# command:# Seed set to 1041883401 # 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= 10530 msec, elapsed time= 10549.6 msec) # Prefix for input files set to Created new target YGR038W from YGR038W.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 YGR038W.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= 21920 msec, elapsed time= 21967.9 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= 26660 msec, elapsed time= 26707.3 msec) # command:# Prefix for input files set to # command:# reading script from file YGR038W.t2k.undertaker-align.under # Reading fragments from alignment file # YGR038W read from 1dms/1dmr-YGR038W-fssp-global-adpstyle5.a2m # 1dms read from 1dms/1dmr-YGR038W-fssp-global-adpstyle5.a2m # adding 1dms to template set 1dms:# found chain 1dms in template set YGR038W 6 :YQGTA 1dms 8 :VMSGS Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR038W 21 :QTDLKPFPSAGSASSSIKTT 1dms 26 :ATAFTPWEKDPHPTPMLEGV Fragment has 5 clashes (null) has 5 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 22 residues other bump:1.8069 Ang F8.CD2 and S10.OG other bump:1.62792 Ang F8.CE2 and S10.OG other bump:3.00109 Ang F8.CZ and S10.OG other bump:2.99907 Ang F8.CD2 and S10.CB other bump:2.69339 Ang F8.CE2 and S10.CB YGR038W 41 :EPVKDHRRRRSS 1dms 53 :TRIKYPMVRREF Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues YGR038W 54 :IIS 1dms 230 :FFG Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues YGR038W 58 :VEPETFEDENDQQLLPNMN 1dms 233 :ADHVTPKPQTDVAIMLGMA Fragment has 15 clashes (null) has 15 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 21 residues other bump:1.52817 Ang Q13.O and P17.CD other bump:2.7227 Ang Q13.C and P17.CD other bump:3.07777 Ang Q14.C and P17.CD other bump:2.21911 Ang Q13.O and P17.CG other bump:1.96612 Ang F7.CE2 and D12.OD2 other bump:2.09074 Ang F7.CE1 and D12.OD1 other bump:2.8927 Ang F7.CE2 and D12.CG other bump:2.67068 Ang F7.CD1 and N11.OD1 neighbor-bump: 2.36795 Ang D9.CB and E10.N self-bump: 2.17525 Ang D9.CB and D9.C other bump:2.20112 Ang F7.CD1 and D9.OD1 other bump:1.8976 Ang F7.CE1 and D9.OD1 self-bump: 1.29649 Ang D9.CA and D9.CB other bump:2.26908 Ang V2.O and P4.CD other bump:2.53307 Ang V2.O and P4.CG YGR038W 83 :R 1dms 395 :S Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR038W 87 :IIHVV 1dms 396 :VIPVA Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR038W 92 :IIILLKLFYNLFPGVTTEWSWTLT 1dms 442 :RNRMVKAWEKLETFIVHDFQWTPT Fragment has 14 clashes (null) has 14 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 26 residues other bump:2.93023 Ang E19.CD and T23.OG1 other bump:2.23094 Ang E19.OE2 and T23.OG1 neighbor-bump: 2.87754 Ang W20.CE3 and S21.OG neighbor-bump: 2.85911 Ang W20.CZ3 and S21.OG neighbor-bump: 2.33519 Ang F13.CA and P14.CD neighbor-bump: 2.44516 Ang F13.CB and P14.CD neighbor-bump: 1.90096 Ang F13.CG and P14.CD neighbor-bump: 1.71334 Ang F13.CD1 and P14.CD neighbor-bump: 1.79393 Ang F13.C and P14.CD neighbor-bump: 2.76616 Ang F13.CG and P14.CG neighbor-bump: 1.73288 Ang F13.CD1 and P14.CG neighbor-bump: 2.35676 Ang F13.CE1 and P14.CG neighbor-bump: 2.57198 Ang F13.C and P14.CG neighbor-bump: 3.11279 Ang F13.CD1 and P14.CB YGR038W 116 :NMTYVIGSYVM 1dms 482 :NDIETIGDYSN Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues neighbor-bump: 2.43985 Ang Y5.CE2 and V6.O neighbor-bump: 2.33805 Ang Y5.CD2 and V6.O YGR038W 127 :FHL 1dms 520 :ERL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues YGR038W 130 :IKGTPFDFNGGAYDNLTMWEQIDDE 1dms 565 :EGIVEFPVTDGADFVRYASFREDPL Fragment has 26 clashes (null) has 26 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 27 residues other bump:1.62291 Ang E21.O and D25.OD2 other bump:2.4772 Ang E21.C and D25.OD2 other bump:2.63808 Ang E21.CG and D25.OD2 other bump:2.53162 Ang N16.CG and M19.SD other bump:2.84016 Ang N16.ND2 and M19.SD other bump:3.26197 Ang N16.CA and M19.SD other bump:1.96556 Ang N16.CB and M19.SD other bump:2.26023 Ang N16.CG and M19.CG other bump:2.79066 Ang N16.ND2 and M19.CG other bump:2.51864 Ang N16.OD1 and M19.CG other bump:2.56573 Ang N16.CB and M19.CG neighbor-bump: 2.62327 Ang L17.C and T18.CB self-bump: 2.21312 Ang L17.CB and L17.C self-bump: 1.28423 Ang L17.CA and L17.CB other bump:2.84346 Ang F9.CE1 and A13.CB other bump:2.68755 Ang F9.CZ and A13.CB other bump:2.37959 Ang F9.CZ and A13.CA other bump:2.3821 Ang F9.CE1 and A13.N other bump:2.40877 Ang F9.CE2 and A13.N other bump:1.39529 Ang F9.CZ and A13.N other bump:2.45951 Ang F9.CE2 and G12.C other bump:2.13267 Ang F9.CZ and G12.C other bump:2.62118 Ang F9.CE2 and G12.CA other bump:2.64542 Ang F9.CZ and G12.CA other bump:2.89164 Ang F9.CZ and G12.N self-bump: 1.3619 Ang N10.CA and N10.CB YGR038W 155 :TLYTPSRKFLISVP 1dms 592 :PLGTPTGLIEIYSK Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues other bump:2.40136 Ang L3.CD1 and F10.CE1 other bump:2.71166 Ang L3.CD1 and F10.CD1 other bump:2.98716 Ang T2.CG2 and R8.C other bump:2.50901 Ang T2.OG1 and R8.NH1 neighbor-bump: 2.3478 Ang S7.O and R8.CG neighbor-bump: 2.66116 Ang S7.C and R8.CG other bump:3.04129 Ang T2.CG2 and R8.CG neighbor-bump: 2.16248 Ang S7.O and R8.CB neighbor-bump: 2.56583 Ang S7.C and R8.CB other bump:2.23879 Ang T2.CG2 and R8.CB other bump:2.43976 Ang T2.CG2 and R8.CA YGR038W 169 :IALFLVSTHY 1dms 635 :YPLHIAASHP Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues other bump:2.89855 Ang V7.CG1 and T9.CG2 YGR038W 179 :AHYDLKLFSWNCFLTTFGAVVPKLPV 1dms 742 :DIGTSKLAQGNCGQTVLAEVEKYTGP Fragment has 29 clashes (null) has 29 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 28 residues other bump:3.26313 Ang K24.CA and P26.CD other bump:2.66449 Ang K24.CG and P26.CD other bump:2.77681 Ang K24.C and P26.CD neighbor-bump: 2.13605 Ang L25.N and P26.CD other bump:2.4212 Ang K24.CG and P26.CG other bump:2.83795 Ang K24.CE and P26.CG neighbor-bump: 2.49755 Ang T16.O and T17.CG2 neighbor-bump: 2.8899 Ang T16.C and T17.CG2 other bump:2.89927 Ang N12.CB and F14.CE2 other bump:2.33907 Ang N12.CG and F14.CE2 other bump:2.89926 Ang N12.ND2 and F14.CE2 other bump:2.34398 Ang N12.OD1 and F14.CE2 other bump:2.24056 Ang N12.CG and F14.CD2 other bump:1.51793 Ang N12.OD1 and F14.CD2 other bump:2.40316 Ang N12.OD1 and F14.CG other bump:2.91796 Ang F9.CB and W11.NE1 other bump:2.88064 Ang F9.CB and W11.CD1 other bump:2.5009 Ang D5.OD2 and W11.CG other bump:2.28728 Ang D5.OD2 and W11.CB other bump:2.83 Ang Y4.CD1 and S10.C other bump:2.64136 Ang Y4.CD1 and S10.O other bump:2.5963 Ang Y4.CE1 and S10.CB other bump:2.47676 Ang Y4.CD1 and S10.CB other bump:3.19326 Ang Y4.CG and S10.CA other bump:2.59535 Ang Y4.CD1 and S10.CA neighbor-bump: 2.40185 Ang L8.CD1 and F9.CZ neighbor-bump: 2.21915 Ang L8.CD1 and F9.CE1 neighbor-bump: 2.79705 Ang L8.CD1 and F9.CD1 self-bump: 1.39563 Ang D5.CA and D5.CB Number of specific fragments= 14 total=14 Number of alignments=1 # Reading fragments from alignment file # YGR038W read from 2at9/YGR038W-2at9-local-str-0.3-adpstyle5.a2m # 2at9 read from 2at9/YGR038W-2at9-local-str-0.3-adpstyle5.a2m # adding 2at9 to template set 2at9:# found chain 2at9 in template set YGR038W 88 :IHVVIIILLKLFYNLFPGVTTE 2at9 17 :TALMGLGTLYFLVKGMGVSDPD Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 24 residues other bump:2.58767 Ang Y14.O and F17.CE1 other bump:2.45353 Ang L12.O and L16.CB other bump:3.20507 Ang F13.C and L16.N other bump:2.42044 Ang V4.O and I8.CD1 other bump:2.18661 Ang V4.O and I8.CG1 other bump:1.74717 Ang I2.CG2 and I6.CD1 other bump:2.94301 Ang I2.CB and I6.CD1 other bump:2.50727 Ang I2.O and I6.CD1 other bump:3.12966 Ang I2.CG2 and I6.CG1 other bump:2.19589 Ang I2.O and I6.CG1 other bump:2.42003 Ang I2.O and I6.CB YGR038W 110 :WSWTLTNMTYVIGSYVMFHLIKGTPFD 2at9 41 :KFYAITTLVPAIAFTMYLSMLLGYGLT Fragment has 21 clashes (null) has 21 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 29 residues neighbor-bump: 2.37012 Ang T25.N and P26.CD neighbor-bump: 2.05013 Ang T25.CA and P26.CD neighbor-bump: 2.32102 Ang T25.CB and P26.CD other bump:2.32468 Ang H20.O and P26.CD neighbor-bump: 1.62623 Ang T25.C and P26.CD self-bump: 1.32541 Ang P26.N and P26.CD other bump:2.3153 Ang H20.NE2 and P26.CG other bump:2.62984 Ang H20.CG and P26.CG other bump:2.19817 Ang H20.O and P26.CG other bump:2.94938 Ang H20.C and P26.CG neighbor-bump: 2.80261 Ang T25.C and P26.CG self-bump: 2.15497 Ang P26.N and P26.CG other bump:2.40332 Ang H20.CD2 and P26.CG self-bump: 2.14312 Ang P26.N and P26.CB other bump:2.75164 Ang H20.CD2 and P26.CB other bump:3.06038 Ang L21.CD2 and P26.CB other bump:2.33546 Ang M18.O and I22.CD1 other bump:2.77223 Ang M18.C and I22.CD1 other bump:2.04019 Ang M18.O and I22.CG1 other bump:3.05746 Ang M18.C and I22.CG1 other bump:2.65724 Ang M18.O and I22.CB YGR038W 138 :NGGAYDNLTMW 2at9 70 :PFGGEQNPIYW Fragment has 5 clashes (null) has 5 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues other bump:2.02958 Ang N2.CG and D7.OD1 other bump:1.16107 Ang N2.OD1 and D7.OD1 other bump:2.2636 Ang N2.OD1 and D7.CG neighbor-bump: 2.23001 Ang G4.O and A5.CB neighbor-bump: 2.5512 Ang G4.C and A5.CB YGR038W 158 :TPSRKFLISVPIALFLVSTHYAHYDLKLFSWNCFLTTFGAV 2at9 81 :ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGT Fragment has 22 clashes (null) has 22 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.60956 Ang L15.CD1 and L36.CD1 other bump:2.71787 Ang V11.CG1 and L36.CD1 self-bump: 1.39191 Ang L36.CA and L36.CB other bump:2.76363 Ang F16.CE1 and N33.ND2 other bump:2.47911 Ang F16.CZ and N33.ND2 other bump:2.36989 Ang K28.O and W32.CD1 other bump:2.60806 Ang S19.CB and L29.CD2 other bump:2.80596 Ang Y22.CA and H24.NE2 other bump:1.65791 Ang Y22.CB and H24.NE2 other bump:2.92854 Ang Y22.C and H24.NE2 other bump:2.50453 Ang Y22.CB and H24.CE1 other bump:2.90842 Ang S19.CA and H24.CD2 other bump:2.63749 Ang Y22.CB and H24.CD2 other bump:1.88298 Ang Y22.O and H24.CD2 other bump:2.88261 Ang Y22.C and H24.CD2 other bump:2.28184 Ang Y22.O and H24.CG other bump:2.72258 Ang S19.O and Y22.C other bump:2.17362 Ang S19.O and Y22.O self-bump: 1.35878 Ang T20.CA and T20.CB other bump:2.46483 Ang P12.O and F16.CE1 other bump:1.93744 Ang P12.O and F16.CD1 other bump:2.35574 Ang I9.O and I13.CD1 Number of specific fragments= 4 total=18 Number of alignments=2 # Reading fragments from alignment file # YGR038W read from 1a7m/YGR038W-1a7m-local-str-0.3-adpstyle5.a2m # 1a7m read from 1a7m/YGR038W-1a7m-local-str-0.3-adpstyle5.a2m # adding 1a7m to template set 1a7m:# found chain 1a7m in template set YGR038W 119 :YVIGSYVMFHLIKGTPFDFN 1a7m 36 :SANALFISYYTAQGEPFPNN Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 22 residues other bump:2.7303 Ang L12.CD1 and D19.OD2 other bump:2.45439 Ang K14.NZ and F18.CZ other bump:2.41158 Ang K14.NZ and F18.CE2 other bump:2.67005 Ang M9.O and I13.CD1 other bump:2.46869 Ang V8.CA and H11.CE1 other bump:2.2302 Ang Y7.O and H11.ND1 other bump:2.91056 Ang Y7.C and H11.ND1 other bump:2.89888 Ang V8.CA and H11.ND1 self-bump: 1.37159 Ang S6.CA and S6.CB other bump:3.22762 Ang Y2.C and S6.N other bump:3.24017 Ang Y2.C and G5.N YGR038W 142 :YDNLTMWEQ 1a7m 61 :GPNVTDFPP Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues neighbor-bump: 2.58754 Ang N4.O and L5.CD1 other bump:2.09932 Ang G1.O and D3.OD1 other bump:2.81506 Ang G1.C and D3.OD1 YGR038W 153 :DETLYTPSRKFLISVPIALFLVSTHYAHYDLKLF 1a7m 70 :FHANGTEKAKLVELYRMVAYLSASLTNITRDQKV Fragment has 15 clashes (null) has 15 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 36 residues other bump:3.24927 Ang K33.C and G36.N other bump:2.01095 Ang D31.OD1 and F35.CE1 other bump:2.69256 Ang D31.OD1 and F35.CD1 neighbor-bump: 2.78607 Ang F21.CD1 and L22.N other bump:2.88748 Ang I18.O and F21.CE2 other bump:2.51852 Ang I14.O and I18.CD1 other bump:2.22281 Ang I14.O and I18.CG1 self-bump: 1.36378 Ang S15.CA and S15.CB other bump:2.80717 Ang D2.CA and I14.CG2 other bump:2.29697 Ang T4.CG2 and K11.CD other bump:2.34604 Ang T4.CG2 and K11.CG other bump:1.47583 Ang E3.OE1 and L5.CD1 other bump:2.08295 Ang E3.CD and L5.CD1 other bump:2.86627 Ang E3.CG and L5.CG other bump:2.95276 Ang E3.CD and L5.CG Number of specific fragments= 3 total=21 Number of alignments=3 # Reading fragments from alignment file # YGR038W read from 1dxrM/YGR038W-1dxrM-local-str-0.3-adpstyle5.a2m # 1dxrM read from 1dxrM/YGR038W-1dxrM-local-str-0.3-adpstyle5.a2m # adding 1dxrM to template set 1dxrM:Skipped atom 8190, because occupancy 0.5 <= existing 0.500001 Skipped atom 8191, because occupancy 0.5 <= existing 0.500001 Skipped atom 8192, because occupancy 0.5 <= existing 0.500001 Skipped atom 8193, because occupancy 0.5 <= existing 0.500001 Skipped atom 8194, because occupancy 0.5 <= existing 0.500001 Skipped atom 8195, because occupancy 0.5 <= existing 0.500001 Skipped atom 8196, because occupancy 0.5 <= existing 0.500001 Skipped atom 8197, because occupancy 0.5 <= existing 0.500001 Skipped atom 8548, because occupancy 0.5 <= existing 0.500001 Skipped atom 8549, because occupancy 0.5 <= existing 0.500001 Skipped atom 8550, because occupancy 0.5 <= existing 0.500001 Skipped atom 8551, because occupancy 0.5 <= existing 0.500001 Skipped atom 8552, because occupancy 0.5 <= existing 0.500001 Skipped atom 8553, because occupancy 0.5 <= existing 0.500001 # found chain 1dxrM in template set YGR038W 31 :G 1dxrM 98 :A Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR038W 66 :ENDQQLLPNMNATWVDQRGAWIIHVVIIILLKLFYN 1dxrM 99 :QYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSR Fragment has 42 clashes (null) has 42 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 38 residues other bump:2.56534 Ang Q18.CD and W22.CH2 other bump:2.65396 Ang Q18.OE1 and W22.CH2 other bump:2.08544 Ang Q18.NE2 and W22.CH2 other bump:2.89088 Ang Q18.CD and W22.CZ3 other bump:2.56402 Ang Q18.OE1 and W22.CZ3 other bump:2.47474 Ang Q18.NE2 and W22.CZ3 other bump:2.51933 Ang Q18.CD and W22.CZ2 other bump:3.17755 Ang Q18.OE1 and W22.CZ2 other bump:1.57391 Ang Q18.NE2 and W22.CZ2 other bump:2.44214 Ang Q18.NE2 and W22.NE1 other bump:3.15243 Ang Q18.CD and W22.CE3 other bump:3.03365 Ang Q18.OE1 and W22.CE3 other bump:2.45638 Ang Q18.NE2 and W22.CE3 other bump:2.77418 Ang Q18.CD and W22.CE2 other bump:1.46541 Ang Q18.NE2 and W22.CE2 other bump:3.09817 Ang Q18.CD and W22.CD2 other bump:2.00044 Ang Q18.NE2 and W22.CD2 other bump:2.70284 Ang N10.CA and T14.OG1 other bump:2.78873 Ang P9.CA and T14.OG1 other bump:1.95117 Ang P9.C and T14.OG1 other bump:2.18014 Ang N10.N and T14.OG1 other bump:1.81839 Ang L8.O and T14.OG1 other bump:2.6512 Ang L8.C and T14.OG1 other bump:2.2371 Ang P9.O and T14.OG1 other bump:3.16144 Ang N10.CA and T14.CG2 other bump:2.38425 Ang N10.CA and T14.CB other bump:3.04706 Ang N10.CB and T14.CB other bump:2.94761 Ang P9.C and T14.CB other bump:2.69281 Ang N10.N and T14.CB neighbor-bump: 1.99256 Ang N12.O and A13.CB neighbor-bump: 2.44292 Ang N12.C and A13.CB other bump:2.98755 Ang L8.CB and A13.CB other bump:2.32068 Ang L8.CD1 and A13.CB self-bump: 1.3764 Ang N10.CA and N10.CB other bump:1.74637 Ang N3.OD1 and L8.CD2 other bump:2.85532 Ang N3.CG and L8.CD2 self-bump: 2.20352 Ang D4.CB and D4.C other bump:2.33647 Ang E2.OE1 and D4.OD1 self-bump: 1.26254 Ang D4.CA and D4.CB other bump:2.8683 Ang E2.OE1 and D4.CA other bump:2.49764 Ang E2.OE1 and D4.N self-bump: 2.18518 Ang N3.CB and N3.C YGR038W 102 :LFPGVTTEWSWTLTNMTYVIGSYVMFH 1dxrM 136 :RALGLGTHIAWNFAAAIFFVLCIGCIH Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 29 residues neighbor-bump: 2.97189 Ang Y24.CE1 and V25.CG2 other bump:2.53268 Ang I21.O and V25.CG2 other bump:2.60137 Ang I21.CG2 and Y24.OH other bump:3.141 Ang I21.CA and Y24.CZ other bump:2.97691 Ang I21.CA and Y24.CE2 other bump:3.0273 Ang G1.C and V6.CG2 neighbor-bump: 2.51353 Ang F3.CB and P4.CD neighbor-bump: 2.43899 Ang F3.N and P4.CD neighbor-bump: 2.28989 Ang F3.CA and P4.CD neighbor-bump: 1.94185 Ang F3.C and P4.CD self-bump: 1.30648 Ang P4.N and P4.CD self-bump: 2.16317 Ang P4.N and P4.CG YGR038W 129 :LIKGTPFD 1dxrM 169 :WSEGVPFG Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues YGR038W 166 :SVPIALFLVSTHY 1dxrM 177 :IWPHIDWLTAFSI Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.53814 Ang V10.CG2 and Y14.CE1 other bump:2.6337 Ang V10.O and Y14.CD1 YGR038W 180 :HYDLKLFSWNCFLTT 1dxrM 190 :RYGNFYYCPWHGFSI Fragment has 18 clashes (null) has 18 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.61886 Ang W10.CE3 and L14.CD2 other bump:2.94009 Ang W10.CZ3 and L14.CD2 neighbor-bump: 2.05869 Ang W10.CE3 and N11.OD1 neighbor-bump: 1.53376 Ang W10.CZ3 and N11.OD1 neighbor-bump: 2.95548 Ang W10.CE2 and N11.OD1 neighbor-bump: 2.64084 Ang W10.CZ2 and N11.OD1 neighbor-bump: 1.92071 Ang W10.CH2 and N11.OD1 neighbor-bump: 2.64034 Ang W10.CZ2 and N11.ND2 neighbor-bump: 2.77931 Ang W10.CH2 and N11.ND2 neighbor-bump: 2.9782 Ang W10.CE3 and N11.CG neighbor-bump: 2.70344 Ang W10.CZ3 and N11.CG neighbor-bump: 2.94491 Ang W10.CZ2 and N11.CG neighbor-bump: 2.67778 Ang W10.CH2 and N11.CG neighbor-bump: 2.54289 Ang Y3.C and D4.CB neighbor-bump: 2.50276 Ang H2.CD2 and Y3.CZ neighbor-bump: 2.8034 Ang H2.NE2 and Y3.CZ neighbor-bump: 2.64012 Ang H2.CD2 and Y3.CE2 neighbor-bump: 2.88653 Ang H2.CD2 and Y3.CE1 Number of specific fragments= 6 total=27 Number of alignments=4 # Reading fragments from alignment file # YGR038W read from 1is2A/YGR038W-1is2A-local-str-0.3-adpstyle5.a2m # 1is2A read from 1is2A/YGR038W-1is2A-local-str-0.3-adpstyle5.a2m # adding 1is2A to template set 1is2A:# found chain 1is2A in template set YGR038W 17 :YSRNQTDLKPFP 1is2A 448 :VGGMVSYLNDLP Fragment has 24 clashes (null) has 24 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues other bump:2.28603 Ang L9.CD2 and F12.CE1 other bump:2.95429 Ang L9.CA and F12.CD1 other bump:2.91023 Ang D8.C and P11.CD neighbor-bump: 2.13936 Ang K10.N and P11.CD other bump:2.43677 Ang D8.O and P11.CD neighbor-bump: 2.66304 Ang K10.CB and P11.CD other bump:2.81429 Ang L9.C and P11.CD neighbor-bump: 2.24219 Ang K10.CA and P11.CD neighbor-bump: 1.88913 Ang K10.C and P11.CD self-bump: 1.27772 Ang P11.N and P11.CD self-bump: 2.13439 Ang P11.N and P11.CG other bump:2.14838 Ang Y2.CA and K10.NZ other bump:1.47896 Ang Y2.O and K10.NZ other bump:1.95712 Ang Y2.C and K10.NZ other bump:2.41702 Ang G1.C and K10.NZ other bump:1.6717 Ang Y2.N and K10.NZ other bump:2.85852 Ang G1.C and K10.CE other bump:2.58123 Ang Y2.N and K10.CE other bump:2.84706 Ang S3.CA and T7.OG1 other bump:2.69414 Ang S3.C and T7.OG1 neighbor-bump: 1.96415 Ang S3.O and R4.CG neighbor-bump: 2.79234 Ang S3.C and R4.CG neighbor-bump: 1.97772 Ang S3.O and R4.CB neighbor-bump: 2.49439 Ang S3.C and R4.CB YGR038W 72 :LPNMNATWVDQRGAWIIHVVIIILLKLFYNLFPGVTTEWSWTLTNMTYVIGSYVMFHLI 1is2A 476 :DINSLEGLTEAYKLRAARLVEIAAKNLQTHVSHRKSKEVAWNLTSVDLVRASEAHCHYV Fragment has 93 clashes (null) has 93 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 61 residues other bump:1.87474 Ang I17.CD1 and L59.CB other bump:3.117 Ang I17.CD1 and L59.CA other bump:2.83423 Ang I17.CG1 and V55.C other bump:2.28416 Ang I17.CG1 and V55.O other bump:2.48855 Ang I17.CD1 and V55.O other bump:3.07831 Ang W16.CE3 and V55.CG2 other bump:2.39431 Ang W16.CZ3 and V55.CG2 other bump:2.08486 Ang W16.CH2 and V55.CG2 other bump:2.57319 Ang W16.CZ2 and V55.CG2 other bump:2.41008 Ang W16.CE3 and V55.CG1 other bump:2.69728 Ang W16.CZ3 and V55.CG1 other bump:2.83044 Ang I17.CG1 and V55.CG1 other bump:3.0925 Ang W16.CD2 and V55.CG1 other bump:3.00831 Ang I17.N and V55.CG1 other bump:2.66572 Ang I17.CA and V55.CG1 other bump:3.10465 Ang W16.CE3 and V55.CB other bump:2.64994 Ang W16.CZ3 and V55.CB other bump:3.09049 Ang W16.CH2 and V55.CB other bump:2.69579 Ang W16.CZ3 and V55.CA other bump:2.93159 Ang V20.CG1 and G52.CA other bump:2.14581 Ang L28.CD2 and Y49.OH other bump:2.206 Ang L28.CG and Y49.OH other bump:2.65704 Ang L28.CD1 and Y49.OH other bump:1.94528 Ang L28.CB and Y49.OH other bump:2.9975 Ang I24.CG2 and Y49.CZ other bump:2.50042 Ang I24.CG2 and Y49.CE2 other bump:2.69099 Ang T45.CB and Y49.CE1 other bump:2.49595 Ang T45.CG2 and Y49.CE1 other bump:2.37951 Ang I24.CG2 and Y49.CD2 other bump:2.56909 Ang T45.O and Y49.CD1 other bump:2.80188 Ang I24.CG2 and Y49.CG other bump:2.89499 Ang I24.CD1 and Y49.CA other bump:2.81874 Ang I24.CG1 and T48.C other bump:2.74043 Ang I24.CD1 and T48.C other bump:2.49081 Ang I24.CG1 and T48.O other bump:1.99284 Ang I24.CD1 and T48.O other bump:2.73087 Ang K27.CE and T48.OG1 other bump:2.43484 Ang I24.CG1 and T48.CG2 other bump:2.95889 Ang K27.CE and T48.CG2 other bump:3.12928 Ang I24.CA and T48.CG2 other bump:2.83513 Ang K27.NZ and T48.CG2 other bump:2.12985 Ang W42.O and N46.OD1 other bump:2.89854 Ang W40.CH2 and L44.CD2 other bump:2.90357 Ang W40.NE1 and L44.CD1 other bump:2.64063 Ang W40.CE2 and L44.CD1 other bump:2.71245 Ang W40.CZ2 and L44.CD1 other bump:3.22577 Ang W40.CZ2 and L44.CG other bump:2.63184 Ang V36.CG2 and S41.OG other bump:2.69961 Ang N31.CB and S41.OG other bump:2.51792 Ang N31.O and V36.CG2 other bump:3.05411 Ang N31.C and V36.CG2 other bump:2.76028 Ang L32.C and P34.CD other bump:3.09939 Ang N31.C and P34.CD other bump:3.14244 Ang Y30.C and P34.CD neighbor-bump: 2.1423 Ang F33.N and P34.CD neighbor-bump: 1.71571 Ang F33.C and P34.CD other bump:2.34119 Ang Y30.O and P34.CD self-bump: 1.34747 Ang P34.N and P34.CD neighbor-bump: 2.18329 Ang F33.CA and P34.CD neighbor-bump: 2.8331 Ang F33.CB and P34.CD other bump:3.27882 Ang N31.C and P34.CG other bump:2.71742 Ang Y30.C and P34.CG other bump:1.5451 Ang Y30.O and P34.CG self-bump: 2.19351 Ang P34.N and P34.CG other bump:2.92981 Ang F29.CE2 and F33.CZ other bump:3.08174 Ang F29.CG and F33.CZ other bump:2.12946 Ang F29.CD2 and F33.CZ other bump:2.722 Ang F29.CA and F33.CE2 other bump:2.7366 Ang F29.O and F33.CE2 other bump:3.01981 Ang F29.C and F33.CE2 other bump:2.3311 Ang F29.CB and F33.CE2 other bump:2.5221 Ang F29.CG and F33.CE2 other bump:2.25609 Ang F29.CD2 and F33.CE2 other bump:2.89171 Ang F29.CA and F33.CD2 other bump:1.69448 Ang F29.O and F33.CD2 other bump:2.44016 Ang F29.C and F33.CD2 other bump:2.99542 Ang F29.CB and F33.CD2 other bump:1.87563 Ang I23.CG2 and K27.NZ other bump:2.88718 Ang W9.CE3 and Q12.OE1 other bump:3.15425 Ang W9.CZ3 and Q12.OE1 other bump:2.32364 Ang P3.O and W9.NE1 other bump:2.83102 Ang P3.O and W9.CE2 other bump:1.42011 Ang L2.O and T8.CG2 other bump:3.11996 Ang G1.C and T8.CG2 other bump:2.27877 Ang L2.N and T8.CG2 other bump:2.43316 Ang L2.CA and T8.CG2 other bump:1.89991 Ang L2.C and T8.CG2 other bump:2.98131 Ang P3.N and T8.CG2 other bump:1.84511 Ang L2.O and T8.CB other bump:2.87967 Ang L2.C and T8.CB other bump:2.44655 Ang G1.O and P3.CD self-bump: 1.35585 Ang P3.N and P3.CD self-bump: 2.20999 Ang P3.N and P3.CG Number of specific fragments= 2 total=29 Number of alignments=5 # command:superimposing iter= 0 total_weight= 1442 weighted rmsd= 0 superimposing iter= 1 total_weight= 14420 weighted rmsd= 0 superimposing iter= 2 total_weight= 14420 weighted rmsd= 0 superimposing iter= 3 total_weight= 14420 weighted rmsd= 0 superimposing iter= 4 total_weight= 14420 weighted rmsd= 0 superimposing iter= 5 total_weight= 14420 weighted rmsd= 0 superimposing iter= 0 total_weight= 826 weighted rmsd= 17.8207 superimposing iter= 1 total_weight= 1670.21 weighted rmsd= 12.2809 superimposing iter= 2 total_weight= 1017.07 weighted rmsd= 10.9323 superimposing iter= 3 total_weight= 935.879 weighted rmsd= 10.1614 superimposing iter= 4 total_weight= 886.346 weighted rmsd= 9.71477 superimposing iter= 5 total_weight= 852.025 weighted rmsd= 9.47814 superimposing iter= 0 total_weight= 533 weighted rmsd= 17.062 superimposing iter= 1 total_weight= 1145.81 weighted rmsd= 11.1632 superimposing iter= 2 total_weight= 728.632 weighted rmsd= 9.32016 superimposing iter= 3 total_weight= 668.964 weighted rmsd= 8.21019 superimposing iter= 4 total_weight= 619.334 weighted rmsd= 7.5694 superimposing iter= 5 total_weight= 575.276 weighted rmsd= 7.26045 superimposing iter= 0 total_weight= 754 weighted rmsd= 21.6992 superimposing iter= 1 total_weight= 1379.73 weighted rmsd= 15.6161 superimposing iter= 2 total_weight= 908.435 weighted rmsd= 14.0286 superimposing iter= 3 total_weight= 857.783 weighted rmsd= 13.0458 superimposing iter= 4 total_weight= 831.787 weighted rmsd= 12.3499 superimposing iter= 5 total_weight= 814.037 weighted rmsd= 11.8312 superimposing iter= 0 total_weight= 484 weighted rmsd= 17.2788 superimposing iter= 1 total_weight= 820.744 weighted rmsd= 12.9893 superimposing iter= 2 total_weight= 598.98 weighted rmsd= 11.4677 superimposing iter= 3 total_weight= 571.393 weighted rmsd= 10.3288 superimposing iter= 4 total_weight= 574.799 weighted rmsd= 9.28333 superimposing iter= 5 total_weight= 550.555 weighted rmsd= 8.57323 # command: