# command:# Seed set to 1041696009 # 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= 10554.2 msec) # Prefix for input files set to Created new target YGR230W from YGR230W.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 YGR230W.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= 19450 msec, elapsed time= 19505.1 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= 24200 msec, elapsed time= 24250.2 msec) # command:# Prefix for input files set to # command:# reading script from file YGR230W.t2k.undertaker-align.under # Reading fragments from alignment file # YGR230W read from 1ihuA/YGR230W-1ihuA-local-str-0.3-adpstyle5.a2m # 1ihuA read from 1ihuA/YGR230W-1ihuA-local-str-0.3-adpstyle5.a2m # adding 1ihuA to template set 1ihuA:# found chain 1ihuA in template set YGR230W 2 :SYGGSASQDIVTKLIRKIQNTSVS 1ihuA 334 :GKGGVGKTTMAAAIAVRLADMGFD Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 26 residues other bump:2.83214 Ang I19.CB and V24.CG1 other bump:1.74201 Ang I19.CG2 and V24.CG1 other bump:2.51765 Ang I19.C and V24.CG1 other bump:3.03096 Ang I19.CA and V24.CG1 other bump:2.76633 Ang I19.CG2 and V24.CB neighbor-bump: 1.67197 Ang S6.O and A7.CB neighbor-bump: 2.23022 Ang S6.C and A7.CB YGR230W 26 :CTRR 1ihuA 362 :TSDP Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR230W 42 :M 1ihuA 379 :N Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues YGR230W 44 :LKVAHNTKTFAKHCLHRQVFKNT 1ihuA 380 :LQVSRIDPHEETERYRQHVLETK Fragment has 11 clashes (null) has 11 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 25 residues other bump:1.52277 Ang Q19.NE2 and N23.OD1 other bump:2.51844 Ang Q19.NE2 and N23.CG other bump:1.79031 Ang K13.CG and H17.NE2 other bump:2.38335 Ang K13.NZ and H17.NE2 other bump:2.6825 Ang K13.CD and H17.NE2 other bump:2.7778 Ang K13.CE and H17.NE2 other bump:2.47436 Ang K13.NZ and H17.CE1 other bump:3.42119 Ang K13.NZ and H17.ND1 other bump:2.30827 Ang K13.O and H17.CD2 other bump:2.64651 Ang K13.CG and H17.CD2 other bump:2.64771 Ang K13.C and H17.CD2 YGR230W 70 :RKAVEDQRKNLNT 1ihuA 403 :GKELDEAGKRLLE Fragment has 21 clashes (null) has 21 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.74683 Ang R2.CZ and T14.OG1 other bump:2.27578 Ang R2.NH2 and T14.OG1 other bump:2.846 Ang R2.NH2 and T14.CB other bump:2.31227 Ang R2.NH2 and T14.CA other bump:2.74191 Ang R2.CZ and T14.N other bump:2.07391 Ang R2.NH2 and T14.N other bump:3.16146 Ang R2.CZ and N13.C other bump:2.60428 Ang R2.NH2 and N13.C other bump:1.76597 Ang R2.NE and N13.OD1 other bump:2.55875 Ang R2.NE and N13.CG other bump:2.7712 Ang R2.CZ and N13.CB other bump:2.22058 Ang R9.NH1 and L12.CD2 other bump:2.21431 Ang R2.NH1 and K10.C other bump:1.38655 Ang R2.NH1 and K10.O other bump:2.51729 Ang R2.CZ and K10.O other bump:2.91852 Ang V5.CG1 and K10.CG other bump:2.63344 Ang R2.NH1 and K10.CA other bump:2.99555 Ang V5.CG2 and R9.C other bump:1.99077 Ang V5.CG2 and R9.CB other bump:2.99831 Ang V5.CG2 and R9.CA other bump:2.16023 Ang R2.O and V5.CG1 YGR230W 93 :DNLLSPCSRKLNDHK 1ihuA 416 :EDLRSPCTEEIAVFQ Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:2.67075 Ang D2.O and L5.CB Number of specific fragments= 6 total=6 Number of alignments=1 # Reading fragments from alignment file # YGR230W read from 1dszA/YGR230W-1dszA-local-str-0.3-adpstyle5.a2m # 1dszA read from 1dszA/YGR230W-1dszA-local-str-0.3-adpstyle5.a2m # adding 1dszA to template set 1dszA:# found chain 1dszA in template set YGR230W 3 :YGGSASQDIVTKLIRKIQNTSVSCTRRDENLD 1dszA 1147 :YGVSACEGCKGFFRRSIQKNMVYTCHRDKNCI Fragment has 21 clashes (null) has 21 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 34 residues other bump:2.56095 Ang R28.NE and L32.CD1 other bump:2.37943 Ang R28.CG and L32.CD1 other bump:2.56964 Ang R28.CB and L32.CD1 other bump:1.3147 Ang R28.CD and L32.CD1 other bump:2.67235 Ang R28.CD and L32.CG other bump:2.68498 Ang R28.NH1 and L32.CB other bump:3.01791 Ang R28.NE and N31.N other bump:2.51525 Ang R28.NE and E30.CA other bump:3.08343 Ang R28.NH2 and E30.CA other bump:2.67025 Ang R28.NE and E30.N other bump:2.59975 Ang R28.CG and E30.N neighbor-bump: 2.25105 Ang R28.CG and D29.N neighbor-bump: 2.39234 Ang R28.CB and D29.N other bump:2.77908 Ang T26.CG2 and R28.NH2 other bump:2.9705 Ang T26.CG2 and R28.NE other bump:1.96972 Ang T12.CG2 and R16.NH1 other bump:2.76797 Ang Y2.CZ and I15.CD1 other bump:1.57943 Ang Y2.OH and I15.CD1 other bump:2.99047 Ang Y2.CE2 and I15.CG1 other bump:2.47986 Ang Y2.CZ and I15.CG1 other bump:1.75369 Ang Y2.OH and I15.CG1 YGR230W 46 :VAHNTKTFAKHCLHRQVFKNTYRKRKAVE 1dszA 1179 :INKVTRNRCQYCRLQKCFEVGMSKESVRN Fragment has 13 clashes (null) has 13 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 31 residues other bump:2.96247 Ang N21.ND2 and Y23.CE1 other bump:2.71827 Ang V18.CG1 and Y23.CD2 other bump:2.94107 Ang N21.OD1 and Y23.CD1 other bump:2.81485 Ang V18.CG1 and Y23.CG other bump:2.89134 Ang V18.CG1 and Y23.CB neighbor-bump: 1.9889 Ang N21.O and T22.OG1 neighbor-bump: 2.33368 Ang N21.C and T22.OG1 neighbor-bump: 1.72164 Ang N21.O and T22.CB neighbor-bump: 2.2031 Ang N21.C and T22.CB other bump:2.19438 Ang V18.O and N21.OD1 other bump:2.94401 Ang H15.NE2 and F19.CZ other bump:2.96365 Ang H15.CD2 and F19.CE2 other bump:2.53512 Ang H15.NE2 and F19.CE2 Number of specific fragments= 2 total=8 Number of alignments=2 # Reading fragments from alignment file # YGR230W read from 1nzyA/YGR230W-1nzyA-local-str-0.3-adpstyle5.a2m # 1nzyA read from 1nzyA/YGR230W-1nzyA-local-str-0.3-adpstyle5.a2m # adding 1nzyA to template set 1nzyA:Skipped atom 910, because occupancy 0.5 <= existing 0.500001 # found chain 1nzyA in template set YGR230W 8 :SQDIVTKLIR 1nzyA 191 :FREVAWKVAR Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues other bump:2.33832 Ang T7.CG2 and R11.NH2 other bump:2.93173 Ang T7.CG2 and R11.CZ YGR230W 52 :TFAKHCLHRQVFKNTYRKRKAVEDQRKNLNTQLRQKFASPSDNLLSPC 1nzyA 201 :ELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPC Fragment has 56 clashes (null) has 56 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 50 residues other bump:2.60295 Ang R10.CZ and L45.CD2 other bump:1.72769 Ang R10.NH1 and L45.CD2 other bump:2.80816 Ang R10.NH2 and L45.CD2 other bump:2.14774 Ang C7.SG and L45.CD1 other bump:2.43324 Ang H9.CE1 and L45.CD1 other bump:2.21953 Ang H9.NE2 and D43.OD2 self-bump: 1.32455 Ang P41.N and P41.CD neighbor-bump: 2.6633 Ang S40.N and P41.CD neighbor-bump: 2.18704 Ang S40.OG and P41.CD other bump:1.65446 Ang K37.O and P41.CD other bump:2.86958 Ang K37.C and P41.CD self-bump: 2.19412 Ang P41.N and P41.CG other bump:2.1147 Ang K37.O and P41.CG other bump:3.18754 Ang K37.C and P41.CG other bump:2.2224 Ang F13.CG and Q36.NE2 other bump:2.87706 Ang F13.CD1 and Q36.NE2 other bump:1.67158 Ang F13.CD2 and Q36.NE2 other bump:2.04474 Ang F13.CE2 and Q36.NE2 other bump:2.75396 Ang F13.CZ and Q36.NE2 other bump:2.75479 Ang F13.CD2 and Q36.CD other bump:3.14646 Ang F13.CE2 and Q36.CD other bump:2.52222 Ang K21.NZ and Q33.NE2 other bump:2.99818 Ang Y17.CZ and Q33.CD other bump:2.59148 Ang K21.NZ and Q33.CD other bump:2.87028 Ang Y17.OH and N29.CB other bump:1.66654 Ang E24.OE1 and K28.NZ other bump:2.3547 Ang E24.CG and K28.NZ other bump:1.42082 Ang E24.CD and K28.NZ other bump:1.86361 Ang E24.OE2 and K28.NZ other bump:2.674 Ang E24.OE1 and K28.CE other bump:2.48916 Ang E24.OE1 and K28.CG other bump:2.26992 Ang Y17.CG and K21.NZ other bump:2.53608 Ang Y17.CD1 and K21.NZ other bump:1.5782 Ang Y17.CD2 and K21.NZ other bump:2.33426 Ang Y17.CE1 and K21.NZ other bump:1.18761 Ang Y17.CE2 and K21.NZ other bump:1.71047 Ang Y17.CZ and K21.NZ other bump:1.53235 Ang Y17.CG and K21.CE other bump:1.38694 Ang Y17.CD1 and K21.CE other bump:1.48495 Ang Y17.CD2 and K21.CE other bump:1.29343 Ang Y17.CE1 and K21.CE other bump:1.36827 Ang Y17.CE2 and K21.CE other bump:1.27652 Ang Y17.CZ and K21.CE other bump:2.34122 Ang Y17.CG and K21.CD other bump:2.56598 Ang Y17.CD1 and K21.CD other bump:1.78009 Ang Y17.CD2 and K21.CD other bump:2.40024 Ang Y17.CE1 and K21.CD other bump:1.49661 Ang Y17.CE2 and K21.CD other bump:1.8768 Ang Y17.CZ and K21.CD other bump:2.87545 Ang Y17.OH and K21.CD other bump:3.07834 Ang Y17.CG and K21.CG other bump:2.37423 Ang Y17.O and K21.CG other bump:2.66736 Ang Y17.O and K21.CB other bump:3.0782 Ang T16.CG2 and R20.CZ other bump:2.01598 Ang C7.SG and H9.CE1 other bump:2.17781 Ang C7.SG and H9.ND1 YGR230W 100 :SRKLNDHKS 1nzyA 250 :TRFLDGHRA Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 11 residues other bump:2.82613 Ang N6.ND2 and H8.CE1 Number of specific fragments= 3 total=11 Number of alignments=3 # Reading fragments from alignment file # YGR230W read from 1jhwA/YGR230W-1jhwA-local-adpstyle1.a2m # 1jhwA read from 1jhwA/YGR230W-1jhwA-local-adpstyle1.a2m # adding 1jhwA to template set 1jhwA:# found chain 1jhwA in template set YGR230W 11 :IVTKLIRKIQNTSVSCTRRDENLDSFNQHLKMSLKVAH 1jhwA 134 :VVQRLYQVKGAKNIRATERALNWDSFNTGDCFILDLGQ Fragment has 49 clashes (null) has 49 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 40 residues self-bump: 1.37081 Ang A38.CA and A38.CB other bump:2.33546 Ang F27.CD2 and M33.CE other bump:2.51249 Ang F27.CG and M33.SD other bump:1.96055 Ang F27.CD2 and M33.SD other bump:2.63856 Ang F27.CE2 and M33.SD other bump:2.60978 Ang R8.NH1 and L31.CD1 other bump:2.61001 Ang T4.CG2 and E22.OE2 other bump:2.55049 Ang T4.C and E22.OE1 other bump:2.75318 Ang T4.CB and E22.OE1 other bump:2.29546 Ang T4.CG2 and E22.OE1 other bump:2.77211 Ang T4.CG2 and E22.CD other bump:2.55309 Ang K5.CD and R19.NH1 other bump:2.70862 Ang K5.CE and R19.CD other bump:1.9539 Ang K5.CE and R19.CG other bump:2.98542 Ang K5.CG and R19.CG other bump:2.94832 Ang K5.CD and R19.CG other bump:2.41815 Ang K5.CE and R19.CB other bump:2.84806 Ang I7.CG2 and T18.N other bump:2.70434 Ang I7.CG2 and C17.C other bump:1.36498 Ang I7.CG2 and C17.SG other bump:2.04851 Ang I7.CB and C17.SG other bump:2.92336 Ang I7.CG1 and C17.SG other bump:2.96541 Ang I7.CD1 and C17.SG other bump:2.38153 Ang I7.CG2 and C17.CB other bump:2.77043 Ang I7.CG2 and C17.CA other bump:2.97076 Ang Q11.CD and V15.CA other bump:2.5878 Ang Q11.OE1 and V15.CA other bump:2.15272 Ang Q11.CD and V15.N other bump:1.30175 Ang Q11.OE1 and V15.N other bump:1.00986 Ang Q11.CD and S14.C other bump:0.462924 Ang Q11.OE1 and S14.C other bump:2.18356 Ang Q11.NE2 and S14.C other bump:2.85524 Ang Q11.CB and S14.C other bump:2.02002 Ang Q11.CG and S14.C other bump:0.825533 Ang Q11.CD and S14.O other bump:1.64333 Ang Q11.OE1 and S14.O other bump:1.70696 Ang Q11.CB and S14.O other bump:1.06891 Ang Q11.CG and S14.O other bump:2.3576 Ang Q11.CD and S14.CB other bump:2.16078 Ang Q11.OE1 and S14.CB other bump:2.568 Ang Q11.NE2 and S14.CB other bump:1.91165 Ang Q11.CD and S14.CA other bump:1.2636 Ang Q11.OE1 and S14.CA other bump:2.8463 Ang Q11.NE2 and S14.CA other bump:2.68848 Ang Q11.CG and S14.CA other bump:2.76964 Ang Q11.CD and S14.N other bump:2.43262 Ang Q11.OE1 and S14.N other bump:2.75538 Ang Q11.CG and S14.N neighbor-bump: 2.93735 Ang K9.C and I10.CG1 YGR230W 51 :KTFAKHCLHRQVFKNTYRKRKAV 1jhwA 172 :NIFAWCGGKSNILERNKARDLAL Fragment has 27 clashes (null) has 27 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 25 residues other bump:2.2335 Ang K20.O and V24.CG2 other bump:2.88523 Ang K20.CD and V24.CG2 other bump:1.88044 Ang K20.CE and V24.CG2 other bump:2.86903 Ang H7.N and R19.NH2 other bump:2.27123 Ang H7.CB and R19.NH2 other bump:1.1229 Ang K6.O and R19.NH1 other bump:2.57422 Ang A5.C and R19.NH1 other bump:2.47762 Ang K6.N and R19.NH1 other bump:2.32824 Ang K6.CA and R19.NH1 other bump:1.30135 Ang K6.C and R19.NH1 other bump:2.1286 Ang H7.N and R19.NH1 other bump:2.3955 Ang K6.O and R19.CZ other bump:3.12946 Ang H7.CA and R19.CZ other bump:2.20991 Ang A5.O and R19.CZ other bump:2.59539 Ang A5.C and R19.CZ other bump:2.4765 Ang K6.C and R19.CZ other bump:2.87092 Ang H7.N and R19.CZ other bump:2.81829 Ang A5.CB and R19.NE other bump:2.86426 Ang A5.C and R19.NE other bump:3.09073 Ang A5.CA and R19.CD other bump:2.99814 Ang A5.CB and R19.CD other bump:3.03422 Ang A5.CB and R19.CG other bump:2.05409 Ang Q12.CG and K15.NZ other bump:3.18826 Ang C8.SG and R11.CZ other bump:2.82398 Ang C8.SG and R11.NE other bump:2.87056 Ang C8.SG and R11.CD other bump:2.05358 Ang C8.SG and R11.CG YGR230W 74 :EDQRKNLNTQLR 1jhwA 197 :RDSERQGKAQVE Fragment has 28 clashes (null) has 28 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues other bump:2.17071 Ang Q11.OE1 and R13.NH1 other bump:2.49707 Ang Q11.OE1 and R13.CZ other bump:3.18423 Ang E2.CD and L12.CD2 other bump:2.44986 Ang E2.OE1 and L12.CD2 other bump:2.46315 Ang E2.CD and L12.CD1 other bump:1.24276 Ang E2.OE1 and L12.CD1 other bump:2.18514 Ang E2.CD and L12.CG other bump:1.27959 Ang E2.OE1 and L12.CG other bump:2.5786 Ang E2.OE1 and L12.CB other bump:2.5945 Ang E2.OE2 and Q11.C other bump:2.10666 Ang E2.OE2 and Q11.O other bump:2.93351 Ang K6.CD and T10.OG1 other bump:2.01468 Ang K6.CE and T10.OG1 neighbor-bump: 1.97328 Ang N9.O and T10.OG1 neighbor-bump: 2.60649 Ang N9.C and T10.OG1 other bump:2.9558 Ang K6.CD and T10.CG2 other bump:2.16983 Ang K6.CE and T10.CG2 other bump:2.603 Ang K6.NZ and T10.CG2 other bump:2.81262 Ang K6.CD and T10.CB other bump:1.44694 Ang K6.CE and T10.CB other bump:2.21775 Ang K6.NZ and T10.CB other bump:2.81695 Ang K6.CE and T10.CA self-bump: 1.39929 Ang L8.CA and L8.CB other bump:2.21473 Ang E2.CB and K6.NZ other bump:1.73062 Ang E2.CG and K6.NZ other bump:2.42563 Ang E2.CD and K6.NZ other bump:2.97729 Ang E2.CG and K6.CE other bump:3.029 Ang E2.CA and K6.CD Number of specific fragments= 3 total=14 Number of alignments=4 # Reading fragments from alignment file # YGR230W read from 1krcC/1ubpC-YGR230W-fssp-global-adpstyle5.a2m # 1krcC read from 1krcC/1ubpC-YGR230W-fssp-global-adpstyle5.a2m # adding 1krcC to template set 1krcC:# found chain 1krcC in template set YGR230W 4 :GGSASQDIVTKLIRKIQN 1krcC 131 :IDTHIHWICPQQAEEALV Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 20 residues neighbor-bump: 3.06477 Ang I9.C and V10.CG1 YGR230W 22 :TSVS 1krcC 153 :TMVG Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR230W 26 :CTRRDENLDSFNQHL 1krcC 170 :CTPGPWYISRMLQAA Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 17 residues other bump:3.10174 Ang T3.CB and L9.CD2 YGR230W 42 :MSLKVAHN 1krcC 214 :IGLKIHED Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 10 residues self-bump: 1.37595 Ang H8.CA and H8.CB YGR230W 53 :FAKHCLHRQVFK 1krcC 227 :AAIDCALTVADE Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues other bump:2.30538 Ang H8.O and F12.CD1 YGR230W 65 :NTYRKRKAVEDQRKNL 1krcC 254 :GFVEDTLAAIGGRTIH Fragment has 13 clashes (null) has 13 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues other bump:2.69211 Ang Y4.CD2 and R7.NH2 other bump:2.98423 Ang Y4.CE2 and R7.NH2 other bump:2.57925 Ang N2.CB and K6.NZ other bump:2.26592 Ang N2.CA and K6.NZ other bump:2.75843 Ang N2.C and K6.NZ other bump:1.68304 Ang N2.CB and K6.CE other bump:2.11003 Ang N2.CA and K6.CE other bump:2.56848 Ang N2.CB and K6.CD other bump:2.95517 Ang N2.CB and K6.CG other bump:2.69518 Ang N2.CB and K6.CB other bump:2.73286 Ang N2.CG and K6.CB other bump:2.56919 Ang N2.ND2 and K6.CB neighbor-bump: 2.19538 Ang N2.ND2 and T3.O YGR230W 81 :NT 1krcC 271 :FH Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues YGR230W 84 :LRQKFASPSDNLLSPCSRKLN 1krcC 283 :DIITACAHPNILPSSTNPTLP Fragment has 15 clashes (null) has 15 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 23 residues other bump:2.98413 Ang A7.CA and L14.CD1 other bump:2.16895 Ang A7.CB and L14.CD1 other bump:2.21202 Ang P9.CG and N12.OD1 other bump:2.7658 Ang F6.CE1 and N12.ND2 other bump:2.47883 Ang F6.CE2 and N12.ND2 other bump:1.80957 Ang F6.CZ and N12.ND2 other bump:2.73314 Ang F6.CE2 and N12.CG other bump:2.10333 Ang F6.CE1 and N12.CB other bump:2.57476 Ang F6.CZ and N12.CB other bump:2.90502 Ang F6.CD1 and N12.CB other bump:1.8179 Ang F6.O and P9.CD neighbor-bump: 2.55964 Ang S8.N and P9.CD other bump:2.80575 Ang F6.C and P9.CD other bump:2.33301 Ang F6.O and P9.CG other bump:2.74138 Ang L2.CD2 and K5.CE YGR230W 109 :KLFS 1krcC 346 :DVLH Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR230W 113 :AKSQ 1krcC 359 :SDSQ Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR230W 118 :KTLEFVRGKQ 1krcC 375 :WQVAHRMKVQ Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues other bump:2.85826 Ang V7.CG1 and Q11.NE2 other bump:2.40291 Ang G1.O and E5.OE2 other bump:2.18357 Ang G1.C and E5.OE1 other bump:1.45168 Ang G1.O and E5.OE1 other bump:2.26236 Ang K2.CA and E5.OE1 other bump:2.97136 Ang G1.C and E5.CD other bump:2.11045 Ang G1.O and E5.CD YGR230W 128 :NIPR 1krcC 399 :RVKR Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 6 residues YGR230W 132 :KP 1krcC 418 :AH Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues other bump:2.81414 Ang G1.C and P3.CD neighbor-bump: 2.44875 Ang K2.N and P3.CD YGR230W 134 :NVDI 1krcC 544 :RVDG Fragment has 1 clashes (null) has 1 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues neighbor-bump: 2.66596 Ang D4.C and I5.CB Number of specific fragments= 14 total=28 Number of alignments=5 # command:superimposing iter= 0 total_weight= 641 weighted rmsd= 0 superimposing iter= 1 total_weight= 6410 weighted rmsd= 0 superimposing iter= 2 total_weight= 6410 weighted rmsd= 0 superimposing iter= 3 total_weight= 6410 weighted rmsd= 0 superimposing iter= 4 total_weight= 6410 weighted rmsd= 0 superimposing iter= 5 total_weight= 6410 weighted rmsd= 0 superimposing iter= 0 total_weight= 422 weighted rmsd= 17.8707 superimposing iter= 1 total_weight= 686.288 weighted rmsd= 13.4928 superimposing iter= 2 total_weight= 536.281 weighted rmsd= 11.6601 superimposing iter= 3 total_weight= 550.871 weighted rmsd= 9.95695 superimposing iter= 4 total_weight= 556.605 weighted rmsd= 8.53496 superimposing iter= 5 total_weight= 514.821 weighted rmsd= 7.6393 superimposing iter= 0 total_weight= 438 weighted rmsd= 13.1808 superimposing iter= 1 total_weight= 989.963 weighted rmsd= 8.57246 superimposing iter= 2 total_weight= 541.442 weighted rmsd= 7.64108 superimposing iter= 3 total_weight= 475.58 weighted rmsd= 7.26578 superimposing iter= 4 total_weight= 468.461 weighted rmsd= 6.95957 superimposing iter= 5 total_weight= 468.833 weighted rmsd= 6.68151 superimposing iter= 0 total_weight= 446 weighted rmsd= 17.7741 superimposing iter= 1 total_weight= 970.911 weighted rmsd= 11.7219 superimposing iter= 2 total_weight= 599.246 weighted rmsd= 9.9784 superimposing iter= 3 total_weight= 513.522 weighted rmsd= 9.21455 superimposing iter= 4 total_weight= 476.624 weighted rmsd= 8.83617 superimposing iter= 5 total_weight= 457.453 weighted rmsd= 8.64342 superimposing iter= 0 total_weight= 573 weighted rmsd= 13.1621 superimposing iter= 1 total_weight= 1245.97 weighted rmsd= 8.62855 superimposing iter= 2 total_weight= 799.634 weighted rmsd= 7.18425 superimposing iter= 3 total_weight= 680.356 weighted rmsd= 6.53176 superimposing iter= 4 total_weight= 617.576 weighted rmsd= 6.24958 superimposing iter= 5 total_weight= 584.991 weighted rmsd= 6.1486 # command: