# command:# Seed set to 1042106492 # 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= 10534.4 msec) # Prefix for input files set to Created new target YGR018C from YGR018C.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 YGR018C.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= 18650 msec, elapsed time= 18669 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= 23390 msec, elapsed time= 23408.1 msec) # command:# Prefix for input files set to # command:# reading script from file YGR018C.t2k.undertaker-align.under # Reading fragments from alignment file # YGR018C read from 1gosA/YGR018C-1gosA-local-str-0.3-adpstyle5.a2m # 1gosA read from 1gosA/YGR018C-1gosA-local-str-0.3-adpstyle5.a2m # adding 1gosA to template set 1gosA:# found chain 1gosA in template set YGR018C 17 :SSLPSVFWKIHLSPPLPSFKF 1gosA 263 :AIPPTLGMKIHFNPPLPMMRN Fragment has 10 clashes (null) has 10 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues self-bump: 1.37834 Ang S19.CA and S19.CB other bump:2.75419 Ang F8.CZ and L17.CD2 other bump:2.05809 Ang F8.CE2 and L17.CD1 other bump:2.77708 Ang F8.CZ and L17.CD1 neighbor-bump: 2.86907 Ang S14.CA and P15.C neighbor-bump: 2.74657 Ang S14.CA and P15.O neighbor-bump: 2.72085 Ang S14.CA and P15.CA neighbor-bump: 3.06603 Ang S14.CB and P15.CA self-bump: 1.31485 Ang S14.CA and S14.CB other bump:2.58858 Ang F8.CZ and L13.CD1 YGR018C 58 :SLAPSTPLWSLSSCLLVSEVSFWPGAGFL 1gosA 284 :QMITRVPLGSVIKCIVYYKEPFWRKKDYC Fragment has 56 clashes (null) has 56 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 31 residues other bump:2.87539 Ang S22.CB and P25.CD neighbor-bump: 3.10713 Ang F23.CE1 and W24.CZ3 self-bump: 2.8227 Ang W24.N and W24.CE3 other bump:2.98126 Ang W10.CZ3 and L12.C other bump:2.64642 Ang W10.CH2 and L12.C other bump:2.65727 Ang W10.CE3 and L12.CD2 other bump:2.46314 Ang W10.CZ2 and L12.CD2 other bump:2.51801 Ang W10.CZ3 and L12.CD2 other bump:2.4112 Ang W10.CH2 and L12.CD2 other bump:2.66121 Ang W10.CZ3 and L12.CD1 other bump:2.63234 Ang W10.CH2 and L12.CD1 other bump:2.93604 Ang W10.CE2 and L12.CG other bump:2.36319 Ang W10.CE3 and L12.CG other bump:2.3118 Ang W10.CZ2 and L12.CG other bump:1.46972 Ang W10.CZ3 and L12.CG other bump:1.43902 Ang W10.CH2 and L12.CG other bump:2.64783 Ang W10.CE2 and L12.CB other bump:2.95127 Ang W10.CE3 and L12.CB other bump:1.43027 Ang W10.CZ2 and L12.CB other bump:1.89558 Ang W10.CZ3 and L12.CB other bump:0.573761 Ang W10.CH2 and L12.CB other bump:3.27208 Ang W10.CE3 and L12.CA other bump:2.42363 Ang W10.CZ2 and L12.CA other bump:2.07507 Ang W10.CZ3 and L12.CA other bump:1.41178 Ang W10.CH2 and L12.CA other bump:2.66416 Ang W10.CE3 and L12.N other bump:2.85534 Ang W10.CZ2 and L12.N other bump:1.91203 Ang W10.CZ3 and L12.N other bump:2.0584 Ang W10.CH2 and L12.N neighbor-bump: 2.79126 Ang W10.CD2 and S11.C neighbor-bump: 2.83124 Ang W10.CE2 and S11.C neighbor-bump: 2.65003 Ang W10.CE3 and S11.C neighbor-bump: 2.76768 Ang