# command:# Seed set to 1041573631 # 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= 10760 msec, elapsed time= 10832.2 msec) # Prefix for input files set to Created new target YGR206W from YGR206W.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 YGR206W.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= 18700 msec, elapsed time= 18809 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= 23450 msec, elapsed time= 23556.6 msec) # command:# Prefix for input files set to # command:# reading script from file YGR206W.t2k.undertaker-align.under # Reading fragments from alignment file # YGR206W read from 1pou/YGR206W-1pou-local-str-0.3-adpstyle5.a2m # 1pou read from 1pou/YGR206W-1pou-local-str-0.3-adpstyle5.a2m # adding 1pou to template set 1pou:# found chain 1pou in template set YGR206W 12 :IPLYNKYGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYE 1pou 32 :LAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLN Fragment has 52 clashes (null) has 52 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.43685 Ang K7.NZ and W40.NE1 other bump:2.78088 Ang K7.NZ and W40.CD1 other bump:3.14045 Ang F12.CZ and T33.CG2 other bump:2.99369 Ang L27.CD1 and Q31.NE2 other bump:2.80838 Ang F20.CD1 and L30.CD2 other bump:3.07244 Ang R19.CZ and F25.CZ other bump:2.47255 Ang R19.CB and F25.CZ other bump:2.93041 Ang R19.CG and F25.CZ other bump:2.38391 Ang R19.CD and F25.CZ other bump:2.24441 Ang R19.NE and F25.CZ other bump:2.89234 Ang R19.CZ and F25.CE2 other bump:2.66689 Ang R19.NE and F25.CE2 other bump:2.96125 Ang R19.CA and F25.CE1 other bump:1.82038 Ang R19.CB and F25.CE1 other bump:3.07319 Ang R19.C and F25.CE1 other bump:2.94942 Ang R19.NE and F25.CE1 other bump:2.9802 Ang R19.CB and F25.CD1 other bump:2.04301 Ang M22.CE and E24.OE1 self-bump: 2.19077 Ang P23.CA and P23.CD neighbor-bump: 1.72788 Ang M22.C and P23.CD neighbor-bump: 2.14777 Ang M22.O and P23.CD other bump:1.76876 Ang V17.O and Q21.OE1 other bump:2.37785 Ang V17.C and Q21.OE1 other bump:3.22757 Ang D11.CA and P13.CD other bump:2.29096 Ang D11.C and P13.CD neighbor-bump: 1.94356 Ang F12.N and P13.CD neighbor-bump: 2.3514 Ang F12.CA and P13.CD neighbor-bump: 2.03614 Ang F12.C and P13.CD self-bump: 1.36835 Ang P13.N and P13.CD neighbor-bump: 3.1175 Ang F12.N and P13.CG self-bump: 2.05074 Ang P13.N and P13.CG self-bump: 2.14321 Ang P13.N and P13.CB other bump:2.82898 Ang L4.CD1 and F12.CD1 other bump:2.40683 Ang Y5.CZ and K10.NZ other bump:1.70147 Ang Y5.OH and K10.NZ other bump:2.48495 Ang Y5.CE2 and K10.NZ other bump:2.81394 Ang Y5.CE1 and K10.CE other bump:2.45038 Ang Y5.CD2 and K10.CE other bump:1.4647 Ang Y5.CZ and K10.CE other bump:1.76724 Ang Y5.OH and K10.CE other bump:1.09442 Ang Y5.CE2 and K10.CE other bump:2.34311 Ang Y5.CD2 and K10.CD other bump:2.78447 Ang Y5.CZ and K10.CD other bump:1.63898 Ang Y5.CE2 and K10.CD other bump:2.81251 Ang Y5.CG and K10.CG other bump:1.64229 Ang Y5.CD2 and K10.CG other bump:1.96849 Ang Y5.CE2 and K10.CG other bump:2.99632 Ang Y5.CD2 and K10.CB other bump:2.43764 Ang L4.CD2 and Y8.CD2 other bump:2.97812 Ang L4.CD2 and Y8.CB other bump:2.67868 Ang I2.O and Y5.CB neighbor-bump: 2.66102 Ang I2.CG2 and P3.CD Number of specific fragments= 1 total=1 Number of alignments=1 # Reading fragments from alignment file # YGR206W read from 1hf0A/YGR206W-1hf0A-global-adpstyle5.a2m # 1hf0A read from 1hf0A/YGR206W-1hf0A-global-adpstyle5.a2m # adding 1hf0A to template set 1hf0A:# found chain 1hf0A in template set YGR206W 6 :EELL 1hf0A 7 :EELE Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR206W 10 :RRIPL 1hf0A 19 :RRIKL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR206W 15 :YNKYGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYEEC 1hf0A 35 :GKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDA Fragment has 57 clashes (null) has 57 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 42 residues other bump:3.13905 Ang W37.CG and C41.SG other bump:2.73796 Ang W37.CD1 and C41.SG other bump:2.02054 Ang W37.NE1 and C41.SG other bump:2.56984 Ang W37.CZ2 and C41.SG other bump:2.76865 Ang W37.CD2 and C41.SG other bump:2.03638 Ang W37.CE2 and C41.SG other bump:3.51918 Ang W37.CH2 and C41.SG other bump:3.15587 Ang L33.C and P36.CD other bump:1.45255 Ang D32.O and P36.CD other bump:2.68118 Ang D32.C and P36.CD other bump:2.45164 Ang D32.O and P36.CG other bump:3.10812 Ang F22.CB and L27.CD2 other bump:3.07821 Ang T13.C and F22.CZ other bump:2.07936 Ang T13.O and F22.CZ other bump:2.57342 Ang F17.N and F22.CZ other bump:3.22311 Ang F17.CA and F22.CZ other bump:3.22061 Ang R16.CA and F22.CZ other bump:2.69336 Ang R16.CB and F22.CZ other bump:2.86269 Ang R16.C and F22.CZ other bump:1.68814 Ang F17.N and F22.CE1 other bump:2.12954 Ang F17.CA and F22.CE1 other bump:2.85913 Ang F17.CB and F22.CE1 other bump:2.85844 Ang R16.CA and F22.CE1 other bump:2.87634 Ang R16.CB and F22.CE1 other bump:2.35134 Ang R16.O and F22.CE1 other bump:1.89234 Ang R16.C and F22.CE1 other bump:2.79349 Ang F17.N and F22.CD1 other bump:2.74142 Ang F17.CA and F22.CD1 other bump:2.35131 Ang R16.O and F22.CD1 other bump:2.61889 Ang R16.C and F22.CD1 other bump:2.41641 Ang M19.CE and E21.OE2 other bump:2.74255 Ang M19.CE and E21.CD neighbor-bump: 2.07258 Ang M19.O and P20.CD neighbor-bump: 1.58385 Ang M19.C and P20.CD self-bump: 2.21685 Ang P20.CA and P20.CD other bump:2.99189 Ang Y5.CZ and F9.CE2 other bump:2.26605 Ang Y5.OH and F9.CE2 other bump:2.85696 Ang Y5.CZ and F9.CD2 other bump:1.62634 Ang Y5.OH and F9.CD2 other bump:2.8398 Ang Y5.OH and F9.CG neighbor-bump: 2.41743 Ang K7.CB and D8.N neighbor-bump: 2.28891 Ang G6.O and K7.O other bump:2.8389 Ang Y5.CD1 and K7.CD other bump:2.7439 Ang Y5.CG and K7.CG other bump:1.4041 Ang Y5.CD1 and K7.CG other bump:1.064 Ang Y5.CE1 and K7.CG other bump:2.0496 Ang Y5.CD1 and K7.CB other bump:1.19321 Ang Y5.CE1 and K7.CB other bump:2.12382 Ang Y5.CZ and K7.CB other bump:2.76007 Ang Y5.OH and K7.CB other bump:2.90288 Ang Y5.CE1 and K7.CA other bump:3.29884 Ang G1.C and Y5.CZ other bump:2.07888 Ang G1.O and Y5.CE2 other bump:2.39107 Ang G1.C and Y5.CE2 other bump:1.6899 Ang G1.O and Y5.CD2 other bump:2.56446 Ang G1.C and Y5.CD2 other bump:2.42642 Ang G1.O and Y5.CG YGR206W 82 :KKPPGIVGNTLL 1hf0A 103 :KKRTSIETNIRV Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues Number of specific fragments= 4 total=5 Number of alignments=2 # Reading fragments from alignment file # YGR206W read from 1g9pA/YGR206W-1g9pA-local-str-1.5-adpstyle5.a2m # 1g9pA read from 1g9pA/YGR206W-1g9pA-local-str-1.5-adpstyle5.a2m # adding 1g9pA to template set 1g9pA:# found chain 1g9pA in template set YGR206W 37 :LPALQPTR 1g9pA 2 :LACLFGNG Fragment has 25 clashes (null) has 25 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues neighbor-bump: 2.7581 Ang T8.C and R9.CG neighbor-bump: 2.25506 Ang T8.O and R9.CB neighbor-bump: 2.63163 Ang T8.C and R9.CB self-bump: 1.37465 Ang P7.N and P7.CD neighbor-bump: 1.70973 Ang Q6.CA and P7.CD neighbor-bump: 2.78009 Ang Q6.CB and P7.CD neighbor-bump: 1.78606 Ang Q6.O and P7.CD neighbor-bump: 0.929744 Ang Q6.C and P7.CD neighbor-bump: 2.01909 Ang Q6.N and P7.CD self-bump: 2.15775 Ang P7.N and P7.CG neighbor-bump: 2.68725 Ang Q6.CA and P7.CG neighbor-bump: 0.943323 Ang Q6.O and P7.CG neighbor-bump: 1.47298 Ang Q6.C and P7.CG neighbor-bump: 3.15635 Ang Q6.N and P7.CG neighbor-bump: 2.07017 Ang Q6.O and P7.CB neighbor-bump: 2.39924 Ang Q6.C and P7.CB self-bump: 1.39041 Ang Q6.CA and Q6.CB neighbor-bump: 2.11312 Ang L2.N and P3.CD neighbor-bump: 1.76069 Ang L2.CA and P3.CD neighbor-bump: 1.66215 Ang L2.O and P3.CD neighbor-bump: 0.875089 Ang L2.C and P3.CD self-bump: 1.38014 Ang P3.N and P3.CD neighbor-bump: 3.19329 Ang L2.CA and P3.CG neighbor-bump: 1.96158 Ang L2.O and P3.CG neighbor-bump: 2.06433 Ang L2.C and P3.CG YGR206W 47 :LCPWYEECDNITKVCQLH 1g9pA 10 :RCSSNRDCCELTPVCKRG Fragment has 37 clashes (null) has 37 clashes, 1 disulphide bonds, and 0 hydrogen bonds in 20 residues other bump:3.084 Ang W5.C and C16.CB other bump:2.80507 Ang Y6.CE2 and C16.N other bump:2.72272 Ang Y6.CD2 and C16.N other bump:3.19722 Ang Y6.CD2 and V15.C other bump:2.57716 Ang Y6.CE2 and V15.CG2 other bump:2.99785 Ang Y6.CE2 and V15.CA other bump:2.86551 Ang Y6.CD2 and V15.CA other bump:2.34328 Ang N11.O and K14.CD self-bump: 1.34754 Ang N11.CA and N11.CB other bump:1.8115 Ang P4.CG and E8.OE2 other bump:2.31376 Ang P4.CD and E8.OE2 other bump:2.1305 Ang P4.CB and E8.OE2 other bump:2.38412 Ang P4.C and E8.OE1 other bump:2.22438 Ang W5.N and E8.OE1 other bump:2.30758 Ang C3.C and E8.OE1 other bump:1.08974 Ang P4.N and E8.OE1 other bump:1.82891 Ang P4.CA and E8.OE1 other bump:2.13886 Ang P4.CG and E8.OE1 other bump:1.22028 Ang P4.CD and E8.OE1 other bump:2.36021 Ang P4.CB and E8.OE1 other bump:2.91008 Ang P4.C and E8.CD other bump:2.51357 Ang W5.N and E8.CD other bump:2.31474 Ang P4.N and E8.CD other bump:2.64484 Ang P4.CA and E8.CD other bump:2.10907 Ang P4.CG and E8.CD other bump:1.66814 Ang P4.CD and E8.CD other bump:2.56731 Ang P4.CB and E8.CD other bump:2.71848 Ang P4.CD and E8.CG other bump:2.98951 Ang P4.CD and E8.CB other bump:2.22279 Ang W5.CD1 and E7.CB other bump:2.60584 Ang W5.NE1 and E7.CB other bump:2.6579 Ang W5.CD1 and E7.CA other bump:2.89311 Ang W5.CG and E7.N other bump:1.90174 Ang W5.CD1 and E7.N other bump:2.60666 Ang W5.NE1 and E7.N neighbor-bump: 2.99601 Ang W5.CD1 and Y6.C neighbor-bump: 2.57402 Ang W5.CG and Y6.N SS bond: 2.01961 Ang C3.SG and C16.SG YGR206W 81 :SKKPPGIVGNTLLSP 1g9pA 30 :VSSGPGLVGGILGGI Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.87177 Ang L14.C and P16.CD neighbor-bump: 2.26432 Ang S15.N and P16.CD neighbor-bump: 2.37955 Ang P5.CB and P6.CD self-bump: 2.16359 Ang P5.CB and P5.C self-bump: 2.18066 Ang P5.CA and P5.CD self-bump: 1.93989 Ang P5.CA and P5.CG self-bump: 1.15847 Ang P5.CA and P5.CB Number of specific fragments= 3 total=8 Number of alignments=3 # Reading fragments from alignment file # YGR206W read from 1cydA/YGR206W-1cydA-global-alpha-0.3-adpstyle5.a2m # 1cydA read from 1cydA/YGR206W-1cydA-global-alpha-0.3-adpstyle5.a2m # adding 1cydA to template set 1cydA:# found chain 1cydA in template set YGR206W 4 :NVEEL 1cydA 4 :NFSGL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR206W 12 :IPLYNKYGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYEECDNITKVCQLHDS 1cydA 9 :RALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLGD Fragment has 163 clashes (null) has 163 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 57 residues other bump:2.8885 Ang N6.OD1 and H54.CE1 other bump:2.74706 Ang N6.CG and H54.CE1 other bump:2.94453 Ang N6.ND2 and H54.CE1 other bump:3.17621 Ang R34.NH1 and C51.SG other bump:3.13402 Ang L30.CD2 and V50.CG1 other bump:2.51499 Ang L30.CD2 and V50.CB other bump:2.56176 Ang Y41.OH and K49.C other bump:1.39509 Ang L37.O and K49.NZ other bump:2.07367 Ang L37.C and K49.NZ other bump:2.4271 Ang C38.N and K49.NZ other bump:2.24893 Ang C38.CA and K49.NZ other bump:2.76446 Ang C38.C and K49.NZ other bump:1.796 Ang Y41.CD1 and K49.NZ other bump:2.70928 Ang Y41.CB and K49.NZ other bump:1.39844 Ang L37.O and K49.CE other bump:2.42651 Ang L37.C and K49.CE other bump:1.61762 Ang Y41.CG and K49.CE other bump:0.510852 Ang Y41.CD1 and K49.CE other bump:2.76029 Ang Y41.CD2 and K49.CE other bump:1.72162 Ang Y41.CE1 and K49.CE other bump:2.49451 Ang Y41.CB and K49.CE other bump:3.19156 Ang L37.CA and K49.CD other bump:2.3617 Ang L37.O and K49.CD other bump:2.79862 Ang L37.C and K49.CD other bump:2.49801 Ang Y41.CG and K49.CD other bump:1.26005 Ang Y41.CD1 and K49.CD other bump:0.607658 Ang Y41.CE1 and K49.CD other bump:2.89409 Ang Y41.CE2 and K49.CD other bump:1.93588 Ang Y41.CZ and K49.CD other bump:2.86802 Ang Y41.OH and K49.CD other bump:2.82706 Ang L37.CB and K49.CD other bump:3.01419 Ang Y41.CG and K49.CG other bump:2.24847 Ang Y41.CD1 and K49.CG other bump:0.960907 Ang Y41.CE1 and K49.CG other bump:2.15937 Ang Y41.CE2 and K49.CG other bump:0.857598 Ang Y41.CZ and K49.CG other bump:1.53603 Ang Y41.OH and K49.CG other bump:2.14817 Ang Y41.CE1 and K49.CB other bump:2.9792 Ang Y41.CE2 and K49.CB other bump:1.71018 Ang Y41.CZ and K49.CB other bump:0.990762 Ang Y41.OH and K49.CB other bump:2.52339 Ang Y41.CZ and K49.CA other bump:1.1469 Ang Y41.OH and K49.CA other bump:2.82842 Ang Y41.CE2 and K49.N other bump:2.59338 Ang Y41.CZ and K49.N other bump:1.67016 Ang Y41.OH and K49.N other bump:2.91228 Ang Y41.CE2 and I47.O other bump:2.38286 Ang W40.CD2 and I47.CD1 other bump:3.12709 Ang W40.CZ2 and I47.CD1 other bump:1.13695 Ang W40.CZ3 and I47.CD1 other bump:2.33316 Ang W40.CH2 and I47.CD1 other bump:1.20027 Ang W40.CE3 and I47.CD1 other bump:2.62939 Ang W40.CZ2 and I47.CG2 other bump:2.87484 Ang W40.CZ3 and I47.CG2 other bump:2.1102 Ang W40.CH2 and I47.CG2 other bump:2.02078 Ang W40.CZ3 and I47.CG1 other bump:2.71854 Ang W40.CH2 and I47.CG1 other bump:2.68773 Ang W40.CE3 and I47.CG1 other bump:3.00254 Ang Y41.CD2 and I47.CG1 other bump:3.02755 Ang Y41.CE2 and I47.CG1 other bump:2.33624 Ang W40.CZ3 and I47.CB other bump:2.24283 Ang W40.CH2 and I47.CB other bump:2.71908 Ang Q21.NE2 and C44.CA other bump:3.24072 Ang L37.C and Y41.CE1 other bump:3.10568 Ang L37.CB and Y41.CE1 other bump:1.87872 Ang L37.O and Y41.CD1 other bump:2.9447 Ang V17.CG1 and W40.CH2 other bump:1.81579 Ang V17.CG1 and W40.CZ2 other bump:2.66385 Ang V17.CG1 and W40.NE1 other bump:2.379 Ang V17.CG1 and W40.CE2 other bump:1.83857 Ang D35.O and P39.CD other bump:3.00112 Ang D35.C and P39.CD other bump:2.7803 Ang K10.NZ and L36.CD1 other bump:2.14305 Ang K7.CA and Q31.NE2 other bump:1.70734 Ang K7.C and Q31.NE2 other bump:1.87916 Ang Y8.N and Q31.NE2 other bump:2.88074 Ang Y8.CA and Q31.NE2 other bump:2.70074 Ang N6.C and Q31.OE1 other bump:2.06823 Ang K7.N and Q31.OE1 other bump:2.37195 Ang K7.CA and Q31.OE1 other bump:2.07663 Ang K7.C and Q31.OE1 other bump:1.23912 Ang Y8.N and Q31.OE1 other bump:2.4375 Ang Y8.CA and Q31.OE1 neighbor-bump: 1.86324 Ang L30.O and Q31.OE1 other bump:2.84117 Ang K7.N and Q31.CD other bump:2.5537 Ang K7.CA and Q31.CD other bump:2.08366 Ang K7.C and Q31.CD other bump:2.88518 Ang Y8.C and Q31.CD other bump:2.58158 Ang G9.N and Q31.CD other bump:1.36352 Ang Y8.N and Q31.CD other bump:2.37441 Ang Y8.CA and Q31.CD other bump:2.88574 Ang Y8.C and Q31.CG other bump:2.38828 Ang G9.N and Q31.CG other bump:2.58401 Ang Y8.N and Q31.CG other bump:2.91085 Ang Y8.CA and Q31.CG other bump:2.59575 Ang Y8.CD1 and L30.N other bump:3.06628 Ang Y8.CD1 and A29.CA other bump:1.59938 Ang P3.O and P28.CD other bump:2.8279 Ang P3.C and P28.CD other bump:2.49925 Ang P3.CB and L27.CD2 other bump:2.75952 Ang P3.CG and L27.CD2 other bump:2.87108 Ang F20.CB and L27.CD1 other bump:2.1996 Ang P3.CD and K26.O neighbor-bump: 2.68659 Ang M22.CB and P23.CD neighbor-bump: 1.90324 Ang M22.C and P23.CD self-bump: 1.29552 Ang P23.N and P23.CD other bump:2.92722 Ang R19.C and P23.CD other bump:1.86469 Ang R19.O and P23.CD neighbor-bump: 2.24934 Ang M22.N and P23.CD neighbor-bump: 2.2652 Ang M22.CA and P23.CD other bump:3.09577 Ang F20.C and P23.CD self-bump: 2.15048 Ang P23.N and P23.CG other bump:2.71531 Ang R19.C and P23.CG other bump:1.52321 Ang R19.O and P23.CG other bump:3.05128 Ang Y5.CE2 and F20.CZ other bump:2.80633 Ang Y5.CZ and F20.CZ other bump:2.00539 Ang Y5.OH and F20.CZ other bump:2.41705 Ang Y5.OH and F20.CE2 other bump:2.27254 Ang Y5.CE2 and F20.CE1 other bump:2.2408 Ang Y5.CZ and F20.CE1 other bump:2.93696 Ang T16.CG2 and F20.CE1 other bump:2.17123 Ang Y5.OH and F20.CE1 other bump:3.03144 Ang Y5.CE2 and F20.CD1 other bump:2.61561 Ang Y5.CZ and F20.CD1 other bump:2.6913 Ang Y5.OH and F20.CD1 other bump:2.28985 Ang Y8.CD2 and V17.CG2 other bump:2.99147 Ang Y8.CE2 and V17.CG2 other bump:2.44568 Ang K7.O and P13.CG other bump:2.00924 Ang K7.O and P13.CB other bump:2.86111 Ang K7.C and P13.CB self-bump: 1.34857 Ang D11.CA and D11.CB other bump:0.658065 Ang Y5.N and Y8.OH other bump:1.16334 Ang Y5.CA and Y8.OH other bump:1.87073 Ang Y5.CB and Y8.OH other bump:2.34473 Ang Y5.CG and Y8.OH other bump:2.45817 Ang Y5.CD1 and Y8.OH other bump:1.70754 Ang L4.C and Y8.OH other bump:2.42987 Ang Y5.C and Y8.OH other bump:1.69216 Ang Y5.N and Y8.CZ other bump:1.27532 Ang Y5.CA and Y8.CZ other bump:1.5887 Ang Y5.CB and Y8.CZ other bump:2.78231 Ang Y5.CG and Y8.CZ other bump:2.99728 Ang L4.C and Y8.CZ other bump:1.95446 Ang Y5.O and Y8.CZ other bump:1.81143 Ang Y5.C and Y8.CZ other bump:2.88202 Ang Y5.N and Y8.CE2 other bump:2.19501 Ang Y5.CA and Y8.CE2 other bump:1.32327 Ang Y5.CB and Y8.CE2 other bump:2.49557 Ang Y5.CG and Y8.CE2 other bump:2.83448 Ang Y5.O and Y8.CE2 other bump:2.75529 Ang Y5.C and Y8.CE2 other bump:2.30844 Ang Y5.N and Y8.CE1 other bump:2.07618 Ang Y5.CA and Y8.CE1 other bump:2.82494 Ang Y5.CB and Y8.CE1 other bump:2.69846 Ang N6.N and Y8.CE1 other bump:0.755612 Ang Y5.O and Y8.CE1 other bump:1.4416 Ang Y5.C and Y8.CE1 other bump:2.55268 Ang Y5.CB and Y8.CD2 other bump:1.23761 Ang Y5.O and Y8.CD1 other bump:2.31819 Ang Y5.C and Y8.CD1 other bump:2.42232 Ang Y5.O and Y8.CG other bump:3.14618 Ang Y5.C and Y8.CG other bump:2.81384 Ang P3.CB and Y5.CE1 YGR206W 71 :FD 1cydA 64 :WD Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues YGR206W 75 :YKEQYLSKKPP 1cydA 66 :ATEKALGGIGP Fragment has 10 clashes (null) has 10 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues neighbor-bump: 2.3627 Ang P11.CB and P12.CD neighbor-bump: 2.48836 Ang P11.CB and P12.N self-bump: 2.14809 Ang P11.CB and P11.C neighbor-bump: 1.92484 Ang K10.O and P11.CD self-bump: 2.16616 Ang P11.CA and P11.CD neighbor-bump: 1.96948 Ang K10.C and P11.CD self-bump: 1.94333 Ang P11.CA and P11.CG self-bump: 1.20745 Ang P11.CA and P11.CB other bump:2.56949 Ang L7.CD2 and K10.CD other bump:2.34154 Ang E4.O and S8.CB YGR206W 86 :GIVGNTLL 1cydA 79 :LLVNNAAL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues Number of specific fragments= 5 total=13 Number of alignments=4 # command:superimposing iter= 0 total_weight= 351 weighted rmsd= 0 superimposing iter= 1 total_weight= 3510 weighted rmsd= 0 superimposing iter= 2 total_weight= 3510 weighted rmsd= 0 superimposing iter= 3 total_weight= 3510 weighted rmsd= 0 superimposing iter= 4 total_weight= 3510 weighted rmsd= 0 superimposing iter= 5 total_weight= 3510 weighted rmsd= 0 superimposing iter= 0 total_weight= 351 weighted rmsd= 4.7246 superimposing iter= 1 total_weight= 1853.08 weighted rmsd= 1.63253 superimposing iter= 2 total_weight= 813.286 weighted rmsd= 1.03306 superimposing iter= 3 total_weight= 498.651 weighted rmsd= 0.850835 superimposing iter= 4 total_weight= 450.14 weighted rmsd= 0.739223 superimposing iter= 5 total_weight= 417.295 weighted rmsd= 0.665734 superimposing iter= 0 total_weight= 118 weighted rmsd= 7.03202 superimposing iter= 1 total_weight= 416.473 weighted rmsd= 3.46857 superimposing iter= 2 total_weight= 223.756 weighted rmsd= 2.46259 superimposing iter= 3 total_weight= 149.763 weighted rmsd= 2.1625 superimposing iter= 4 total_weight= 127.264 weighted rmsd= 2.06055 superimposing iter= 5 total_weight= 119.582 weighted rmsd= 2.02251 superimposing iter= 0 total_weight= 351 weighted rmsd= 9.62763 superimposing iter= 1 total_weight= 970.102 weighted rmsd= 5.58063 superimposing iter= 2 total_weight= 476.374 weighted rmsd= 4.72742 superimposing iter= 3 total_weight= 401.962 weighted rmsd= 4.38853 superimposing iter= 4 total_weight= 363.339 weighted rmsd= 4.28782 superimposing iter= 5 total_weight= 353.591 weighted rmsd= 4.24689 # command: