# command:# Seed set to 1041309588 # 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= 10524.4 msec) # Prefix for input files set to Created new target YGR039W from YGR039W.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 YGR039W.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= 18450 msec, elapsed time= 18476 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= 23190 msec, elapsed time= 23215.5 msec) # command:# Prefix for input files set to # command:# reading script from file YGR039W.t2k.undertaker-align.under # Reading fragments from alignment file # YGR039W read from 1bwfO/1glcG-YGR039W-fssp-local-adpstyle5.a2m # 1bwfO read from 1bwfO/1glcG-YGR039W-fssp-local-adpstyle5.a2m # adding 1bwfO to template set 1bwfO:# found chain 1bwfO in template set YGR039W 3 :FFTGLVILSYLLGGKKDWLLIMYEASDYLE 1bwfO 126 :SNTGLVIDPYFSGTKVKWILDHVEGSRERA Fragment has 42 clashes (null) has 42 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 32 residues other bump:2.17379 Ang S27.CA and E31.OE2 other bump:2.40797 Ang S27.CB and E31.OE2 other bump:1.99341 Ang S27.C and E31.OE2 other bump:3.05471 Ang L21.CD1 and E31.OE2 other bump:1.75722 Ang D28.CA and E31.OE1 other bump:2.1042 Ang D28.C and E31.OE1 other bump:1.26754 Ang S27.O and E31.OE1 other bump:1.36487 Ang S27.C and E31.OE1 other bump:1.59753 Ang D28.N and E31.OE1 other bump:2.64628 Ang D28.CA and E31.CD other bump:2.83012 Ang S27.CA and E31.CD other bump:1.90734 Ang S27.O and E31.CD other bump:1.87559 Ang S27.C and E31.CD other bump:2.26631 Ang D28.N and E31.CD other bump:2.16353 Ang W19.CZ2 and M23.CE other bump:1.76673 Ang W19.CH2 and M23.CE other bump:2.8257 Ang W19.CZ3 and M23.CE other bump:2.4563 Ang W19.CD2 and M23.SD other bump:2.15523 Ang W19.CE2 and M23.SD other bump:2.37215 Ang W19.CE3 and M23.SD other bump:3.31541 Ang W19.NE1 and M23.SD other bump:1.7341 Ang W19.CZ2 and M23.SD other bump:1.57058 Ang W19.CH2 and M23.SD other bump:1.91247 Ang W19.CZ3 and M23.SD other bump:3.28516 Ang W19.CH2 and M23.CG other bump:2.37285 Ang D18.OD2 and I22.CD1 neighbor-bump: 3.1674 Ang W19.CE3 and L20.CD2 neighbor-bump: 3.06805 Ang W19.CZ3 and L20.CD2 self-bump: 2.98185 Ang W19.CE3 and W19.C neighbor-bump: 2.67972 Ang K17.C and D18.C other bump:3.28087 Ang L13.CA and K16.CD neighbor-bump: 2.11754 Ang L13.O and G14.C neighbor-bump: 2.60889 Ang L13.C and G14.C neighbor-bump: 2.29141 Ang L13.O and G14.O neighbor-bump: 2.44728 Ang I8.O and L9.CG self-bump: 2.54478 Ang L6.CA and L6.CD2 neighbor-bump: 2.7385 Ang F2.CD2 and F3.CZ neighbor-bump: 2.92794 Ang F2.CE2 and F3.CZ neighbor-bump: 2.06225 Ang F2.CD2 and F3.CE1 neighbor-bump: 2.11344 Ang F2.CE2 and F3.CE1 neighbor-bump: 2.65853 Ang F2.CD2 and F3.CD1 neighbor-bump: 3.0615 Ang F2.CE2 and F3.CD1 YGR039W 33 :FLNRLSSMLFK 1bwfO 165 :VDTWLIWKMTQ Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 13 residues self-bump: 1.38199 Ang K12.CA and K12.CB neighbor-bump: 2.34552 Ang S7.O and S8.C neighbor-bump: 2.66342 Ang S7.C and S8.C YGR039W 47 :FEHLSSTFLIFSHS 1bwfO 183 :YTNASRTMLFNIHT Fragment has 28 clashes (null) has 28 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues other bump:2.12757 Ang F12.CG and S15.OG other bump:1.88319 Ang F12.CD1 and S15.OG other bump:1.95673 Ang F12.CB and S15.OG other bump:2.90009 Ang F12.CA and S15.OG other bump:2.79008 Ang F12.C and S15.OG other bump:2.90901 Ang F12.CG and S15.CB other bump:2.11851 Ang F12.CD1 and S15.CB other bump:2.94399 Ang F12.CE1 and S15.CB other bump:2.70468 Ang F12.CD1 and S15.CA other bump:2.56428 Ang F12.CD1 and S15.N other bump:2.72633 Ang F12.CE1 and S15.N neighbor-bump: 2.24885 Ang H14.N and S15.N other bump:2.72181 Ang F12.CD1 and H14.C other bump:2.19971 Ang F12.CE1 and H14.C other bump:2.06618 Ang F12.CE1 and H14.O other bump:3.13658 Ang F12.CZ and H14.ND1 other bump:2.84086 Ang F12.CE1 and H14.CA other bump:2.91256 Ang F12.CE1 and H14.N other bump:1.473 Ang L5.CG and I11.CD1 other bump:2.63992 Ang L5.CD1 and I11.CD1 other bump:2.1242 Ang L5.CD2 and I11.CD1 other bump:2.45485 Ang L5.CB and I11.CD1 other bump:2.71671 Ang L5.C and I11.CD1 neighbor-bump: 1.69116 Ang L10.O and I11.CG2 other bump:3.04731 Ang L5.CD1 and I11.CG2 neighbor-bump: 2.57592 Ang L10.C and I11.CG2 other bump:2.81453 Ang L5.CG and I11.CG1 other bump:2.54905 Ang H4.O and S7.CB Number of specific fragments= 3 total=3 Number of alignments=1 # Reading fragments from alignment file # YGR039W read from 1pciA/1cs8A-YGR039W-fssp-local-adpstyle5.a2m # 1pciA read from 1pciA/1cs8A-YGR039W-fssp-local-adpstyle5.a2m # adding 1pciA to template set 1pciA:WARNING: atom 813 has residue number 1 < previous residue 106P # found chain 1pciA in template set YGR039W 17 :KKDWLLIMYEASDYLEFLNR 1pciA 19P:IQLFNSWMLNHNKFYENVDE Fragment has 13 clashes (null) has 13 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 22 residues other bump:1.8008 Ang L16.CA and R21.NH2 other bump:2.59714 Ang L16.CB and R21.NH2 other bump:2.2648 Ang L16.C and R21.NH2 other bump:2.15483 Ang E17.N and R21.NH2 other bump:2.86136 Ang L16.CA and R21.CZ other bump:2.78317 Ang E17.OE1 and R21.CZ other bump:3.0362 Ang L16.CD1 and R21.NE other bump:2.97447 Ang F18.CE2 and R21.N other bump:2.8342 Ang L7.CD2 and Y10.CE2 other bump:2.97064 Ang W5.CZ2 and M9.SD other bump:2.52743 Ang W5.CH2 and M9.SD other bump:3.43137 Ang W5.CE3 and M9.SD other bump:2.79639 Ang W5.CZ3 and M9.SD YGR039W 37 :LSSMLFKFELFEHLS 1pciA 40P:LYRFEIFKDNLNYID Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues Number of specific fragments= 2 total=5 Number of alignments=2 # Reading fragments from alignment file # YGR039W read from 1hf2A/YGR039W-1hf2A-local-str-0.3-adpstyle5.a2m # 1hf2A read from 1hf2A/YGR039W-1hf2A-local-str-0.3-adpstyle5.a2m # adding 1hf2A to template set 1hf2A:# found chain 1hf2A in template set YGR039W 17 :KKDWLLIMYEASDYLEFLNRLSSMLFKFELFEHLSSTFLIF 1hf2A 8 :KEGLVLLIKDYQNLEEVLNAISARITQMGGFFAKGDRISLM Fragment has 47 clashes (null) has 47 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 43 residues other bump:2.29623 Ang L6.CG and L40.CD2 other bump:1.36205 Ang L6.CD2 and L40.CD2 other bump:2.67877 Ang L6.CD2 and L40.CG other bump:2.43988 Ang W5.CH2 and F32.CZ other bump:2.80801 Ang W5.CE2 and F32.CZ other bump:1.91225 Ang W5.CZ2 and F32.CZ other bump:3.245 Ang W5.CH2 and F32.CE2 other bump:2.65467 Ang W5.CZ2 and F32.CE2 other bump:3.25432 Ang W5.CH2 and F32.CE1 other bump:3.04851 Ang W5.CZ2 and F32.CE1 neighbor-bump: 3.04672 Ang E30.CD and L31.CD1 neighbor-bump: 2.77971 Ang E30.CG and L31.CG neighbor-bump: 2.90614 Ang E30.CD and L31.CG neighbor-bump: 3.13366 Ang E30.CG and L31.CA neighbor-bump: 2.41334 Ang E30.CB and L31.N neighbor-bump: 2.01591 Ang E30.CG and L31.N self-bump: 2.15105 Ang E30.CB and E30.C self-bump: 2.42609 Ang E30.CG and E30.C self-bump: 1.26812 Ang E30.CA and E30.CB other bump:2.70822 Ang M25.CG and F29.CZ other bump:3.08087 Ang M25.SD and F29.CZ other bump:2.26851 Ang M25.CG and F29.CE1 other bump:3.1531 Ang M25.SD and F29.CE1 other bump:3.13222 Ang M25.C and F29.CE1 other bump:2.39095 Ang M25.O and F29.CD1 other bump:2.81029 Ang F18.CE1 and L22.CD1 other bump:2.69246 Ang Y15.CZ and L19.CD2 other bump:2.42325 Ang Y15.OH and L19.CD2 other bump:2.04692 Ang Y15.CE1 and L19.CD1 other bump:2.78981 Ang Y15.CZ and L19.CD1 other bump:2.87083 Ang Y15.OH and L19.CD1 other bump:2.18852 Ang M9.CG and F18.CZ other bump:2.53186 Ang M9.CB and F18.CZ other bump:2.07249 Ang M9.SD and F18.CZ other bump:1.49699 Ang M9.CG and F18.CE2 other bump:2.47678 Ang M9.CB and F18.CE2 other bump:2.07327 Ang M9.SD and F18.CE2 other bump:2.2671 Ang M9.SD and F18.CE1 other bump:2.34291 Ang M9.CG and F18.CD2 other bump:2.26772 Ang M9.SD and F18.CD2 other bump:2.45182 Ang M9.SD and F18.CD1 other bump:2.46585 Ang M9.SD and F18.CG other bump:2.32588 Ang D4.O and L6.CD1 neighbor-bump: 2.66566 Ang K3.C and D4.CG neighbor-bump: 1.75817 Ang K3.O and D4.CG neighbor-bump: 2.67455 Ang K3.C and D4.CB neighbor-bump: 2.30661 Ang K3.O and D4.CB YGR039W 58 :SHSKRAVKLLEIYRSRHISIYNVF 1hf2A 54 :KHSQDIPRIVSHLRNLGLEVSQIL Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 26 residues neighbor-bump: 2.55747 Ang Y22.O and N23.CG other bump:2.92796 Ang L11.CD2 and I21.CD1 other bump:2.19196 Ang L11.CD2 and I21.CG2 other bump:3.04992 Ang L11.CD2 and I21.CB Number of specific fragments= 2 total=7 Number of alignments=3 # Reading fragments from alignment file # YGR039W read from 1f03A/1cyo-YGR039W-fssp-global-adpstyle5.a2m # 1f03A read from 1f03A/1cyo-YGR039W-fssp-global-adpstyle5.a2m # adding 1f03A to template set 1f03A:# found chain 1f03A in template set YGR039W 1 :MLFFTGLVILSYLLGGKKDWLLIMYEASDYLEFLNRLSS 1f03A 3 :AVKYYTLEEIQKHNNSKSTWLILHYKVYDLTKFLEEHPG Fragment has 34 clashes (null) has 34 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 40 residues other bump:1.99481 Ang F33.CD1 and L37.CD2 other bump:1.76243 Ang F33.CE1 and L37.CD2 other bump:2.29483 Ang F33.CD1 and L37.CG other bump:2.73997 Ang D19.OD2 and L34.CD1 other bump:3.07773 Ang D19.C and L31.CD2 other bump:2.20538 Ang K18.C and L31.CD2 other bump:2.14385 Ang D19.CA and L31.CD2 other bump:2.63743 Ang D19.CB and L31.CD2 other bump:2.88267 Ang D19.CG and L31.CD2 other bump:2.76253 Ang K18.CA and L31.CD2 other bump:1.17082 Ang D19.N and L31.CD2 other bump:2.56348 Ang K18.C and L31.CD1 other bump:2.87622 Ang K18.CB and L31.CD1 other bump:2.86326 Ang K18.N and L31.CD1 other bump:1.78586 Ang K18.CA and L31.CD1 other bump:2.62788 Ang D19.N and L31.CD1 other bump:2.81473 Ang K18.C and L31.CG other bump:3.13402 Ang D19.CA and L31.CG other bump:2.75996 Ang K18.CA and L31.CG other bump:2.11437 Ang D19.N and L31.CG other bump:2.78633 Ang S28.CB and Y30.CE1 other bump:2.63932 Ang W20.NE1 and D29.OD2 other bump:2.72649 Ang L10.CD1 and L22.CD2 other bump:2.88469 Ang L10.CD2 and W20.CE3 other bump:2.77557 Ang L13.C and K18.O other bump:2.94033 Ang L13.CG and K18.CD other bump:1.84903 Ang L13.CD2 and K18.CD other bump:2.22305 Ang L13.CD2 and K18.CG other bump:1.88268 Ang L13.CD2 and K18.CB other bump:2.49932 Ang S11.O and L14.CD1 other bump:2.46203 Ang S11.O and L14.CG other bump:2.53745 Ang T5.CG2 and L10.CD2 other bump:2.44035 Ang T5.CG2 and L10.CG neighbor-bump: 2.83113 Ang F3.CE2 and F4.O YGR039W 40 :MLFKFELFEHLSSTFLIFSHSKRAVKLLEIYRSRHISI 1f03A 44 :AVLRAQAGGDATANFEAVGHSTDARELSKTFIIGELHP Fragment has 32 clashes (null) has 32 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 40 residues other bump:2.53832 Ang E30.CD and R33.NH1 other bump:2.62445 Ang E30.N and R33.NH1 other bump:2.18083 Ang E30.CA and R33.NH1 other bump:1.93885 Ang E30.CB and R33.NH1 other bump:1.1028 Ang E30.CG and R33.NH1 other bump:2.95712 Ang E30.N and R33.CZ other bump:2.89927 Ang E30.CA and R33.CZ other bump:2.3706 Ang E30.CG and R33.CZ other bump:3.15975 Ang L29.CG and R33.NE other bump:3.08135 Ang E30.N and R33.NE other bump:3.08415 Ang L29.C and R33.CD other bump:2.98334 Ang E30.N and R33.CD other bump:2.5006 Ang E30.CA and R33.CD other bump:3.22578 Ang F16.CD1 and H21.ND1 other bump:2.86529 Ang T15.CG2 and F19.CE1 self-bump: 1.37596 Ang F19.CA and F19.CB other bump:1.5725 Ang H11.CE1 and S13.OG other bump:2.36888 Ang H11.NE2 and S13.OG other bump:2.77345 Ang H11.CE1 and S13.CB other bump:3.26983 Ang E7.CA and L12.CD2 other bump:2.78187 Ang E7.CB and L12.CD2 other bump:2.31051 Ang E7.O and L12.CD2 other bump:2.66724 Ang E7.C and L12.CD2 other bump:2.85921 Ang E7.CA and L12.CD1 other bump:2.90778 Ang E7.CB and L12.CD1 other bump:2.27111 Ang E7.OE1 and L12.CD1 other bump:2.01128 Ang E7.O and L12.CD1 other bump:2.7422 Ang E7.C and L12.CD1 other bump:3.05214 Ang E7.CD and L12.CD1 other bump:2.66628 Ang E7.CB and L12.CG other bump:3.17584 Ang E7.C and L12.CG other bump:2.88298 Ang K5.CD and L8.CD1 Number of specific fragments= 2 total=9 Number of alignments=4 # Reading fragments from alignment file # YGR039W read from 1h2eA/YGR039W-1h2eA-local-str-0.3-adpstyle5.a2m # 1h2eA read from 1h2eA/YGR039W-1h2eA-local-str-0.3-adpstyle5.a2m # adding 1h2eA to template set 1h2eA:Skipped atom 173, because occupancy 0.5 <= existing 0.500001 Skipped atom 174, because occupancy 0.5 <= existing 0.500001 Skipped atom 175, because occupancy 0.5 <= existing 0.500001 Skipped atom 176, because occupancy 0.5 <= existing 0.500001 Skipped atom 177, because occupancy 0.5 <= existing 0.500001 Skipped atom 178, because occupancy 0.5 <= existing 0.500001 Skipped atom 179, because occupancy 0.5 <= existing 0.500001 Skipped atom 180, because occupancy 0.5 <= existing 0.500001 Skipped atom 231, because occupancy 0.5 <= existing 0.500001 Skipped atom 232, because occupancy 0.5 <= existing 0.500001 Skipped atom 233, because occupancy 0.5 <= existing 0.500001 Skipped atom 234, because occupancy 0.5 <= existing 0.500001 Skipped atom 235, because occupancy 0.5 <= existing 0.500001 Skipped atom 236, because occupancy 0.5 <= existing 0.500001 Skipped atom 292, because occupancy 0.5 <= existing 0.500001 Skipped atom 293, because occupancy 0.5 <= existing 0.500001 Skipped atom 294, because occupancy 0.5 <= existing 0.500001 Skipped atom 295, because occupancy 0.5 <= existing 0.500001 Skipped atom 296, because occupancy 0.5 <= existing 0.500001 Skipped atom 297, because occupancy 0.5 <= existing 0.500001 Skipped atom 298, because occupancy 0.5 <= existing 0.500001 Skipped atom 299, because occupancy 0.5 <= existing 0.500001 Skipped atom 300, because occupancy 0.5 <= existing 0.500001 Skipped atom 301, because occupancy 0.5 <= existing 0.500001 Skipped atom 302, because occupancy 0.5 <= existing 0.500001 Skipped atom 393, because occupancy 0.5 <= existing 0.500001 Skipped atom 394, because occupancy 0.5 <= existing 0.500001 Skipped atom 395, because occupancy 0.5 <= existing 0.500001 Skipped atom 396, because occupancy 0.5 <= existing 0.500001 Skipped atom 397, because occupancy 0.5 <= existing 0.500001 Skipped atom 398, because occupancy 0.5 <= existing 0.500001 Skipped atom 399, because occupancy 0.5 <= existing 0.500001 Skipped atom 400, because occupancy 0.5 <= existing 0.500001 Skipped atom 401, because occupancy 0.5 <= existing 0.500001 Skipped atom 423, because occupancy 0.5 <= existing 0.500001 Skipped atom 424, because occupancy 0.5 <= existing 0.500001 Skipped atom 425, because occupancy 0.5 <= existing 0.500001 Skipped atom 426, because occupancy 0.5 <= existing 0.500001 Skipped atom 427, because occupancy 0.5 <= existing 0.500001 Skipped atom 428, because occupancy 0.5 <= existing 0.500001 Skipped atom 429, because occupancy 0.5 <= existing 0.500001 Skipped atom 430, because occupancy 0.5 <= existing 0.500001 Skipped atom 431, because occupancy 0.5 <= existing 0.500001 Skipped atom 533, because occupancy 0.5 <= existing 0.500001 Skipped atom 534, because occupancy 0.5 <= existing 0.500001 Skipped atom 535, because occupancy 0.5 <= existing 0.500001 Skipped atom 536, because occupancy 0.5 <= existing 0.500001 Skipped atom 537, because occupancy 0.5 <= existing 0.500001 Skipped atom 538, because occupancy 0.5 <= existing 0.500001 Skipped atom 539, because occupancy 0.5 <= existing 0.500001 Skipped atom 540, because occupancy 0.5 <= existing 0.500001 Skipped atom 541, because occupancy 0.5 <= existing 0.500001 Skipped atom 852, because occupancy 0.5 <= existing 0.500001 Skipped atom 853, because occupancy 0.5 <= existing 0.500001 Skipped atom 854, because occupancy 0.5 <= existing 0.500001 Skipped atom 855, because occupancy 0.5 <= existing 0.500001 Skipped atom 856, because occupancy 0.5 <= existing 0.500001 Skipped atom 857, because occupancy 0.5 <= existing 0.500001 Skipped atom 858, because occupancy 0.5 <= existing 0.500001 Skipped atom 859, because occupancy 0.5 <= existing 0.500001 Skipped atom 860, because occupancy 0.5 <= existing 0.500001 Skipped atom 877, because occupancy 0.5 <= existing 0.500001 Skipped atom 878, because occupancy 0.5 <= existing 0.500001 Skipped atom 879, because occupancy 0.5 <= existing 0.500001 Skipped atom 880, because occupancy 0.5 <= existing 0.500001 Skipped atom 881, because occupancy 0.5 <= existing 0.500001 Skipped atom 882, because occupancy 0.5 <= existing 0.500001 Skipped atom 883, because occupancy 0.5 <= existing 0.500001 Skipped atom 884, because occupancy 0.5 <= existing 0.500001 Skipped atom 900, because occupancy 0.5 <= existing 0.500001 Skipped atom 901, because occupancy 0.5 <= existing 0.500001 Skipped atom 902, because occupancy 0.5 <= existing 0.500001 Skipped atom 903, because occupancy 0.5 <= existing 0.500001 Skipped atom 904, because occupancy 0.5 <= existing 0.500001 Skipped atom 905, because occupancy 0.5 <= existing 0.500001 Skipped atom 906, because occupancy 0.5 <= existing 0.500001 Skipped atom 907, because occupancy 0.5 <= existing 0.500001 Skipped atom 1074, because occupancy 0.5 <= existing 0.500001 Skipped atom 1075, because occupancy 0.5 <= existing 0.500001 Skipped atom 1076, because occupancy 0.5 <= existing 0.500001 Skipped atom 1077, because occupancy 0.5 <= existing 0.500001 Skipped atom 1078, because occupancy 0.5 <= existing 0.500001 Skipped atom 1079, because occupancy 0.5 <= existing 0.500001 Skipped atom 1080, because occupancy 0.5 <= existing 0.500001 Skipped atom 1081, because occupancy 0.5 <= existing 0.500001 Skipped atom 1082, because occupancy 0.5 <= existing 0.500001 Skipped atom 1083, because occupancy 0.5 <= existing 0.500001 Skipped atom 1084, because occupancy 0.5 <= existing 0.500001 Skipped atom 1102, because occupancy 0.5 <= existing 0.500001 Skipped atom 1103, because occupancy 0.5 <= existing 0.500001 Skipped atom 1104, because occupancy 0.5 <= existing 0.500001 Skipped atom 1105, because occupancy 0.5 <= existing 0.500001 Skipped atom 1106, because occupancy 0.5 <= existing 0.500001 Skipped atom 1107, because occupancy 0.5 <= existing 0.500001 Skipped atom 1141, because occupancy 0.5 <= existing 0.500001 Skipped atom 1142, because occupancy 0.5 <= existing 0.500001 Skipped atom 1143, because occupancy 0.5 <= existing 0.500001 Skipped atom 1144, because occupancy 0.5 <= existing 0.500001 Skipped atom 1145, because occupancy 0.5 <= existing 0.500001 Skipped atom 1146, because occupancy 0.5 <= existing 0.500001 Skipped atom 1147, because occupancy 0.5 <= existing 0.500001 Skipped atom 1148, because occupancy 0.5 <= existing 0.500001 Skipped atom 1149, because occupancy 0.5 <= existing 0.500001 Skipped atom 1174, because occupancy 0.5 <= existing 0.500001 Skipped atom 1175, because occupancy 0.5 <= existing 0.500001 Skipped atom 1176, because occupancy 0.5 <= existing 0.500001 Skipped atom 1177, because occupancy 0.5 <= existing 0.500001 Skipped atom 1178, because occupancy 0.5 <= existing 0.500001 Skipped atom 1179, because occupancy 0.5 <= existing 0.500001 Skipped atom 1180, because occupancy 0.5 <= existing 0.500001 Skipped atom 1181, because occupancy 0.5 <= existing 0.500001 Skipped atom 1191, because occupancy 0.5 <= existing 0.500001 Skipped atom 1192, because occupancy 0.5 <= existing 0.500001 Skipped atom 1193, because occupancy 0.5 <= existing 0.500001 Skipped atom 1194, because occupancy 0.5 <= existing 0.500001 Skipped atom 1195, because occupancy 0.5 <= existing 0.500001 Skipped atom 1196, because occupancy 0.5 <= existing 0.500001 Skipped atom 1197, because occupancy 0.5 <= existing 0.500001 Skipped atom 1198, because occupancy 0.5 <= existing 0.500001 Skipped atom 1199, because occupancy 0.5 <= existing 0.500001 Skipped atom 1227, because occupancy 0.5 <= existing 0.500001 Skipped atom 1228, because occupancy 0.5 <= existing 0.500001 Skipped atom 1229, because occupancy 0.5 <= existing 0.500001 Skipped atom 1230, because occupancy 0.5 <= existing 0.500001 Skipped atom 1231, because occupancy 0.5 <= existing 0.500001 Skipped atom 1232, because occupancy 0.5 <= existing 0.500001 Skipped atom 1256, because occupancy 0.5 <= existing 0.500001 Skipped atom 1257, because occupancy 0.5 <= existing 0.500001 Skipped atom 1258, because occupancy 0.5 <= existing 0.500001 Skipped atom 1259, because occupancy 0.5 <= existing 0.500001 Skipped atom 1260, because occupancy 0.5 <= existing 0.500001 Skipped atom 1261, because occupancy 0.5 <= existing 0.500001 Skipped atom 1262, because occupancy 0.5 <= existing 0.500001 Skipped atom 1263, because occupancy 0.5 <= existing 0.500001 Skipped atom 1449, because occupancy 0.5 <= existing 0.500001 Skipped atom 1450, because occupancy 0.5 <= existing 0.500001 Skipped atom 1451, because occupancy 0.5 <= existing 0.500001 Skipped atom 1452, because occupancy 0.5 <= existing 0.500001 Skipped atom 1453, because occupancy 0.5 <= existing 0.500001 Skipped atom 1454, because occupancy 0.5 <= existing 0.500001 Skipped atom 1455, because occupancy 0.5 <= existing 0.500001 Skipped atom 1456, because occupancy 0.5 <= existing 0.500001 Skipped atom 1457, because occupancy 0.5 <= existing 0.500001 Skipped atom 1480, because occupancy 0.5 <= existing 0.500001 Skipped atom 1481, because occupancy 0.5 <= existing 0.500001 Skipped atom 1482, because occupancy 0.5 <= existing 0.500001 Skipped atom 1483, because occupancy 0.5 <= existing 0.500001 Skipped atom 1484, because occupancy 0.5 <= existing 0.500001 Skipped atom 1485, because occupancy 0.5 <= existing 0.500001 Skipped atom 1486, because occupancy 0.5 <= existing 0.500001 Skipped atom 1541, because occupancy 0.5 <= existing 0.500001 Skipped atom 1542, because occupancy 0.5 <= existing 0.500001 Skipped atom 1543, because occupancy 0.5 <= existing 0.500001 Skipped atom 1544, because occupancy 0.5 <= existing 0.500001 Skipped atom 1545, because occupancy 0.5 <= existing 0.500001 Skipped atom 1546, because occupancy 0.5 <= existing 0.500001 Skipped atom 1554, because occupancy 0.5 <= existing 0.500001 Skipped atom 1555, because occupancy 0.5 <= existing 0.500001 Skipped atom 1556, because occupancy 0.5 <= existing 0.500001 Skipped atom 1557, because occupancy 0.5 <= existing 0.500001 Skipped atom 1558, because occupancy 0.5 <= existing 0.500001 Skipped atom 1559, because occupancy 0.5 <= existing 0.500001 Skipped atom 1560, because occupancy 0.5 <= existing 0.500001 Skipped atom 1686, because occupancy 0.5 <= existing 0.500001 Skipped atom 1687, because occupancy 0.5 <= existing 0.500001 Skipped atom 1688, because occupancy 0.5 <= existing 0.500001 Skipped atom 1689, because occupancy 0.5 <= existing 0.500001 Skipped atom 1690, because occupancy 0.5 <= existing 0.500001 Skipped atom 1691, because occupancy 0.5 <= existing 0.500001 Skipped atom 1692, because occupancy 0.5 <= existing 0.500001 Skipped atom 1714, because occupancy 0.5 <= existing 0.500001 Skipped atom 1715, because occupancy 0.5 <= existing 0.500001 Skipped atom 1716, because occupancy 0.5 <= existing 0.500001 Skipped atom 1717, because occupancy 0.5 <= existing 0.500001 Skipped atom 1718, because occupancy 0.5 <= existing 0.500001 Skipped atom 1719, because occupancy 0.5 <= existing 0.500001 Skipped atom 1720, because occupancy 0.5 <= existing 0.500001 Skipped atom 1721, because occupancy 0.5 <= existing 0.500001 Skipped atom 1722, because occupancy 0.5 <= existing 0.500001 Skipped atom 1723, because occupancy 0.5 <= existing 0.500001 # found chain 1h2eA in template set YGR039W 35 :NRLSSMLFK 1h2eA 33 :GRQDAMRLG Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues YGR039W 45 :ELFEHLSSTFLIFSHSKRAVKLLEIYRS 1h2eA 42 :KRLEAVELAAIYTSTSGRALETAEIVRG Fragment has 30 clashes (null) has 30 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 30 residues other bump:2.71563 Ang I26.C and S29.OG other bump:1.78631 Ang I26.O and S29.OG other bump:2.88336 Ang F4.CB and Y27.OH other bump:2.93975 Ang F4.CD1 and Y27.OH other bump:2.13128 Ang F4.CD1 and Y27.CE1 other bump:3.10186 Ang F4.CE1 and Y27.CE1 other bump:1.53034 Ang F14.CZ and L24.CD2 other bump:2.93951 Ang F14.CG and L24.CD2 other bump:2.01911 Ang F14.CD2 and L24.CD2 other bump:0.975579 Ang F14.CE2 and L24.CD2 other bump:2.05699 Ang F14.CB and L24.CD1 other bump:1.51168 Ang F14.CD1 and L24.CD1 other bump:2.20158 Ang F14.CE1 and L24.CD1 other bump:2.32928 Ang F14.CZ and L24.CD1 other bump:0.640147 Ang F14.CG and L24.CD1 other bump:0.980231 Ang F14.CD2 and L24.CD1 other bump:1.86606 Ang F14.CE2 and L24.CD1 other bump:2.61253 Ang F14.CD1 and L24.CG other bump:1.64131 Ang F14.CZ and L24.CG other bump:2.1273 Ang F14.CG and L24.CG other bump:1.10237 Ang F14.CD2 and L24.CG other bump:0.565976 Ang F14.CE2 and L24.CG other bump:3.07203 Ang F14.CD1 and L24.CB other bump:2.45526 Ang F14.CE1 and L24.CB other bump:1.67105 Ang F14.CZ and L24.CB other bump:2.52281 Ang F14.CD2 and L24.CB other bump:1.72225 Ang F14.CE2 and L24.CB other bump:2.63347 Ang F14.CZ and L24.CA other bump:2.56411 Ang F14.CE2 and L24.CA neighbor-bump: 2.52341 Ang T10.OG1 and F11.CD1 YGR039W 73 :RHISIYNVFLLR 1h2eA 71 :RLIPIYQDERLR Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues Number of specific fragments= 3 total=12 Number of alignments=5 # command:superimposing iter= 0 total_weight= 458 weighted rmsd= 0 superimposing iter= 1 total_weight= 4580 weighted rmsd= 0 superimposing iter= 2 total_weight= 4580 weighted rmsd= 0 superimposing iter= 3 total_weight= 4580 weighted rmsd= 0 superimposing iter= 4 total_weight= 4580 weighted rmsd= 0 superimposing iter= 5 total_weight= 4580 weighted rmsd= 0 superimposing iter= 0 total_weight= 279 weighted rmsd= 11.2601 superimposing iter= 1 total_weight= 509.142 weighted rmsd= 8.21351 superimposing iter= 2 total_weight= 338.364 weighted rmsd= 7.37138 superimposing iter= 3 total_weight= 320.154 weighted rmsd= 6.80848 superimposing iter= 4 total_weight= 304.683 weighted rmsd= 6.45514 superimposing iter= 5 total_weight= 293.082 weighted rmsd= 6.24647 superimposing iter= 0 total_weight= 352 weighted rmsd= 11.9 superimposing iter= 1 total_weight= 770.877 weighted rmsd= 7.63307 superimposing iter= 2 total_weight= 519.104 weighted rmsd= 6.12079 superimposing iter= 3 total_weight= 469.951 weighted rmsd= 5.20389 superimposing iter= 4 total_weight= 437.992 weighted rmsd= 4.59836 superimposing iter= 5 total_weight= 415.959 weighted rmsd= 4.17664 superimposing iter= 0 total_weight= 458 weighted rmsd= 14.9367 superimposing iter= 1 total_weight= 1030.75 weighted rmsd= 9.68043 superimposing iter= 2 total_weight= 607.269 weighted rmsd= 8.24346 superimposing iter= 3 total_weight= 537.15 weighted rmsd= 7.49478 superimposing iter= 4 total_weight= 498.009 weighted rmsd= 7.10125 superimposing iter= 5 total_weight= 481.53 weighted rmsd= 6.86411 superimposing iter= 0 total_weight= 192 weighted rmsd= 10.2822 superimposing iter= 1 total_weight= 392.507 weighted rmsd= 7.00391 superimposing iter= 2 total_weight= 241.431 weighted rmsd= 6.18759 superimposing iter= 3 total_weight= 202.296 weighted rmsd= 5.98633 superimposing iter= 4 total_weight= 194.522 weighted rmsd= 5.90544 superimposing iter= 5 total_weight= 193.002 weighted rmsd= 5.84546 # command: