1c7nA to template set 1c7nA:# found chain 1c7nA in template set YGR022C 1 :MDEEESSE 1c7nA 1 :MIYDFTTK Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 9 residues other bump:2.42521 Ang E4.CD and S7.OG other bump:1.27946 Ang E4.OE2 and S7.OG other bump:3.165 Ang E4.CD and S7.CB other bump:2.38044 Ang E4.OE2 and S7.CB YGR022C 9 :DNVDERVSSEELCGKEVKD 1c7nA 27 :PEVGNEVVPLSVADMEFKN Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 21 residues self-bump: 1.33464 Ang E12.CA and E12.CB YGR022C 28 :TEAILGVDKLA 1c7nA 47 :PELIEGLKKYL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues YGR022C 39 :L 1c7nA 80 :K Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR022C 40 :LVAS 1c7nA 105 :AVRE Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR022C 44 :VLDVN 1c7nA 137 :IIECE Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR022C 49 :DSTAESEVMEGAVLDVVLLAGT 1c7nA 152 :DFQKLEKLSKDKNNKALLFCSP Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 24 residues other bump:1.79455 Ang V9.O and L15.CD1 other bump:2.76481 Ang V9.C and L15.CD1 YGR022C 71 :NSCERTLS 1c7nA 175 :NPVGRVWK Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues neighbor-bump: 2.83994 Ang N2.OD1 and S3.CA YGR022C 91 :IDRLEAELFFLVGLQL 1c7nA 183 :KDELQKIKDIVLKSDL Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues other bump:2.79476 Ang L15.CD1 and L17.CD1 other bump:3.00623 Ang E8.CD and L12.CD1 other bump:2.57208 Ang E8.OE2 and L12.CD1 Number of specific fragments= 9 total=23 Number of alignments=5 # command:superimposing iter= 0 total_weight= 343 weighted rmsd= 0 superimposing iter= 1 total_weight= 3430 weighted rmsd= 0 superimposing iter= 2 total_weight= 3430 weighted rmsd= 0 superimposing iter= 3 total_weight= 3430 weighted rmsd= 0 superimposing iter= 4 total_weight= 3430 weighted rmsd= 0 superimposing iter= 5 total_weight= 3430 weighted rmsd= 0 superimposing iter= 0 total_weight= 208 weighted rmsd= 7.72034 superimposing iter= 1 total_weight= 502.081 weighted rmsd= 4.92793 superimposing iter= 2 total_weight= 217.183 weighted rmsd= 4.812 superimposing iter= 3 total_weight= 209.319 weighted rmsd= 4.78735 superimposing iter= 4 total_weight= 210.688 weighted rmsd= 4.74779 superimposing iter= 5 total_weight= 212.322 weighted rmsd= 4.6908 superimposing iter= 0 total_weight= 235 weighted rmsd= 14.7295 superimposing iter= 1 total_weight= 519.752 weighted rmsd= 9.55235 superimposing iter= 2 total_weight= 311.923 weighted rmsd= 8.19655 superimposing iter= 3 total_weight= 257.482 weighted rmsd= 7.77652 superimposing iter= 4 total_weight= 241.832 weighted rmsd= 7.61179 superimposing iter= 5 total_weight= 239.259 weighted rmsd= 7.48306 superimposing iter= 0 total_weight= 334 weighted rmsd= 12.0675 superimposing iter= 1 total_weight= 882.264 weighted rmsd= 7.03306 superimposing iter= 2 total_weight= 566.635 weighted rmsd= 5.18484 superimposing iter= 3 total_weight= 459.553 weighted rmsd= 4.34111 superimposing iter= 4 total_weight= 379.282 weighted rmsd= 4.04337 superimposing iter= 5 total_weight= 342.735 weighted rmsd= 3.96918 superimposing iter= 0 total_weight= 326 weighted rmsd= 19.3549 superimposing iter= 1 total_weight= 797.044 weighted rmsd= 9.26462 superimposing iter= 2 total_weight= 543.18 weighted rmsd= 6.64777 superimposing iter= 3 total_weight= 402.755 weighted rmsd= 5.83232 superimposing iter= 4 total_weight= 384.661 weighted rmsd= 5.30567 superimposing iter= 5 total_weight= 387.56 weighted rmsd= 4.83267 # command: