# command:# Seed set to 1042094731 # 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= 10533.4 msec) # Prefix for input files set to Created new target YGR016W from YGR016W.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 YGR016W.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= 21000 msec, elapsed time= 21019.2 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= 25740 msec, elapsed time= 25758.8 msec) # command:# Prefix for input files set to # command:# reading script from file YGR016W.t2k.undertaker-align.under # Reading fragments from alignment file # YGR016W read from 1cqa/3nul-YGR016W-fssp-global-adpstyle5.a2m # 1cqa read from 1cqa/3nul-YGR016W-fssp-global-adpstyle5.a2m # adding 1cqa to template set 1cqa:# found chain 1cqa in template set YGR016W 1 :MSRLRRFN 1cqa 2 :SWQTYVDE Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 9 residues other bump:2.71422 Ang L4.O and N8.CB other bump:2.71749 Ang R3.NE and F7.CZ other bump:2.4685 Ang R3.CZ and F7.CZ other bump:2.25913 Ang R3.NH2 and F7.CZ other bump:3.2545 Ang R3.NH2 and F7.CE2 other bump:2.32268 Ang R3.NE and F7.CE1 other bump:2.78491 Ang R3.CZ and F7.CE1 other bump:3.00616 Ang R3.NH2 and F7.CE1 neighbor-bump: 2.34463 Ang M1.CB and S2.N self-bump: 2.1331 Ang M1.CB and M1.C self-bump: 1.2498 Ang M1.CA and M1.CB YGR016W 13 :SLSSDYTHDGESDQEDVSILPLDTEEQEELIQKFETNAHITNK 1cqa 23 :AASAIVGHDGSVWAQSSSFPQFKPQEITGIMKDFEEPGHLAPT Fragment has 36 clashes (null) has 36 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 45 residues other bump:2.8581 Ang K34.CB and I41.CD1 neighbor-bump: 2.24071 Ang N38.O and A39.CB neighbor-bump: 2.55389 Ang N38.C and A39.CB other bump:1.01546 Ang E26.O and E30.OE1 other bump:2.08166 Ang E26.C and E30.OE1 other bump:1.9496 Ang E26.O and E30.CD other bump:2.94768 Ang E26.C and E30.CD other bump:2.90083 Ang Y7.CE2 and Q28.NE2 other bump:2.5406 Ang Y7.CD2 and Q28.NE2 other bump:2.27044 Ang S5.CB and I20.CD1 other bump:2.38545 Ang S5.OG and I20.CD1 other bump:3.01493 Ang E16.CD and I20.CG2 other bump:2.80152 Ang E16.OE1 and I20.CG2 other bump:3.11577 Ang L3.CD1 and I20.CG1 other bump:2.31942 Ang L3.CD1 and I20.CB other bump:2.82753 Ang L3.CG and I20.CA other bump:2.9327 Ang L3.CD2 and I20.CA other bump:1.88235 Ang L3.CD1 and I20.CA other bump:2.0409 Ang L3.CD1 and I20.N other bump:2.69293 Ang L3.CD1 and S19.C other bump:2.64637 Ang L3.CA and D17.OD2 other bump:2.85736 Ang L3.C and D17.OD2 other bump:2.20223 Ang L3.CD1 and D17.OD1 other bump:2.97271 Ang S4.N and D17.CG other bump:2.67663 Ang D10.CG and E12.OE2 other bump:1.99515 Ang D10.OD2 and E12.OE2 other bump:2.75856 Ang D10.CB and E12.OE1 other bump:2.21071 Ang T8.OG1 and E12.OE1 other bump:1.49952 Ang D10.OD1 and E12.OE1 other bump:1.39669 Ang D10.CG and E12.OE1 other bump:1.44718 Ang D10.OD2 and E12.OE1 other bump:2.31151 Ang D10.CG and E12.CD other bump:1.85251 Ang D10.OD2 and E12.CD other bump:2.36666 Ang T8.CB and D10.OD1 other bump:1.21983 Ang T8.OG1 and D10.OD1 other bump:2.43279 Ang T8.OG1 and D10.CG YGR016W 65 :YLLYGGLLMILVRKSRG 1cqa 66 :GLHLGGIKYMVIQGEAG Fragment has 15 clashes (null) has 15 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.48625 Ang Y2.CB and L9.CD1 other bump:1.64298 Ang Y2.CG and L9.CD1 other bump:2.55088 Ang Y2.CD2 and L9.CD1 other bump:1.32896 Ang Y2.CD1 and L9.CD1 other bump:2.18709 Ang Y2.CE1 and L9.CD1 other bump:2.94649 Ang Y2.CZ and L9.CD1 other bump:2.85487 Ang Y2.CG and L9.CG other bump:2.96245 Ang Y2.CD1 and L4.CD2 other bump:2.07582 Ang Y2.CE1 and L4.CD2 neighbor-bump: 2.36622 Ang G1.O and Y2.CE2 neighbor-bump: 2.63839 Ang G1.C and Y2.CD2 neighbor-bump: 1.56514 Ang G1.O and Y2.CD2 neighbor-bump: 2.64235 Ang G1.O and Y2.CD1 neighbor-bump: 2.72428 Ang G1.C and Y2.CG neighbor-bump: 1.77676 Ang G1.O and Y2.CG YGR016W 88 :LA 1cqa 85 :IR Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues Number of specific fragments= 4 total=4 Number of alignments=1 # Reading fragments from alignment file # YGR016W read from 1g5hA/YGR016W-1g5hA-local-str-0.3-adpstyle5.a2m # 1g5hA read from 1g5hA/YGR016W-1g5hA-local-str-0.3-adpstyle5.a2m # adding 1g5hA to template set 1g5hA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # found chain 1g5hA in template set YGR016W 4 :LRRFNRKILSLSSDYTHDGESDQEDVSILPLDTEEQEELIQ 1g5hA 92 :MVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQ Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.28927 Ang E36.O and E39.OE1 other bump:2.7376 Ang D33.CB and E36.OE2 other bump:2.64712 Ang R3.NH2 and S11.OG other bump:2.15268 Ang R3.NH2 and S11.CB other bump:3.13762 Ang R3.NH2 and S11.CA other bump:2.08853 Ang L2.C and I9.CD1 other bump:1.0537 Ang L2.O and I9.CD1 other bump:2.68695 Ang R3.N and I9.CD1 other bump:2.67447 Ang R3.CA and I9.CD1 neighbor-bump: 2.81481 Ang R4.NH1 and F5.CZ neighbor-bump: 2.08026 Ang R4.NH1 and F5.CE1 YGR016W 50 :AHITNKLYINLL 1g5hA 138 :KEQLVAFLENLL Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues other bump:2.83463 Ang N6.OD1 and I10.CD1 YGR016W 78 :KSRGYIKLALLAGANSLICSCI 1g5hA 150 :KTSGKLRATLLHGALEHYVNCL Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 24 residues other bump:2.94811 Ang N16.CA and I19.CD1 other bump:2.86964 Ang N16.OD1 and I19.CD1 YGR016W 104 :DIVNDYLLFKKFKLRVSNFSI 1g5hA 172 :DLVNRKLPFGLAQIGVCFHPV Fragment has 17 clashes (null) has 17 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues other bump:1.70561 Ang K14.CE and R16.NH2 other bump:0.590294 Ang K14.NZ and R16.NH2 other bump:2.56399 Ang K14.NZ and R16.NH1 other bump:2.19301 Ang K14.CE and R16.CZ other bump:1.79339 Ang K14.NZ and R16.CZ other bump:2.91109 Ang K14.CE and R16.NE other bump:2.09134 Ang K11.NZ and F13.CZ other bump:2.96181 Ang K11.CG and F13.CZ other bump:1.50756 Ang K11.CD and F13.CZ other bump:2.18405 Ang K11.CE and F13.CZ other bump:2.50804 Ang K11.NZ and F13.CE2 other bump:2.37743 Ang K11.CD and F13.CE2 other bump:2.5313 Ang K11.CG and F13.CE1 other bump:1.64868 Ang K11.CD and F13.CE1 other bump:2.9508 Ang K11.CE and F13.CE1 other bump:3.09606 Ang K11.CD and F13.CD2 other bump:2.60001 Ang K11.CD and F13.CD1 YGR016W 142 :HVVEDKKTVLCLQVP 1g5hA 204 :RVGEKTEASLVWFTP Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues self-bump: 1.39304 Ang C12.CA and C12.CB other bump:2.58625 Ang K8.CG and V10.CG1 other bump:2.49635 Ang K8.CD and V10.CG1 YGR016W 157 :MFLFWVAVLVK 1g5hA 225 :WLDFWLRHRLL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues Number of specific fragments= 6 total=10 Number of alignments=2 # Reading fragments from alignment file # YGR016W read from 1yasA/YGR016W-1yasA-local-str-0.3-adpstyle5.a2m # 1yasA read from 1yasA/YGR016W-1yasA-local-str-0.3-adpstyle5.a2m # adding 1yasA to template set 1yasA:# found chain 1yasA in template set YGR016W 26 :QEDVS 1yasA 48 :IEEIG Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YGR016W 45 :K 1yasA 53 :S Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR016W 53 :TNKLYINLLSILYLLYGGLLMILVRKSRGYIKLALLAGANSLICSCITLRYDIVNDY 1yasA 54 :FDEYSEPLLTFLEALPPGEKVILVGESCGGLNIAIAADKYCEKIAAAVFHNSVLPDT Fragment has 133 clashes (null) has 133 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 59 residues other bump:3.00364 Ang Y31.CE2 and N56.CA other bump:2.61174 Ang Y31.CD2 and N56.N other bump:1.57903 Ang Y31.CE2 and N56.N other bump:2.40554 Ang Y31.CZ and N56.N other bump:2.8713 Ang Y31.CD2 and V55.C other bump:2.29747 Ang Y31.OH and V55.C other bump:1.63439 Ang Y31.CE2 and V55.C other bump:2.17735 Ang Y31.CZ and V55.C other bump:2.85445 Ang Y31.CE2 and V55.O other bump:2.92919 Ang Y31.CE1 and V55.CG2 other bump:3.02532 Ang Y31.CZ and V55.CG2 other bump:1.43864 Ang Y31.OH and V55.CG1 other bump:2.60099 Ang Y31.CE1 and V55.CG1 other bump:2.14312 Ang Y31.CZ and V55.CG1 other bump:2.19002 Ang Y31.OH and V55.CB other bump:2.74961 Ang Y31.CE1 and V55.CB other bump:2.70856 Ang Y31.CE2 and V55.CB other bump:2.15631 Ang Y31.CZ and V55.CB other bump:2.35141 Ang Y31.CD2 and V55.CA other bump:2.23893 Ang Y31.OH and V55.CA other bump:3.13004 Ang Y31.CG and V55.CA other bump:2.57741 Ang Y31.CE1 and V55.CA other bump:1.40974 Ang Y31.CE2 and V55.CA other bump:1.61432 Ang Y31.CZ and V55.CA other bump:2.23091 Ang Y31.CD2 and V55.N other bump:3.10916 Ang Y31.CG and V55.N other bump:2.07573 Ang Y31.CE2 and V55.N other bump:2.87053 Ang Y31.CZ and V55.N other bump:1.95801 Ang Y31.CD2 and I54.C other bump:3.01081 Ang Y31.CB and I54.C other bump:2.42223 Ang Y31.CG and I54.C other bump:2.60204 Ang Y31.CE2 and I54.C other bump:1.71716 Ang Y31.CD2 and I54.O other bump:2.03359 Ang Y31.CB and I54.O other bump:1.40267 Ang Y31.CG and I54.O other bump:2.16649 Ang Y31.CD1 and I54.O other bump:2.62233 Ang Y31.CE2 and I54.O other bump:2.96746 Ang Y31.CD2 and I54.CG2 other bump:3.21062 Ang Y31.CD2 and I54.CA other bump:1.57087 Ang R26.O and D53.OD2 other bump:2.46668 Ang R26.C and D53.OD2 other bump:2.28521 Ang K27.CA and D53.OD1 other bump:2.26044 Ang K27.C and D53.OD1 other bump:1.96221 Ang S28.N and D53.OD1 other bump:2.4302 Ang R26.O and D53.CG other bump:3.16431 Ang R26.C and D53.CG other bump:3.21704 Ang K27.CA and D53.CG other bump:3.1305 Ang S28.N and D53.CG other bump:2.94067 Ang R51.N and D53.CG other bump:2.6921 Ang V25.CG1 and R51.NE other bump:3.03112 Ang Y31.CG and L50.CD2 other bump:1.92094 Ang Y31.CD1 and L50.CD2 other bump:2.60869 Ang L34.CD1 and I48.CG2 other bump:2.91808 Ang N41.OD1 and I44.CD1 other bump:2.7367 Ang M22.CE and I44.CG2 other bump:2.0188 Ang A38.O and S42.OG other bump:2.11955 Ang L13.CD1 and L37.CD2 other bump:1.81847 Ang L13.CD1 and L37.CD1 other bump:2.10959 Ang L13.CD1 and L37.CG other bump:2.18594 Ang N3.OD1 and L36.CD2 other bump:2.29988 Ang N3.OD1 and L36.CD1 other bump:2.79655 Ang Y6.CD1 and L36.CD1 other bump:2.8876 Ang Y6.CE1 and L36.CD1 other bump:2.86237 Ang L24.CD1 and L34.CD2 other bump:2.76772 Ang L24.CB and L34.CD2 other bump:3.04173 Ang R26.CB and L34.CD1 other bump:2.61001 Ang Y6.CD2 and K33.CD other bump:2.57842 Ang Y6.CE2 and K33.CD other bump:2.88573 Ang Y6.CG and K33.CG other bump:1.57173 Ang Y6.CD2 and K33.CG other bump:1.08691 Ang Y6.CE2 and K33.CG other bump:2.09997 Ang Y6.CD2 and K33.CB other bump:1.76893 Ang Y6.CE2 and K33.CB other bump:2.57337 Ang Y6.CD2 and K33.CA other bump:2.04731 Ang Y6.CE2 and K33.CA other bump:2.67718 Ang Y6.CZ and K33.CA other bump:2.54677 Ang Y6.CE2 and K33.N other bump:2.62595 Ang Y6.CZ and K33.N other bump:2.50171 Ang Y6.OH and K33.N other bump:3.24063 Ang Y6.CZ and I32.C other bump:2.77934 Ang Y6.OH and I32.CB other bump:3.12607 Ang R26.NH2 and I32.CB other bump:2.30207 Ang R26.NH1 and I32.CA other bump:3.1179 Ang R26.CZ and I32.CA other bump:0.91399 Ang R26.NH1 and I32.N other bump:3.07082 Ang R26.NE and I32.N other bump:2.06008 Ang R26.CZ and I32.N other bump:2.78502 Ang R26.NH2 and I32.N other bump:3.06682 Ang R26.CD and Y31.C other bump:1.51926 Ang R26.NH1 and Y31.C other bump:2.68367 Ang R26.CZ and Y31.C other bump:2.3178 Ang R26.CD and Y31.CA other bump:2.0478 Ang R26.NH1 and Y31.CA other bump:2.87877 Ang R26.NE and Y31.CA other bump:2.80431 Ang R26.CZ and Y31.CA other bump:1.28635 Ang R26.CD and Y31.N other bump:2.09365 Ang R26.NH1 and Y31.N other bump:1.64883 Ang R26.NE and Y31.N other bump:2.04979 Ang R26.CZ and Y31.N other bump:2.50675 Ang R26.CG and Y31.N other bump:0.538222 Ang R26.CD and G30.C other bump:2.57521 Ang R26.NH1 and G30.C other bump:0.950696 Ang R26.NE and G30.C other bump:2.02913 Ang R26.CZ and G30.C other bump:3.01179 Ang R26.CB and G30.C other bump:1.81745 Ang R26.CG and G30.C other bump:1.27784 Ang R26.CD and G30.O other bump:1.88848 Ang R26.NE and G30.O other bump:2.6699 Ang R26.CZ and G30.O other bump:2.31734 Ang R26.CG and G30.O other bump:1.83379 Ang R26.CD and G30.CA other bump:1.27211 Ang R26.NE and G30.CA other bump:2.51639 Ang R26.CZ and G30.CA other bump:3.15176 Ang R26.NH2 and G30.CA other bump:1.89574 Ang R26.CG and G30.CA other bump:2.82781 Ang R26.CD and G30.N other bump:1.82201 Ang R26.NE and G30.N other bump:2.45038 Ang R26.CZ and G30.N other bump:2.6515 Ang R26.NH2 and G30.N other bump:3.04264 Ang R26.CG and G30.N other bump:2.20097 Ang R26.NE and R29.C other bump:2.00191 Ang R26.CZ and R29.C other bump:1.65168 Ang R26.NH2 and R29.C other bump:1.29412 Ang R26.CZ and R29.O other bump:0.431044 Ang R26.NH2 and R29.O other bump:2.71678 Ang R26.NH2 and R29.CA other bump:1.76526 Ang L16.CD1 and M22.CE other bump:2.60641 Ang L13.CD2 and M22.CE other bump:2.8275 Ang L16.CD1 and M22.SD other bump:3.28339 Ang L13.CD2 and M22.SD other bump:3.12247 Ang T2.CG2 and Y6.CZ other bump:2.40587 Ang T2.CG2 and Y6.CE1 other bump:2.15195 Ang T2.O and Y6.CD1 YGR016W 120 :SNFSINIINIILLVLMAWI 1yasA 111 :EHCPSYVVDKLMEVFPDWK Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 21 residues neighbor-bump: 2.46919 Ang I20.CG2 and G21.N self-bump: 1.34509 Ang I20.CA and I20.CB other bump:2.21354 Ang L13.O and M17.CG other bump:2.39495 Ang N3.ND2 and N7.ND2 other bump:2.94595 Ang N3.CG and N7.CG other bump:2.93387 Ang N3.CG and N7.CB other bump:2.36065 Ang N3.OD1 and N7.CB other bump:2.22512 Ang F4.CE2 and I6.CD1 other bump:3.06748 Ang F4.CD2 and I6.CG1 other bump:2.65466 Ang F4.CE2 and I6.CG1 other bump:2.98069 Ang F4.CD2 and I6.CB YGR016W 139 :SFNHVVEDKKTVLCLQVPMFLF 1yasA 132 :TYFTYTKDGKEITGLKLGFTLL Fragment has 16 clashes (null) has 16 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 24 residues other bump:2.81302 Ang V18.CG2 and F23.CZ other bump:2.53353 Ang V18.CB and F23.CZ other bump:2.62387 Ang V18.CG1 and F23.CZ other bump:2.90733 Ang V18.CG2 and F23.CE1 other bump:2.54415 Ang V18.CB and F23.CE1 other bump:1.8714 Ang V18.CG1 and F23.CE1 other bump:2.91738 Ang M20.CE and F23.CD2 other bump:2.3322 Ang V18.CG1 and F23.CD1 other bump:3.15663 Ang N4.ND2 and C15.SG other bump:2.93615 Ang H5.CE1 and T12.C other bump:1.96818 Ang H5.ND1 and T12.CG2 other bump:1.43972 Ang H5.CE1 and T12.CG2 other bump:2.22798 Ang H5.NE2 and T12.CG2 other bump:2.89854 Ang H5.CG and T12.CG2 other bump:2.15735 Ang H5.CE1 and T12.CB other bump:2.34445 Ang H5.CE1 and T12.CA Number of specific fragments= 5 total=15 Number of alignments=3 # Reading fragments from alignment file # YGR016W read from 1go5A/YGR016W-1go5A-local-str-0.3-adpstyle5.a2m # 1go5A read from 1go5A/YGR016W-1go5A-local-str-0.3-adpstyle5.a2m # adding 1go5A to template set 1go5A:Bad short name: OT1 for alphabet: pdb_atoms Bad short name: OT2 for alphabet: pdb_atoms # found chain 1go5A in template set YGR016W 26 :QEDVSILPLDTEEQEELIQKFETNAHITNKL 1go5A 5 :TPSSSPVPTLSPEQQEMLQAFSTQSGMNLEW Fragment has 29 clashes (null) has 29 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 33 residues other bump:3.14562 Ang I28.CG1 and G33.CA other bump:1.99124 Ang I28.CD1 and G33.CA other bump:2.4532 Ang I28.CD1 and G33.N other bump:2.69398 Ang T29.CB and L32.CD1 other bump:2.42789 Ang T29.CG2 and L32.CD1 other bump:2.12015 Ang T29.OG1 and L32.CD1 other bump:2.56443 Ang T29.OG1 and L32.N other bump:2.37077 Ang I19.CG2 and N30.ND2 other bump:2.91165 Ang E23.OE1 and N30.CB other bump:3.16522 Ang E23.CD and T29.C other bump:2.8521 Ang E23.CG and T29.C other bump:3.20074 Ang E23.CG and T29.CA other bump:3.29646 Ang E23.CG and I28.C other bump:2.42102 Ang E23.O and I28.O other bump:2.4072 Ang E23.CG and I28.O other bump:2.30575 Ang F22.O and I28.CG2 other bump:2.98377 Ang F22.C and I28.CG2 other bump:2.58343 Ang E23.CA and I28.CG2 other bump:2.95097 Ang E23.C and I28.CG2 self-bump: 1.34337 Ang N25.CA and N25.CB other bump:3.01778 Ang Q15.CD and I19.CD1 other bump:2.57571 Ang Q15.CG and I19.CD1 neighbor-bump: 2.32737 Ang I7.O and L8.CD2 neighbor-bump: 2.4283 Ang V5.CG1 and S6.N neighbor-bump: 2.44353 Ang D4.O and V5.CG2 neighbor-bump: 2.84854 Ang D4.OD1 and V5.CG2 neighbor-bump: 2.77576 Ang D4.C and V5.CG2 neighbor-bump: 1.97446 Ang D4.O and V5.CB neighbor-bump: 2.44892 Ang D4.C and V5.CB Number of specific fragments= 1 total=16 Number of alignments=4 # Reading fragments from alignment file # YGR016W read from 1cl3A/2jhbA-YGR016W-fssp-global-adpstyle5.a2m # 1cl3A read from 1cl3A/2jhbA-YGR016W-fssp-global-adpstyle5.a2m # adding 1cl3A to template set 1cl3A:# found chain 1cl3A in template set YGR016W 1 :M 1cl3A 4 :V Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 2 residues YGR016W 7 :FNRKILSLSSDYTHDGESDQEDVSILPLDTEEQEELIQKFE 1cl3A 5 :VPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQTRFQ Fragment has 16 clashes (null) has 16 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.60682 Ang L37.O and F41.CD1 other bump:2.68032 Ang E36.O and K40.CB other bump:1.9613 Ang E35.OE1 and Q39.OE1 self-bump: 2.64602 Ang E35.OE1 and E35.C self-bump: 2.3655 Ang E35.OE1 and E35.O other bump:2.98483 Ang L29.CB and E32.CG other bump:2.05816 Ang I26.O and P28.CD other bump:2.65172 Ang I26.C and P28.CD neighbor-bump: 2.38674 Ang L27.CA and P28.CD neighbor-bump: 1.81263 Ang L27.C and P28.CD other bump:2.26978 Ang E18.O and E22.OE1 other bump:2.80506 Ang H15.CA and S19.OG other bump:2.64752 Ang H15.C and S19.OG self-bump: 1.39593 Ang E18.CA and E18.CB other bump:2.50198 Ang F2.CE2 and R4.CB other bump:2.46883 Ang F2.CD2 and R4.CB YGR016W 54 :NKLYINLLSILYLLYGGLLMILVRK 1cl3A 46 :NACRDGRSEIAFVATGTNLSLQFFP Fragment has 45 clashes (null) has 45 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 27 residues other bump:2.62142 Ang L23.CD2 and K26.NZ other bump:0.46212 Ang L8.CG and K26.NZ other bump:1.72997 Ang L8.CD1 and K26.NZ other bump:1.2483 Ang L8.CD2 and K26.NZ other bump:2.47613 Ang L8.CA and K26.NZ other bump:1.41419 Ang L8.CB and K26.NZ other bump:2.75247 Ang L23.CD2 and K26.CE other bump:1.3978 Ang L8.CG and K26.CE other bump:2.82638 Ang L8.CD1 and K26.CE other bump:2.12701 Ang L8.CD2 and K26.CE other bump:1.78333 Ang L8.CA and K26.CE other bump:1.73716 Ang L8.CB and K26.CE other bump:2.66447 Ang N7.C and K26.CE other bump:1.93554 Ang L8.N and K26.CE other bump:2.06786 Ang L8.CG and K26.CD other bump:2.92288 Ang L8.CD1 and K26.CD other bump:2.90031 Ang L8.CD2 and K26.CD other bump:3.21281 Ang L8.CA and K26.CD other bump:2.98395 Ang L8.CB and K26.CD other bump:3.1515 Ang N7.C and K26.CD other bump:2.72794 Ang L8.N and K26.CD other bump:3.01625 Ang N7.CB and K26.CG other bump:2.36909 Ang N7.N and K26.CG other bump:2.64474 Ang N7.CA and K26.CG other bump:2.64812 Ang N7.C and K26.CG other bump:2.8303 Ang L8.N and K26.CG other bump:3.2172 Ang I6.C and K26.CG other bump:2.95714 Ang N7.N and K26.CB other bump:3.26027 Ang N7.N and K26.CA other bump:3.19072 Ang N7.CB and K26.N other bump:3.20186 Ang N7.CB and R25.C other bump:2.65612 Ang N7.OD1 and V24.CB other bump:2.85201 Ang N7.OD1 and V24.CA other bump:2.98162 Ang L8.CG and L23.CD2 other bump:1.9818 Ang L8.CD2 and L23.CD2 neighbor-bump: 2.5947 Ang I22.O and L23.CD2 other bump:2.84307 Ang L8.CA and L23.CD2 other bump:3.04478 Ang L8.CB and L23.CD2 other bump:2.14569 Ang L8.CD2 and L23.CD1 other bump:2.49823 Ang L8.CD2 and L23.CG other bump:2.30405 Ang Y13.O and Y16.O other bump:2.34559 Ang K3.O and I6.O neighbor-bump: 2.53964 Ang Y5.CE1 and I6.CD1 neighbor-bump: 2.92113 Ang Y5.CE1 and I6.CG1 neighbor-bump: 3.06138 Ang Y5.CZ and I6.CG1 YGR016W 143 :VVEDKKTVLCLQVPMFLFWVAVLVKRWARN 1cl3A 87 :DLEREAGKVYLKAPMILNGVCVIWKGWIDL Fragment has 13 clashes (null) has 13 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 32 residues other bump:2.98385 Ang R30.CG and G32.N other bump:2.82021 Ang V9.CG2 and A29.C other bump:2.14145 Ang V9.CG2 and A29.O other bump:2.33823 Ang C11.SG and W28.CB other bump:2.9455 Ang C11.SG and W28.CA neighbor-bump: 1.89091 Ang F19.O and W20.CD1 neighbor-bump: 2.39462 Ang F19.O and W20.CG self-bump: 1.30359 Ang W20.CA and W20.CB other bump:3.169 Ang E4.CA and L10.CD2 other bump:2.68444 Ang E4.CB and L10.CD2 other bump:2.80097 Ang E4.CG and L10.CD2 neighbor-bump: 2.1344 Ang K7.O and T8.OG1 self-bump: 1.29797 Ang K6.CA and K6.CB YGR016W 175 :DEIADLRCLKYKYKNA 1cl3A 117 :HRLDGMGCLEFDEERA Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.69686 Ang Y14.O and A17.CB other bump:2.53207 Ang Y14.CB and N16.OD1 neighbor-bump: 2.4833 Ang L10.O and K11.CG Number of specific fragments= 5 total=21 Number of alignments=5 # command:superimposing iter= 0 total_weight= 567 weighted rmsd= 0 superimposing iter= 1 total_weight= 5670 weighted rmsd= 0 superimposing iter= 2 total_weight= 5670 weighted rmsd= 0 superimposing iter= 3 total_weight= 5670 weighted rmsd= 0 superimposing iter= 4 total_weight= 5670 weighted rmsd= 0 superimposing iter= 5 total_weight= 5670 weighted rmsd= 0 superimposing iter= 0 total_weight= 392 weighted rmsd= 14.1895 superimposing iter= 1 total_weight= 673.664 weighted rmsd= 10.5124 superimposing iter= 2 total_weight= 548.208 weighted rmsd= 8.73718 superimposing iter= 3 total_weight= 471.572 weighted rmsd= 7.88174 superimposing iter= 4 total_weight= 431.899 weighted rmsd= 7.42252 superimposing iter= 5 total_weight= 428.254 weighted rmsd= 7.01091 superimposing iter= 0 total_weight= 221 weighted rmsd= 11.563 superimposing iter= 1 total_weight= 574.072 weighted rmsd= 6.81837 superimposing iter= 2 total_weight= 371.593 weighted rmsd= 5.08132 superimposing iter= 3 total_weight= 303.839 weighted rmsd= 4.19537 superimposing iter= 4 total_weight= 274.532 weighted rmsd= 3.65998 superimposing iter= 5 total_weight= 251.882 weighted rmsd= 3.33934 superimposing iter= 0 total_weight= 246 weighted rmsd= 8.947 superimposing iter= 1 total_weight= 654.014 weighted rmsd= 5.19967 superimposing iter= 2 total_weight= 346.764 weighted rmsd= 4.19506 superimposing iter= 3 total_weight= 346.21 weighted rmsd= 3.38998 superimposing iter= 4 total_weight= 356.946 weighted rmsd= 2.73886 superimposing iter= 5 total_weight= 310.708 weighted rmsd= 2.39974 superimposing iter= 0 total_weight= 441 weighted rmsd= 13.2766 superimposing iter= 1 total_weight= 1027.98 weighted rmsd= 8.44682 superimposing iter= 2 total_weight= 576.992 weighted rmsd= 7.26129 superimposing iter= 3 total_weight= 491.886 weighted rmsd= 6.76949 superimposing iter= 4 total_weight= 481.818 weighted rmsd= 6.39211 superimposing iter= 5 total_weight= 478.105 weighted rmsd= 6.07198 # command: