# command:# Seed set to 1041178712 # 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= 10618.6 msec) # Prefix for input files set to Created new target YCL020W from YCL020W.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 YCL020W.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= 28200 msec, elapsed time= 28336.3 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= 32930 msec, elapsed time= 33074.9 msec) # command:# Prefix for input files set to # command:# reading script from file YCL020W.t2k.undertaker-align.under # Reading fragments from alignment file # YCL020W read from 1kgsA/YCL020W-1kgsA-local-str-0.3-adpstyle5.a2m # 1kgsA read from 1kgsA/YCL020W-1kgsA-local-str-0.3-adpstyle5.a2m # found chain 1kgsA in training set YCL020W 242 :ADILTVLCKSVSKMQ 1kgsA 12 :RDLADLITEALKKEM Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues YCL020W 258 :NNQELKDWIALANLEY 1kgsA 33 :YDGEEGMYMALNEPFD Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues YCL020W 287 :STIIQRLKENNINVS 1kgsA 62 :WEILKSMRESGVNTP Fragment has 9 clashes (null) has 9 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.19268 Ang L8.CD2 and I13.CD1 other bump:2.92201 Ang L8.CD2 and I13.CG1 other bump:3.16182 Ang N11.ND2 and I13.CG1 other bump:2.74299 Ang L8.CA and N11.OD1 other bump:2.31686 Ang L8.C and N11.OD1 other bump:1.45864 Ang L8.O and N11.OD1 other bump:2.73784 Ang I5.CG2 and K9.NZ other bump:2.67976 Ang T3.CG2 and R7.NH2 other bump:2.36064 Ang T3.OG1 and R7.NH1 YCL020W 304 :LACQLILKGLSGDFK 1kgsA 84 :SDVEYRVKGLNMGAD Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues YCL020W 324 :YRTKTNMKLSQLFAEIQLIYDENKIMNLN 1kgsA 99 :DYLPKPFDLRELIARVRALIRRKSESKST Fragment has 24 clashes (null) has 24 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 31 residues other bump:2.90647 Ang N28.OD1 and N30.C other bump:2.74225 Ang N28.OD1 and N30.CA other bump:2.13411 Ang N28.OD1 and N30.N neighbor-bump: 2.58405 Ang I26.CG2 and M27.N other bump:2.68919 Ang Y21.CD2 and K25.NZ other bump:2.61093 Ang L19.C and D22.OD1 other bump:2.0141 Ang L19.O and D22.OD1 other bump:2.73617 Ang L19.CA and D22.OD1 other bump:2.06529 Ang Y2.OH and E16.OE2 other bump:1.94877 Ang Y2.CE2 and E16.OE2 other bump:1.80489 Ang T4.OG1 and E16.OE2 other bump:2.30747 Ang Y2.CZ and E16.OE2 other bump:0.690763 Ang Y2.OH and E16.OE1 other bump:2.88587 Ang Y2.CE2 and E16.OE1 other bump:1.99666 Ang Y2.CZ and E16.OE1 other bump:0.982098 Ang Y2.OH and E16.CD other bump:2.14372 Ang Y2.CE2 and E16.CD other bump:2.82949 Ang T4.OG1 and E16.CD other bump:1.6925 Ang Y2.CZ and E16.CD other bump:1.88447 Ang Y2.OH and E16.CG other bump:2.72541 Ang Y2.CE2 and E16.CG other bump:2.87578 Ang Y2.CE2 and E16.CB other bump:2.88744 Ang M8.CE and L13.CD1 other bump:2.24026 Ang Y2.CE2 and T4.OG1 Number of specific fragments= 5 total=5 Number of alignments=1 # Reading fragments from alignment file # YCL020W read from 1ljrA/YCL020W-1ljrA-local-str-0.3-adpstyle5.a2m # 1ljrA read from 1ljrA/YCL020W-1ljrA-local-str-0.3-adpstyle5.a2m # adding 1ljrA to template set 1ljrA:# found chain 1ljrA in template set YCL020W 186 :RFLKNSNLGDIIPNDQGEIKRQMTYE 1ljrA 44 :EFLQINSLGKLPTLKDGDFILTESSA Fragment has 40 clashes (null) has 40 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 28 residues other bump:2.88579 Ang R22.CZ and G28.N other bump:2.85043 Ang R22.NE and E27.C other bump:1.99297 Ang R22.CZ and E27.C other bump:2.17901 Ang R22.NH1 and E27.C other bump:2.08599 Ang R22.NH2 and E27.C other bump:1.81862 Ang R22.CZ and E27.O other bump:1.34812 Ang R22.NH1 and E27.O other bump:2.09797 Ang R22.NH2 and E27.O other bump:2.58509 Ang R22.CG and E27.OE2 other bump:2.45526 Ang R22.NE and E27.OE2 other bump:2.24423 Ang R22.NE and E27.CD other bump:3.11796 Ang R22.CZ and E27.CD other bump:2.70684 Ang R22.CD and E27.CG other bump:1.31962 Ang R22.NE and E27.CG other bump:1.73597 Ang R22.CZ and E27.CG other bump:1.81499 Ang R22.NH2 and E27.CG other bump:2.55508 Ang R22.NE and E27.CB other bump:2.50997 Ang R22.CZ and E27.CB other bump:2.02942 Ang R22.NH2 and E27.CB other bump:2.48133 Ang R22.CZ and E27.CA other bump:1.7735 Ang R22.NH2 and E27.CA other bump:2.40352 Ang L9.CD1 and Q23.NE2 other bump:2.68563 Ang L9.CD1 and Q23.OE1 other bump:2.89809 Ang L9.CD1 and Q23.CD other bump:1.32004 Ang N6.CA and K21.NZ other bump:1.59443 Ang N6.CB and K21.NZ other bump:1.50219 Ang N6.O and K21.NZ other bump:1.11393 Ang N6.C and K21.NZ other bump:2.25568 Ang S7.N and K21.NZ other bump:2.76607 Ang N6.CA and K21.CE other bump:2.57974 Ang N6.CB and K21.CE other bump:1.8564 Ang N6.O and K21.CE other bump:2.34724 Ang N6.C and K21.CE other bump:1.73354 Ang N6.O and K21.CD other bump:2.704 Ang N6.C and K21.CD other bump:2.28431 Ang D16.OD1 and G18.O self-bump: 1.39971 Ang Q17.CA and Q17.CB other bump:3.16722 Ang I12.CA and P14.CD neighbor-bump: 1.94697 Ang I13.C and P14.CD self-bump: 1.39444 Ang N6.CA and N6.CB YCL020W 214 :AYIYNTFQAFAPFHLLPTWVK 1ljrA 70 :ILIYLSCKYQTPDHWYPSDLQ Fragment has 17 clashes (null) has 17 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues other bump:2.52741 Ang W20.CD1 and G23.N other bump:2.72077 Ang W20.NE1 and K22.CB other bump:2.90275 Ang F14.CZ and W20.N other bump:2.19413 Ang F14.CZ and T19.OG1 other bump:2.11076 Ang F14.CE1 and T19.OG1 other bump:2.64682 Ang F14.CE1 and T19.CG2 other bump:2.96465 Ang F14.CZ and T19.CB other bump:2.43908 Ang F14.CE1 and T19.CB other bump:2.80887 Ang F14.CZ and T19.CA other bump:2.45706 Ang F14.CE1 and T19.CA other bump:1.94716 Ang F14.CZ and T19.N other bump:1.63338 Ang F14.CE1 and T19.N other bump:2.90497 Ang F14.CZ and P18.C other bump:2.65938 Ang F14.CE1 and P18.C other bump:3.12827 Ang F14.CZ and P18.CA other bump:2.47445 Ang Y5.CE1 and Q9.NE2 other bump:2.67747 Ang Y5.CZ and Q9.NE2 YCL020W 237 :LEINYADILTVLCKSVSKMQTNNQELKDWIALANLE 1ljrA 91 :ARARVHEYLGWHADCIRGTFGIPLWVQVLGPLIGVQ Fragment has 16 clashes (null) has 16 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 38 residues other bump:2.69686 Ang I31.CG2 and L36.C other bump:2.64045 Ang I31.C and L36.O other bump:1.8267 Ang I31.CG2 and L36.O other bump:3.15873 Ang W30.CE3 and L33.CD1 other bump:2.97565 Ang W30.CZ3 and L33.CD1 other bump:2.86909 Ang L27.N and I31.CD1 other bump:2.80741 Ang L27.CA and I31.CD1 other bump:2.84713 Ang E26.C and I31.CG1 other bump:2.66396 Ang E26.O and I31.CB other bump:2.8803 Ang Q25.NE2 and W30.NE1 other bump:2.3527 Ang V17.O and Q21.OE1 other bump:2.77897 Ang V17.CA and Q21.OE1 other bump:2.99666 Ang L13.CD2 and V17.CG2 other bump:2.89106 Ang L13.CD2 and V17.CG1 other bump:2.66461 Ang L13.CD2 and V17.CB other bump:2.75981 Ang Y6.CE1 and L10.CD1 YCL020W 277 :TS 1ljrA 127 :VP Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues YCL020W 283 :EITVSTIIQRL 1ljrA 129 :EEKVERNRTAM Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues YCL020W 303 :RLACQLILKGLSGDFKYLRNQY 1ljrA 140 :DQALQWLEDKFLGDRPFLAGQQ Fragment has 26 clashes (null) has 26 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 24 residues other bump:2.97786 Ang Y18.CD2 and G24.CA other bump:2.56966 Ang Y18.CE2 and G24.CA other bump:2.79285 Ang Y18.CD2 and G24.N other bump:2.1405 Ang Y18.CE2 and G24.N other bump:2.58417 Ang Y18.CZ and G24.N other bump:3.11825 Ang Y18.CG and Y23.C other bump:2.76803 Ang Y18.CD2 and Y23.C other bump:2.63043 Ang Y18.CE2 and Y23.C other bump:2.84426 Ang Y18.CZ and Y23.C other bump:2.30552 Ang N21.OD1 and Y23.O other bump:2.69555 Ang Y18.CE1 and Y23.CA other bump:2.83059 Ang Y18.CZ and Y23.CA other bump:3.07548 Ang Y18.CD1 and Y23.CA other bump:2.80636 Ang Y18.CD1 and Y23.N other bump:1.88099 Ang N21.OD1 and Y23.N other bump:3.02538 Ang N21.CG and Y23.N other bump:2.80086 Ang Y18.CE1 and Q22.C other bump:2.65471 Ang Y18.CD1 and Q22.C neighbor-bump: 2.70944 Ang N21.OD1 and Q22.C other bump:2.34997 Ang Y18.CE1 and Q22.O other bump:2.71313 Ang Y18.CD1 and Q22.O other bump:2.59296 Ang F16.CD1 and Q22.NE2 neighbor-bump: 2.45911 Ang N21.CB and Q22.N neighbor-bump: 2.62342 Ang R20.C and N21.CB other bump:2.15101 Ang Q6.CD and K10.NZ other bump:1.28954 Ang Q6.OE1 and K10.NZ YCL020W 330 :MKLSQLFAEIQLI 1ljrA 162 :VTLADLMALEELM Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.57912 Ang L7.O and I11.CD1 Number of specific fragments= 7 total=12 Number of alignments=2 # Reading fragments from alignment file # YCL020W read from 1iq3A/YCL020W-1iq3A-local-str-0.3-adpstyle5.a2m # 1iq3A read from 1iq3A/YCL020W-1iq3A-local-str-0.3-adpstyle5.a2m # adding 1iq3A to template set 1iq3A:# found chain 1iq3A in template set YCL020W 205 :KRQMTYEEHAYIYNTFQAFAPFHLL 1iq3A 13 :PWRITEEQREYYVNQFRSLQPDPSS Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 27 residues neighbor-bump: 2.48694 Ang L26.CB and G27.N self-bump: 2.20536 Ang L26.CB and L26.C self-bump: 1.24758 Ang L26.CA and L26.CB other bump:2.07158 Ang Y14.CE2 and L25.CD2 self-bump: 1.37323 Ang L25.CA and L25.CB self-bump: 1.38608 Ang H24.CA and H24.CB self-bump: 2.77765 Ang F17.CD1 and F17.C other bump:2.70164 Ang H10.CE1 and Y14.CZ other bump:2.92626 Ang H10.NE2 and Y14.CZ other bump:2.71704 Ang H10.ND1 and Y14.CE1 other bump:1.95477 Ang H10.CE1 and Y14.CE1 other bump:2.453 Ang H10.NE2 and Y14.CE1 YCL020W 245 :LTVLCKSVSKMQTNNQELKDWIALANLEYDGSTSADTFEITVSTIIQRLKENNI 1iq3A 41 :GSVAKNFFTKSKLSIPELSYIWELSDADCDGALTLPEFCAAFHLIVARKNGYPL Fragment has 49 clashes (null) has 49 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 56 residues other bump:2.31817 Ang K51.CD and N53.OD1 other bump:2.26311 Ang M12.SD and L50.CD2 other bump:1.43182 Ang M12.CE and L50.CD2 other bump:2.57366 Ang M12.CG and L50.CD1 other bump:0.943454 Ang M12.SD and L50.CD1 other bump:2.42427 Ang M12.CE and L50.CD1 other bump:1.58777 Ang M12.SD and L50.CG other bump:1.59952 Ang M12.CE and L50.CG other bump:2.24568 Ang M12.SD and L50.CB other bump:1.69001 Ang M12.CE and L50.CB other bump:2.91378 Ang M12.SD and L50.CA other bump:2.95484 Ang M12.SD and L50.N other bump:2.56987 Ang T42.O and I46.CD1 other bump:3.07817 Ang F39.CE1 and V43.CG2 other bump:3.06046 Ang F39.CE2 and V43.CG2 other bump:2.53237 Ang F39.CZ and V43.CG2 other bump:2.85 Ang T34.CB and T38.CG2 other bump:2.10403 Ang T34.OG1 and T38.CG2 other bump:2.42862 Ang D31.OD2 and S33.O other bump:2.61652 Ang L2.CG and S33.N other bump:2.02209 Ang L2.CG and G32.C other bump:2.31112 Ang L2.CD1 and G32.C other bump:3.12778 Ang L2.CD2 and G32.C other bump:3.06887 Ang L2.CB and G32.C other bump:2.39717 Ang L2.CG and G32.O other bump:2.22607 Ang L2.CG and G32.CA other bump:1.44725 Ang L2.CD1 and G32.CA other bump:3.16181 Ang L2.CB and G32.CA other bump:2.25755 Ang L2.CD1 and G32.N neighbor-bump: 2.34865 Ang L28.O and E29.CG other bump:2.64492 Ang D21.O and L25.CD1 other bump:2.94118 Ang Q13.CB and W22.CH2 other bump:2.94227 Ang Q13.OE1 and W22.CH2 other bump:2.98367 Ang L19.CD2 and W22.CZ3 other bump:2.65152 Ang Q13.OE1 and W22.CZ3 other bump:2.42356 Ang L19.CD2 and W22.CE3 other bump:2.87193 Ang V9.CG1 and L19.CD2 other bump:1.37437 Ang S10.OG and L19.CD1 other bump:2.62773 Ang S10.CB and L19.CD1 other bump:2.57607 Ang S10.OG and L19.CG neighbor-bump: 2.68009 Ang N15.C and N16.CB neighbor-bump: 2.31712 Ang N15.CB and N16.N self-bump: 2.1079 Ang N15.CB and N15.C self-bump: 1.27655 Ang N15.CA and N15.CB self-bump: 1.29473 Ang T14.CA and T14.CB other bump:2.45708 Ang S10.OG and Q13.NE2 other bump:1.98971 Ang L5.O and V9.CG2 other bump:2.93492 Ang L5.C and V9.CG2 other bump:2.38034 Ang L2.O and C6.SG Number of specific fragments= 2 total=14 Number of alignments=3 # Reading fragments from alignment file # YCL020W read from 1g8iA/YCL020W-1g8iA-local-str-0.3-adpstyle5.a2m # 1g8iA read from 1g8iA/YCL020W-1g8iA-local-str-0.3-adpstyle5.a2m # adding 1g8iA to template set 1g8iA:Skipped atom 300, because occupancy 0.5 <= existing 0.500001 Skipped atom 565, because occupancy 0.5 <= existing 0.500001 Skipped atom 567, because occupancy 0.5 <= existing 0.500001 Skipped atom 670, because occupancy 0.5 <= existing 0.500001 Skipped atom 733, because occupancy 0.5 <= existing 0.500001 Skipped atom 735, because occupancy 0.5 <= existing 0.500001 Skipped atom 749, because occupancy 0.5 <= existing 0.500001 Skipped atom 963, because occupancy 0.5 <= existing 0.500001 Skipped atom 965, because occupancy 0.5 <= existing 0.500001 Skipped atom 967, because occupancy 0.5 <= existing 0.500001 Skipped atom 969, because occupancy 0.5 <= existing 0.500001 Skipped atom 1451, because occupancy 0.5 <= existing 0.500001 # found chain 1g8iA in template set YCL020W 173 :SEENFSTWVKFYIRFL 1g8iA 23 :TEKEVQQWYKGFIKDC Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues neighbor-bump: 2.41796 Ang R15.CZ and F16.CZ neighbor-bump: 1.24695 Ang R15.NH2 and F16.CZ other bump:3.08186 Ang F12.CZ and F16.CZ other bump:2.35147 Ang F12.CE1 and F16.CZ neighbor-bump: 2.36347 Ang R15.NH2 and F16.CE2 neighbor-bump: 2.73694 Ang R15.NE and F16.CE1 neighbor-bump: 2.36914 Ang R15.CZ and F16.CE1 neighbor-bump: 1.70083 Ang R15.NH2 and F16.CE1 other bump:3.13575 Ang F12.CZ and F16.CE1 other bump:2.3807 Ang F12.CD1 and F16.CE1 other bump:2.19098 Ang F12.CE1 and F16.CE1 other bump:2.49797 Ang F12.O and F16.CD1 YCL020W 200 :D 1g8iA 39 :P Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YCL020W 205 :KRQMTYEEHAYIYNTFQAFAPFHLLPTWVKQILEIN 1g8iA 40 :SGQLDAAGFQKIYKQFFPFGDPTKFATFVFNVFDEN Fragment has 56 clashes (null) has 56 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 38 residues other bump:1.43504 Ang E35.OE1 and N37.OD1 other bump:1.71644 Ang Y7.CE1 and K31.NZ other bump:1.57236 Ang Y7.CZ and K31.NZ other bump:1.8703 Ang Y7.CG and K31.NZ other bump:1.84509 Ang Y7.CD1 and K31.NZ other bump:1.72121 Ang Y7.CD2 and K31.NZ other bump:1.58234 Ang Y7.CE2 and K31.NZ other bump:2.95622 Ang Y7.CE1 and K31.CE other bump:2.4334 Ang Y7.CB and K31.CE other bump:1.71628 Ang Y7.CG and K31.CE other bump:2.3528 Ang Y7.CD1 and K31.CE other bump:1.86171 Ang Y7.CD2 and K31.CE other bump:2.5745 Ang Y7.CE2 and K31.CE other bump:2.6794 Ang Y7.N and K31.CE other bump:2.37665 Ang Y7.CA and K31.CE other bump:3.06283 Ang Y7.CB and K31.CD other bump:2.62082 Ang Y7.CG and K31.CD other bump:1.98645 Ang Y7.CD2 and K31.CD other bump:2.73393 Ang Y7.CE2 and K31.CD other bump:2.87472 Ang Y7.CA and K31.CD other bump:3.1706 Ang L25.CG and W29.CZ2 other bump:3.1592 Ang L25.CD2 and W29.CZ2 other bump:1.34995 Ang F23.O and P27.CD other bump:2.54575 Ang F23.C and P27.CD other bump:1.82861 Ang F23.O and P27.CG other bump:2.82777 Ang F23.C and P27.CG other bump:1.48667 Ang Q18.CG and F23.CZ other bump:1.5396 Ang Q18.CD and F23.CZ other bump:2.38706 Ang Q18.OE1 and F23.CZ other bump:2.04518 Ang Q18.NE2 and F23.CZ other bump:2.93973 Ang Q18.CA and F23.CZ other bump:1.50652 Ang Q18.CB and F23.CZ other bump:2.56734 Ang Q18.O and F23.CE2 other bump:2.75787 Ang Q18.C and F23.CE2 other bump:2.04291 Ang Q18.CG and F23.CE2 other bump:2.5484 Ang Q18.CD and F23.CE2 other bump:2.95512 Ang Q18.OE1 and F23.CE2 other bump:3.08051 Ang Q18.N and F23.CE2 other bump:2.2012 Ang Q18.CA and F23.CE2 other bump:0.858469 Ang Q18.CB and F23.CE2 other bump:2.372 Ang Q18.CG and F23.CE1 other bump:1.27217 Ang Q18.CD and F23.CE1 other bump:1.72115 Ang Q18.OE1 and F23.CE1 other bump:1.44341 Ang Q18.NE2 and F23.CE1 other bump:2.75606 Ang Q18.CB and F23.CE1 other bump:3.1445 Ang Q18.CD and F23.CD2 other bump:3.24628 Ang Q18.CA and F23.CD2 other bump:2.12275 Ang Q18.CB and F23.CD2 other bump:2.2339 Ang Q18.CD and F23.CD1 other bump:1.80365 Ang Q18.OE1 and F23.CD1 other bump:2.68748 Ang Q18.NE2 and F23.CD1 other bump:3.03895 Ang Q18.CD and F23.CG other bump:2.52187 Ang Q18.OE1 and F23.CG neighbor-bump: 2.71093 Ang K2.C and R3.CG neighbor-bump: 2.19162 Ang K2.O and R3.CB neighbor-bump: 2.52568 Ang K2.C and R3.CB YCL020W 241 :YADILTVL 1g8iA 82 :FSEFIQAL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues YCL020W 251 :SVSKMQTNNQELKDWIALANLEYDGSTSADTFEITVSTIIQR 1g8iA 90 :SVTSRGTLDEKLRWAFKLYDLDNDGYITRNEMLDIVDAIYQM Fragment has 22 clashes (null) has 22 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 44 residues other bump:2.49471 Ang T36.O and T39.CG2 other bump:2.23698 Ang A20.O and T32.CG2 other bump:2.7917 Ang L22.CG and T32.CG2 other bump:3.28199 Ang W16.CZ3 and L19.CD2 other bump:2.49328 Ang E12.O and W16.CD1 other bump:2.85155 Ang Q7.OE1 and E12.CA self-bump: 1.37715 Ang N9.CA and N9.CB other bump:2.54478 Ang V3.CA and Q7.NE2 other bump:1.90366 Ang V3.CG2 and Q7.NE2 other bump:1.36565 Ang V3.CB and Q7.NE2 other bump:0.800358 Ang V3.CG1 and Q7.NE2 other bump:1.52055 Ang V3.CG1 and Q7.OE1 other bump:2.39667 Ang V3.CA and Q7.CD other bump:2.98743 Ang V3.CG2 and Q7.CD other bump:1.95176 Ang V3.CB and Q7.CD other bump:0.88178 Ang V3.CG1 and Q7.CD other bump:2.67962 Ang V3.C and Q7.CD other bump:2.07886 Ang V3.CA and Q7.CG other bump:2.59024 Ang V3.CB and Q7.CG other bump:2.29437 Ang V3.CG1 and Q7.CG other bump:2.45977 Ang V3.C and Q7.CG other bump:2.2562 Ang V3.O and Q7.CG Number of specific fragments= 5 total=19 Number of alignments=4 # Reading fragments from alignment file # YCL020W read from 1qkkA/YCL020W-1qkkA-local-str-0.3-adpstyle5.a2m # 1qkkA read from 1qkkA/YCL020W-1qkkA-local-str-0.3-adpstyle5.a2m # adding 1qkkA to template set 1qkkA:Skipped atom 606, because occupancy 0.5 <= existing 0.500001 Skipped atom 607, because occupancy 0.5 <= existing 0.500001 Skipped atom 608, because occupancy 0.5 <= existing 0.500001 Skipped atom 609, because occupancy 0.5 <= existing 0.500001 Skipped atom 610, because occupancy 0.5 <= existing 0.500001 Skipped atom 611, because occupancy 0.25 <= existing 0.500001 Skipped atom 612, because occupancy 0.25 <= existing 0.500001 Skipped atom 613, because occupancy 0.25 <= existing 0.500001 Skipped atom 614, because occupancy 0.25 <= existing 0.500001 Skipped atom 615, because occupancy 0.25 <= existing 0.500001 # found chain 1qkkA in template set YCL020W 288 :TIIQRLKENNINVSDRLACQLILKGLSGDFKYLRNQYRTKTNMKLSQLFAEIQLI 1qkkA 19 :AMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILAL Fragment has 114 clashes (null) has 114 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 57 residues other bump:2.81327 Ang R35.CD and I53.CD1 other bump:2.99798 Ang R35.NH1 and L49.C other bump:3.21027 Ang R35.CD and L49.CD2 other bump:1.87953 Ang R35.NE and L49.CD2 other bump:0.835934 Ang R35.CZ and L49.CD2 other bump:1.89425 Ang R35.NH1 and L49.CD2 other bump:0.503824 Ang R35.NH2 and L49.CD2 other bump:1.59564 Ang Q37.CD and L49.CD2 other bump:1.50885 Ang Q37.OE1 and L49.CD2 other bump:1.4836 Ang Q37.NE2 and L49.CD2 other bump:2.55853 Ang R35.CZ and L49.CD1 other bump:2.32638 Ang R35.NH1 and L49.CD1 other bump:2.69781 Ang R35.NH2 and L49.CD1 other bump:2.74995 Ang R35.NE and L49.CG other bump:1.49531 Ang R35.CZ and L49.CG other bump:1.13927 Ang R35.NH1 and L49.CG other bump:1.76858 Ang R35.NH2 and L49.CG other bump:3.00733 Ang Q37.CD and L49.CG other bump:2.27013 Ang Q37.NE2 and L49.CG other bump:2.71682 Ang R35.CZ and L49.CB other bump:2.24409 Ang R35.NH1 and L49.CB other bump:2.45449 Ang R35.NH2 and L49.CB other bump:2.41715 Ang R39.NH1 and S47.N other bump:2.3237 Ang R39.NH1 and L46.C other bump:2.4647 Ang Q37.O and L46.CD2 other bump:2.59729 Ang R39.NE and L46.CD2 other bump:3.07038 Ang R39.CB and L46.CD2 other bump:2.44554 Ang Y38.C and L46.CD2 other bump:2.25294 Ang R39.N and L46.CD2 other bump:2.40123 Ang R39.CA and L46.CD2 other bump:2.54918 Ang R39.CZ and L46.CD2 other bump:2.25894 Ang R39.NH2 and L46.CD2 other bump:2.88264 Ang Q37.CA and L46.CD1 other bump:2.57618 Ang Q37.O and L46.CD1 other bump:2.4363 Ang Q37.C and L46.CD1 other bump:2.924 Ang Y38.N and L46.CD1 other bump:2.06066 Ang Y38.O and L46.CD1 other bump:2.7802 Ang Y38.C and L46.CD1 other bump:2.3026 Ang Q37.CB and L46.CD1 other bump:2.36191 Ang Y38.O and L46.CG other bump:2.83533 Ang Y38.C and L46.CG other bump:3.09547 Ang R39.N and L46.CG other bump:2.94228 Ang R39.CA and L46.CG other bump:2.01655 Ang R39.NH2 and L46.CG other bump:2.86461 Ang R39.C and L46.CB other bump:2.29816 Ang Y38.O and L46.CB other bump:3.00242 Ang Y38.C and L46.CB other bump:3.08652 Ang R39.N and L46.CB other bump:2.41593 Ang R39.CA and L46.CB other bump:2.79171 Ang R39.CZ and L46.CB other bump:3.05511 Ang R39.NH2 and L46.CB self-bump: 2.14782 Ang N43.CB and N43.C self-bump: 1.19869 Ang N43.CA and N43.CB other bump:2.52097 Ang R35.CD and Q37.NE2 other bump:1.52124 Ang R35.NE and Q37.NE2 other bump:1.06998 Ang R35.CZ and Q37.NE2 other bump:1.80618 Ang R35.NH1 and Q37.NE2 other bump:1.77756 Ang R35.NH2 and Q37.NE2 other bump:2.88066 Ang C20.SG and Q37.OE1 other bump:2.39732 Ang R35.NE and Q37.OE1 other bump:2.1092 Ang R35.CZ and Q37.OE1 other bump:1.27882 Ang R35.NH2 and Q37.OE1 other bump:3.03714 Ang R35.CD and Q37.CD other bump:1.71442 Ang R35.NE and Q37.CD other bump:1.72115 Ang R35.CZ and Q37.CD other bump:1.64799 Ang R35.NH2 and Q37.CD other bump:2.53114 Ang R35.NE and Q37.CG other bump:3.25522 Ang F31.CE2 and Y33.C other bump:2.24971 Ang F31.CE1 and Y33.CD2 other bump:2.58473 Ang F31.CZ and Y33.CD2 other bump:3.06772 Ang F31.CD1 and Y33.CD2 other bump:2.34213 Ang F31.CZ and Y33.CB other bump:2.3908 Ang F31.CE2 and Y33.CB other bump:2.44395 Ang Q21.CD and K25.NZ other bump:1.93541 Ang Q21.OE1 and K25.NZ other bump:3.11558 Ang R17.CZ and I23.C other bump:2.68479 Ang R17.CB and I23.CD1 other bump:2.61855 Ang R17.CD and I23.CD1 other bump:3.05577 Ang R17.CD and I23.CG2 other bump:2.79775 Ang R17.NE and I23.CG2 other bump:2.54541 Ang R17.CB and I23.CG1 other bump:2.09172 Ang R17.CG and I23.CG1 other bump:1.16844 Ang R17.CD and I23.CG1 other bump:2.24878 Ang R17.NE and I23.CG1 other bump:2.01516 Ang R17.CD and I23.CB other bump:2.30849 Ang R17.NE and I23.CB other bump:2.21021 Ang R17.CD and I23.CA other bump:1.97495 Ang R17.NE and I23.CA other bump:2.31804 Ang R17.CZ and I23.CA other bump:2.68106 Ang R17.NH1 and I23.CA other bump:2.55387 Ang R17.CD and I23.N other bump:2.86036 Ang R17.NE and I23.N other bump:2.96637 Ang R17.CZ and I23.N other bump:2.62578 Ang R17.NH1 and I23.N other bump:3.12811 Ang R17.CZ and L22.C other bump:2.30523 Ang R17.NH1 and L22.C other bump:2.7756 Ang R17.CZ and L22.O other bump:1.95584 Ang R17.NH1 and L22.O other bump:2.43869 Ang I4.CG1 and D16.OD2 other bump:2.83291 Ang I4.CG2 and D16.OD2 other bump:1.73153 Ang I4.CD1 and D16.OD2 other bump:2.94653 Ang V14.CG1 and D16.OD1 other bump:1.97248 Ang I4.CG1 and D16.OD1 other bump:2.15718 Ang I4.CD1 and D16.OD1 other bump:2.3706 Ang I4.CG1 and D16.CG other bump:1.74293 Ang I4.CD1 and D16.CG other bump:2.68997 Ang I4.CD1 and D16.CB other bump:2.60717 Ang L7.CA and N10.OD1 other bump:1.16303 Ang L7.O and N10.OD1 other bump:2.06362 Ang L7.C and N10.OD1 other bump:3.09448 Ang L7.CA and N10.CG other bump:2.36298 Ang L7.O and N10.CG other bump:3.03957 Ang L7.C and N10.CG other bump:2.97846 Ang I4.CG2 and K8.NZ Number of specific fragments= 1 total=20 Number of alignments=5 # command:superimposing iter= 0 total_weight= 724 weighted rmsd= 0 superimposing iter= 1 total_weight= 7240 weighted rmsd= 0 superimposing iter= 2 total_weight= 7240 weighted rmsd= 0 superimposing iter= 3 total_weight= 7240 weighted rmsd= 0 superimposing iter= 4 total_weight= 7240 weighted rmsd= 0 superimposing iter= 5 total_weight= 7240 weighted rmsd= 0 superimposing iter= 0 total_weight= 521 weighted rmsd= 13.5351 superimposing iter= 1 total_weight= 1067.51 weighted rmsd= 9.09756 superimposing iter= 2 total_weight= 726.088 weighted rmsd= 7.56233 superimposing iter= 3 total_weight= 601.185 weighted rmsd= 6.98088 superimposing iter= 4 total_weight= 545.928 weighted rmsd= 6.78019 superimposing iter= 5 total_weight= 527.1 weighted rmsd= 6.70594 superimposing iter= 0 total_weight= 325 weighted rmsd= 12.4775 superimposing iter= 1 total_weight= 653.239 weighted rmsd= 8.62175 superimposing iter= 2 total_weight= 390.899 weighted rmsd= 7.73428 superimposing iter= 3 total_weight= 385.39 weighted rmsd= 6.98517 superimposing iter= 4 total_weight= 370.101 weighted rmsd= 6.43523 superimposing iter= 5 total_weight= 370.3 weighted rmsd= 5.95476 superimposing iter= 0 total_weight= 281 weighted rmsd= 10.5345 superimposing iter= 1 total_weight= 738.696 weighted rmsd= 6.34969 superimposing iter= 2 total_weight= 351.141 weighted rmsd= 5.64136 superimposing iter= 3 total_weight= 294.76 weighted rmsd= 5.47501 superimposing iter= 4 total_weight= 284.334 weighted rmsd= 5.40659 superimposing iter= 5 total_weight= 283.342 weighted rmsd= 5.34672 superimposing iter= 0 total_weight= 385 weighted rmsd= 8.56849 superimposing iter= 1 total_weight= 880.736 weighted rmsd= 5.33877 superimposing iter= 2 total_weight= 610.025 weighted rmsd= 4.00663 superimposing iter= 3 total_weight= 578.033 weighted rmsd= 3.1526 superimposing iter= 4 total_weight= 503.174 weighted rmsd= 2.69104 superimposing iter= 5 total_weight= 456.907 weighted rmsd= 2.42772 # command: