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 10:28:31 X-PLOR>remarks file XSOLMASK.INP -- test solvent mask 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>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> set message=all end XREFINE> XREFINE> solmask MASK> probe=1.4 MASK> end NBUPDA: type-based van der Waals parameters retrieved. XMASK: 327 atoms have been selected for mask calculation. 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 Number of deleted points in ASU= 0 Number of non-zero lattice points in ASU= 2304 Number of special positions in ASU= 0 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. XREDUC: mapping reflections into standard asymmetric unit. XREDU2: mapping all reflections into asymmetric unit. XREDU2: sorting all reflections. XREDU2: checking for multiple entries. Removing systematic absences. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 150 CUSHA= -2,..., 25 CUSHB= -2,..., 7 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 1.4000 shrink radius= 0.0000 XMASK: volume inside mask= 88.8455% (MAP1<=0) XMASK: volume outside mask= 11.1545% (MAP1=1) XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XREFINE> do (fpart=fpart * 0.4 ) ( all ) DO: bypassing selection. Total of 150 structure factor elements were selected. XREFINE> XREFINE> do complex (fcalc=fpart) DO> DO> write reflection fpart end DO: using default selection. XRTEST: number of selected reflections 150 Total of 150 structure factor elements were selected. XRTEST: number of selected reflections 150 NREFlection= 150 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FPART DOMAin=RECIprocal TYPE=COMP END INDE 5 0 0 FPART= 4.484 0.000 INDE 6 0 0 FPART= 20.905 0.000 INDE 7 0 0 FPART= 13.401 180.000 INDE 8 0 0 FPART= 28.371 0.000 INDE 4 1 0 FPART= 50.062 90.397 INDE 5 1 0 FPART= 49.356 343.129 INDE 6 1 0 FPART= 46.768 30.000 INDE 7 1 0 FPART= 31.134 259.809 INDE 0 2 0 FPART= 68.687 300.000 INDE 1 2 0 FPART= 57.830 115.029 INDE 2 2 0 FPART= 97.613 271.871 INDE 3 2 0 FPART= 57.710 89.746 INDE 4 2 0 FPART= 15.589 335.496 INDE 5 2 0 FPART= 19.959 338.819 INDE 6 2 0 FPART= 18.650 103.898 INDE 1 3 0 FPART= 33.363 122.481 INDE 2 3 0 FPART= 59.992 296.815 INDE 3 3 0 FPART= 12.488 99.736 INDE 4 3 0 FPART= 5.783 296.565 INDE -8 0 1 FPART= 7.249 180.000 INDE -7 0 1 FPART= 4.652 180.000 INDE -6 0 1 FPART= 19.437 180.000 INDE -5 0 1 FPART= 58.195 180.000 INDE -4 0 1 FPART= 78.860 180.000 INDE 4 0 1 FPART= 17.704 0.000 INDE 5 0 1 FPART= 6.244 180.000 INDE 6 0 1 FPART= 12.492 0.000 INDE 7 0 1 FPART= 1.082 180.000 INDE -7 1 1 FPART= 43.673 18.677 INDE -6 1 1 FPART= 40.231 80.073 INDE -5 1 1 FPART= 28.043 210.941 INDE -4 1 1 FPART= 69.037 358.134 INDE -3 1 1 FPART= 61.841 50.003 INDE 3 1 1 FPART= 31.119 166.368 INDE 4 1 1 FPART= 54.842 182.372 INDE 5 1 1 FPART= 23.475 134.071 INDE 6 1 1 FPART= 24.381 167.128 INDE 7 1 1 FPART= 11.695 190.490 INDE -6 2 1 FPART= 43.257 164.456 INDE -5 2 1 FPART= 48.058 295.194 INDE -4 2 1 FPART= 47.445 83.488 INDE -3 2 1 FPART= 21.547 204.034 INDE -2 2 1 FPART= 33.072 44.280 INDE -1 2 1 FPART= 16.033 120.769 INDE 0 2 1 FPART= 21.738 134.925 INDE 1 2 1 FPART= 73.883 61.307 INDE 2 2 1 FPART= 68.176 220.363 INDE 3 2 1 FPART= 38.990 86.050 INDE 4 2 1 FPART= 6.844 243.991 INDE 5 2 1 FPART= 48.864 134.524 INDE 6 2 1 FPART= 22.207 243.572 INDE -4 3 1 FPART= 24.887 265.121 INDE -3 3 1 FPART= 22.279 316.836 INDE -2 3 1 FPART= 22.408 199.769 INDE -1 3 1 FPART= 28.013 355.912 INDE 0 3 1 FPART= 34.487 187.998 INDE 1 3 1 FPART= 29.455 35.614 INDE 2 3 1 FPART= 40.456 170.533 INDE 3 3 1 FPART= 40.211 319.598 INDE 4 3 1 FPART= 58.150 128.952 INDE -7 0 2 FPART= 26.768 0.000 INDE -6 0 2 FPART= 71.735 0.000 INDE -5 0 2 FPART= 43.631 180.000 INDE -4 0 2 FPART= 19.526 0.000 INDE -3 0 2 FPART= 101.811 0.000 INDE -2 0 2 FPART= 97.067 0.000 INDE 2 0 2 FPART= 16.588 0.000 INDE 3 0 2 FPART= 24.253 180.000 INDE 4 0 2 FPART= 24.624 180.000 INDE 5 0 2 FPART= 22.968 0.000 INDE 6 0 2 FPART= 69.261 180.000 INDE 7 0 2 FPART= 5.053 0.000 INDE -7 1 2 FPART= 23.410 333.125 INDE -6 1 2 FPART= 29.401 137.949 INDE -5 1 2 FPART= 55.388 217.422 INDE -4 1 2 FPART= 66.815 329.617 INDE -3 1 2 FPART= 19.440 270.345 INDE -2 1 2 FPART= 53.442 168.332 INDE -1 1 2 FPART= 94.915 21.784 INDE 0 1 2 FPART= 122.025 280.627 INDE 1 1 2 FPART= 107.323 88.374 INDE 2 1 2 FPART= 33.830 306.220 INDE 3 1 2 FPART= 42.650 16.899 INDE 4 1 2 FPART= 18.679 286.534 INDE 5 1 2 FPART= 21.597 86.219 INDE 6 1 2 FPART= 16.402 112.434 INDE -5 2 2 FPART= 19.259 312.066 INDE -4 2 2 FPART= 24.626 182.911 INDE -3 2 2 FPART= 50.831 300.000 INDE -2 2 2 FPART= 9.647 206.949 INDE -1 2 2 FPART= 60.567 270.743 INDE 0 2 2 FPART= 14.402 276.251 INDE 1 2 2 FPART= 42.161 335.989 INDE 2 2 2 FPART= 15.015 241.039 INDE 3 2 2 FPART= 57.061 300.446 INDE 4 2 2 FPART= 18.754 26.105 INDE 5 2 2 FPART= 19.481 353.780 INDE -3 3 2 FPART= 39.561 118.362 INDE -2 3 2 FPART= 14.742 281.407 INDE -1 3 2 FPART= 6.268 88.299 INDE 0 3 2 FPART= 20.761 268.586 INDE 1 3 2 FPART= 9.280 224.924 INDE 2 3 2 FPART= 9.630 10.280 INDE 3 3 2 FPART= 41.766 285.371 INDE -6 0 3 FPART= 7.277 180.000 INDE -5 0 3 FPART= 63.381 180.000 INDE -4 0 3 FPART= 7.261 180.000 INDE -3 0 3 FPART= 29.851 180.000 INDE -2 0 3 FPART= 62.950 0.000 INDE -1 0 3 FPART= 152.168 180.000 INDE 0 0 3 FPART= 105.955 0.000 INDE 1 0 3 FPART= 34.035 180.000 INDE 2 0 3 FPART= 33.473 0.000 INDE 3 0 3 FPART= 26.465 180.000 INDE 4 0 3 FPART= 18.197 0.000 INDE 5 0 3 FPART= 43.510 0.000 INDE 6 0 3 FPART= 41.919 180.000 INDE -5 1 3 FPART= 3.277 306.916 INDE -4 1 3 FPART= 11.707 25.100 INDE -3 1 3 FPART= 18.922 135.954 INDE -2 1 3 FPART= 24.670 225.389 INDE -1 1 3 FPART= 59.394 106.669 INDE 0 1 3 FPART= 89.741 269.136 INDE 1 1 3 FPART= 30.408 84.750 INDE 2 1 3 FPART= 36.537 185.963 INDE 3 1 3 FPART= 29.745 309.357 INDE 4 1 3 FPART= 31.475 319.388 INDE 5 1 3 FPART= 15.638 232.667 INDE -4 2 3 FPART= 41.781 118.387 INDE -3 2 3 FPART= 32.829 5.496 INDE -2 2 3 FPART= 50.104 138.760 INDE -1 2 3 FPART= 31.861 87.100 INDE 0 2 3 FPART= 14.239 191.673 INDE 1 2 3 FPART= 28.367 126.838 INDE 2 2 3 FPART= 44.307 116.457 INDE 3 2 3 FPART= 47.700 244.375 INDE 4 2 3 FPART= 22.421 95.539 INDE -3 0 4 FPART= 8.959 0.000 INDE -2 0 4 FPART= 42.795 0.000 INDE -1 0 4 FPART= 40.412 180.000 INDE 0 0 4 FPART= 35.837 0.000 INDE 1 0 4 FPART= 17.270 180.000 INDE 2 0 4 FPART= 25.091 0.000 INDE 3 0 4 FPART= 15.657 180.000 INDE -3 1 4 FPART= 3.876 173.448 INDE -2 1 4 FPART= 25.064 338.565 INDE -1 1 4 FPART= 31.230 116.546 INDE 0 1 4 FPART= 18.130 310.765 INDE 1 1 4 FPART= 20.240 36.003 INDE 2 1 4 FPART= 39.610 154.246 XREFINE> XREFINE> mask MASK> probe=1.4 to=map1 MASK> end XMASK: 327 atoms have been selected for mask calculation. XMAPAL: allocating space for real space object. CUSHA= -2,..., 25 CUSHB= -2,..., 7 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 1.4000 shrink radius= 0.0000 XMASK: volume inside mask= 88.8455% (MAP1<=0) XMASK: volume outside mask= 11.1545% (MAP1=1) XREFINE> do (map1=0.4 ) (map1=1) Total of 257 map elements were selected. XREFINE> do (deri1=ft(map1)) ( all ) DO: bypassing selection. XMAPAL: allocating space for real space object. DO: executing operations right of FT. Total of 2304 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XSFAL: allocating space for complex reciprocal space object. Total of 150 structure factor elements were selected. DO: executing operations left of FT. XREFINE> XREFINE> show max (abs(deri1-fpart)) ( all ) Maximum of 150 elements = 0.0000 XREFINE> do (fpart=deri1) ( all ) DO: bypassing selection. Total of 150 structure factor elements were selected. XREFINE> write reflection fpart end XRTEST: number of selected reflections 150 NREFlection= 150 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FPART DOMAin=RECIprocal TYPE=COMP END INDE 5 0 0 FPART= 4.484 0.000 INDE 6 0 0 FPART= 20.905 0.000 INDE 7 0 0 FPART= 13.401 180.000 INDE 8 0 0 FPART= 28.371 0.000 INDE 4 1 0 FPART= 50.062 90.397 INDE 5 1 0 FPART= 49.356 343.129 INDE 6 1 0 FPART= 46.768 30.000 INDE 7 1 0 FPART= 31.134 259.809 INDE 0 2 0 FPART= 68.687 300.000 INDE 1 2 0 FPART= 57.830 115.029 INDE 2 2 0 FPART= 97.613 271.871 INDE 3 2 0 FPART= 57.710 89.746 INDE 4 2 0 FPART= 15.589 335.496 INDE 5 2 0 FPART= 19.959 338.819 INDE 6 2 0 FPART= 18.650 103.898 INDE 1 3 0 FPART= 33.363 122.481 INDE 2 3 0 FPART= 59.992 296.815 INDE 3 3 0 FPART= 12.488 99.736 INDE 4 3 0 FPART= 5.783 296.565 INDE -8 0 1 FPART= 7.249 180.000 INDE -7 0 1 FPART= 4.652 180.000 INDE -6 0 1 FPART= 19.437 180.000 INDE -5 0 1 FPART= 58.195 180.000 INDE -4 0 1 FPART= 78.860 180.000 INDE 4 0 1 FPART= 17.704 0.000 INDE 5 0 1 FPART= 6.244 180.000 INDE 6 0 1 FPART= 12.492 0.000 INDE 7 0 1 FPART= 1.082 180.000 INDE -7 1 1 FPART= 43.673 18.677 INDE -6 1 1 FPART= 40.231 80.073 INDE -5 1 1 FPART= 28.043 210.941 INDE -4 1 1 FPART= 69.037 358.134 INDE -3 1 1 FPART= 61.841 50.003 INDE 3 1 1 FPART= 31.119 166.368 INDE 4 1 1 FPART= 54.842 182.372 INDE 5 1 1 FPART= 23.475 134.071 INDE 6 1 1 FPART= 24.381 167.128 INDE 7 1 1 FPART= 11.695 190.490 INDE -6 2 1 FPART= 43.257 164.456 INDE -5 2 1 FPART= 48.058 295.194 INDE -4 2 1 FPART= 47.445 83.488 INDE -3 2 1 FPART= 21.547 204.034 INDE -2 2 1 FPART= 33.072 44.280 INDE -1 2 1 FPART= 16.033 120.769 INDE 0 2 1 FPART= 21.738 134.925 INDE 1 2 1 FPART= 73.883 61.307 INDE 2 2 1 FPART= 68.176 220.363 INDE 3 2 1 FPART= 38.990 86.050 INDE 4 2 1 FPART= 6.844 243.991 INDE 5 2 1 FPART= 48.864 134.524 INDE 6 2 1 FPART= 22.207 243.572 INDE -4 3 1 FPART= 24.887 265.121 INDE -3 3 1 FPART= 22.279 316.836 INDE -2 3 1 FPART= 22.408 199.769 INDE -1 3 1 FPART= 28.013 355.912 INDE 0 3 1 FPART= 34.487 187.998 INDE 1 3 1 FPART= 29.455 35.614 INDE 2 3 1 FPART= 40.456 170.533 INDE 3 3 1 FPART= 40.211 319.598 INDE 4 3 1 FPART= 58.150 128.952 INDE -7 0 2 FPART= 26.768 0.000 INDE -6 0 2 FPART= 71.735 0.000 INDE -5 0 2 FPART= 43.631 180.000 INDE -4 0 2 FPART= 19.526 0.000 INDE -3 0 2 FPART= 101.811 0.000 INDE -2 0 2 FPART= 97.067 0.000 INDE 2 0 2 FPART= 16.588 0.000 INDE 3 0 2 FPART= 24.253 180.000 INDE 4 0 2 FPART= 24.624 180.000 INDE 5 0 2 FPART= 22.968 0.000 INDE 6 0 2 FPART= 69.261 180.000 INDE 7 0 2 FPART= 5.053 0.000 INDE -7 1 2 FPART= 23.410 333.125 INDE -6 1 2 FPART= 29.401 137.949 INDE -5 1 2 FPART= 55.388 217.422 INDE -4 1 2 FPART= 66.815 329.617 INDE -3 1 2 FPART= 19.440 270.345 INDE -2 1 2 FPART= 53.442 168.332 INDE -1 1 2 FPART= 94.915 21.784 INDE 0 1 2 FPART= 122.025 280.627 INDE 1 1 2 FPART= 107.323 88.374 INDE 2 1 2 FPART= 33.830 306.220 INDE 3 1 2 FPART= 42.650 16.899 INDE 4 1 2 FPART= 18.679 286.534 INDE 5 1 2 FPART= 21.597 86.219 INDE 6 1 2 FPART= 16.402 112.434 INDE -5 2 2 FPART= 19.259 312.066 INDE -4 2 2 FPART= 24.626 182.911 INDE -3 2 2 FPART= 50.831 300.000 INDE -2 2 2 FPART= 9.647 206.949 INDE -1 2 2 FPART= 60.567 270.743 INDE 0 2 2 FPART= 14.402 276.251 INDE 1 2 2 FPART= 42.161 335.989 INDE 2 2 2 FPART= 15.015 241.039 INDE 3 2 2 FPART= 57.061 300.446 INDE 4 2 2 FPART= 18.754 26.105 INDE 5 2 2 FPART= 19.481 353.780 INDE -3 3 2 FPART= 39.561 118.362 INDE -2 3 2 FPART= 14.742 281.407 INDE -1 3 2 FPART= 6.268 88.299 INDE 0 3 2 FPART= 20.761 268.586 INDE 1 3 2 FPART= 9.280 224.924 INDE 2 3 2 FPART= 9.630 10.280 INDE 3 3 2 FPART= 41.766 285.371 INDE -6 0 3 FPART= 7.277 180.000 INDE -5 0 3 FPART= 63.381 180.000 INDE -4 0 3 FPART= 7.261 180.000 INDE -3 0 3 FPART= 29.851 180.000 INDE -2 0 3 FPART= 62.950 0.000 INDE -1 0 3 FPART= 152.168 180.000 INDE 0 0 3 FPART= 105.955 0.000 INDE 1 0 3 FPART= 34.035 180.000 INDE 2 0 3 FPART= 33.473 0.000 INDE 3 0 3 FPART= 26.465 180.000 INDE 4 0 3 FPART= 18.197 0.000 INDE 5 0 3 FPART= 43.510 0.000 INDE 6 0 3 FPART= 41.919 180.000 INDE -5 1 3 FPART= 3.277 306.916 INDE -4 1 3 FPART= 11.707 25.100 INDE -3 1 3 FPART= 18.922 135.954 INDE -2 1 3 FPART= 24.670 225.389 INDE -1 1 3 FPART= 59.394 106.669 INDE 0 1 3 FPART= 89.741 269.136 INDE 1 1 3 FPART= 30.408 84.750 INDE 2 1 3 FPART= 36.537 185.963 INDE 3 1 3 FPART= 29.745 309.357 INDE 4 1 3 FPART= 31.475 319.388 INDE 5 1 3 FPART= 15.638 232.667 INDE -4 2 3 FPART= 41.781 118.387 INDE -3 2 3 FPART= 32.829 5.496 INDE -2 2 3 FPART= 50.104 138.760 INDE -1 2 3 FPART= 31.861 87.100 INDE 0 2 3 FPART= 14.239 191.673 INDE 1 2 3 FPART= 28.367 126.838 INDE 2 2 3 FPART= 44.307 116.457 INDE 3 2 3 FPART= 47.700 244.375 INDE 4 2 3 FPART= 22.421 95.539 INDE -3 0 4 FPART= 8.959 0.000 INDE -2 0 4 FPART= 42.795 0.000 INDE -1 0 4 FPART= 40.412 180.000 INDE 0 0 4 FPART= 35.837 0.000 INDE 1 0 4 FPART= 17.270 180.000 INDE 2 0 4 FPART= 25.091 0.000 INDE 3 0 4 FPART= 15.657 180.000 INDE -3 1 4 FPART= 3.876 173.448 INDE -2 1 4 FPART= 25.064 338.565 INDE -1 1 4 FPART= 31.230 116.546 INDE 0 1 4 FPART= 18.130 310.765 INDE 1 1 4 FPART= 20.240 36.003 INDE 2 1 4 FPART= 39.610 154.246 XREFINE> XREFINE> XREFINE> solmask MASK> probe=0. MASK> end XMASK: 327 atoms have been selected for mask calculation. XMAPAL: allocating space for real space object. XRTEST: number of selected reflections 150 CUSHA= -1,..., 24 CUSHB= -1,..., 6 CUSHC= -2,..., 17 MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 0.0000 shrink radius= 0.0000 XMASK: volume inside mask= 58.9844% (MAP1<=0) XMASK: volume outside mask= 41.0156% (MAP1=1) XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XREFINE> do (fpart=fpart * 0.4 ) ( all ) DO: bypassing selection. Total of 150 structure factor elements were selected. XREFINE> XREFINE> mask MASK> probe=0. to=map1 MASK> end XMASK: 327 atoms have been selected for mask calculation. CUSHA= -1,..., 24 CUSHB= -1,..., 6 CUSHC= -2,..., 17 MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 0.0000 shrink radius= 0.0000 XMASK: volume inside mask= 58.9844% (MAP1<=0) XMASK: volume outside mask= 41.0156% (MAP1=1) XREFINE> do (map1=0.4 ) (map1=1) Total of 945 map elements were selected. XREFINE> do (deri1=ft(map1)) ( all ) DO: bypassing selection. XMAPAL: allocating space for real space object. DO: executing operations right of FT. Total of 2304 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 Total of 150 structure factor elements were selected. DO: executing operations left of FT. XREFINE> XREFINE> show max (abs(deri1-fpart)) ( all ) Maximum of 150 elements = 0.0000 XREFINE> XREFINE> target=packing XREFINE> print target CUSHA= -1,..., 24 CUSHB= -1,..., 6 CUSHC= -2,..., 17 MASKX2: volume inside molecule= 58.9844% MASKX2: volume outside molecule= 41.0156% XREFINE> XREFINE> solmask MASK> probe=1.6 shrink=3. MASK> end XMASK: 327 atoms have been selected for mask calculation. XMAPAL: allocating space for real space object. XRTEST: number of selected reflections 150 CUSHA= -2,..., 25 CUSHB= -2,..., 7 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 65.9722% (MAP1<=0) XMASK: volume outside mask= 34.0278% (MAP1=1) XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XREFINE> do (fpart=fpart * 1.4 ) ( all ) DO: bypassing selection. Total of 150 structure factor elements were selected. XREFINE> XREFINE> mask MASK> probe=1.6 shrink=3. to=map1 MASK> end XMASK: 327 atoms have been selected for mask calculation. CUSHA= -2,..., 25 CUSHB= -2,..., 7 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.9848 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 65.9722% (MAP1<=0) XMASK: volume outside mask= 34.0278% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 784 map elements were selected. XREFINE> XREFINE> do (deri1=ft(map1)) ( all ) DO: bypassing selection. XMAPAL: allocating space for real space object. DO: executing operations right of FT. Total of 2304 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 Total of 150 structure factor elements were selected. DO: executing operations left of FT. XREFINE> XREFINE> show max (abs(deri1-fpart)) ( all ) Maximum of 150 elements = 0.0000 XREFINE> XREFINE>end X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> {* test shell mode *} XREFINE> mask MASK> solrad=1.4 MASK> shrink=1.2 MASK> to=map1 MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. CUSHA= -2,..., 25 CUSHB= -2,..., 7 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.7728 A XMASK: probe radius= 1.4000 shrink radius= 1.2000 XMASK: volume inside mask= 88.8455% (MAP1<=0) XMASK: volume outside mask= 11.1545% (MAP1=1) XREFINE> XREFINE> mask MASK> solrad=2.4 MASK> shrink=0. MASK> to=map2 MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. XMAPAL: allocating space for real space object. CUSHA= -3,..., 26 CUSHB= -3,..., 8 CUSHC= -3,..., 18 MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.7728 A XMASK: probe radius= 2.4000 shrink radius= 0.0000 XMASK: volume inside mask= 96.0503% (MAP2<=0) XMASK: volume outside mask= 3.9497% (MAP2=1) XREFINE> XREFINE> mask MASK> solrad=3.4 MASK> shrink=0. MASK> to=map3 MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. XMAPAL: allocating space for real space object. CUSHA= -3,..., 26 CUSHB= -3,..., 9 CUSHC= -4,..., 19 MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.7728 A XMASK: probe radius= 3.4000 shrink radius= 0.0000 XMASK: volume inside mask= 99.1753% (MAP3<=0) XMASK: volume outside mask= 0.8247% (MAP3=1) XREFINE> XREFINE> do (map4=3) ( map3=1 ) XMAPAL: allocating space for real space object. Total of 19 map elements were selected. XREFINE> do (map4=2) ( map3=0 and map2=1) Total of 72 map elements were selected. XREFINE> do (map4=1) ( map2=0 and map1=1) Total of 166 map elements were selected. XREFINE> XREFINE> show sum ( 1 ) ( map4=1) Sum of 166 elements = 166.0000 XREFINE> show sum ( 1 ) ( map4=2) Sum of 72 elements = 72.0000 XREFINE> show sum ( 1 ) ( map4=3) Sum of 19 elements = 19.0000 XREFINE> XREFINE> mask MASK> solrad=1.4 MASK> shrink=1.2 MASK> nshell=3 MASK> thickness=1. MASK> to=map1 MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. CUSHA= -3,..., 26 CUSHB= -3,..., 9 CUSHC= -4,..., 19 MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.7728 A XMASK: probe radius= 1.4000 shrink radius= 1.2000 XMASK: shell= 0 from= 0 to 1.97 A, volume= 88.845% (MAP1=0) XMASK: shell= 1 from= 1.97 to 4.17 A, volume= 7.205% (MAP1= 1) XMASK: shell= 2 from= 4.17 to 5.17 A, volume= 3.125% (MAP1= 2) XMASK: shell= 3 from= 5.17 to infin. A, volume= 0.825% (MAP1= 3) XMASK: volume inside mask= 88.8455% (MAP1<=0) XMASK: volume outside mask= 11.1545% (MAP1>0) XREFINE> XREFINE> show sum ( 1 ) ( map1=1) Sum of 166 elements = 166.0000 XREFINE> show sum ( 1 ) ( map1=2) Sum of 72 elements = 72.0000 XREFINE> show sum ( 1 ) ( map1=3) Sum of 19 elements = 19.0000 XREFINE> XREFINE> show max (abs(map1-map4)) ( all ) Maximum of 2304 elements = 0.0000 XREFINE>end X-PLOR> X-PLOR>{* test selection of atoms *} X-PLOR>set message=normal end X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> a=16. b=16. c=18. alpha=90.0 beta=90.00 gamma=90.0 XRMAPR: symmetry or unitcell changed. Real space obj. deleted. XREFINE> XREFINE> symmetry reset XREFINE> symmetry=( X,Y,Z ) {* test with tetragonal space group P4(3)22 *} XREFINE> symmetry=( -X,-Y,1/2+Z ) XREFINE> symmetry=( -Y,X,3/4+Z ) XREFINE> symmetry=( Y,-X,1/4+Z ) XREFINE> symmetry=( -X,Y,-Z ) XREFINE> symmetry=( X,-Y,1/2-Z ) XREFINE> symmetry=( Y,X,1/4-Z ) XREFINE> symmetry=( -Y,-X,3/4-Z ) XREFINE> XREFINE> reflection reset end REFLection: data will be merged with existing data. XRRR: all existing reciprocal data will be scratched. XRRR2: 0 new reflections have been added. 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: 16 new reflections have been generated. XREFINE> XREFINE> resolution 10. 5. XREFINE> XREFINE> asymm=( 0<=x<1 ASYMmetric> and 0<=y<1 ASYMmetric> and 0<=z<=1/8 ) XREFINE> XREFINE> XREFINE> mask MASK> probe=1.6 shrink=3. to=map1 MASK> selection=( resid 10:14 ) SELRPN: 59 atoms have been selected out of 396 MASK> end XMASK: 59 atoms have been selected for mask calculation. XMAPASU: using grid [ 9, 9, 12] and sublattice [ 9, 9, 12] Minimum brick that covers asymmetric unit: A= 0,..., 8 B= 0,..., 8 C= 0,..., 1 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.6419 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 81.4815% (MAP1<=0) XMASK: volume outside mask= 18.5185% (MAP1=1) XREFINE> do (fpart=fpart * 1.4 ) ( all ) XREDUC: mapping reflections into standard asymmetric unit. Total of 16 structure factor elements were selected. XREFINE> XREFINE>end X-PLOR> X-PLOR>delete selection=( not resid 10:14 ) end SELRPN: 337 atoms have been selected out of 396 MAPIC: Atom numbers being modified SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 59(MAXA= 400) NBOND= 59(MAXB= 800) NTHETA= 81(MAXT= 800) NGRP= 23(MAXGRP= 200) NPHI= 31(MAXP= 400) NIMPHI= 26(MAXIMP= 200) NDON= 15(MAXPAD= 100) NACC= 8(MAXPAD= 100) NNB= 3(MAXNB= 100) X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> a=20. b=20. c=20. alpha=90.0 beta=90.00 gamma=90.0 XRMAPR: symmetry or unitcell changed. Real space obj. deleted. XREFINE> XREFINE> symmetry reset XREFINE> symmetry=( X,Y,Z ) {* test with tetragonal space group P4(3)22 *} XREFINE> symmetry=( -X,-Y,1/2+Z ) XREFINE> symmetry=( -Y,X,3/4+Z ) XREFINE> symmetry=( Y,-X,1/4+Z ) XREFINE> symmetry=( -X,Y,-Z ) XREFINE> symmetry=( X,-Y,1/2-Z ) XREFINE> symmetry=( Y,X,1/4-Z ) XREFINE> symmetry=( -Y,-X,3/4-Z ) XREFINE> hermitian=true XREFINE> XREFINE> SCATter ( chemical C* ) SELRPN: 26 atoms have been selected out of 59 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 10 atoms have been selected out of 59 SCATTER_A1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> XREFINE> SCATter ( chemical O* ) SELRPN: 8 atoms have been selected out of 59 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 0 atoms have been selected out of 59 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> reflection reset end REFLection: data will be merged with existing data. XRRR: all existing reciprocal data will be scratched. XRRR2: 0 new reflections have been added. 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: 25 new reflections have been generated. XREFINE> update XREDUC: mapping reflections into standard asymmetric unit. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 25 %XREFIN-error: zero occupancies --> all set to one CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 44 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 12, 12, 12] and sublattice [ 12( 13), 12( 13), 12] XFFT: CPU-time: electron-density-calc= 0.0000 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 25 structure factor elements were selected. XREFINE> XREFINE> resolution 10. 5. XREFINE> XREFINE> asymm=( 0<=x<1 ASYMmetric> and 0<=y<1 ASYMmetric> and 0<=z<=1/8 ) XREFINE> XREFINE> XREFINE> mask MASK> probe=1.6 shrink=3. to=map1 MASK> selection=( all ) SELRPN: 59 atoms have been selected out of 59 MASK> end XMASK: 59 atoms have been selected for mask calculation. XMAPASU: using grid [ 12, 12, 12] and sublattice [ 12, 12, 12] Minimum brick that covers asymmetric unit: A= 0,..., 11 B= 0,..., 11 C= 0,..., 1 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.6419 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 75.4630% (MAP1<=0) XMASK: volume outside mask= 24.5370% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 55 map elements were selected. XREFINE> XREFINE> do (fpart=ft(map1)) ( all ) XMAPAL: allocating space for real space object. Total of 228 map elements were selected. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XREFINE> XREFINE> hermitian=false expand hermitian=true XPARSE: expanding data set (h,k,l)->{(h,k,l),(-h,-k,-l)} XEXPA2: 25 new reflections have been generated. XRMAPR: symmetry or unitcell changed. Real space obj. deleted. XREDUC: mapping reflections into standard asymmetric unit. XREDU2: 19 reflections have been deleted. XEXPA2: 195 new reflections have been generated. %XPARSE-warning: data reduced to hemisphere. Anomalous signal may be lost. XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR>{* expand model to P1 *} X-PLOR>vector do ( segid="1" ) ( all ) SELRPN: 59 atoms have been selected out of 59 X-PLOR>duplicate selection=( segid "1" ) segid="2" end SELRPN: 59 atoms have been selected out of 59 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 118(MAXA= 400) NBOND= 118(MAXB= 800) NTHETA= 162(MAXT= 800) NGRP= 46(MAXGRP= 200) NPHI= 62(MAXP= 400) NIMPHI= 52(MAXIMP= 200) NDON= 30(MAXPAD= 100) NACC= 16(MAXPAD= 100) NNB= 6(MAXNB= 100) X-PLOR>coor symmetry=( -X,-Y,1/2+Z ) selection=( segid "2" ) end SELRPN: 59 atoms have been selected out of 118 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="3" end SELRPN: 59 atoms have been selected out of 118 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 177(MAXA= 400) NBOND= 177(MAXB= 800) NTHETA= 243(MAXT= 800) NGRP= 69(MAXGRP= 200) NPHI= 93(MAXP= 400) NIMPHI= 78(MAXIMP= 200) NDON= 45(MAXPAD= 100) NACC= 24(MAXPAD= 100) NNB= 9(MAXNB= 100) X-PLOR>coor symmetry=( -Y,X,3/4+Z ) selection=( segid "3" ) end SELRPN: 59 atoms have been selected out of 177 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="4" end SELRPN: 59 atoms have been selected out of 177 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 236(MAXA= 400) NBOND= 236(MAXB= 800) NTHETA= 324(MAXT= 800) NGRP= 92(MAXGRP= 200) NPHI= 124(MAXP= 400) NIMPHI= 104(MAXIMP= 200) NDON= 60(MAXPAD= 100) NACC= 32(MAXPAD= 100) NNB= 12(MAXNB= 100) X-PLOR>coor symmetry=( Y,-X,1/4+Z ) selection=( segid "4" ) end SELRPN: 59 atoms have been selected out of 236 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="5" end SELRPN: 59 atoms have been selected out of 236 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 295(MAXA= 400) NBOND= 295(MAXB= 800) NTHETA= 405(MAXT= 800) NGRP= 115(MAXGRP= 200) NPHI= 155(MAXP= 400) NIMPHI= 130(MAXIMP= 200) NDON= 75(MAXPAD= 100) NACC= 40(MAXPAD= 100) NNB= 15(MAXNB= 100) X-PLOR>coor symmetry=( -X,Y,-Z ) selection=( segid "5" ) end SELRPN: 59 atoms have been selected out of 295 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="6" end SELRPN: 59 atoms have been selected out of 295 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 354(MAXA= 400) NBOND= 354(MAXB= 800) NTHETA= 486(MAXT= 800) NGRP= 138(MAXGRP= 200) NPHI= 186(MAXP= 400) NIMPHI= 156(MAXIMP= 200) NDON= 90(MAXPAD= 100) NACC= 48(MAXPAD= 100) NNB= 18(MAXNB= 100) X-PLOR>coor symmetry=( X,-Y,1/2-Z ) selection=( segid "6" ) end SELRPN: 59 atoms have been selected out of 354 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="7" end SELRPN: 59 atoms have been selected out of 354 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 413(MAXA= 800) NBOND= 413(MAXB= 800) NTHETA= 567(MAXT= 800) NGRP= 161(MAXGRP= 200) NPHI= 217(MAXP= 400) NIMPHI= 182(MAXIMP= 200) NDON= 105(MAXPAD= 200) NACC= 56(MAXPAD= 200) NNB= 21(MAXNB= 100) X-PLOR>coor symmetry=( Y,X,1/4-Z ) selection=( segid "7" ) end SELRPN: 59 atoms have been selected out of 413 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR>duplicate selection=( segid "1" ) segid="8" end SELRPN: 59 atoms have been selected out of 413 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 472(MAXA= 800) NBOND= 472(MAXB= 800) NTHETA= 648(MAXT= 800) NGRP= 184(MAXGRP= 200) NPHI= 248(MAXP= 400) NIMPHI= 208(MAXIMP= 400) NDON= 120(MAXPAD= 200) NACC= 64(MAXPAD= 200) NNB= 24(MAXNB= 100) X-PLOR>coor symmetry=( -Y,-X,3/4-Z ) selection=( segid "8" ) end SELRPN: 59 atoms have been selected out of 472 COOR: using atom subset. COOR: applied symmetry operator to selected coordinates X-PLOR> X-PLOR> X-PLOR>xrefin XREFINE> SCATter ( chemical C* ) SELRPN: 208 atoms have been selected out of 472 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 80 atoms have been selected out of 472 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 472 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 0 atoms have been selected out of 472 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> update XREDUC: mapping reflections into standard asymmetric unit. XREDU2: 113 reflections have been deleted. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 113 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 352 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 12, 12, 12] and sublattice [ 12( 13), 12( 13), 12] XFFT: CPU-time: electron-density-calc= 0.0000 XFFT: CPU-time: FFT of electron density= 0.0000 XFFT: CPU-time: transformation into A, B= 0.0000 XREFINE> XREFINE> show max (abs(fobs-fcalc) ) ( all ) Maximum of 113 elements = 0.0000 XREFINE> XREFINE> resolution 10. 5. XREFINE> XREFINE> asymm=( 0<=x<1 ASYMmetric> and 0<=y<1 ASYMmetric> and 0<=z<1) XREFINE> XREFINE> mask MASK> probe=1.6 shrink=3. to=map1 MASK> selection=( all ) SELRPN: 472 atoms have been selected out of 472 MASK> end XMASK: 472 atoms have been selected for mask calculation. XMAPASU: using grid [ 12, 12, 12] and sublattice [ 12, 12, 12] Minimum brick that covers asymmetric unit: A= 0,..., 11 B= 0,..., 11 C= 0,..., 11 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.6419 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 75.4630% (MAP1<=0) XMASK: volume outside mask= 24.5370% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 424 map elements were selected. XREFINE> XREFINE> do (deri1=ft(map1)) ( all ) XMAPAL: allocating space for real space object. Total of 1728 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 Total of 113 structure factor elements were selected. XREFINE> XREFINE> show max (abs(deri1-fpart)) ( all ) Maximum of 113 elements = 0.0000 XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR>ncs strict {* invoke strict non-crystallographic symmetry*} NCS-strict> NCS-strict> xncsrel SKEW TRANSFORMATION HAS NOT BEEN GIVEN, ASSUMING IDENTITY XNCS> matrix= MATRix-first-row= (-.5 0. .866025) MATRix-second-row= (0. 1. 0. ) MATRix-third-row= (-.866025 0. -.5 ) XNCS> translation= TRANslation= (0. 0. 0.) XNCS> end NCS-strict> xncsrel SKEW TRANSFORMATION HAS NOT BEEN GIVEN, ASSUMING IDENTITY XNCS> matrix= MATRix-first-row= (-.5 0. -.866025) MATRix-second-row= (0. 1. 0.) MATRix-third-row= (.866025 0. -.5) XNCS> translation= TRANslation= (0. 0. 0.) XNCS> end NCS-strict>end X-PLOR> X-PLOR>xrefin XREFINE> mask MASK> probe=1.6 shrink=3. to=map1 MASK> selection=( resid 11 ) SELRPN: 64 atoms have been selected out of 472 MASK> end XMASK: 64 atoms have been selected for mask calculation. XMASK: applying non-crystallographic symmetry. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.6375 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 20.8333% (MAP1<=0) XMASK: volume outside mask= 79.1667% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 1368 map elements were selected. XREFINE> XREFINE> do (deri1=ft(map1)) ( all ) XMAPAL: allocating space for real space object. Total of 1728 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 Total of 113 structure factor elements were selected. XREFINE>end X-PLOR> X-PLOR>vector do (segid="1") ( all ) SELRPN: 472 atoms have been selected out of 472 X-PLOR>duplicate selection=( segid "1" ) segid="2" end SELRPN: 472 atoms have been selected out of 472 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 944(MAXA= 1600) NBOND= 944(MAXB= 1600) NTHETA= 1296(MAXT= 1600) NGRP= 368(MAXGRP= 400) NPHI= 496(MAXP= 800) NIMPHI= 416(MAXIMP= 800) NDON= 240(MAXPAD= 400) NACC= 128(MAXPAD= 400) NNB= 48(MAXNB= 100) X-PLOR>coor rotate COOR-ROTA> matrix= MATRix-first-row= (-.5 0. .866025) MATRix-second-row= (0. 1. 0. ) MATRix-third-row= (-.866025 0. -.5 ) Rotation matrix = -0.500000 0.000000 0.866025 0.000000 1.000000 0.000000 -0.866025 0.000000 -0.500000 Corresp. Eulerian angles (theta1,theta2,theta3) 270.0000 120.0000 90.0000 Corresp. spherical polar angles (psi,phi,kappa) 0.0000 0.0000 240.0000 Corresp. rotation angle 120.0000 about axis 0.0000 -1.0000 0.0000 Corresp. quaternions 0.5000 0.0000 -0.8660 0.0000 COOR-ROTA> selection=( segid "2" ) SELRPN: 472 atoms have been selected out of 944 COOR: using atom subset. COOR-ROTA>end COOR: rotation center = 0.000000 0.000000 0.000000 COOR: selected coordinates rotated X-PLOR>duplicate selection=( segid "1" ) segid="3" end SELRPN: 472 atoms have been selected out of 944 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 1416(MAXA= 1600) NBOND= 1416(MAXB= 1600) NTHETA= 1944(MAXT= 3200) NGRP= 552(MAXGRP= 800) NPHI= 744(MAXP= 800) NIMPHI= 624(MAXIMP= 800) NDON= 360(MAXPAD= 400) NACC= 192(MAXPAD= 400) NNB= 72(MAXNB= 100) X-PLOR>coor rotate COOR-ROTA> matrix= MATRix-first-row= (-.5 0. -.866025) MATRix-second-row= (0. 1. 0.) MATRix-third-row= (.866025 0. -.5) Rotation matrix = -0.500000 0.000000 -0.866025 0.000000 1.000000 0.000000 0.866025 0.000000 -0.500000 Corresp. Eulerian angles (theta1,theta2,theta3) 90.0000 120.0000 270.0000 Corresp. spherical polar angles (psi,phi,kappa) 0.0000 0.0000 120.0000 Corresp. rotation angle 120.0000 about axis 0.0000 1.0000 0.0000 Corresp. quaternions 0.5000 0.0000 0.8660 0.0000 COOR-ROTA> selection=( segid "3" ) SELRPN: 472 atoms have been selected out of 1416 COOR: using atom subset. COOR-ROTA>end COOR: rotation center = 0.000000 0.000000 0.000000 COOR: selected coordinates rotated X-PLOR> X-PLOR>ncs strict init end X-PLOR>xrefin XREFINE> mask MASK> solrad=1.6 shrink=3. to=map1 MASK> selection=( resid 11 ) SELRPN: 192 atoms have been selected out of 1416 MASK> end XMASK: 192 atoms have been selected for mask calculation. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.6375 A XMASK: probe radius= 1.6000 shrink radius= 3.0000 XMASK: volume inside mask= 20.8333% (MAP1<=0) XMASK: volume outside mask= 79.1667% (MAP1=1) XREFINE> do (deri2=ft(map1 * 1.4)) ( all ) XMAPAL: allocating space for real space object. Total of 1728 map elements were selected. XSFAL: allocating space for complex reciprocal space object. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XSFAL: allocating space for complex reciprocal space object. Total of 113 structure factor elements were selected. XREFINE> XREFINE> show max (abs(deri1-deri2)) ( all ) Maximum of 113 elements = 0.0000 XREFINE> XREFINE>end X-PLOR>xrefin XREFINE> {* test probe mode *} XREFINE> mask MASK> probe=5. shrink=3. to=map1 MASK> mode=probe MASK> selection=( resid 11 ) SELRPN: 192 atoms have been selected out of 1416 MASK> end XMASK: 192 atoms have been selected for mask calculation. MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 0.0000 A XMASK: probe radius= 5.0000 shrink radius= 3.0000 XMASK: volume inside mask= 78.6458% (MAP1<=0) XMASK: volume outside mask= 21.3542% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 369 map elements were selected. XREFINE> XREFINE> {* test vdw mode *} XREFINE> mask MASK> probe=5. shrink=3. to=map1 MASK> mode=vdw MASK> selection=( resid 11 ) SELRPN: 192 atoms have been selected out of 1416 MASK> end XMASK: 192 atoms have been selected for mask calculation. MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.6375 A XMASK: probe radius= 5.0000 shrink radius= 3.0000 XMASK: volume inside mask= 98.4375% (MAP1<=0) XMASK: volume outside mask= 1.5625% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 27 map elements were selected. XREFINE> XREFINE> {* test sigma mode *} XREFINE> mask MASK> probe=5. shrink=3. to=map1 MASK> mode=sigma MASK> selection=( resid 11 ) SELRPN: 192 atoms have been selected out of 1416 MASK> end XMASK: 192 atoms have been selected for mask calculation. MASKX2: CPU-time: mask-calc= 0.0100 XMASK: average mask radius around selected atoms 1.4589 A XMASK: probe radius= 5.0000 shrink radius= 3.0000 XMASK: volume inside mask= 97.9167% (MAP1<=0) XMASK: volume outside mask= 2.0833% (MAP1=1) XREFINE> do (map1=1.4 ) (map1=1) Total of 36 map elements were selected. XREFINE> XREFINE> show max (real(map1)) ( all ) Maximum of 1728 elements = 1.4000 XREFINE> show min (real(map1)) ( all ) Minimum of 1728 elements = 0.0000 XREFINE> XREFINE> {* test sigma mode *} XREFINE> mask MASK> probe=5. shrink=3. to=map1 MASK> mode=sigma MASK> selection=( resid 11 ) SELRPN: 192 atoms have been selected out of 1416 MASK> end XMASK: 192 atoms have been selected for mask calculation. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 1.4589 A XMASK: probe radius= 5.0000 shrink radius= 3.0000 XMASK: volume inside mask= 97.9167% (MAP1<=0) XMASK: volume outside mask= 2.0833% (MAP1=1) XREFINE> XREFINE> display $inside $outside $averadius 0.979167 2.083333E-02 1.45885 XREFINE> XREFINE> do (map1=1.4 ) (map1=1) Total of 36 map elements were selected. XREFINE> XREFINE> do (map1=10) ( map1=0) Total of 1692 map elements were selected. XREFINE> XREFINE> show max (real(map1)) ( all ) Maximum of 1728 elements = 10.0000 XREFINE> show min (real(map1)) ( all ) Minimum of 1728 elements = 1.4000 XREFINE> XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR>structure reset end XPLOR: current counts (number in parenthesis is maximum) NATOM= 0(MAXA= 1600) NBOND= 0(MAXB= 1600) NTHETA= 0(MAXT= 3200) NGRP= 0(MAXGRP= 800) NPHI= 0(MAXP= 800) NIMPHI= 0(MAXIMP= 800) NDON= 0(MAXPAD= 400) NACC= 0(MAXPAD= 400) NNB= 0(MAXNB= 100) 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= 1600) NBOND= 403(MAXB= 1600) NTHETA= 581(MAXT= 3200) NGRP= 165(MAXGRP= 800) NPHI= 235(MAXP= 800) NIMPHI= 182(MAXIMP= 800) NDON= 69(MAXPAD= 400) NACC= 64(MAXPAD= 400) 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> X-PLOR>xrefin XREFINE> {* test averaging mode *} XREFINE> symmetry=(x,y,z) XRMAPR: symmetry or unitcell changed. Real space obj. deleted. XREFINE> symmetry=(-x,y+1/2,-z) XREFINE> hermitian=true XREFINE> asymmetric=(0<=x<1 and 0<=y<1/2 and 0<=z<1) XREFINE> XREFINE> a=40.96 b=18.65 c=22.52 alpha=90.0 beta=90.77 gamma=90.0 XREFINE> XREFINE>!! a=30. b=30. c=30. alpha=90.0 beta=90.00 gamma=90.0 XREFINE> XREFINE>!! symmetry reset XREFINE>!! symmetry=( X,Y,Z ) {* test with tetragonal space group P4(3)22 *} XREFINE>!! symmetry=( -X,-Y,1/2+Z ) XREFINE>!! symmetry=( -Y,X,3/4+Z ) XREFINE>!! symmetry=( Y,-X,1/4+Z ) XREFINE>!! symmetry=( -X,Y,-Z ) XREFINE>!! symmetry=( X,-Y,1/2-Z ) XREFINE>!! symmetry=( Y,X,1/4-Z ) XREFINE>!! symmetry=( -Y,-X,3/4-Z ) XREFINE>!! hermitian=true XREFINE>!! asymm=( 0<=x<1 XREFINE>!! and 0<=y<1 XREFINE>!! and 0<=z<=1/8 ) XREFINE> XREFINE> mask MASK> average=true MASK> probe=1.4 shrink=1. to=map1 MASK> mode=probe MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. 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. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 0.0000 A XMASK: probe radius= 1.4000 shrink radius= 1.0000 XMASK: volume inside mask= 34.0278% (MAP1<=0) XMASK: volume outside mask= 65.9722% (MAP1=1) XREFINE> XREFINE> show sum ( map1 ) ( map1<0) XREDUC: mapping reflections into standard asymmetric unit. XREDU2: 47 reflections have been deleted. Sum of 784 elements = -388165236.0000 XREFINE> show rms ( map1 ) ( map1<0) Rms of 784 elements = 45558.1844 XREFINE> show ave ( map1 ) ( map1<0) SHOW: average of 784 elements= -495108.7194 XREFINE> XREFINE>end X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> a=30. b=30. c=30. alpha=90.0 beta=90.00 gamma=90.0 XRMAPR: symmetry or unitcell changed. Real space obj. deleted. XREFINE> XREFINE> symmetry reset XREFINE> symmetry=( X,Y,Z ) {* test with tetragonal space group P4(3)22 *} XREFINE> symmetry=( -X,-Y,1/2+Z ) XREFINE> symmetry=( -Y,X,3/4+Z ) XREFINE> symmetry=( Y,-X,1/4+Z ) XREFINE> symmetry=( -X,Y,-Z ) XREFINE> symmetry=( X,-Y,1/2-Z ) XREFINE> symmetry=( Y,X,1/4-Z ) XREFINE> symmetry=( -Y,-X,3/4-Z ) XREFINE> hermitian=true XREFINE> asymm=( 0<=x<1 ASYMmetric> and 0<=y<1 ASYMmetric> and 0<=z<=1/8 ) XREFINE> XREFINE> mask MASK> average=true MASK> probe=1.4 shrink=1. to=map1 MASK> mode=probe MASK> selection=( all ) SELRPN: 396 atoms have been selected out of 396 MASK> end XMASK: 396 atoms have been selected for mask calculation. XMAPASU: using grid [ 20, 20, 20] and sublattice [ 20, 20, 20] Minimum brick that covers asymmetric unit: A= 0,..., 19 B= 0,..., 19 C= 0,..., 2 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. MASKX2: CPU-time: mask-calc= 0.0000 XMASK: average mask radius around selected atoms 0.0000 A XMASK: probe radius= 1.4000 shrink radius= 1.0000 XMASK: volume inside mask= 58.8000% (MAP1<=0) XMASK: volume outside mask= 41.2000% (MAP1=1) XREFINE> XREFINE> show sum ( map1 ) ( map1<0) XREDUC: mapping reflections into standard asymmetric unit. XREDU2: 41 reflections have been deleted. Sum of 596 elements = -287383439.0000 XREFINE> show rms ( map1 ) ( map1<0) Rms of 596 elements = 47106.1268 XREFINE> show ave ( map1 ) ( map1<0) SHOW: average of 596 elements= -482186.9782 XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>stop HEAP: maximum use= 2393724 current use= 1028007 X-PLOR: total CPU time= 0.3400 s X-PLOR: entry time at 10:28:31 04-Jun-04 X-PLOR: exit time at 10:28:31 04-Jun-04