XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:28:23 X-PLOR>remarks file XMREAD.INP -- test map read and write facility X-PLOR>remarks Author: Axel T. Brunger X-PLOR> X-PLOR>topology @TOPPAR:toph19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pro opened. RTFRDR>REMARKS TOPH19.PRO ( protein topology ) RTFRDR>REMARKS =============================== RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>param @TOPPAR:param19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param19.pro opened. PARRDR>remark - parameter file PARAM19 - PARRDR>remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR> PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> chain CHAIN> @TOPPAR:toph19.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pep opened. CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE ASN VAL CYS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = ARG LEU PRO GLY THR PRO GLU ALA ILE CYS ALA THR TYR THR GLY CYS SEQUence-element (terminate with END) = ILE ILE ILE PRO GLY ALA THR CYS PRO GLY ASP TYR ALA ASN SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 46 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 396(MAXA= 400) NBOND= 403(MAXB= 800) NTHETA= 581(MAXT= 800) NGRP= 165(MAXGRP= 200) NPHI= 235(MAXP= 400) NIMPHI= 182(MAXIMP= 200) NDON= 69(MAXPAD= 100) NACC= 64(MAXPAD= 100) NNB= 9(MAXNB= 100) X-PLOR> X-PLOR> X-PLOR>coor COOR>ATOM 1 HT1 THR 1 16.206 14.668 3.850 0.00 0.00 COOR>ATOM 2 HT2 THR 1 17.090 13.935 2.599 0.00 0.00 X-PLOR> X-PLOR>set timing=on end X-PLOR> X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> method=fft XREFINE> a=40.96 b=18.65 c=22.52 alpha=90.0 beta=90.77 gamma=90.0 XREFINE> fft XFFT> grid=0.33333333 prime=5 avoid=2 ! sampling grid of Patterson XFFT> end XREFINE> !! scattering tables, from SCATT input XREFINE> !! XREFINE> SCATter ( chemical C* ) SELRPN: 202 atoms have been selected out of 396 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 55 atoms have been selected out of 396 SCATTER_A1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> XREFINE> SCATter ( chemical O* ) SELRPN: 64 atoms have been selected out of 396 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 6 atoms have been selected out of 396 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(-x,y+1/2,-z) XREFINE> XREFINE> asymmetric=(0<=x<1 and 0<=y<1/2 and 0<=z<1) XREFINE> XREFINE> resolution 10. 5.0 XREFINE> XREFINE> nreflection=40000 XREFIN: allocating space for 40000 reflections. XREFINE> generate XGENER: generating reflections to produce a full set for the specified resolution range. The new Fobs are set to 1 and weight is set to 1, all other reciprocal space objects are set to 0. XGENE2: 150 new reflections have been generated. XREFINE> XREFINE> update XREDUC: mapping reflections into standard asymmetric unit. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 150 %XREFIN-error: zero occupancies --> all set to one CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 24, 12, 16] and sublattice [ 24( 25), 12( 13), 16] XFFT: CPU-time: electron-density-calc= 0.0100 XFFT: CPU-time: FFT of electron density= 0.0000 XFFT: CPU-time: transformation into A, B= 0.0000 XREFINE> do (fobs=fcalc) ( all ) Total of 150 structure factor elements were selected. XREFINE> XREFINE> print R XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 150 PRRFAC: optimum Fobs/Fcalc scale = 1.000 {{ (* resol.-range #reflections R-value Accum.*) { 8.11, 10.00, 23, 0.0000, 0.0000 }, { 7.14, 8.11, 17, 0.0000, 0.0000 }, { 6.51, 7.14, 23, 0.0000, 0.0000 }, { 6.06, 6.51, 13, 0.0000, 0.0000 }, { 5.71, 6.06, 19, 0.0000, 0.0000 }, { 5.43, 5.71, 19, 0.0000, 0.0000 }, { 5.20, 5.43, 21, 0.0000, 0.0000 }, { 5.00, 5.20, 15, 0.0000, 0.0000 }}, { (* Fobs-ampl-range #reflections R-value Accum.*) { 10.277, 85.744, 39, 0.0000, 0.0000 }, { 85.744, 161.211, 52, 0.0000, 0.0000 }, { 161.211, 236.678, 40, 0.0000, 0.0000 }, { 236.678, 312.144, 11, 0.0000, 0.0000 }, { 312.144, 387.611, 5, 0.0000, 0.0000 }, { 387.611, 463.078, 1, 0.0000, 0.0000 }, { 463.078, 538.545, 1, 0.0000, 0.0000 }, { 538.545, 614.012, 1, 0.0000, 0.0000 }}} XREFINE> XREFINE>end X-PLOR> X-PLOR>vector do (b=b+20) ( all ) SELRPN: 396 atoms have been selected out of 396 X-PLOR> X-PLOR>xrefin XREFINE> predict to=map1 end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XMAPASU: using grid [ 24, 12, 16] and sublattice [ 24, 12, 16] Minimum brick that covers asymmetric unit: A= 0,..., 23 B= 0,..., 5 C= 0,..., 15 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. XPRED: CPU-time: predict-calc= 0.0000 XREFINE> XREFINE> write map extend=unit output=xmread.dat formatted=true end ASSFIL: file xmread.dat opened. XMAPX: map will be scaled. XMAPX: extend NA=( 24 0 24) NB=( 12 0 12) NC=( 16 0 16) XMAPX: ave. density (real) in unit cell= 0.25527 sigma= 0.38560 e/A^3 XMAPX: real part of section # 0 ave. dens.= 0.16910 sigma= 0.31299 e/A^3 XMAPX: real part of section # 1 ave. dens.= 0.16697 sigma= 0.32558 e/A^3 XMAPX: real part of section # 2 ave. dens.= 0.22243 sigma= 0.37290 e/A^3 XMAPX: real part of section # 3 ave. dens.= 0.22981 sigma= 0.33767 e/A^3 XMAPX: real part of section # 4 ave. dens.= 0.28320 sigma= 0.39521 e/A^3 XMAPX: real part of section # 5 ave. dens.= 0.29892 sigma= 0.38334 e/A^3 XMAPX: real part of section # 6 ave. dens.= 0.32396 sigma= 0.44152 e/A^3 XMAPX: real part of section # 7 ave. dens.= 0.24299 sigma= 0.38072 e/A^3 XMAPX: real part of section # 8 ave. dens.= 0.25483 sigma= 0.42263 e/A^3 XMAPX: real part of section # 9 ave. dens.= 0.24290 sigma= 0.37682 e/A^3 XMAPX: real part of section # 10 ave. dens.= 0.32763 sigma= 0.44678 e/A^3 XMAPX: real part of section # 11 ave. dens.= 0.29231 sigma= 0.38186 e/A^3 XMAPX: real part of section # 12 ave. dens.= 0.28357 sigma= 0.39187 e/A^3 XMAPX: real part of section # 13 ave. dens.= 0.22568 sigma= 0.33334 e/A^3 XMAPX: real part of section # 14 ave. dens.= 0.20890 sigma= 0.35314 e/A^3 XMAPX: real part of section # 15 ave. dens.= 0.17490 sigma= 0.34703 e/A^3 XMAPX: real part of section # 16 ave. dens.= 0.16910 sigma= 0.31299 e/A^3 XMAPX: CPU-time: expansion= 0.0000 XREFINE> XREFINE> read map input=xmread.dat formatted=true to=map2 end XMAPAL: allocating space for real space object. ASSFIL: file xmread.dat opened. REMARKS FILENAME="xmread.dat" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:04-Jun-04 10:28:23 created by user: [unknown] XREADX: extend NA=( 24 0 24) NB=( 12 0 12) NC=( 16 0 16) XMREAD2: CPU-time: expansion= 0.0000 XREFINE> XREFINE> show max (abs(map1-map2)) ( all ) Maximum of 2304 elements = 0.0001 XREFINE> XREFINE> XREFINE> write map extend=unit output=xmread.dat formatted=false end ASSFIL: file xmread.dat opened. XMAPX: map will be scaled. XMAPX: extend NA=( 24 0 24) NB=( 12 0 12) NC=( 16 0 16) XMAPX: ave. density (real) in unit cell= 0.25527 sigma= 0.38560 e/A^3 XMAPX: real part of section # 0 ave. dens.= 0.16910 sigma= 0.31299 e/A^3 XMAPX: real part of section # 1 ave. dens.= 0.16697 sigma= 0.32558 e/A^3 XMAPX: real part of section # 2 ave. dens.= 0.22243 sigma= 0.37290 e/A^3 XMAPX: real part of section # 3 ave. dens.= 0.22981 sigma= 0.33767 e/A^3 XMAPX: real part of section # 4 ave. dens.= 0.28320 sigma= 0.39521 e/A^3 XMAPX: real part of section # 5 ave. dens.= 0.29892 sigma= 0.38334 e/A^3 XMAPX: real part of section # 6 ave. dens.= 0.32396 sigma= 0.44152 e/A^3 XMAPX: real part of section # 7 ave. dens.= 0.24299 sigma= 0.38072 e/A^3 XMAPX: real part of section # 8 ave. dens.= 0.25483 sigma= 0.42263 e/A^3 XMAPX: real part of section # 9 ave. dens.= 0.24290 sigma= 0.37682 e/A^3 XMAPX: real part of section # 10 ave. dens.= 0.32763 sigma= 0.44678 e/A^3 XMAPX: real part of section # 11 ave. dens.= 0.29231 sigma= 0.38186 e/A^3 XMAPX: real part of section # 12 ave. dens.= 0.28357 sigma= 0.39187 e/A^3 XMAPX: real part of section # 13 ave. dens.= 0.22568 sigma= 0.33334 e/A^3 XMAPX: real part of section # 14 ave. dens.= 0.20890 sigma= 0.35314 e/A^3 XMAPX: real part of section # 15 ave. dens.= 0.17490 sigma= 0.34703 e/A^3 XMAPX: real part of section # 16 ave. dens.= 0.16910 sigma= 0.31299 e/A^3 XMAPX: CPU-time: expansion= 0.0000 XREFINE> XREFINE> read map input=xmread.dat formatted=false to=map8 end XMAPAL: allocating space for real space object. ASSFIL: file xmread.dat opened. REMARKS FILENAME="xmread.dat" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:04-Jun-04 10:28:23 created by user: [unknown] XREADX: extend NA=( 24 0 24) NB=( 12 0 12) NC=( 16 0 16) XMREAD2: CPU-time: expansion= 0.0000 XREFINE> XREFINE> show max (abs(map1-map8)) ( all ) Maximum of 2304 elements = 0.0000 XREFINE> XREFINE> XREFINE> write map extend=asymmetric output=xmread.dat formatted=false end ASSFIL: file xmread.dat opened. XMAPX: map will be scaled. XMAPX: extend NA=( 24 0 23) NB=( 12 0 5) NC=( 16 0 15) XMAPX: ave. density (real) in unit cell= 0.25527 sigma= 0.38560 e/A^3 XMAPX: real part of section # 0 ave. dens.= 0.17884 sigma= 0.32764 e/A^3 XMAPX: real part of section # 1 ave. dens.= 0.14527 sigma= 0.30227 e/A^3 XMAPX: real part of section # 2 ave. dens.= 0.26124 sigma= 0.40560 e/A^3 XMAPX: real part of section # 3 ave. dens.= 0.24477 sigma= 0.36460 e/A^3 XMAPX: real part of section # 4 ave. dens.= 0.22943 sigma= 0.37561 e/A^3 XMAPX: real part of section # 5 ave. dens.= 0.25793 sigma= 0.35023 e/A^3 XMAPX: real part of section # 6 ave. dens.= 0.28743 sigma= 0.43624 e/A^3 XMAPX: real part of section # 7 ave. dens.= 0.18969 sigma= 0.31081 e/A^3 XMAPX: real part of section # 8 ave. dens.= 0.27199 sigma= 0.42875 e/A^3 XMAPX: real part of section # 9 ave. dens.= 0.32492 sigma= 0.44600 e/A^3 XMAPX: real part of section # 10 ave. dens.= 0.37594 sigma= 0.44383 e/A^3 XMAPX: real part of section # 11 ave. dens.= 0.36303 sigma= 0.42740 e/A^3 XMAPX: real part of section # 12 ave. dens.= 0.34397 sigma= 0.40090 e/A^3 XMAPX: real part of section # 13 ave. dens.= 0.22257 sigma= 0.31838 e/A^3 XMAPX: real part of section # 14 ave. dens.= 0.18568 sigma= 0.32100 e/A^3 XMAPX: real part of section # 15 ave. dens.= 0.20167 sigma= 0.36410 e/A^3 XMAPX: CPU-time: expansion= 0.0000 XREFINE> XREFINE> read map input=xmread.dat formatted=false to=map8 end ASSFIL: file xmread.dat opened. REMARKS FILENAME="xmread.dat" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:04-Jun-04 10:28:23 created by user: [unknown] XREADX: extend NA=( 24 0 23) NB=( 12 0 5) NC=( 16 0 15) XMREAD2: CPU-time: expansion= 0.0000 XREFINE> XREFINE> show max (abs(map1-map8)) ( all ) Maximum of 2304 elements = 0.0000 XREFINE> XREFINE> XREFINE> write map extend=molecule selection=( all ) cushion=5. SELRPN: 396 atoms have been selected out of 396 WRITe MAP> output=xmread.dat formatted=false end ASSFIL: file xmread.dat opened. XMAPX: map will be scaled. XMAPX: extend NA=( 24 -5 18) NB=( 12 -4 17) NC=( 16 -9 17) XMAPX: ave. density (real) in unit cell= 0.25527 sigma= 0.38560 e/A^3 XMAPX: real part of section # 0 ave. dens.= 0.24551 sigma= 0.37089 e/A^3 XMAPX: real part of section # 1 ave. dens.= 0.27637 sigma= 0.43326 e/A^3 XMAPX: real part of section # 2 ave. dens.= 0.26816 sigma= 0.39900 e/A^3 XMAPX: real part of section # 3 ave. dens.= 0.33912 sigma= 0.44743 e/A^3 XMAPX: real part of section # 4 ave. dens.= 0.31360 sigma= 0.39825 e/A^3 XMAPX: real part of section # 5 ave. dens.= 0.28363 sigma= 0.38244 e/A^3 XMAPX: real part of section # 6 ave. dens.= 0.22776 sigma= 0.33892 e/A^3 XMAPX: real part of section # 7 ave. dens.= 0.21170 sigma= 0.35578 e/A^3 XMAPX: real part of section # 8 ave. dens.= 0.17609 sigma= 0.34242 e/A^3 XMAPX: real part of section # 9 ave. dens.= 0.18712 sigma= 0.33645 e/A^3 XMAPX: real part of section # 10 ave. dens.= 0.17318 sigma= 0.33000 e/A^3 XMAPX: real part of section # 11 ave. dens.= 0.22991 sigma= 0.37531 e/A^3 XMAPX: real part of section # 12 ave. dens.= 0.23986 sigma= 0.34948 e/A^3 XMAPX: real part of section # 13 ave. dens.= 0.29023 sigma= 0.39544 e/A^3 XMAPX: real part of section # 14 ave. dens.= 0.32066 sigma= 0.40213 e/A^3 XMAPX: real part of section # 15 ave. dens.= 0.32251 sigma= 0.43312 e/A^3 XMAPX: real part of section # 16 ave. dens.= 0.24551 sigma= 0.37089 e/A^3 XMAPX: real part of section # 17 ave. dens.= 0.27637 sigma= 0.43326 e/A^3 XMAPX: real part of section # 18 ave. dens.= 0.26816 sigma= 0.39900 e/A^3 XMAPX: real part of section # 19 ave. dens.= 0.33912 sigma= 0.44743 e/A^3 XMAPX: real part of section # 20 ave. dens.= 0.31360 sigma= 0.39825 e/A^3 XMAPX: real part of section # 21 ave. dens.= 0.28363 sigma= 0.38244 e/A^3 XMAPX: real part of section # 22 ave. dens.= 0.22776 sigma= 0.33892 e/A^3 XMAPX: real part of section # 23 ave. dens.= 0.21170 sigma= 0.35578 e/A^3 XMAPX: real part of section # 24 ave. dens.= 0.17609 sigma= 0.34242 e/A^3 XMAPX: real part of section # 25 ave. dens.= 0.18712 sigma= 0.33645 e/A^3 XMAPX: real part of section # 26 ave. dens.= 0.17318 sigma= 0.33000 e/A^3 XMAPX: CPU-time: expansion= 0.0100 XREFINE> XREFINE> read map input=xmread.dat formatted=false to=map8 end ASSFIL: file xmread.dat opened. REMARKS FILENAME="xmread.dat" REMARKS TOPH19.pep -MACRO for protein sequence REMARKS DATE:04-Jun-04 10:28:23 created by user: [unknown] XREADX: extend NA=( 24 -5 18) NB=( 12 -4 17) NC=( 16 -9 17) XMREAD2: CPU-time: expansion= 0.0100 XREFINE> XREFINE> show max (abs(map1-map8)) ( all ) Maximum of 2304 elements = 0.0000 XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 1997522 current use= 905732 X-PLOR: total CPU time= 0.2300 s X-PLOR: entry time at 10:28:23 04-Jun-04 X-PLOR: exit time at 10:28:23 04-Jun-04