X-PLOR: V3.1f user: white on: sgi at: 22-Oct-96 10:34:04 Author: Axel T. Brunger Copyright: 1988-92 (Yale University), 1987 (Harvard University) X-PLOR> remarks file xtalrefine/baoverall.inp X-PLOR> remarks Overall anisotropic B-factor refinement X-PLOR> remarks This job will produce a scaled data set X-PLOR> X-PLOR>{===>} parameter @TOPPAR:parhcsdx.pro end {*Read parameters.*} ASSFIL: file /usr/people/programs/xplor/toppar/parhcsdx.pro opened. PARRDR>REMARK Parameter file including bond and angle parameters PARRDR>REMARK derived from Cambridge Data Base model structures PARRDR>REMARK (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991). PARRDR>REMARK Dihedral, improper, and non-bonded parameters taken PARRDR>REMARK from param19x (XPLOR--Axel T. Brunger, Yale University, PARRDR>REMARK BRUNGER@YALEVMS) and assigned to new atom types PARRDR>REMARK where appropriate. PARRDR> PARRDR>set echo=false end PARRDR> end {*Read parameters.*} X-PLOR> X-PLOR>{===>} structure @generate.psf end {*Read structure file.*} ASSFIL: file generate.psf opened. STRUcture>PSF REMARKS FILENAME="generate.psf" REMARKS User: white REMARKS Directory: /data2/white/nuc011Y27W/proc/ REMARKS Input File: (PDB): y27w_M2.pdb REMARKS Output File: (this file): y27w_M2a.pdb REMARKS PDB file written by xfit(XtalView) on Mon Oct 21 16:40:16 1996 REMARKS User: white REMARKS Directory: /data2/white/nuc011Y27W/proc/ REMARKS Input File: (PDB): y27w_M2a.pdb REMARKS Output File: (this file): Exercise1.pdb REMARKS DATE:22-Oct-96 10:03:11 created by user: white XPLOR: current counts (number in parenthesis is maximum) NATOM= 1339(MAXA= 36000) NBOND= 1359(MAXB= 36000) NTHETA= 1965(MAXT= 50000) NGRP= 138(MAXGRP= 36000) NPHI= 818(MAXP= 60000) NIMPHI= 587(MAXIMP= 24000) NDON= 268(MAXPAD= 10000) NACC= 194(MAXPAD= 10000) NNB= 0(MAXNB= 4000) STRUcture> end {*Read structure file.*} X-PLOR> X-PLOR>{===>} coor @generate.pdb {*Read coordinates.*} ASSFIL: file generate.pdb opened. COOR>REMARK FILENAME="generate.pdb" COOR>REMARK User: white COOR>REMARK Directory: /data2/white/nuc011Y27W/proc/ COOR>REMARK Input File: (PDB): y27w_M2.pdb COOR>REMARK Output File: (this file): y27w_M2a.pdb COOR>REMARK PDB file written by xfit(XtalView) on Mon Oct 21 16:40:16 1996 COOR>REMARK User: white COOR>REMARK Directory: /data2/white/nuc011Y27W/proc/ COOR>REMARK Input File: (PDB): y27w_M2a.pdb COOR>REMARK Output File: (this file): Exercise1.pdb COOR>REMARK DATE:22-Oct-96 10:03:10 created by user: white COOR>ATOM 1 CB LYS 6 -1.644 40.734 21.408 1.00 34.83 COOR>ATOM 2 CG LYS 6 -2.960 40.861 20.655 1.00 37.38 X-PLOR> {*Read coordinates.*} X-PLOR> X-PLOR> X-PLOR> xrefine {*This invokes the *} XREFINE> {*crystallographic data parser.*} XREFINE>{===>} XREFINE> @cell.inp {*Unit cell+.Symmetry operators *} ASSFIL: file cell.inp opened. XREFINE>{*This is the unit cell and symmetry file read by ALL other *.inp files *} XREFINE> XREFINE>a=48.50 b=48.50 c=63.51 alpha=90.0 beta=90.0 gamma=90.0 {*Unit cell Y27W.*} XREFINE> XREFINE>{a=47.706 b=47.706 c=63.837 alpha=90.0 beta=90.0 gamma=90.0} {*Unit cell H124C_HG.*} XREFINE> XREFINE>{a=47.770 b=47.770 c=63.896 alpha=90.0 beta=90.0 gamma=90.0} {*native nuc026*} XREFINE>{a=47.706 b=47.706 c=63.837 alpha=90.0 beta=90.0 gamma=90.0} {*Hg deriv. nnuc025*} XREFINE> XREFINE>{===>} XREFINE> symmetry=(x,y,z) {*Symmetry operators for space *} XREFINE> symmetry=(-x, -y, z+1/2) {*group P41; notation as in*} XREFINE> symmetry=(-y, x, z+1/4) {*Int. Tables. *} XREFINE> symmetry=(y, -x, z+3/4) XREFINE> XREFINE> {*Unit cell+.Symmetry operators *} XREFINE> XREFINE> SCATter ( chemical C* ) SELRPN: 681 atoms have been selected out of 1339 a1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> SCATter ( chemical N* ) SELRPN: 193 atoms have been selected out of 1339 a1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> SCATter ( chemical O* ) SELRPN: 194 atoms have been selected out of 1339 a1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> SCATter ( chemical S* ) SELRPN: 3 atoms have been selected out of 1339 a1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> SCATter ( chemical P* ) SELRPN: 0 atoms have been selected out of 1339 a1= 6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490 XREFINE> SCATter ( chemical FE* ) SELRPN: 0 atoms have been selected out of 1339 a1= 11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070 XREFINE> SCATter ( chemical MR* ) SELRPN: 0 atoms have been selected out of 1339 a1= 11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070 XREFINE> {IMAGinary 2.2} XREFINE> {hermitian=false} {* Turns off FREIDEL symmetry *} XREFINE> XREFINE>{===>} XREFINE> nreflections=300000 XREFIN: allocating space for 300000 reflections. XREFINE> reflection @Exercise1.fob end {*Read reflections.*} ASSFIL: file Exercise1.fob opened. REFLection> INDE 7 0 0 FOBS= 12.371 PHAS= 0.000 SIGMA= 1.400 XRRR2: 12287 new reflections have been added. XREFINE> XREFINE>{###} XREFINE> fwind=0.1=100000 XREFINE> resolution 50.0 1.0 XREFINE> update-fcalc {*Compute fcalcs with current *} XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 12287 XRFILL: #scatt.= 1071 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [150,150,200] and sublattice [150(151),150(151), 20] XREFINE> {*B-factors stored in array B.*} XREFINE> GENErate XGENER: existing reflections will be conserved reducing existing reflections appending new reflections to produce a full set for the specified resolution range XRTEST: number of selected reflections 12287 XREDU2: 0 reflections have been deleted. The new Fobs are set to 1 except for systematic absences which are set to 0, Fcalc, Fpart are set to 0, weight, sigma, FOM are set to 1, test set to 0. XGENE2: 66909 new reflections have been generated. XREFINE> UPDAte XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 79149 XRFILL: #scatt.= 1071 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [150,150,200] and sublattice [150(151),150(151), 20] XREFINE> print rfactor XRTEST: number of selected reflections 79149 PRRFAC: optimum Fobs/Fcalc scale = 0.304 {{ (* resol.-range #reflections R-value Accum.*) { 2.00, 50.00, 10001, 0.5687, 0.5687 }, { 1.59, 2.00, 9910, 1.3324, 0.6940 }, { 1.39, 1.59, 9906, 20.8522, 0.8449 }, { 1.26, 1.39, 9879, 17.4528, 0.9680 }, { 1.17, 1.26, 9890, 16.3030, 1.0809 }, { 1.10, 1.17, 9812, 16.0599, 1.1895 }, { 1.05, 1.10, 9888, 14.6911, 1.2875 }, { 1.00, 1.05, 9863, 12.4339, 1.3676 }}, { (* Fobs-ampl-range #reflections R-value Accum.*) { 1.000, 55.636, 69771, 6.8510, 6.8510 }, { 55.636, 110.273, 4814, 0.4947, 2.5202 }, { 110.273, 164.909, 2578, 0.5276, 1.7709 }, { 164.909, 219.546, 1090, 0.5438, 1.5465 }, { 219.546, 274.182, 516, 0.5465, 1.4459 }, { 274.182, 328.818, 245, 0.5564, 1.3968 }, { 328.818, 383.455, 108, 0.5781, 1.3739 }, { 383.455, 438.091, 27, 0.5780, 1.3676 }}} XREFINE> write write-object= reflections fcalc {*Write FCALC to file.*} WRITE>{===>} WRITE> output=Exercise1.fcalc WRITE> end {*write*} ASSFIL: file Exercise1.fcalc opened. XRTEST: number of selected reflections 79149 XREFINE> XREFINE> end {*end xrefin*} X-PLOR> X-PLOR> stop CSTACK: size= 40000 used= 140 current= 0 HEAP: maximum use= 8928264 current use= 0 X-PLOR: total CPU time= 63.1188 s X-PLOR: entry time at 10:34:04 22-Oct-96 X-PLOR: exit time at 10:35:08 22-Oct-96