W10.CZ2 and S11.C neighbor-bump: 2.53433 Ang W10.CZ3 and S11.C neighbor-bump: 2.59648 Ang W10.CH2 and S11.C neighbor-bump: 2.43256 Ang W10.CE2 and S11.O neighbor-bump: 2.38041 Ang W10.CZ2 and S11.O neighbor-bump: 2.79469 Ang W10.CH2 and S11.O neighbor-bump: 3.02689 Ang W10.CE3 and S11.CA neighbor-bump: 2.71459 Ang W10.CD2 and S11.N other bump:2.55398 Ang S2.O and P5.CD other bump:2.93851 Ang S2.C and P5.CD other bump:3.16787 Ang L3.CA and P5.CD self-bump: 1.31823 Ang P5.N and P5.CD neighbor-bump: 2.29731 Ang A4.CB and P5.CD neighbor-bump: 1.72817 Ang A4.N and P5.CD neighbor-bump: 1.9026 Ang A4.CA and P5.CD neighbor-bump: 1.71819 Ang A4.C and P5.CD other bump:2.14642 Ang L3.C and P5.CD other bump:3.01505 Ang S2.C and P5.CG self-bump: 2.15768 Ang P5.N and P5.CG neighbor-bump: 2.92376 Ang A4.CB and P5.CG neighbor-bump: 3.11232 Ang A4.N and P5.CG neighbor-bump: 3.16966 Ang A4.CA and P5.CG neighbor-bump: 2.72413 Ang A4.C and P5.CG other bump:2.5451 Ang S2.O and P5.CB YGR018C 89 :DLVCLDRED 1gosA 313 :GTMIIDGEE Fragment has 6 clashes (null) has 6 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues neighbor-bump: 2.18684 Ang D7.O and R8.CG neighbor-bump: 2.20075 Ang D7.O and R8.CB neighbor-bump: 2.6726 Ang D7.C and R8.CB other bump:2.6295 Ang V4.CG1 and L6.CD2 other bump:2.65295 Ang V4.CG1 and L6.CD1 other bump:2.30851 Ang V4.CG1 and L6.CG Number of specific fragments= 3 total=3 Number of alignments=1 # Reading fragments from alignment file # YGR018C read from 1bcpC/YGR018C-1bcpC-local-str-0.3-adpstyle5.a2m # 1bcpC read from 1bcpC/YGR018C-1bcpC-local-str-0.3-adpstyle5.a2m # adding 1bcpC to template set 1bcpC:# found chain 1bcpC in template set YGR018C 61 :PSTPLWSLSSCLLVSEV 1bcpC 50 :PGWSIYGLYDGTYLGQA Fragment has 28 clashes (null) has 28 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.72098 Ang T4.N and V18.CG2 other bump:2.65239 Ang S3.C and V18.CG2 other bump:1.16341 Ang S3.CB and V18.CG2 other bump:2.19854 Ang S3.OG and V18.CG2 other bump:2.09346 Ang S3.CA and V18.CG2 other bump:2.97893 Ang T4.N and V18.CB other bump:2.68387 Ang S3.CB and V18.CB other bump:2.49143 Ang T4.N and S16.OG other bump:2.54263 Ang P5.CD and S16.OG other bump:3.04795 Ang P5.CD and S16.CB other bump:3.18453 Ang P5.N and S16.CB other bump:2.60388 Ang P5.O and S16.CB other bump:3.16179 Ang W7.CZ3 and S16.CB other bump:2.76739 Ang L9.CD2 and C12.SG self-bump: 1.27373 Ang S11.CA and S11.CB self-bump: 1.39082 Ang S10.CA and S10.CB neighbor-bump: 2.06848 Ang T4.N and P5.CD neighbor-bump: 2.46634 Ang T4.CA and P5.CD neighbor-bump: 1.90178 Ang T4.C and P5.CD other bump:2.52524 Ang P2.O and P5.CD other bump:2.22026 Ang S3.O and P5.CD other bump:1.95407 Ang S3.C and P5.CD other bump:2.93283 Ang S3.CA and P5.CD neighbor-bump: 2.79122 Ang T4.C and P5.CG other bump:1.94852 Ang P2.O and P5.CG other bump:2.97351 Ang S3.C and P5.CG other bump:3.12027 Ang P2.C and P5.CG neighbor-bump: 2.22155 Ang S3.O and T4.OG1 YGR018C 78 :SFWPGAGFLYNDLVCLD 1bcpC 73 :DAPPGAGFIYRETFCIT Fragment has 8 clashes (null) has 8 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.96825 Ang G1.C and F3.CE1 other bump:2.46827 Ang G1.O and F3.CE1 neighbor-bump: 2.43065 Ang S2.O and F3.CE1 other bump:2.35604 Ang G1.O and F3.CD1 neighbor-bump: 1.78487 Ang S2.O and F3.CD1 neighbor-bump: 2.56934 Ang S2.C and F3.CD1 neighbor-bump: 2.09475 Ang S2.O and F3.CG neighbor-bump: 2.80701 Ang S2.C and F3.CG Number of specific fragments= 2 total=5 Number of alignments=2 # Reading fragments from alignment file # YGR018C read from 1ac6A/YGR018C-1ac6A-local-str-0.3-adpstyle5.a2m # 1ac6A read from 1ac6A/YGR018C-1ac6A-local-str-0.3-adpstyle5.a2m # adding 1ac6A to template set 1ac6A:# found chain 1ac6A in template set YGR018C 13 :SHRSSSLPSVFWKIHLSPPLPSFKFKKSTEST 1ac6A 23 :NYSASGYPALFWYVQYPGEGPQFLFRASRDKE Fragment has 27 clashes (null) has 27 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 34 residues other bump:2.8067 Ang K28.NZ and G34.CA neighbor-bump: 2.31848 Ang E31.O and S32.CB neighbor-bump: 2.60491 Ang E31.C and S32.CB other bump:2.40581 Ang I15.CG2 and K25.NZ other bump:2.93912 Ang I15.CD1 and K25.NZ other bump:2.02765 Ang I15.CG2 and K25.CE other bump:2.21625 Ang I15.CB and K25.CE other bump:3.12298 Ang H16.CD2 and L21.C other bump:2.67907 Ang H16.CD2 and P20.C other bump:2.12912 Ang H16.NE2 and P20.C other bump:2.21473 Ang H16.CE1 and P20.O other bump:2.18586 Ang H16.CD2 and P20.O other bump:1.13096 Ang H16.NE2 and P20.O self-bump: 1.26328 Ang P19.N and P19.CD neighbor-bump: 1.61322 Ang S18.CA and P19.CD neighbor-bump: 1.87704 Ang S18.CB and P19.CD neighbor-bump: 1.99752 Ang S18.O and P19.CD neighbor-bump: 0.963163 Ang S18.C and P19.CD self-bump: 2.1174 Ang P19.N and P19.CG neighbor-bump: 2.89214 Ang S18.CA and P19.CG neighbor-bump: 2.80518 Ang S18.CB and P19.CG neighbor-bump: 1.97775 Ang S18.O and P19.CG neighbor-bump: 1.86925 Ang S18.C and P19.CG neighbor-bump: 1.91313 Ang S18.O and P19.CB neighbor-bump: 2.23482 Ang S18.C and P19.CB self-bump: 1.35548 Ang S18.CA and S18.CB self-bump: 1.39759 Ang S7.CA and S7.CB Number of specific fragments= 1 total=6 Number of alignments=3 # Reading fragments from alignment file # YGR018C read from 3gcb/YGR018C-3gcb-local-str-0.3-adpstyle5.a2m # 3gcb read from 3gcb/YGR018C-3gcb-local-str-0.3-adpstyle5.a2m # adding 3gcb to template set 3gcb:# found chain 3gcb in template set YGR018C 19 :LPSVFWKIHLSPPLPSFKFKKSTESTQRQTIP 3gcb 219 :LMSLFMDIPPVQPNEQFTWEYVDKDKKIHTIK Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 34 residues other bump:2.67719 Ang T24.CG2 and Q30.NE2 other bump:2.07301 Ang Q28.O and Q30.NE2 other bump:2.65811 Ang Q28.C and Q30.NE2 other bump:2.59289 Ang T24.CG2 and Q30.OE1 other bump:2.69275 Ang T24.CG2 and Q30.CD other bump:2.98067 Ang K21.CE and R29.NH2 neighbor-bump: 2.66182 Ang F6.O and W7.CD1 YGR018C 51 :KFSSPASSLAPSTP 3gcb 255 :EFASKYAKLDPSTP Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues other bump:2.20667 Ang S4.O and S8.OG other bump:2.82418 Ang S4.CA and S8.OG other bump:2.7847 Ang S4.C and S8.OG YGR018C 77 :VSFWPGAGFLYNDLVCLDREDHCLSNSA 3gcb 269 :VSLINDPRHPYGKLIKIDRLGNVLGGDA Fragment has 20 clashes (null) has 20 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 30 residues other bump:1.80291 Ang D22.OD2 and N27.OD1 other bump:1.8013 Ang C24.O and N27.OD1 other bump:2.26336 Ang D22.CG and N27.OD1 other bump:2.2579 Ang D22.OD2 and N27.ND2 other bump:1.9529 Ang D22.CG and N27.ND2 other bump:1.18242 Ang D22.OD1 and N27.ND2 other bump:2.18357 Ang D22.OD2 and N27.CG other bump:2.50552 Ang C24.O and N27.CG other bump:2.40298 Ang D22.CG and N27.CG other bump:2.12302 Ang D22.OD1 and N27.CG neighbor-bump: 2.29404 Ang L25.O and S26.CB neighbor-bump: 2.49854 Ang L25.C and S26.CB neighbor-bump: 2.66284 Ang H23.CD2 and C24.SG neighbor-bump: 2.98784 Ang H23.NE2 and C24.SG neighbor-bump: 2.59779 Ang H23.CD2 and C24.N self-bump: 1.28048 Ang H23.CA and H23.CB other bump:3.00491 Ang S3.CB and W5.CH2 other bump:2.59226 Ang S3.O and W5.CZ3 other bump:3.21743 Ang S3.C and W5.CZ3 other bump:3.19017 Ang S3.CB and W5.CZ2 Number of specific fragments= 3 total=9 Number of alignments=4 # Reading fragments from alignment file # YGR018C read from 1ueaB/1br9-YGR018C-fssp-global-adpstyle5.a2m # 1ueaB read from 1ueaB/1br9-YGR018C-fssp-global-adpstyle5.a2m # adding 1ueaB to template set 1ueaB:# found chain 1ueaB in template set YGR018C 1 :MI 1ueaB 1 :CT Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR018C 3 :DI 1ueaB 16 :DL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues YGR018C 5 :S 1ueaB 32 :T Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR018C 14 :HRSSSLPSVFWKIHL 1ueaB 33 :TLYQRYEIKMTKMYK Fragment has 14 clashes (null) has 14 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.79855 Ang F11.CD1 and I14.CD1 other bump:2.11922 Ang F11.CE1 and I14.CD1 other bump:2.67072 Ang F11.CZ and I14.CD1 other bump:3.00406 Ang F11.CZ and I14.CG2 other bump:2.66874 Ang F11.CE2 and I14.CG1 other bump:2.58027 Ang F11.CD1 and I14.CG1 other bump:1.31415 Ang F11.CE1 and I14.CG1 other bump:1.39039 Ang F11.CZ and I14.CG1 other bump:2.72206 Ang F11.CE1 and I14.CB other bump:2.32589 Ang F11.CZ and I14.CB other bump:2.65288 Ang F11.CZ and I14.CA other bump:3.01507 Ang F11.CZ and I14.N other bump:3.09691 Ang F11.CZ and K13.C other bump:2.75673 Ang F11.CZ and K13.O YGR018C 29 :SPPLPSFKFKKST 1ueaB 64 :PAMESVCGYFHRS Fragment has 39 clashes (null) has 39 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.10208 Ang S2.C and K9.NZ other bump:2.42592 Ang P3.N and K9.NZ other bump:2.45264 Ang P3.CD and K9.NZ other bump:1.19212 Ang S2.CA and K9.NZ other bump:1.14038 Ang S2.CB and K9.NZ other bump:2.40619 Ang S2.OG and K9.NZ other bump:2.11966 Ang S2.O and K9.CE other bump:1.14773 Ang S2.C and K9.CE other bump:2.00327 Ang P3.N and K9.CE other bump:2.7023 Ang P3.CD and K9.CE other bump:1.72885 Ang S2.N and K9.CE other bump:0.628673 Ang S2.CA and K9.CE other bump:2.07705 Ang S2.CB and K9.CE other bump:2.85616 Ang S2.OG and K9.CE other bump:2.40204 Ang G1.O and K9.CE other bump:2.37746 Ang G1.C and K9.CE other bump:1.28018 Ang S2.O and K9.CD other bump:1.38119 Ang S2.C and K9.CD other bump:2.70521 Ang P3.N and K9.CD other bump:1.65873 Ang S2.N and K9.CD other bump:1.53226 Ang S2.CA and K9.CD other bump:2.40783 Ang S2.CB and K9.CD other bump:2.3617 Ang S2.OG and K9.CD other bump:2.61132 Ang G1.O and K9.CD other bump:2.23363 Ang G1.C and K9.CD other bump:1.33664 Ang S2.O and K9.CG other bump:1.73433 Ang S2.C and K9.CG other bump:2.63541 Ang P3.N and K9.CG other bump:3.14516 Ang P3.C and K9.CG other bump:2.93221 Ang P4.N and K9.CG other bump:3.10049 Ang S2.N and K9.CG other bump:2.52969 Ang S2.CA and K9.CG other bump:2.72028 Ang S2.CB and K9.CG other bump:2.08268 Ang S2.OG and K9.CG other bump:2.34388 Ang S2.O and K9.CB other bump:3.16184 Ang S2.C and K9.CB other bump:2.3715 Ang S2.OG and K9.N neighbor-bump: 2.83705 Ang P3.CB and P4.CD neighbor-bump: 2.50714 Ang P3.CG and P4.CD YGR018C 42 :ESTQRQTIPKFSSPA 1ueaB 78 :ARSEEFLIAGKLQDG Fragment has 5 clashes (null) has 5 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues neighbor-bump: 2.8135 Ang S14.OG and P15.CD self-bump: 2.1251 Ang P15.CA and P15.CG self-bump: 1.20145 Ang P15.CA and P15.CB other bump:2.59662 Ang I9.CG2 and K11.CE other bump:2.94549 Ang I9.CG2 and K11.CG YGR018C 57 :SSLAPST 1ueaB 100 :SFVAPWN Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 9 residues YGR018C 64 :PLWSLSSCLLVSEVSFWPGAGFLYNDLVCLDREDHCLSNSA 1ueaB 138 :KLQSGTHCLWTDQLLQGSEKGFQSRHLACLPREPGLCTWQS Fragment has 50 clashes (null) has 50 clashes, 1 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.74617 Ang C9.CB and N40.OD1 other bump:3.02106 Ang C9.SG and N40.OD1 other bump:2.6637 Ang S7.C and L38.CD1 other bump:3.03047 Ang S7.N and L38.CD1 other bump:1.82286 Ang S7.CA and L38.CD1 other bump:2.19026 Ang S7.CB and L38.CD1 other bump:3.1772 Ang S7.CA and L38.CG other bump:2.23675 Ang L6.CG and C37.SG other bump:2.93195 Ang L6.CD1 and C37.SG other bump:1.40442 Ang L6.CD2 and C37.SG other bump:2.98534 Ang L6.CG and C37.CB other bump:2.7812 Ang L6.CD2 and C37.CB other bump:3.07074 Ang L6.CG and C37.CA other bump:3.16713 Ang L6.CD2 and C37.CA other bump:3.22221 Ang L6.CB and H36.C other bump:3.31224 Ang L6.CG and H36.C other bump:2.95766 Ang L6.CD2 and H36.C other bump:2.02538 Ang L6.CB and H36.O other bump:2.46636 Ang L6.CG and H36.O other bump:2.49263 Ang L6.CD2 and H36.O other bump:3.08233 Ang V29.CG1 and L31.CD2 other bump:2.28804 Ang L24.CD2 and L28.CD2 other bump:1.83986 Ang G22.O and N26.OD1 other bump:2.87405 Ang G22.C and N26.OD1 other bump:2.53993 Ang G22.O and N26.CG other bump:1.48174 Ang L11.CD2 and Y25.OH other bump:1.84441 Ang L11.CD2 and Y25.CZ other bump:3.08924 Ang L11.CG and Y25.CZ other bump:1.93018 Ang L11.CD2 and Y25.CE1 other bump:2.5748 Ang L11.CG and Y25.CE1 other bump:2.19136 Ang L11.CD1 and Y25.CE1 other bump:2.865 Ang L11.CD1 and Y25.CD1 neighbor-bump: 2.34787 Ang W18.N and P19.CD neighbor-bump: 2.10333 Ang W18.C and P19.CD other bump:2.73741 Ang F17.CD2 and P19.CD other bump:2.90001 Ang F17.C and P19.CD other bump:2.24659 Ang F17.CD2 and P19.CG other bump:2.9606 Ang F17.CE2 and P19.CG other bump:2.78345 Ang F17.CD2 and P19.CB other bump:2.78254 Ang F17.CE2 and P19.CB neighbor-bump: 2.62329 Ang F17.C and W18.CB neighbor-bump: 2.6902 Ang S16.C and F17.CB self-bump: 1.22596 Ang S16.CA and S16.CB self-bump: 1.31865 Ang S13.CA and S13.CB other bump:3.2502 Ang W4.CE3 and S8.C other bump:2.70911 Ang W4.CE3 and S8.OG other bump:2.85275 Ang W4.CD2 and S8.CB other bump:1.78664 Ang W4.CE3 and S8.CB other bump:2.61354 Ang W4.CZ3 and S8.CB other bump:3.00917 Ang W4.CE3 and S8.CA SS bond: 2.03342 Ang C9.SG and C30.SG Number of specific fragments= 8 total=17 Number of alignments=5 # command:superimposing iter= 0 total_weight= 460 weighted rmsd= 0 superimposing iter= 1 total_weight= 4600 weighted rmsd= 0 superimposing iter= 2 total_weight= 4600 weighted rmsd= 0 superimposing iter= 3 total_weight= 4600 weighted rmsd= 0 superimposing iter= 4 total_weight= 4600 weighted rmsd= 0 superimposing iter= 5 total_weight= 4600 weighted rmsd= 0 superimposing iter= 0 total_weight= 241 weighted rmsd= 14.3877 superimposing iter= 1 total_weight= 621.898 weighted rmsd= 8.71432 superimposing iter= 2 total_weight= 303.082 weighted rmsd= 7.65459 superimposing iter= 3 total_weight= 270.147 weighted rmsd= 7.09648 superimposing iter= 4 total_weight= 270.424 weighted rmsd= 6.5612 superimposing iter= 5 total_weight= 275.356 weighted rmsd= 6.03073 superimposing iter= 0 total_weight= 172 weighted rmsd= 8.55897 superimposing iter= 1 total_weight= 325.804 weighted rmsd= 6.1089 superimposing iter= 2 total_weight= 200.142 weighted rmsd= 5.6428 superimposing iter= 3 total_weight= 176.748 weighted rmsd= 5.56057 superimposing iter= 4 total_weight= 171.881 weighted rmsd= 5.55967 superimposing iter= 5 total_weight= 170.624 weighted rmsd= 5.57996 superimposing iter= 0 total_weight= 356 weighted rmsd= 13.8777 superimposing iter= 1 total_weight= 805.604 weighted rmsd= 9.03899 superimposing iter= 2 total_weight= 437.61 weighted rmsd= 8.10178 superimposing iter= 3 total_weight= 380.877 weighted rmsd= 7.79293 superimposing iter= 4 total_weight= 365.522 weighted rmsd= 7.64951 superimposing iter= 5 total_weight= 360.518 weighted rmsd= 7.55516 superimposing iter= 0 total_weight= 460 weighted rmsd= 18.3699 superimposing iter= 1 total_weight= 850.792 weighted rmsd= 12.0274 superimposing iter= 2 total_weight= 666.145 weighted rmsd= 9.50583 superimposing iter= 3 total_weight= 599.588 weighted rmsd= 7.95209 superimposing iter= 4 total_weight= 634.301 weighted rmsd= 6.58611 superimposing iter= 5 total_weight= 551.282 weighted rmsd= 5.9208 # command: