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 10:28:20 X-PLOR>REMARKS XFFTEST.INP X-PLOR>remarks test the FFT routines of XREFIN X-PLOR> X-PLOR>parameter @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>{* read a ca trace *} X-PLOR>struc STRUcture>PSF XPLOR: current counts (number in parenthesis is maximum) NATOM= 3(MAXA= 200) NBOND= 0(MAXB= 100) NTHETA= 0(MAXT= 100) NGRP= 2(MAXGRP= 100) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 100) STRUcture>end X-PLOR> X-PLOR>coor COOR>ATOM 1 CA LYS 1 8.000 8.000 8.000 1.00 15.00 COOR>ATOM 2 CA LYS 2 1.400 6.200 18.000 1.00 15.00 X-PLOR> X-PLOR>set timer=1 end X-PLOR> X-PLOR>{===================================================================} X-PLOR>{* test with arbitrary unit cell, P1 space group *} X-PLOR>{===================================================================} X-PLOR> X-PLOR>xrefin XREFINE> a=16.2 b=16.5 c=8.2 alpha=81.2 beta=94.5 gamma=100.3 XREFINE> XREFINE> symmetry=(x,y,z) XREFINE> SCATter ( chemical C* ) SELRPN: 3 atoms have been selected out of 3 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> method=direct lookup=false XREFINE> nreflections=1000 XREFIN: allocating space for 1000 reflections. XREFINE> generate update do (fobs=fcalc) 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: 164 new reflections have been generated. XREDUC: mapping reflections into standard asymmetric unit. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 DO> TOLERANCE=0.0 XRTEST: number of selected reflections 164 Total of 164 structure factor elements were selected. XREFINE> wa=200000. XREFINE> wp=61500. {* turn on phase info *} XREFINE> do (fom=1.) ( all ) Total of 164 structure factor elements were selected. XREFINE>end X-PLOR>coor translate vector=( 1.1 0.8 1.4 ) sele=( resid 1 ) end SELRPN: 1 atoms have been selected out of 3 COOR: using atom subset. COOR: translation vector =( 1.100000 0.800000 1.400000 ) COOR: selected coordinates translated X-PLOR> X-PLOR>flags exclu * inclu xref end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.150000 sec. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 0.895 R= 0.388 TRRESI: = 46.409 = 1.000 corr.= 0.000 = 46.409 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.150000 sec. --------------- cycle= 1 -------------------------------------------------- | Etotal =111646.642 grad(E)=17412.332 E(XREF)=111646.642 | ------------------------------------------------------------------------------- X-PLOR>vector do ( xcomp = dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( ycomp = dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( zcomp = dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>xrefin XREFINE> method=fft XREFINE> fft bscale=20.0 memory=50000 prime=5 avoid=2 end XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.150000 sec. XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 TRRESI: Fobs/Fcalc scale= 0.894 R= 0.387 TRRESI: = 46.352 = 1.000 corr.= 0.000 = 46.352 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.160000 sec. --------------- cycle= 2 -------------------------------------------------- | Etotal =111470.830 grad(E)=17092.122 E(XREF)=111470.830 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 25774. ( LYS 2 CA ) 4620.0 ( LYS 3 CA ) -19115. X-PLOR>vector show elem ( xcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 26415. ( LYS 2 CA ) 4367.6 ( LYS 3 CA ) -19523. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 2199.2 ( LYS 2 CA ) 7701.2 ( LYS 3 CA ) -11501. X-PLOR>vector show elem ( ycomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 2733.3 ( LYS 2 CA ) 7450.6 ( LYS 3 CA ) -11194. X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 34913. ( LYS 2 CA ) -2182.5 ( LYS 3 CA ) -12578. X-PLOR>vector show elem ( zcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 35807. ( LYS 2 CA ) -2358.3 ( LYS 3 CA ) -12440. X-PLOR>xrefin fft memory=250 end end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.160000 sec. XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 8( 9), 4( 5), 4] ************************************************ %XFFT-ERR: Warning: Extreme factorization of FFT. %XFFT: Factorization of FFT= 16 %XFFT: This may cause excessive CPU time usage. %XFFT: Resubmit with larger XREFin FFT MEMOry specification. %XFFT: Recommendation: MEMOry= 333 or larger. 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 TRRESI: Fobs/Fcalc scale= 0.894 R= 0.387 TRRESI: = 46.352 = 1.000 corr.= 0.000 = 46.352 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.170000 sec. --------------- cycle= 3 -------------------------------------------------- | Etotal =111470.829 grad(E)=17092.120 E(XREF)=111470.829 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 25774. ( LYS 2 CA ) 4620.0 ( LYS 3 CA ) -19115. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 2199.2 ( LYS 2 CA ) 7701.2 ( LYS 3 CA ) -11501. X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 34913. ( LYS 2 CA ) -2182.5 ( LYS 3 CA ) -12578. X-PLOR>xrefin XREFINE> fft memory=5000 bscale=0.0 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.898 R= 0.378 TRRESI: = 45.939 = 1.000 corr.= 0.000 = 45.939 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft bscale=10.0 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.895 R= 0.385 TRRESI: = 46.242 = 1.000 corr.= 0.000 = 46.242 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft bscale=20.0 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.894 R= 0.387 TRRESI: = 46.352 = 1.000 corr.= 0.000 = 46.352 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft elim=10.0 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.896 R= 0.387 TRRESI: = 46.340 = 1.000 corr.= 0.000 = 46.340 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft elim=3.0 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.925 R= 0.400 TRRESI: = 47.572 = 1.000 corr.= 0.000 = 47.572 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft elim=10.0 grid=0.25 end update print target XRTEST: number of selected reflections 164 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 24, 24, 12] and sublattice [ 24( 25), 24( 25), 6] 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 XRTEST: number of selected reflections 164 TRRESI: Fobs/Fcalc scale= 0.895 R= 0.388 TRRESI: = 46.409 = 1.000 corr.= 0.000 = 46.409 TARPA0: CPU-time: target-function= 0.0000 XREFINE> fft elim=7.00 grid=0.33333333 end XREFINE>end X-PLOR> X-PLOR> X-PLOR>{===================================================================} X-PLOR>{* test with P21 space group *} X-PLOR>{===================================================================} X-PLOR> X-PLOR>xrefin XREFINE> reset XREFIN: symmetry operators set to P1, all reciprocal and real space data scratched, atom scatter factors scratched. XREFINE> a=16.1 b=16.1 c=8.1 alpha=90. beta=130. gamma=90.0 XREFINE> XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(-x,y+1/2,-z) XREFINE> SCATter ( chemical C* ) SELRPN: 3 atoms have been selected out of 3 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> method=direct lookup=false XREFINE> generate update do (fobs=fcalc) 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: 71 new reflections have been generated. XREDUC: mapping reflections into standard asymmetric unit. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 71 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 DO> TOLERANCE=0.0 XRTEST: number of selected reflections 71 Total of 71 structure factor elements were selected. XREFINE> wa=200000. XREFINE> wp=45600.0 {* turn on phase info *} XREFINE> do (fom=1.) ( all ) Total of 71 structure factor elements were selected. XREFINE>end X-PLOR>coor translate vector=( 1.1 0.8 1.4 ) sele=( resid 1 ) end SELRPN: 1 atoms have been selected out of 3 COOR: using atom subset. COOR: translation vector =( 1.100000 0.800000 1.400000 ) COOR: selected coordinates translated X-PLOR> X-PLOR>flags exclu * inclu xref end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.180000 sec. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 71 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 1.004 R= 0.432 TRRESI: = 47.650 = 1.000 corr.= 0.000 = 47.650 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.180000 sec. --------------- cycle= 4 -------------------------------------------------- | Etotal =119618.265 grad(E)=30051.613 E(XREF)=119618.265 | ------------------------------------------------------------------------------- X-PLOR>vector do ( xcomp = dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( ycomp = dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( zcomp = dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>xrefin XREFINE> method=fft XREFINE> fft bscale=20.0 memory=50000 prime=5 avoid=2 end XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.180000 sec. XRTEST: number of selected reflections 71 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 TRRESI: Fobs/Fcalc scale= 1.003 R= 0.432 TRRESI: = 47.592 = 1.000 corr.= 0.000 = 47.592 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.180000 sec. --------------- cycle= 5 -------------------------------------------------- | Etotal =119463.095 grad(E)=30086.630 E(XREF)=119463.095 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 26612. ( LYS 2 CA ) 4119.8 ( LYS 3 CA ) -76404. X-PLOR>vector show elem ( xcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 27475. ( LYS 2 CA ) 3333.6 ( LYS 3 CA ) -75979. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -13056. ( LYS 2 CA ) 4256.7 ( LYS 3 CA ) 12101. X-PLOR>vector show elem ( ycomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -13008. ( LYS 2 CA ) 4115.2 ( LYS 3 CA ) 11927. X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 30479. ( LYS 2 CA ) 14953. ( LYS 3 CA ) 9827.2 X-PLOR>vector show elem ( zcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 30470. ( LYS 2 CA ) 14949. ( LYS 3 CA ) 10434. X-PLOR>xrefin fft memory=250 end end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.180000 sec. XRTEST: number of selected reflections 71 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 8( 9), 4( 5), 4] ************************************************ %XFFT-ERR: Warning: Extreme factorization of FFT. %XFFT: Factorization of FFT= 16 %XFFT: This may cause excessive CPU time usage. %XFFT: Resubmit with larger XREFin FFT MEMOry specification. %XFFT: Recommendation: MEMOry= 333 or larger. 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 TRRESI: Fobs/Fcalc scale= 1.003 R= 0.432 TRRESI: = 47.592 = 1.000 corr.= 0.000 = 47.592 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.190000 sec. --------------- cycle= 6 -------------------------------------------------- | Etotal =119463.093 grad(E)=30086.626 E(XREF)=119463.093 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 26612. ( LYS 2 CA ) 4119.8 ( LYS 3 CA ) -76404. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -13056. ( LYS 2 CA ) 4256.7 ( LYS 3 CA ) 12101. X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 30479. ( LYS 2 CA ) 14953. ( LYS 3 CA ) 9827.2 X-PLOR> X-PLOR>{===============================} X-PLOR>{* test with P31c space group *} X-PLOR>{==============================*} X-PLOR> X-PLOR>xrefin XREFINE> reset XREFIN: symmetry operators set to P1, all reciprocal and real space data scratched, atom scatter factors scratched. XREFINE> a=16.00 b=16.00 c=8.00 alpha=90.0 beta=90.00 gamma=120.0 XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(-y,x-y,z) XREFINE> symmetry=(y-x,-x,z) XREFINE>! symmetry=(y,x,1/2+z) XREFINE>! symmetry=(-x,y-x,1/2+z) XREFINE>! symmetry=(x-y,-y,1/2+z) XREFINE> SCATter ( chemical C* ) SELRPN: 3 atoms have been selected out of 3 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> method=direct lookup=false 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: 47 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 47 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XREFINE> write reflection fobs fcalc end XRTEST: number of selected reflections 47 NREFlection= 47 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END DECLare NAME=FCALC DOMAin=RECIprocal TYPE=COMP END INDE 2 0 0 FOBS= 1.000 0.000 FCALC= 4.500 167.613 INDE 3 0 0 FOBS= 1.000 0.000 FCALC= 5.560 330.486 INDE 4 0 0 FOBS= 1.000 0.000 FCALC= 4.406 37.393 INDE 1 1 0 FOBS= 1.000 0.000 FCALC= 17.536 254.108 INDE 2 1 0 FOBS= 1.000 0.000 FCALC= 12.073 298.670 INDE 3 1 0 FOBS= 1.000 0.000 FCALC= 9.617 56.262 INDE 4 1 0 FOBS= 1.000 0.000 FCALC= 2.030 167.352 INDE 1 2 0 FOBS= 1.000 0.000 FCALC= 4.796 50.965 INDE 2 2 0 FOBS= 1.000 0.000 FCALC= 17.307 143.655 INDE 3 2 0 FOBS= 1.000 0.000 FCALC= 8.599 217.109 INDE 1 3 0 FOBS= 1.000 0.000 FCALC= 3.902 326.960 INDE 2 3 0 FOBS= 1.000 0.000 FCALC= 4.766 7.203 INDE 1 4 0 FOBS= 1.000 0.000 FCALC= 4.727 337.576 INDE 0 0 1 FOBS= 1.000 0.000 FCALC= 29.487 77.163 INDE 1 0 1 FOBS= 1.000 0.000 FCALC= 15.429 148.031 INDE 2 0 1 FOBS= 1.000 0.000 FCALC= 3.717 242.006 INDE 3 0 1 FOBS= 1.000 0.000 FCALC= 8.857 133.938 INDE 4 0 1 FOBS= 1.000 0.000 FCALC= 6.369 176.337 INDE 0 1 1 FOBS= 1.000 0.000 FCALC= 11.754 268.253 INDE 1 1 1 FOBS= 1.000 0.000 FCALC= 24.020 6.869 INDE 2 1 1 FOBS= 1.000 0.000 FCALC= 6.548 81.860 INDE 3 1 1 FOBS= 1.000 0.000 FCALC= 3.683 275.460 INDE -1 2 1 FOBS= 1.000 0.000 FCALC= 18.726 245.062 INDE 0 2 1 FOBS= 1.000 0.000 FCALC= 4.297 331.695 INDE 1 2 1 FOBS= 1.000 0.000 FCALC= 2.538 310.630 INDE 2 2 1 FOBS= 1.000 0.000 FCALC= 3.280 234.020 INDE -2 3 1 FOBS= 1.000 0.000 FCALC= 11.891 333.981 INDE -1 3 1 FOBS= 1.000 0.000 FCALC= 13.697 114.500 INDE 0 3 1 FOBS= 1.000 0.000 FCALC= 12.877 155.290 INDE 1 3 1 FOBS= 1.000 0.000 FCALC= 9.149 190.167 INDE -3 4 1 FOBS= 1.000 0.000 FCALC= 11.188 98.101 INDE -2 4 1 FOBS= 1.000 0.000 FCALC= 11.561 256.075 INDE -1 4 1 FOBS= 1.000 0.000 FCALC= 12.628 355.850 INDE 0 4 1 FOBS= 1.000 0.000 FCALC= 3.708 53.510 INDE 0 0 2 FOBS= 1.000 0.000 FCALC= 11.186 252.000 INDE 1 0 2 FOBS= 1.000 0.000 FCALC= 2.517 163.904 INDE 2 0 2 FOBS= 1.000 0.000 FCALC= 1.881 246.627 INDE 3 0 2 FOBS= 1.000 0.000 FCALC= 5.498 231.539 INDE 0 1 2 FOBS= 1.000 0.000 FCALC= 3.678 245.605 INDE 1 1 2 FOBS= 1.000 0.000 FCALC= 14.080 99.303 INDE 2 1 2 FOBS= 1.000 0.000 FCALC= 13.295 185.304 INDE -1 2 2 FOBS= 1.000 0.000 FCALC= 14.233 339.853 INDE 0 2 2 FOBS= 1.000 0.000 FCALC= 5.857 75.245 INDE 1 2 2 FOBS= 1.000 0.000 FCALC= 6.802 312.603 INDE -2 3 2 FOBS= 1.000 0.000 FCALC= 10.757 26.769 INDE -1 3 2 FOBS= 1.000 0.000 FCALC= 9.002 149.008 INDE 0 3 2 FOBS= 1.000 0.000 FCALC= 9.254 250.254 XREFINE> print completeness XRTEST: number of selected reflections 47 PRRDAT: reducing reflections {{ (* resol.-range %Completeness %Accum.*) { 5.66, 10.00, 100.0000, 100.0000 }, { 4.64, 5.66, 100.0000, 100.0000 }, { 4.10, 4.64, 100.0000, 100.0000 }, { 3.75, 4.10, 100.0000, 100.0000 }, { 3.49, 3.75, 100.0000, 100.0000 }, { 3.29, 3.49, 100.0000, 100.0000 }, { 3.13, 3.29, 100.0000, 100.0000 }, { 3.00, 3.13, 100.0000, 100.0000 }}, XREFINE> do (fobs=fcalc) DO> TOLERANCE=0.0 XRTEST: number of selected reflections 47 Total of 47 structure factor elements were selected. XREFINE> wa=200000. XREFINE> wp=48000.0 {* turn on phase info *} XREFINE> do (fom=1.) ( all ) Total of 47 structure factor elements were selected. XREFINE>end X-PLOR>coor translate vector=( 1.1 0.8 1.4 ) sele=( resid 1 ) end SELRPN: 1 atoms have been selected out of 3 COOR: using atom subset. COOR: translation vector =( 1.100000 0.800000 1.400000 ) COOR: selected coordinates translated X-PLOR> X-PLOR>flags exclu * inclu xref end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 47 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 0.937 R= 0.444 TRRESI: = 57.545 = 1.000 corr.= 0.000 = 57.545 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.200000 sec. --------------- cycle= 7 -------------------------------------------------- | Etotal =122765.402 grad(E)=25011.384 E(XREF)=122765.402 | ------------------------------------------------------------------------------- X-PLOR>vector do ( xcomp = dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( ycomp = dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( zcomp = dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR> X-PLOR>xrefin XREFINE> method=fft XREFINE> fft bscale=20.0 memory=50000 prime=5 avoid=2 end XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. XRTEST: number of selected reflections 47 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 8] 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 TRRESI: Fobs/Fcalc scale= 0.934 R= 0.444 TRRESI: = 57.460 = 1.000 corr.= 0.000 = 57.460 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.200000 sec. --------------- cycle= 8 -------------------------------------------------- | Etotal =122586.155 grad(E)=24737.524 E(XREF)=122586.155 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -3825.4 ( LYS 2 CA ) -9302.3 ( LYS 3 CA ) -2641.7 X-PLOR>vector show elem ( xcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -3514.5 ( LYS 2 CA ) -9338.9 ( LYS 3 CA ) -2654.6 X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 4875.0 ( LYS 2 CA ) 54209. ( LYS 3 CA ) 8370.7 X-PLOR>vector show elem ( ycomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 5166.1 ( LYS 2 CA ) 54087. ( LYS 3 CA ) 8222.5 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 37495. ( LYS 2 CA ) -8461.7 ( LYS 3 CA ) -29823. X-PLOR>vector show elem ( zcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 38989. ( LYS 2 CA ) -8211.2 ( LYS 3 CA ) -30271. X-PLOR>xrefin fft memory=2000 end end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. XRTEST: number of selected reflections 47 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 16( 17), 16( 17), 4] 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 TRRESI: Fobs/Fcalc scale= 0.934 R= 0.444 TRRESI: = 57.460 = 1.000 corr.= 0.000 = 57.460 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.200000 sec. --------------- cycle= 9 -------------------------------------------------- | Etotal =122586.153 grad(E)=24737.525 E(XREF)=122586.153 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -3825.4 ( LYS 2 CA ) -9302.3 ( LYS 3 CA ) -2641.7 X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 4875.0 ( LYS 2 CA ) 54209. ( LYS 3 CA ) 8370.7 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 37495. ( LYS 2 CA ) -8461.7 ( LYS 3 CA ) -29823. X-PLOR>xrefin fft memory=250 end end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.200000 sec. XRTEST: number of selected reflections 47 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 8] and sublattice [ 8( 9), 4( 5), 4] ************************************************ %XFFT-ERR: Warning: Extreme factorization of FFT. %XFFT: Factorization of FFT= 16 %XFFT: This may cause excessive CPU time usage. %XFFT: Resubmit with larger XREFin FFT MEMOry specification. %XFFT: Recommendation: MEMOry= 333 or larger. XFFT: CPU-time: electron-density-calc= 0.0000 XFFT: CPU-time: FFT of electron density= 0.0100 XFFT: CPU-time: transformation into A, B= 0.0000 TRRESI: Fobs/Fcalc scale= 0.934 R= 0.444 TRRESI: = 57.460 = 1.000 corr.= 0.000 = 57.460 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.210000 sec. --------------- cycle= 10 -------------------------------------------------- | Etotal =122586.156 grad(E)=24737.523 E(XREF)=122586.156 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -3825.4 ( LYS 2 CA ) -9302.3 ( LYS 3 CA ) -2641.7 X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 4875.0 ( LYS 2 CA ) 54209. ( LYS 3 CA ) 8370.7 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 37495. ( LYS 2 CA ) -8461.7 ( LYS 3 CA ) -29823. X-PLOR> X-PLOR> X-PLOR>{* ============================ *} X-PLOR>{* test with P2(1)3 space group *} X-PLOR>{* ============================ *} X-PLOR>xrefin XREFINE> reset XREFIN: symmetry operators set to P1, all reciprocal and real space data scratched, atom scatter factors scratched. XREFINE> a=16.00 b=16.00 c=16.00 alpha=90.0 beta=90.00 gamma=90.0 XREFINE> {* space_group=P2(1)3 *} XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(z,x,y) XREFINE> symmetry=(y,z,x) XREFINE> symmetry=(1/2+x,1/2-y,-z) XREFINE> symmetry=(1/2+z,1/2-x,-y) XREFINE> symmetry=(1/2+y,1/2-z,-x) XREFINE> symmetry=(-x,1/2+y,1/2-z) XREFINE> symmetry=(-z,1/2+x,1/2-y) XREFINE> symmetry=(-y,1/2+z,1/2-x) XREFINE> symmetry=(1/2-x,-y,1/2+z) XREFINE> symmetry=(1/2-z,-x,1/2+y) XREFINE> symmetry=(1/2-y,-z,1/2+x) XREFINE> SCATter ( chemical C* ) SELRPN: 3 atoms have been selected out of 3 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> method=direct lookup=false 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: 36 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 36 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XREFINE> write reflection fobs fcalc end XRTEST: number of selected reflections 36 NREFlection= 36 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END DECLare NAME=FCALC DOMAin=RECIprocal TYPE=COMP END INDE 2 0 0 FOBS= 1.000 0.000 FCALC= 5.513 180.000 INDE 4 0 0 FOBS= 1.000 0.000 FCALC= 30.738 180.000 INDE 2 1 0 FOBS= 1.000 0.000 FCALC= 25.677 0.000 INDE 3 1 0 FOBS= 1.000 0.000 FCALC= 26.606 270.000 INDE 4 1 0 FOBS= 1.000 0.000 FCALC= 22.963 180.000 INDE 5 1 0 FOBS= 1.000 0.000 FCALC= 6.105 270.000 INDE 2 2 0 FOBS= 1.000 0.000 FCALC= 29.658 0.000 INDE 3 2 0 FOBS= 1.000 0.000 FCALC= 9.405 90.000 INDE 4 2 0 FOBS= 1.000 0.000 FCALC= 23.927 180.000 INDE 3 3 0 FOBS= 1.000 0.000 FCALC= 3.643 90.000 INDE 4 3 0 FOBS= 1.000 0.000 FCALC= 11.275 180.000 INDE 2 0 1 FOBS= 1.000 0.000 FCALC= 6.759 90.000 INDE 3 0 1 FOBS= 1.000 0.000 FCALC= 40.389 270.000 INDE 4 0 1 FOBS= 1.000 0.000 FCALC= 2.724 90.000 INDE 5 0 1 FOBS= 1.000 0.000 FCALC= 1.780 90.000 INDE 1 1 1 FOBS= 1.000 0.000 FCALC= 72.638 151.054 INDE 2 1 1 FOBS= 1.000 0.000 FCALC= 20.611 236.913 INDE 3 1 1 FOBS= 1.000 0.000 FCALC= 38.452 295.318 INDE 4 1 1 FOBS= 1.000 0.000 FCALC= 7.667 290.421 INDE 5 1 1 FOBS= 1.000 0.000 FCALC= 16.794 4.649 INDE 2 2 1 FOBS= 1.000 0.000 FCALC= 19.711 118.291 INDE 3 2 1 FOBS= 1.000 0.000 FCALC= 14.093 59.040 INDE 4 2 1 FOBS= 1.000 0.000 FCALC= 26.984 8.919 INDE 3 3 1 FOBS= 1.000 0.000 FCALC= 20.947 298.740 INDE 4 3 1 FOBS= 1.000 0.000 FCALC= 19.575 174.094 INDE 3 0 2 FOBS= 1.000 0.000 FCALC= 12.600 180.000 INDE 4 0 2 FOBS= 1.000 0.000 FCALC= 10.236 180.000 INDE 3 1 2 FOBS= 1.000 0.000 FCALC= 22.480 141.117 INDE 4 1 2 FOBS= 1.000 0.000 FCALC= 14.870 33.686 INDE 2 2 2 FOBS= 1.000 0.000 FCALC= 52.876 114.766 INDE 3 2 2 FOBS= 1.000 0.000 FCALC= 26.089 340.615 INDE 4 2 2 FOBS= 1.000 0.000 FCALC= 14.206 141.327 INDE 3 3 2 FOBS= 1.000 0.000 FCALC= 23.255 210.947 INDE 4 0 3 FOBS= 1.000 0.000 FCALC= 23.006 270.000 INDE 4 1 3 FOBS= 1.000 0.000 FCALC= 1.989 145.972 INDE 3 3 3 FOBS= 1.000 0.000 FCALC= 13.211 272.125 XREFINE> print completeness XRTEST: number of selected reflections 36 PRRDAT: reducing reflections {{ (* resol.-range %Completeness %Accum.*) { 5.66, 10.00, 100.0000, 100.0000 }, { 4.64, 5.66, 100.0000, 100.0000 }, { 4.10, 4.64, 100.0000, 100.0000 }, { 3.75, 4.10, 100.0000, 100.0000 }, { 3.49, 3.75, 100.0000, 100.0000 }, { 3.29, 3.49, 100.0000, 100.0000 }, { 3.13, 3.29, 100.0000, 100.0000 }, { 3.00, 3.13, 100.0000, 100.0000 }}, XREFINE> do (fobs=fcalc) DO> TOLERANCE=0.0 XRTEST: number of selected reflections 36 Total of 36 structure factor elements were selected. XREFINE> wa=200000. XREFINE> wp=102000.0 {* turn on phase info *} XREFINE> do (fom=1.) ( all ) Total of 36 structure factor elements were selected. XREFINE>end X-PLOR>coor translate vector=( 1.1 0.8 1.4 ) sele=( resid 1 ) end SELRPN: 1 atoms have been selected out of 3 COOR: using atom subset. COOR: translation vector =( 1.100000 0.800000 1.400000 ) COOR: selected coordinates translated X-PLOR> X-PLOR>flags exclu * inclu xref end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.220000 sec. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 36 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 0.972 R= 0.388 TRRESI: = 50.463 = 1.000 corr.= 0.000 = 50.463 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.220000 sec. --------------- cycle= 11 -------------------------------------------------- | Etotal =245392.633 grad(E)=18423.637 E(XREF)=245392.633 | ------------------------------------------------------------------------------- X-PLOR>vector do ( xcomp = dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( ycomp = dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR>vector do ( zcomp = dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 X-PLOR> X-PLOR>xrefin XREFINE> method=fft XREFINE> fft bscale=20.0 memory=50000 prime=5 avoid=2 end XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.220000 sec. XRTEST: number of selected reflections 36 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 16] and sublattice [ 16( 17), 16( 17), 16] 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 TRRESI: Fobs/Fcalc scale= 0.972 R= 0.388 TRRESI: = 50.427 = 1.000 corr.= 0.000 = 50.427 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.220000 sec. --------------- cycle= 12 -------------------------------------------------- | Etotal =245025.883 grad(E)=18325.269 E(XREF)=245025.883 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 10761. ( LYS 2 CA ) 24340. ( LYS 3 CA ) -2294.5 X-PLOR>vector show elem ( xcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 10659. ( LYS 2 CA ) 24475. ( LYS 3 CA ) -2550.9 X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -17436. ( LYS 2 CA ) 38998. ( LYS 3 CA ) -7791.4 X-PLOR>vector show elem ( ycomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -17289. ( LYS 2 CA ) 39507. ( LYS 3 CA ) -7989.4 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 14066. ( LYS 2 CA ) -7852.9 ( LYS 3 CA ) -12796. X-PLOR>vector show elem ( zcomp ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 13639. ( LYS 2 CA ) -8317.7 ( LYS 3 CA ) -12530. X-PLOR> X-PLOR>xrefin fft memory=1000 end end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.220000 sec. XRTEST: number of selected reflections 36 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 16, 16, 16] and sublattice [ 16( 17), 8( 9), 4] 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 TRRESI: Fobs/Fcalc scale= 0.972 R= 0.388 TRRESI: = 50.427 = 1.000 corr.= 0.000 = 50.427 TARPA0: CPU-time: target-function= 0.0000 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 ENERGY: after XPLOR terms CPU= 0.230000 sec. --------------- cycle= 13 -------------------------------------------------- | Etotal =245025.887 grad(E)=18325.272 E(XREF)=245025.887 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 10761. ( LYS 2 CA ) 24340. ( LYS 3 CA ) -2294.5 X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -17436. ( LYS 2 CA ) 38998. ( LYS 3 CA ) -7791.4 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 14066. ( LYS 2 CA ) -7852.9 ( LYS 3 CA ) -12796. X-PLOR> X-PLOR> X-PLOR>{* check sorting of reflections *} X-PLOR> X-PLOR>xrefin XREFINE> method=FFT XREFINE> resolution 4.01 7.01 wp=32700. XREFINE> fft grid=0.15 memory=500000 end XREFINE> do (fom=1) DO>end XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 11 Total of 11 structure factor elements were selected. X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.230000 sec. XRTEST: number of selected reflections 11 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 27, 27, 30] and sublattice [ 27( 27), 27( 27), 30] 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 TRRESI: Fobs/Fcalc scale= 1.106 R= 0.340 TRRESI: = 70.123 = 1.000 corr.= 0.000 = 70.123 TARPA0: CPU-time: target-function= 0.0000 XFFT: CPU-time: electron-density-calc= 0.0000 XFFT: CPU-time: FFT of electron density= 0.0000 XFFT: CPU-time: transformation into A, B= 0.0100 ENERGY: after XPLOR terms CPU= 0.240000 sec. --------------- cycle= 14 -------------------------------------------------- | Etotal =137962.969 grad(E)=10016.568 E(XREF)=137962.969 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 16464. ( LYS 2 CA ) -10615. ( LYS 3 CA ) -19185. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 3960.7 ( LYS 2 CA ) 6866.4 ( LYS 3 CA ) 4772.6 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -107.61 ( LYS 2 CA ) -7865.2 ( LYS 3 CA ) 1925.5 X-PLOR> X-PLOR>xrefin XREFINE> method=direct lookup=false XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.240000 sec. XRTEST: number of selected reflections 11 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 1.110 R= 0.340 TRRESI: = 70.124 = 1.000 corr.= 0.000 = 70.124 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.240000 sec. --------------- cycle= 15 -------------------------------------------------- | Etotal =137941.917 grad(E)=10074.773 E(XREF)=137941.917 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 16517. ( LYS 2 CA ) -10354. ( LYS 3 CA ) -19445. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 3834.5 ( LYS 2 CA ) 7069.6 ( LYS 3 CA ) 4635.2 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -117.49 ( LYS 2 CA ) -7996.3 ( LYS 3 CA ) 2297.6 X-PLOR> X-PLOR>{* check partial turning off phase information *} X-PLOR>xrefin XREFINE> resolution 5.01 6.01 XREFINE> do (FOM = 0) DO> resolution 4.01 7.01 wp=20400 XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 4 Total of 4 structure factor elements were selected. XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.240000 sec. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 11 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 TRRESI: Fobs/Fcalc scale= 1.110 R= 0.340 TRRESI: = 97.649 = 1.000 corr.= 0.000 = 97.649 TARPA0: CPU-time: target-function= 0.0000 ENERGY: after XPLOR terms CPU= 0.240000 sec. --------------- cycle= 16 -------------------------------------------------- | Etotal =129096.564 grad(E)=10467.081 E(XREF)=129096.564 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 17962. ( LYS 2 CA ) -5032.3 ( LYS 3 CA ) -21139. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 3680.3 ( LYS 2 CA ) 10565. ( LYS 3 CA ) 1501.1 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -293.39 ( LYS 2 CA ) -6544.6 ( LYS 3 CA ) 4573.6 X-PLOR> X-PLOR>xrefin XREFINE> method=FFT XREFINE>end X-PLOR>energy end XPLOR_ENERGY: at entry CPU= 0.240000 sec. XRTEST: number of selected reflections 11 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 3 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 27, 27, 30] and sublattice [ 27( 27), 27( 27), 30] 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 TRRESI: Fobs/Fcalc scale= 1.106 R= 0.340 TRRESI: = 97.647 = 1.000 corr.= 0.000 = 97.647 TARPA0: CPU-time: target-function= 0.0000 XFFT: CPU-time: electron-density-calc= 0.0000 XFFT: CPU-time: FFT of electron density= 0.0000 XFFT: CPU-time: transformation into A, B= 0.0100 ENERGY: after XPLOR terms CPU= 0.250000 sec. --------------- cycle= 17 -------------------------------------------------- | Etotal =129117.239 grad(E)=10363.219 E(XREF)=129117.239 | ------------------------------------------------------------------------------- X-PLOR>vector show elem ( dx ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 17892. ( LYS 2 CA ) -5338.2 ( LYS 3 CA ) -20857. X-PLOR>vector show elem ( dy ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) 3804.9 ( LYS 2 CA ) 10332. ( LYS 3 CA ) 1661.3 X-PLOR>vector show elem ( dz ) ( all ) SELRPN: 3 atoms have been selected out of 3 ( LYS 1 CA ) -274.54 ( LYS 2 CA ) -6427.5 ( LYS 3 CA ) 4188.7 X-PLOR> X-PLOR>stop HEAP: maximum use= 1074581 current use= 868117 X-PLOR: total CPU time= 0.2500 s X-PLOR: entry time at 10:28:20 04-Jun-04 X-PLOR: exit time at 10:28:20 04-Jun-04