# command:# Seed set to 1041960514 # 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= 10540.1 msec) # Prefix for input files set to Created new target YAR033W from YAR033W.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 YAR033W.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= 22270 msec, elapsed time= 22326.4 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= 27020 msec, elapsed time= 27076.8 msec) # command:# Prefix for input files set to # command:# reading script from file YAR033W.t2k.undertaker-align.under # Reading fragments from alignment file # YAR033W read from 1ha2A/YAR033W-1ha2A-local-str-0.3-adpstyle5.a2m # 1ha2A read from 1ha2A/YAR033W-1ha2A-local-str-0.3-adpstyle5.a2m # adding 1ha2A to template set 1ha2A:# found chain 1ha2A in template set YAR033W 6 :ESTDVKLDTLNEPSAHLIEKNVA 1ha2A 294 :ENDEMPADLPSLAADFVESKDVC Fragment has 24 clashes (null) has 24 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 25 residues neighbor-bump: 2.74383 Ang K21.C and N22.CG neighbor-bump: 1.86254 Ang K21.O and N22.CG other bump:1.63391 Ang S15.O and E20.OE2 other bump:2.1801 Ang S15.CA and E20.OE2 other bump:2.31217 Ang S15.CB and E20.OE2 other bump:1.71819 Ang S15.OG and E20.OE2 other bump:1.69173 Ang S15.C and E20.OE2 other bump:0.69279 Ang S15.O and E20.OE1 other bump:2.3329 Ang A16.N and E20.OE1 other bump:1.6552 Ang S15.C and E20.OE1 other bump:2.479 Ang A16.CA and E20.OE1 other bump:0.974366 Ang S15.O and E20.CD other bump:2.73473 Ang A16.N and E20.CD other bump:2.90679 Ang S15.CA and E20.CD other bump:1.85545 Ang S15.C and E20.CD other bump:3.0691 Ang A16.CA and E20.CD other bump:2.3724 Ang S15.O and E20.CG other bump:2.83867 Ang N12.CG and P14.CD other bump:1.91604 Ang N12.OD1 and P14.CD self-bump: 1.34404 Ang P14.N and P14.CD neighbor-bump: 2.44399 Ang E13.N and P14.CD other bump:3.03597 Ang N12.CG and P14.CG other bump:2.25816 Ang N12.OD1 and P14.CG self-bump: 2.21474 Ang P14.N and P14.CG YAR033W 29 :LPKDIFRSYLSYWIYEIARYTPVMILSLVIGVLVLLIIFFNDN 1ha2A 321 :EAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAA Fragment has 34 clashes (null) has 34 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 45 residues other bump:2.48988 Ang F41.CA and N44.ND2 other bump:2.0084 Ang F41.O and N44.ND2 other bump:2.53703 Ang F41.C and N44.ND2 other bump:2.43821 Ang F41.O and N44.CG other bump:2.50528 Ang L36.O and F40.CD2 other bump:2.31604 Ang R8.CD and V35.CG2 other bump:2.52166 Ang S12.CB and I31.CD1 other bump:2.47021 Ang Y16.OH and S28.N other bump:2.45229 Ang Y16.OH and L27.C other bump:2.99169 Ang Y16.CZ and L27.CD1 other bump:2.63879 Ang Y16.CG and L27.CD1 other bump:1.96524 Ang Y16.CD2 and L27.CD1 other bump:2.21429 Ang Y16.CE2 and L27.CD1 other bump:2.83012 Ang Y16.CE2 and L27.CG other bump:2.55411 Ang Y16.CE1 and L27.CB other bump:1.97115 Ang Y16.CZ and L27.CB other bump:2.17229 Ang Y16.OH and L27.CB other bump:2.46698 Ang Y16.CE2 and L27.CB other bump:3.16917 Ang Y16.CZ and L27.CA other bump:2.77202 Ang Y16.OH and L27.CA other bump:2.22914 Ang P23.CG and I26.CD1 other bump:2.63662 Ang P23.CD and I26.CD1 other bump:2.70082 Ang P23.CG and I26.CG1 other bump:2.67 Ang S12.O and Y16.CD1 other bump:2.74847 Ang L11.CD2 and I15.CD1 neighbor-bump: 2.81279 Ang Y13.CD2 and W14.CD1 neighbor-bump: 3.03913 Ang Y13.CE2 and W14.CD1 neighbor-bump: 2.30227 Ang L2.CA and P3.CD neighbor-bump: 1.85877 Ang L2.O and P3.CD neighbor-bump: 1.33082 Ang L2.C and P3.CD neighbor-bump: 2.50749 Ang L2.CB and P3.CD neighbor-bump: 1.56233 Ang L2.O and P3.CG neighbor-bump: 2.03219 Ang L2.C and P3.CG self-bump: 1.39979 Ang P3.CA and P3.CB YAR033W 72 :EACVFNSAIFAFTSLVGLLIILSD 1ha2A 372 :KVFDEFKPLVEEPQNLIKQNCELF Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 26 residues other bump:2.76568 Ang E2.OE1 and V5.CG2 self-bump: 2.14453 Ang E2.CB and E2.C self-bump: 1.28047 Ang E2.CA and E2.CB YAR033W 99 :KLVSRRNFRTELLVDVITRKPAVEGKEWRIITYNMNQ 1ha2A 396 :EQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGK Fragment has 56 clashes (null) has 56 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 39 residues other bump:1.96946 Ang R6.NH2 and Q38.CG other bump:3.11046 Ang R6.NH2 and Q38.CB other bump:2.7594 Ang F9.C and N37.OD1 other bump:2.33948 Ang R10.CA and N37.OD1 other bump:2.59381 Ang R10.CA and N37.ND2 other bump:2.55649 Ang R10.CB and N37.ND2 other bump:2.4175 Ang R10.CG and N37.ND2 other bump:1.91861 Ang T33.O and N37.ND2 other bump:2.90408 Ang T33.C and N37.ND2 other bump:2.62309 Ang R10.CA and N37.CG other bump:2.77627 Ang R10.CB and N37.CG other bump:2.19358 Ang R10.CG and N37.CG other bump:2.43802 Ang R10.CG and N37.CB other bump:2.77349 Ang R10.NE and Y34.CE1 other bump:2.18873 Ang R10.CZ and Y34.CE1 other bump:2.58146 Ang R10.NH2 and Y34.CE1 other bump:2.53474 Ang R6.NH1 and Y34.CE1 other bump:2.29314 Ang R10.NH1 and Y34.CE1 other bump:1.93419 Ang R10.NE and Y34.CD1 other bump:1.57189 Ang R10.CZ and Y34.CD1 other bump:1.6769 Ang R10.NH2 and Y34.CD1 other bump:3.07086 Ang R10.CD and Y34.CD1 other bump:2.46025 Ang R10.NH1 and Y34.CD1 other bump:2.92468 Ang R10.NE and Y34.CG other bump:2.20597 Ang R10.NH2 and Y34.CG other bump:2.66327 Ang R10.NH2 and Y34.CB other bump:2.37921 Ang L14.CD1 and T33.CG2 other bump:2.4565 Ang V17.O and W29.CH2 other bump:3.06415 Ang V17.C and W29.CH2 other bump:3.15494 Ang V17.CB and W29.CH2 other bump:1.88504 Ang V17.CG1 and W29.CH2 other bump:3.20619 Ang V17.CA and W29.CZ3 other bump:3.14496 Ang V17.C and W29.CZ3 other bump:2.29677 Ang V17.CB and W29.CZ3 other bump:0.893918 Ang V17.CG1 and W29.CZ3 other bump:2.73717 Ang V17.O and W29.CZ2 other bump:3.14675 Ang K21.CB and W29.CZ2 other bump:2.82449 Ang K21.O and W29.CZ2 other bump:2.57199 Ang V24.CB and W29.NE1 other bump:3.00134 Ang V17.CB and W29.CE3 other bump:2.02634 Ang V17.CG1 and W29.CE3 other bump:2.14786 Ang N8.O and E12.OE2 other bump:2.30062 Ang F9.CA and E12.OE1 other bump:2.6544 Ang F9.C and E12.OE1 other bump:1.35019 Ang N8.O and E12.OE1 other bump:2.1694 Ang N8.C and E12.OE1 other bump:1.88454 Ang N8.O and E12.CD other bump:2.88777 Ang N8.C and E12.CD other bump:3.2928 Ang V4.CG1 and F9.CA other bump:2.58909 Ang V4.CG1 and F9.N other bump:2.80441 Ang V4.CG1 and N8.C other bump:2.64663 Ang V4.CG1 and N8.CB other bump:3.14912 Ang V4.CG1 and N8.CA neighbor-bump: 2.70722 Ang V4.CG1 and S5.O other bump:2.45135 Ang G1.O and V4.O self-bump: 1.3904 Ang L3.CA and L3.CB YAR033W 138 :FNHGQWHTPY 1ha2A 433 :VGSKCCKHPE Fragment has 20 clashes (null) has 20 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues other bump:2.24103 Ang Q6.O and T9.OG1 other bump:2.56798 Ang H4.O and H8.CD2 other bump:1.42623 Ang N3.ND2 and W7.CH2 other bump:2.33337 Ang N3.CB and W7.CH2 other bump:1.90873 Ang N3.CG and W7.CH2 other bump:2.7696 Ang N3.ND2 and W7.CZ3 other bump:2.55593 Ang N3.CB and W7.CZ3 other bump:2.88647 Ang N3.CG and W7.CZ3 other bump:1.53911 Ang N3.ND2 and W7.CZ2 other bump:2.51867 Ang N3.CB and W7.CZ2 other bump:1.48143 Ang N3.CG and W7.CZ2 other bump:1.90271 Ang N3.OD1 and W7.CZ2 other bump:2.92638 Ang N3.CB and W7.CE3 other bump:2.92184 Ang N3.O and W7.CE3 other bump:3.18446 Ang N3.C and W7.CE3 other bump:2.88125 Ang N3.ND2 and W7.CE2 other bump:2.85409 Ang N3.CB and W7.CE2 other bump:2.30468 Ang N3.CG and W7.CE2 other bump:2.28168 Ang N3.OD1 and W7.CE2 other bump:3.06268 Ang N3.CB and W7.CD2 YAR033W 151 :SDEDCYRYFLRLVEGVTP 1ha2A 444 :KRMPCAEDYLSVVLNQLC Fragment has 5 clashes (null) has 5 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 20 residues other bump:1.43002 Ang E15.O and P19.CD other bump:2.59651 Ang E15.C and P19.CD other bump:2.92311 Ang G16.C and P19.CD other bump:2.0465 Ang E15.O and P19.CG other bump:3.12595 Ang E15.C and P19.CG YAR033W 176 :IGNSPVTAKP 1ha2A 490 :ALEVDETYVP Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues YAR033W 187 :DAIESASPSSRLNYQNFLLKAAEIERQAQENYWRRRHPNI 1ha2A 500 :KEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKA Fragment has 41 clashes (null) has 41 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 42 residues other bump:3.09588 Ang W34.CZ2 and I41.CD1 other bump:3.15061 Ang W34.CZ2 and I41.CG2 other bump:2.2007 Ang W34.CH2 and I41.CG2 other bump:3.02558 Ang W34.CZ3 and I41.CG2 other bump:2.93096 Ang W34.CZ2 and I41.CG1 other bump:2.79796 Ang W34.CH2 and I41.CG1 other bump:2.863 Ang W34.CH2 and I41.CB other bump:2.49808 Ang E5.N and R37.NH2 other bump:2.77532 Ang E5.CB and R37.NH2 other bump:2.54371 Ang S8.OG and R37.NH2 other bump:1.77967 Ang I4.CA and R37.NH1 other bump:2.04284 Ang I4.C and R37.NH1 other bump:2.7344 Ang I4.CG1 and R37.NH1 other bump:1.79221 Ang E5.N and R37.NH1 other bump:3.0939 Ang I4.CA and R37.CZ other bump:3.18295 Ang I4.C and R37.CZ other bump:2.47994 Ang E5.N and R37.CZ other bump:1.84036 Ang N32.OD1 and R36.NH1 other bump:2.31837 Ang N32.OD1 and R36.CZ other bump:2.88752 Ang N14.CB and F18.CZ other bump:2.5759 Ang N14.CA and F18.CE1 other bump:2.33493 Ang N14.CB and F18.CE1 other bump:2.04837 Ang N14.O and F18.CE1 other bump:2.1458 Ang N14.C and F18.CE1 other bump:2.84214 Ang Y15.N and F18.CD1 other bump:2.99154 Ang Y15.CA and F18.CD1 other bump:1.60514 Ang N14.O and F18.CD1 other bump:2.24399 Ang N14.C and F18.CD1 other bump:2.91207 Ang S11.OG and Y15.CE2 other bump:2.4616 Ang R12.O and Y15.CE2 other bump:2.40628 Ang R12.O and Y15.CD2 neighbor-bump: 2.24164 Ang S8.CB and P9.CD neighbor-bump: 1.73142 Ang S8.OG and P9.CD neighbor-bump: 2.54528 Ang S8.N and P9.CD neighbor-bump: 1.99355 Ang S8.CA and P9.CD neighbor-bump: 1.55852 Ang S8.C and P9.CD self-bump: 1.26619 Ang P9.N and P9.CD neighbor-bump: 2.15505 Ang S8.OG and P9.CG neighbor-bump: 2.71258 Ang S8.C and P9.CG self-bump: 2.11549 Ang P9.N and P9.CG self-bump: 2.15157 Ang P9.N and P9.CB Number of specific fragments= 8 total=8 Number of alignments=1 # Reading fragments from alignment file # YAR033W read from 1e7aA/YAR033W-1e7aA-local-str-1.5-adpstyle5.a2m # 1e7aA read from 1e7aA/YAR033W-1e7aA-local-str-1.5-adpstyle5.a2m # adding 1e7aA to template set 1e7aA:# found chain 1e7aA in template set YAR033W 7 :STDVKLDTLNEPSAHLIEKNVAL 1e7aA 292 :EVENDEMPADLPSLAADFVESKD Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 25 residues other bump:2.88474 Ang I18.CA and V22.CG2 other bump:1.9615 Ang T9.OG1 and E12.OE1 other bump:2.68393 Ang T9.OG1 and E12.CD self-bump: 1.35169 Ang L10.CA and L10.CB YAR033W 30 :PK 1e7aA 322 :AK Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues self-bump: 2.13142 Ang P2.CA and P2.CG self-bump: 1.39334 Ang P2.CA and P2.CB YAR033W 35 :RSYLSYWIYEIARYTP 1e7aA 324 :DVFLGMFLYEYARRHP Fragment has 12 clashes (null) has 12 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues neighbor-bump: 2.4153 Ang R14.NH1 and Y15.OH neighbor-bump: 2.74173 Ang R14.CG and Y15.CE1 other bump:2.58096 Ang E11.O and Y15.CD1 neighbor-bump: 2.64072 Ang R14.CG and Y15.CD1 other bump:2.38587 Ang W8.CD2 and I12.CD1 other bump:1.8035 Ang W8.CE2 and I12.CD1 other bump:3.07821 Ang W8.CE3 and I12.CD1 other bump:2.16754 Ang W8.CZ2 and I12.CD1 other bump:2.87821 Ang W8.CH2 and I12.CD1 other bump:2.30597 Ang W8.NE1 and I12.CD1 other bump:3.18356 Ang W8.NE1 and I12.CG1 other bump:2.40118 Ang S3.O and Y7.CD1 YAR033W 51 :VMILSLVIGVLVLLIIFFNDN 1e7aA 344 :VLLLRLAKTYETTLEKCCAAA Fragment has 21 clashes (null) has 21 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues other bump:2.29916 Ang F18.O and D21.OD2 other bump:2.76274 Ang F18.C and D21.OD2 other bump:2.57816 Ang F18.CA and D21.OD2 other bump:3.27945 Ang F18.C and D21.CG other bump:2.74403 Ang L15.CA and F19.CZ other bump:2.26359 Ang L15.CB and F19.CZ other bump:2.32972 Ang L15.CG and F19.CZ other bump:2.02711 Ang L15.CD2 and F19.CZ other bump:2.7176 Ang L15.CD1 and F19.CZ other bump:3.18095 Ang L15.N and F19.CE2 other bump:1.73849 Ang L15.CA and F19.CE2 other bump:1.6725 Ang L15.CB and F19.CE2 other bump:2.10488 Ang L15.O and F19.CE2 other bump:2.08103 Ang L15.C and F19.CE2 other bump:2.60478 Ang L15.CG and F19.CE2 other bump:2.73578 Ang L15.CD2 and F19.CE2 other bump:2.53067 Ang L15.CA and F19.CD2 other bump:2.91274 Ang L15.CB and F19.CD2 other bump:1.17492 Ang L15.O and F19.CD2 other bump:1.96974 Ang L15.C and F19.CD2 other bump:2.29912 Ang L15.O and F19.CG YAR033W 72 :EACVFNSAIFAFTSLVGLLIILSD 1e7aA 377 :FKPLVEEPQNLIKQNCELFEQLGE Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 26 residues neighbor-bump: 1.64459 Ang L23.O and S24.OG neighbor-bump: 2.572 Ang L23.C and S24.OG neighbor-bump: 2.68057 Ang L23.C and S24.CB YAR033W 104 :RNFRTELLVDVITRKPAVEGKEWRIITYNMNQ 1e7aA 401 :YKFQNALLVRYTKKVPQVSTPTLVEVSRNLGK Fragment has 38 clashes (null) has 38 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 34 residues other bump:2.90439 Ang Y29.CE2 and Q33.NE2 other bump:2.72372 Ang N30.CA and Q33.OE1 other bump:2.58774 Ang L8.CG and N32.OD1 other bump:1.82234 Ang L8.CD1 and N32.OD1 other bump:2.25055 Ang R5.N and N32.ND2 other bump:1.28285 Ang R5.CA and N32.ND2 other bump:2.45667 Ang R5.C and N32.ND2 other bump:1.98164 Ang R5.CB and N32.ND2 other bump:2.1907 Ang R5.CG and N32.ND2 other bump:2.75931 Ang L8.CD1 and N32.CG other bump:2.81632 Ang R5.N and N32.CG other bump:2.44325 Ang R5.CA and N32.CG other bump:3.05859 Ang R5.CB and N32.CG other bump:2.65216 Ang R5.CG and N32.CG other bump:2.38543 Ang R5.CG and N32.CB other bump:2.54498 Ang R5.NH1 and Y29.CZ other bump:2.7758 Ang R5.CZ and Y29.CE1 other bump:1.78877 Ang R5.NH1 and Y29.CE1 other bump:2.91778 Ang R5.CD and Y29.CD1 other bump:3.24443 Ang R5.NE and Y29.CD1 other bump:2.60692 Ang R5.NH1 and Y29.CD1 other bump:2.50626 Ang L9.CD2 and T28.CG2 other bump:2.86135 Ang L9.CG and T28.CG2 other bump:2.33143 Ang V12.O and W24.CH2 other bump:3.10695 Ang V12.C and W24.CH2 other bump:2.38489 Ang V12.CG1 and W24.CH2 other bump:3.25355 Ang V12.CA and W24.CZ3 other bump:2.58353 Ang V12.CB and W24.CZ3 other bump:2.80132 Ang V12.O and W24.CZ3 other bump:3.03458 Ang V12.C and W24.CZ3 other bump:1.18167 Ang V12.CG1 and W24.CZ3 other bump:3.19043 Ang K16.CB and W24.CZ2 other bump:2.66588 Ang K16.O and W24.CZ2 other bump:2.82167 Ang V12.O and W24.CZ2 other bump:2.63799 Ang V19.CB and W24.NE1 other bump:1.94537 Ang V12.CG1 and W24.CE3 other bump:2.59441 Ang V19.CG1 and E23.OE1 self-bump: 1.35003 Ang R15.CA and R15.CB YAR033W 138 :FNHGQWHTP 1e7aA 433 :VGSKCCKHP Fragment has 35 clashes (null) has 35 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues other bump:2.23769 Ang Q6.O and T9.OG1 neighbor-bump: 2.84774 Ang W7.CD2 and H8.NE2 neighbor-bump: 2.12438 Ang W7.CE2 and H8.NE2 neighbor-bump: 2.82926 Ang W7.CE3 and H8.NE2 neighbor-bump: 2.09144 Ang W7.CZ3 and H8.NE2 neighbor-bump: 1.01947 Ang W7.CZ2 and H8.NE2 neighbor-bump: 0.958982 Ang W7.CH2 and H8.NE2 neighbor-bump: 2.55418 Ang W7.CZ3 and H8.CE1 neighbor-bump: 2.31068 Ang W7.CZ2 and H8.CE1 neighbor-bump: 1.67944 Ang W7.CH2 and H8.CE1 neighbor-bump: 2.95658 Ang W7.CZ3 and H8.ND1 neighbor-bump: 3.12878 Ang W7.CZ2 and H8.ND1 neighbor-bump: 2.61121 Ang W7.CH2 and H8.ND1 neighbor-bump: 2.09524 Ang W7.CD2 and H8.CD2 neighbor-bump: 1.71842 Ang W7.CE2 and H8.CD2 neighbor-bump: 2.75958 Ang W7.NE1 and H8.CD2 neighbor-bump: 2.3502 Ang W7.CE3 and H8.CD2 neighbor-bump: 2.27982 Ang W7.CZ3 and H8.CD2 neighbor-bump: 1.6694 Ang W7.CZ2 and H8.CD2 neighbor-bump: 1.94731 Ang W7.CH2 and H8.CD2 neighbor-bump: 3.03261 Ang W7.CE3 and H8.CG neighbor-bump: 2.82856 Ang W7.CZ3 and H8.CG neighbor-bump: 2.87149 Ang W7.CZ2 and H8.CG neighbor-bump: 2.73535 Ang W7.CH2 and H8.CG other bump:2.69357 Ang N3.C and W7.NE1 other bump:2.86219 Ang H4.N and W7.NE1 other bump:2.33256 Ang N3.O and W7.NE1 other bump:2.69493 Ang H4.CA and W7.NE1 other bump:2.95314 Ang N3.CA and W7.CD1 other bump:2.00955 Ang N3.C and W7.CD1 other bump:2.81361 Ang H4.N and W7.CD1 other bump:1.37192 Ang N3.O and W7.CD1 other bump:3.21227 Ang N3.C and W7.CG other bump:2.29531 Ang N3.O and W7.CG other bump:2.8344 Ang F2.CD1 and Q6.NE2 YAR033W 151 :SDEDCYRYFLRLVE 1e7aA 444 :KRMPCAEDYLSVVL Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 16 residues other bump:2.21579 Ang Y9.CD2 and R12.NH1 other bump:2.26471 Ang Y9.CE2 and R12.NH1 other bump:2.4794 Ang E4.CD and R8.NH2 other bump:1.92503 Ang E4.OE2 and R8.NH2 other bump:2.3343 Ang E4.OE2 and R8.NH1 other bump:1.6668 Ang E4.OE2 and R8.CZ other bump:2.02055 Ang E4.OE2 and R8.NE YAR033W 165 :GVTP 1e7aA 467 :TPVS Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues neighbor-bump: 2.13666 Ang T4.CG2 and P5.CD neighbor-bump: 2.09487 Ang T4.C and P5.CD neighbor-bump: 2.76821 Ang T4.CG2 and P5.CG neighbor-bump: 2.83855 Ang T4.C and P5.CG YAR033W 169 :KKQTATSIGNSPVTAKP 1e7aA 493 :VDETYVPKEFNAETFTF Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.36873 Ang K3.CE and T5.OG1 YAR033W 186 :EDAIE 1e7aA 511 :ADICT Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YAR033W 196 :SRLNYQNFLLKAAEIER 1e7aA 516 :LSEKERQIKKQTALVEL Fragment has 9 clashes (null) has 9 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.47681 Ang N5.ND2 and F9.CZ other bump:1.69259 Ang N5.OD1 and F9.CZ other bump:2.34016 Ang N5.CG and F9.CZ other bump:2.66655 Ang N5.ND2 and F9.CE2 other bump:2.81277 Ang N5.OD1 and F9.CE2 other bump:3.04435 Ang N5.CG and F9.CE2 other bump:1.60439 Ang N5.OD1 and F9.CE1 other bump:2.71294 Ang N5.CG and F9.CE1 other bump:2.67381 Ang N5.OD1 and F9.CD1 YAR033W 220 :RRRHPNID 1e7aA 533 :VKHKPKAT Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues self-bump: 1.34364 Ang N7.CA and N7.CB Number of specific fragments= 13 total=21 Number of alignments=2 # Reading fragments from alignment file # YAR033W read from 2nllA/YAR033W-2nllA-local-str-0.3-adpstyle5.a2m # 2nllA read from 2nllA/YAR033W-2nllA-local-str-0.3-adpstyle5.a2m # adding 2nllA to template set 2nllA:# found chain 2nllA in template set YAR033W 149 :FYSDEDCYRYFLRLVEGVTP 2nllA 149 :VYSCEGCKGFFKRTVRKDLT Fragment has 9 clashes (null) has 9 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 22 residues neighbor-bump: 1.9916 Ang T20.C and P21.CD other bump:2.72703 Ang V16.CA and V19.CG2 other bump:1.94706 Ang V16.O and V19.CG2 other bump:2.44868 Ang V16.C and V19.CG2 self-bump: 1.2784 Ang E17.CA and E17.CB other bump:3.06433 Ang D5.OD2 and C8.SG neighbor-bump: 2.73261 Ang G1.C and F2.CD1 neighbor-bump: 2.47524 Ang G1.O and F2.CD1 neighbor-bump: 2.47171 Ang G1.O and F2.CG YAR033W 169 :KKQTATSIGNSPV 2nllA 171 :CRDNKDCLIDKRQ Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:3.00657 Ang N11.OD1 and V14.CG2 other bump:2.99589 Ang Q4.CD and S8.CB other bump:2.09119 Ang Q4.NE2 and S8.CB other bump:2.97641 Ang Q4.NE2 and S8.CA other bump:2.41823 Ang K2.NZ and A6.CB other bump:2.99716 Ang K2.CD and A6.CB other bump:3.06613 Ang K2.CD and A6.CA other bump:3.10288 Ang K2.CD and A6.N neighbor-bump: 2.18742 Ang Q4.O and T5.OG1 neighbor-bump: 2.73501 Ang Q4.C and T5.OG1 neighbor-bump: 2.09611 Ang Q4.CB and T5.N Number of specific fragments= 2 total=23 Number of alignments=3 # Reading fragments from alignment file # YAR033W read from 1fkmA/YAR033W-1fkmA-local-str-0.3-adpstyle5.a2m # 1fkmA read from 1fkmA/YAR033W-1fkmA-local-str-0.3-adpstyle5.a2m # adding 1fkmA to template set 1fkmA: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 Skipped atom 1883, because occupancy 0.5 <= existing 0.500001 Skipped atom 1885, because occupancy 0.5 <= existing 0.500001 Skipped atom 1887, because occupancy 0.5 <= existing 0.500001 Skipped atom 1889, because occupancy 0.5 <= existing 0.500001 Skipped atom 1891, because occupancy 0.5 <= existing 0.500001 Skipped atom 1893, because occupancy 0.5 <= existing 0.500001 Skipped atom 1895, because occupancy 0.5 <= existing 0.500001 Skipped atom 1897, because occupancy 0.5 <= existing 0.500001 Skipped atom 1899, because occupancy 0.5 <= existing 0.500001 Skipped atom 1901, because occupancy 0.5 <= existing 0.500001 Skipped atom 1974, because occupancy 0.5 <= existing 0.500001 Skipped atom 1976, because occupancy 0.5 <= existing 0.500001 Skipped atom 1978, because occupancy 0.5 <= existing 0.500001 Skipped atom 1980, because occupancy 0.5 <= existing 0.500001 Skipped atom 1982, because occupancy 0.5 <= existing 0.500001 Skipped atom 1984, because occupancy 0.5 <= existing 0.500001 Skipped atom 1986, because occupancy 0.5 <= existing 0.500001 Skipped atom 1988, because occupancy 0.5 <= existing 0.500001 Skipped atom 1990, because occupancy 0.5 <= existing 0.500001 Skipped atom 1992, because occupancy 0.5 <= existing 0.500001 Skipped atom 1994, because occupancy 0.5 <= existing 0.500001 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 Skipped atom 2603, because occupancy 0.5 <= existing 0.500001 Skipped atom 2605, because occupancy 0.5 <= existing 0.500001 Skipped atom 2607, because occupancy 0.5 <= existing 0.500001 Skipped atom 2609, because occupancy 0.5 <= existing 0.500001 Skipped atom 2611, because occupancy 0.5 <= existing 0.500001 Skipped atom 2613, because occupancy 0.5 <= existing 0.500001 Skipped atom 2615, because occupancy 0.5 <= existing 0.500001 Skipped atom 2617, because occupancy 0.5 <= existing 0.500001 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 Skipped atom 2652, because occupancy 0.5 <= existing 0.500001 Skipped atom 2654, because occupancy 0.5 <= existing 0.500001 Skipped atom 2656, because occupancy 0.5 <= existing 0.500001 Skipped atom 2658, because occupancy 0.5 <= existing 0.500001 Skipped atom 2660, because occupancy 0.5 <= existing 0.500001 Skipped atom 2662, because occupancy 0.5 <= existing 0.500001 Skipped atom 2720, because occupancy 0.5 <= existing 0.500001 Skipped atom 2722, because occupancy 0.5 <= existing 0.500001 Skipped atom 2724, because occupancy 0.5 <= existing 0.500001 Skipped atom 2726, because occupancy 0.5 <= existing 0.500001 Skipped atom 2728, because occupancy 0.5 <= existing 0.500001 Skipped atom 2730, because occupancy 0.5 <= existing 0.500001 # found chain 1fkmA in template set YAR033W 91 :IILSD 1fkmA 321 :HTFSD Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues YAR033W 99 :KLVSRRNFRTELLVDVITRKPAVEGKEWRIITYNMNQYLFNHGQWHTPYYFYSDED 1fkmA 326 :QHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGIN Fragment has 94 clashes (null) has 94 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 58 residues other bump:3.14642 Ang R20.CD and D57.C other bump:2.90932 Ang R20.NE and D57.C other bump:2.39592 Ang R20.CD and D57.O other bump:2.32643 Ang R20.NE and D57.CB other bump:2.28921 Ang R20.CZ and D57.CB other bump:1.90753 Ang R20.NH2 and D57.CB other bump:2.9428 Ang R20.NE and D57.CA other bump:2.92413 Ang R20.CZ and D57.CA other bump:2.94956 Ang R20.NH2 and D57.CA other bump:1.21437 Ang Y53.O and E56.OE1 other bump:2.73965 Ang Y53.CA and E56.OE1 other bump:2.09814 Ang Y53.C and E56.OE1 other bump:2.46155 Ang Y53.O and E56.CD neighbor-bump: 2.47876 Ang S54.O and D55.CG other bump:2.42498 Ang Y50.O and Y53.CZ other bump:2.86639 Ang Y50.CA and Y53.CE2 other bump:1.58038 Ang Y50.O and Y53.CE2 other bump:2.40711 Ang Y50.C and Y53.CE2 other bump:3.10617 Ang Y50.CB and Y53.CE2 other bump:2.52716 Ang Y50.O and Y53.CD2 other bump:3.14229 Ang Y50.C and Y53.CD2 neighbor-bump: 2.39241 Ang Y51.CD1 and F52.C neighbor-bump: 2.92145 Ang Y51.CE1 and F52.C neighbor-bump: 1.61725 Ang Y51.CD1 and F52.O neighbor-bump: 2.06876 Ang Y51.CE1 and F52.O other bump:2.48059 Ang L13.CD2 and F52.CD1 other bump:2.57286 Ang L13.CD2 and F52.CG other bump:2.44676 Ang F9.CE1 and F52.CB neighbor-bump: 2.70969 Ang Y51.CD1 and F52.CA other bump:2.91329 Ang F9.CE1 and F52.CA neighbor-bump: 2.50787 Ang Y51.CG and F52.N neighbor-bump: 2.24481 Ang Y51.CD1 and F52.N other bump:2.53184 Ang F9.CE1 and F52.N other bump:0.684047 Ang E12.CD and Y51.OH other bump:0.650154 Ang E12.OE1 and Y51.OH other bump:1.55482 Ang E12.OE2 and Y51.OH other bump:2.79286 Ang E12.CB and Y51.OH other bump:2.08213 Ang E12.CG and Y51.OH other bump:1.85974 Ang E12.CD and Y51.CZ other bump:1.51658 Ang E12.OE1 and Y51.CZ other bump:1.90727 Ang E12.OE2 and Y51.CZ other bump:3.02892 Ang E12.CD and Y51.CE2 other bump:2.17085 Ang E12.OE1 and Y51.CE2 other bump:2.53913 Ang E12.CD and Y51.CE1 other bump:2.73769 Ang E12.OE1 and Y51.CE1 other bump:1.98918 Ang E12.OE2 and Y51.CE1 neighbor-bump: 1.83028 Ang Y50.O and Y51.CB neighbor-bump: 2.35698 Ang Y50.C and Y51.CB self-bump: 1.38713 Ang Y50.CA and Y50.CB self-bump: 1.37819 Ang P49.N and P49.CD neighbor-bump: 2.55409 Ang T48.N and P49.CD neighbor-bump: 2.78218 Ang T48.OG1 and P49.CD other bump:3.08328 Ang N42.CG and W46.CH2 other bump:2.32602 Ang N42.OD1 and W46.CH2 other bump:2.30513 Ang N42.OD1 and W46.CZ3 other bump:3.0543 Ang N42.CG and W46.CZ2 other bump:2.78434 Ang N42.OD1 and W46.CZ2 other bump:2.60221 Ang N42.ND2 and W46.CZ2 other bump:2.75933 Ang N42.OD1 and W46.CE3 other bump:2.89513 Ang N42.ND2 and W46.CE2 other bump:2.12768 Ang K2.NZ and Q45.OE1 other bump:2.98088 Ang F9.CZ and G44.CA other bump:2.7558 Ang R20.NH1 and L40.CD1 other bump:2.77089 Ang R20.NH1 and M36.CE other bump:2.95354 Ang R30.CG and Y34.CE2 other bump:2.28383 Ang V17.CG2 and T33.OG1 other bump:2.76941 Ang K27.N and I32.CD1 other bump:2.21849 Ang K27.CA and I32.CD1 other bump:2.06401 Ang G26.O and I32.CD1 other bump:2.66221 Ang G26.C and I32.CD1 other bump:2.32697 Ang V24.O and E28.OE1 other bump:2.67391 Ang E25.CA and E28.OE1 other bump:2.32021 Ang E25.O and E28.OE1 other bump:2.56981 Ang E25.C and E28.OE1 other bump:1.33875 Ang K21.CD and K27.NZ other bump:2.42302 Ang K21.CE and K27.NZ other bump:1.83578 Ang K21.CB and K27.NZ other bump:0.750413 Ang K21.CG and K27.NZ other bump:2.16285 Ang K21.CB and K27.CE other bump:1.88301 Ang K21.CG and K27.CE other bump:3.08273 Ang K21.CA and K27.CD other bump:1.75887 Ang K21.CB and K27.CD other bump:2.47476 Ang K21.CG and K27.CD other bump:3.08922 Ang K2.CE and R6.NE other bump:2.02651 Ang K2.CE and R6.CD other bump:2.47607 Ang K2.CE and R6.CG other bump:2.50265 Ang K2.NZ and R6.CG other bump:2.31646 Ang V4.CG2 and R6.CG other bump:2.60079 Ang K2.CD and V4.CG2 other bump:2.45295 Ang K2.CE and V4.CG2 other bump:2.56688 Ang K2.NZ and V4.CG2 other bump:2.9393 Ang K2.CG and V4.CG1 other bump:2.33148 Ang K2.CD and V4.CG1 other bump:2.97116 Ang K2.CD and V4.CB YAR033W 155 :CYRYFLRLVEGVTPKKQTATSIGNSPVTAKPEDA 1fkmA 384 :VTPFFETFLTEYLPPSQIDDVEIKDPSTYMVDEQ Fragment has 6 clashes (null) has 6 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 36 residues other bump:2.57657 Ang V13.CG2 and K31.NZ other bump:2.96922 Ang V13.CG1 and K31.CE other bump:2.92014 Ang V13.CB and K31.CD other bump:2.05929 Ang V13.CG1 and K31.CD other bump:2.30708 Ang V13.CG1 and K31.CG other bump:2.55236 Ang F6.O and V10.CG2 YAR033W 193 :SPSSRLNYQNFLLKA 1fkmA 418 :ITDLEADTFWCLTKL Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues Number of specific fragments= 4 total=27 Number of alignments=4 # Reading fragments from alignment file # YAR033W read from 1zdc/1fc2C-YAR033W-fssp-local-adpstyle5.a2m # 1zdc read from 1zdc/1fc2C-YAR033W-fssp-local-adpstyle5.a2m # adding 1zdc to template set 1zdc:# found chain 1zdc in template set Number of specific fragments= 0 total=27 # command:superimposing iter= 0 total_weight= 1679 weighted rmsd= 0 superimposing iter= 1 total_weight= 16790 weighted rmsd= 0 superimposing iter= 2 total_weight= 16790 weighted rmsd= 0 superimposing iter= 3 total_weight= 16790 weighted rmsd= 0 superimposing iter= 4 total_weight= 16790 weighted rmsd= 0 superimposing iter= 5 total_weight= 16790 weighted rmsd= 0 superimposing iter= 0 total_weight= 1494 weighted rmsd= 9.23836 superimposing iter= 1 total_weight= 6256.49 weighted rmsd= 3.94221 superimposing iter= 2 total_weight= 4335.29 weighted rmsd= 2.08469 superimposing iter= 3 total_weight= 3645.7 weighted rmsd= 1.23461 superimposing iter= 4 total_weight= 2956.61 weighted rmsd= 0.838318 superimposing iter= 5 total_weight= 2322.09 weighted rmsd= 0.655173 superimposing iter= 0 total_weight= 191 weighted rmsd= 8.82826 superimposing iter= 1 total_weight= 468.509 weighted rmsd= 5.44808 superimposing iter= 2 total_weight= 261.21 weighted rmsd= 4.58723 superimposing iter= 3 total_weight= 214.221 weighted rmsd= 4.28461 superimposing iter= 4 total_weight= 197.503 weighted rmsd= 4.17336 superimposing iter= 5 total_weight= 190.505 weighted rmsd= 4.13874 superimposing iter= 0 total_weight= 798 weighted rmsd= 13.5177 superimposing iter= 1 total_weight= 1303.98 weighted rmsd= 10.4204 superimposing iter= 2 total_weight= 923.483 weighted rmsd= 9.43242 superimposing iter= 3 total_weight= 992.783 weighted rmsd= 8.12938 superimposing iter= 4 total_weight= 1070.88 weighted rmsd= 6.7796 superimposing iter= 5 total_weight= 1107.33 weighted rmsd= 5.61254 # command: