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 10:28:24 X-PLOR>remarks file XPRED.INP -- test prediction facility X-PLOR>remarks Author: Axel T. Brunger X-PLOR> X-PLOR>topology @TOPPAR:toph19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pro opened. RTFRDR>REMARKS TOPH19.PRO ( protein topology ) RTFRDR>REMARKS =============================== RTFRDR>REMARKS Charges and atom order modified for neutral GROUPs. RTFRDR>REMARKS Histidine charges set to Del Bene and Cohen sto-3g calculations. RTFRDR>REMARKS Amide charges set to match the experimental dipole moment. RTFRDR>REMARKS Default for HIStidines is the doubly protonated state RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>param @TOPPAR:param19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param19.pro opened. PARRDR>remark - parameter file PARAM19 - PARRDR>remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR> PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>segment SEGMENT> chain CHAIN> @TOPPAR:toph19.pep ASSFIL: file /home/schwitrs/xplor/toppar/toph19.pep opened. CHAIN>REMARKS TOPH19.pep -MACRO for protein sequence CHAIN>SET ECHO=FALSE END CHAIN> sequence SEQUENCE> THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE ASN VAL CYS MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = ARG LEU PRO GLY THR PRO GLU ALA ILE CYS ALA THR TYR THR GLY CYS SEQUence-element (terminate with END) = ILE ILE ILE PRO GLY ALA THR CYS PRO GLY ASP TYR ALA ASN SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN> end SEGMENT>end SEGMNT: 46 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 396(MAXA= 400) NBOND= 403(MAXB= 800) NTHETA= 581(MAXT= 800) NGRP= 165(MAXGRP= 200) NPHI= 235(MAXP= 400) NIMPHI= 182(MAXIMP= 200) NDON= 69(MAXPAD= 100) NACC= 64(MAXPAD= 100) NNB= 9(MAXNB= 100) X-PLOR> X-PLOR> X-PLOR>coor COOR>ATOM 1 HT1 THR 1 16.206 14.668 3.850 0.00 0.00 COOR>ATOM 2 HT2 THR 1 17.090 13.935 2.599 0.00 0.00 X-PLOR> X-PLOR>set timing=on end X-PLOR> X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> method=fft XREFINE> a=40.96 b=18.65 c=22.52 alpha=90.0 beta=90.77 gamma=90.0 XREFINE> fft XFFT> grid=0.33333333 prime=5 avoid=2 ! sampling grid of Patterson XFFT> end XREFINE> !! scattering tables, from SCATT input XREFINE> !! XREFINE> SCATter ( chemical C* ) SELRPN: 202 atoms have been selected out of 396 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 55 atoms have been selected out of 396 SCATTER_A1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> XREFINE> SCATter ( chemical O* ) SELRPN: 64 atoms have been selected out of 396 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 6 atoms have been selected out of 396 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(-x,y+1/2,-z) XREFINE> XREFINE> asymmetric=(0<=x<1 and 0<=y<1/2 and 0<=z<1) XREFINE> XREFINE> resolution 10. 5.0 XREFINE> XREFINE> nreflection=40000 XREFIN: allocating space for 40000 reflections. XREFINE> generate XGENER: generating reflections to produce a full set for the specified resolution range. The new Fobs are set to 1 and weight is set to 1, all other reciprocal space objects are set to 0. XGENE2: 150 new reflections have been generated. XREFINE> XREFINE> method=fft XREFINE> XREFINE> update XREDUC: mapping reflections into standard asymmetric unit. XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 150 %XREFIN-error: zero occupancies --> all set to one CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 24, 12, 16] and sublattice [ 24( 25), 12( 13), 16] XFFT: CPU-time: electron-density-calc= 0.0000 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 150 structure factor elements were selected. XREFINE> XREFINE> print R XREFIN: selected reflections will be sorted by index. XRTEST: number of selected reflections 150 PRRFAC: optimum Fobs/Fcalc scale = 1.000 {{ (* resol.-range #reflections R-value Accum.*) { 8.11, 10.00, 23, 0.0000, 0.0000 }, { 7.14, 8.11, 17, 0.0000, 0.0000 }, { 6.51, 7.14, 23, 0.0000, 0.0000 }, { 6.06, 6.51, 13, 0.0000, 0.0000 }, { 5.71, 6.06, 19, 0.0000, 0.0000 }, { 5.43, 5.71, 19, 0.0000, 0.0000 }, { 5.20, 5.43, 21, 0.0000, 0.0000 }, { 5.00, 5.20, 15, 0.0000, 0.0000 }}, { (* Fobs-ampl-range #reflections R-value Accum.*) { 10.277, 85.744, 39, 0.0000, 0.0000 }, { 85.744, 161.211, 52, 0.0000, 0.0000 }, { 161.211, 236.678, 40, 0.0000, 0.0000 }, { 236.678, 312.144, 11, 0.0000, 0.0000 }, { 312.144, 387.611, 5, 0.0000, 0.0000 }, { 387.611, 463.078, 1, 0.0000, 0.0000 }, { 463.078, 538.545, 1, 0.0000, 0.0000 }, { 538.545, 614.012, 1, 0.0000, 0.0000 }}} XREFINE> XREFINE>end X-PLOR> X-PLOR> X-PLOR> X-PLOR>vector do (b=b+20) ( all ) SELRPN: 396 atoms have been selected out of 396 X-PLOR> X-PLOR> X-PLOR>xrefin XREFINE> predict mode=real to=map1 ? end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 |-----------------------precict------------------------------------- | MODE = REAL | TO = MAP1 |------------------------------------------------------------------- XMAPASU: using grid [ 24, 12, 16] and sublattice [ 24, 12, 16] Minimum brick that covers asymmetric unit: A= 0,..., 23 B= 0,..., 5 C= 0,..., 15 XMAPAS2: CPU-time: fill RHOMASK= 0.0000 XMAPAS2: CPU-time: boundary, special pos. check= 0.0000 XMAPAL: allocating space for real space object. XPRED: CPU-time: predict-calc= 0.0100 XREFINE> XREFINE> do (fcalc=ft(map1)) ( all ) XMAPAL: allocating space for real space object. Total of 2304 map elements were selected. XDOIFT: CPU-time: transformation1= 0.0000 XDOIFT: CPU-time: FFT= 0.0000 XDOIFT: CPU-time: transformation2= 0.0000 XREFINE> XREFINE> do (fcalc=fcalc exp(20. s^2/4) ) ( all ) Total of 150 structure factor elements were selected. XREFINE> XREFINE> print R XRTEST: number of selected reflections 150 PRRFAC: optimum Fobs/Fcalc scale = 1.000 {{ (* resol.-range #reflections R-value Accum.*) { 8.11, 10.00, 23, 0.0000, 0.0000 }, { 7.14, 8.11, 17, 0.0000, 0.0000 }, { 6.51, 7.14, 23, 0.0000, 0.0000 }, { 6.06, 6.51, 13, 0.0000, 0.0000 }, { 5.71, 6.06, 19, 0.0000, 0.0000 }, { 5.43, 5.71, 19, 0.0000, 0.0000 }, { 5.20, 5.43, 21, 0.0000, 0.0000 }, { 5.00, 5.20, 15, 0.0000, 0.0000 }}, { (* Fobs-ampl-range #reflections R-value Accum.*) { 10.277, 85.744, 39, 0.0000, 0.0000 }, { 85.744, 161.211, 52, 0.0000, 0.0000 }, { 161.211, 236.678, 40, 0.0000, 0.0000 }, { 236.678, 312.144, 11, 0.0000, 0.0000 }, { 312.144, 387.611, 5, 0.0000, 0.0000 }, { 387.611, 463.078, 1, 0.0000, 0.0000 }, { 463.078, 538.545, 1, 0.0000, 0.0000 }, { 538.545, 614.012, 1, 0.0000, 0.0000 }}} XREFINE>end X-PLOR> X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> method=direct XREFINE> ? ---------------------------diffraction-data----------------------------------- | a= 40.96, b= 18.65, c= 22.52, alpha= 90.00, beta= 90.77, gamma= 90.00 | ANOMalous=FALSe [equiv. to HERMitian=TRUE] | First group of symmetry operators: | ---------------------------------- | SYMMetry=(X,Y,Z) | SYMMetry=(-X,Y+1/2,-Z) | #Fobs= 150, allocation= 40000 | Fobs-min= 10.28, Fobs-max= 614.01, resolution range: 9.94 to 5.01 | Hmax= 8 Kmax= 3 Lmax= 4 Hmin= -8 Kmin= 0 Lmin= 0 | #atomic scattering factor types= 4 ------------------------------------------------------------------------------ ------------------------refinement-parameters--------------------------------- | Fobs-min= 0.00, Fobs-max= 10000000000.00, resolution range: 10.00 to 5.00 | #atoms contributing to Fcalc= 327 | Weight-A= 1.00 , Weight-P= 0.00 TOLErance= 0.500 | The direct summation method will be used, LOOKup=T | TARGet=RESI | The target is the residual with optimum Fobs/Fcalc scale factor ------------------------------------------------------------------------------ XREFINE> update {compute fcalc} XRTEST: number of selected reflections 150 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XREFINE> XREFINE> declare name=fdrct domain=reci type=complex end XREFINE> XREFINE> predict mode=reci to=fdrct ? end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 |-----------------------precict------------------------------------- | MODE = RECI | TO = FDRCT |------------------------------------------------------------------- XSFAL: allocating space for complex reciprocal space object. XPRED: CPU-time: predict-calc= 0.0500 XREFINE> XREFINE> statistics STATistics> output=OUTPUT STATistics> ( ampl(fcalc) ) STATistics> ( ampl(fdrct) ) STATistics> ( sum(abs(abs(fcalc)-abs(fdrct))) / sum(abs(fcalc)) ) STATistics> sele=( 10.0 >= d >= 5.0 ) Total of 150 structure factor elements were selected. STATistics> end #bin | resolution range | #refl | expressions 1 8.09 9.94 23 177.3022 177.3022 0.0000 2 7.13 8.09 17 156.6596 156.6596 0.0000 3 6.51 7.13 23 119.9843 119.9843 0.0000 4 6.06 6.51 13 123.6918 123.6918 0.0000 5 5.71 6.06 19 87.5411 87.5411 0.0000 6 5.43 5.71 19 125.6518 125.6518 0.0000 7 5.20 5.43 21 111.5206 111.5206 0.0000 8 5.01 5.20 15 127.2810 127.2810 0.0000 XREFINE> XREFINE> method=fft XREFINE> update XRTEST: number of selected reflections 150 CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XFFT: using grid [ 24, 12, 16] and sublattice [ 24( 25), 12( 13), 16] XFFT: CPU-time: electron-density-calc= 0.0100 XFFT: CPU-time: FFT of electron density= 0.0000 XFFT: CPU-time: transformation into A, B= 0.0000 XREFINE> XREFINE> XREFINE>end X-PLOR> X-PLOR>xrefin XREFINE> XREFINE> declare name=ffsum domain=reci type=real end XREFINE> XREFINE> predict mode=ff2 to=ffsum ? end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 |-----------------------precict------------------------------------- | MODE = FF2 | TO = FFSUM |------------------------------------------------------------------- XSFAL: allocating space for real reciprocal space object. XPRED: CPU-time: predict-calc= 0.0000 XREFINE> XREFINE> statistics STATistics> output=OUTPUT STATistics> ( s()^2 ) STATistics> ( amplitude(fobs)^2/100.0 ) STATistics> ( ffsum/100.0 ) STATistics> ( log(AVE[bins=8](ampl(fobs)^2)/AVE[bins=8](ffsum)) ) STATistics> sele=( 10.0 >= d >= 5.0 ) Total of 150 structure factor elements were selected. STATistics> end #bin | resolution range | #refl | expressions 1 8.09 9.94 23 0.0124 534.3471 285.8752 0.6255 2 7.13 8.09 17 0.0175 389.8505 276.0687 0.3451 3 6.51 7.13 23 0.0216 232.9366 268.6930 -0.1428 4 6.06 6.51 13 0.0256 263.2180 261.6701 0.0059 5 5.71 6.06 19 0.0291 147.1603 255.8454 -0.5531 6 5.43 5.71 19 0.0324 315.0957 250.5159 0.2294 7 5.20 5.43 21 0.0351 224.4718 246.1758 -0.0923 8 5.01 5.20 15 0.0385 289.8689 241.0015 0.1846 XREFINE> XREFINE> XREFINE>end X-PLOR> 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> XREFINE> predict mode=real to=map1 end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 327 #anomalous= 0 #special pos.= 0 occupancies=1 XPRED2: applying non-crystallographic symmetry. XPRED: CPU-time: predict-calc= 0.0100 XREFINE> do (deri1=ft(map1)) ( all ) XMAPAL: allocating space for real space object. 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. XREFINE>end X-PLOR> X-PLOR>vector do (segid="1") ( all ) SELRPN: 396 atoms have been selected out of 396 X-PLOR>duplicate selection=( segid "1" ) segid="2" end SELRPN: 396 atoms have been selected out of 396 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 792(MAXA= 800) NBOND= 806(MAXB= 1600) NTHETA= 1162(MAXT= 1600) NGRP= 330(MAXGRP= 400) NPHI= 470(MAXP= 800) NIMPHI= 364(MAXIMP= 400) NDON= 138(MAXPAD= 200) NACC= 128(MAXPAD= 200) NNB= 18(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: 396 atoms have been selected out of 792 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: 396 atoms have been selected out of 792 SCRATC-warning: XREFin SCATter database erased. XPLOR: current counts (number in parenthesis is maximum) NATOM= 1188(MAXA= 1600) NBOND= 1209(MAXB= 1600) NTHETA= 1743(MAXT= 3200) NGRP= 495(MAXGRP= 800) NPHI= 705(MAXP= 800) NIMPHI= 546(MAXIMP= 800) NDON= 207(MAXPAD= 400) NACC= 192(MAXPAD= 400) NNB= 27(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: 396 atoms have been selected out of 1188 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> SCATter ( chemical C* ) SELRPN: 606 atoms have been selected out of 1188 SCATTER_A1= 2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600 XREFINE> XREFINE> SCATter ( chemical N* ) SELRPN: 165 atoms have been selected out of 1188 SCATTER_A1= 12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529 XREFINE> XREFINE> SCATter ( chemical O* ) SELRPN: 192 atoms have been selected out of 1188 SCATTER_A1= 3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800 XREFINE> XREFINE> SCATter ( chemical S* ) SELRPN: 18 atoms have been selected out of 1188 SCATTER_A1= 6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900 XREFINE> XREFINE> predict mode=real to=map1 end CPU-time for XRFILL: 0.0000 XRFILL: #scatt.= 981 #anomalous= 0 #special pos.= 0 occupancies=1 XPRED: CPU-time: predict-calc= 0.0100 XREFINE> XREFINE> do (deri2=ft(map1)) ( all ) XMAPAL: allocating space for real space object. 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. XREFINE> XREFINE> show max (abs(deri1-deri2)) ( all ) Maximum of 150 elements = 0.0000 XREFINE> XREFINE>end X-PLOR> X-PLOR>stop HEAP: maximum use= 2612488 current use= 1028007 X-PLOR: total CPU time= 0.3500 s X-PLOR: entry time at 10:28:24 04-Jun-04 X-PLOR: exit time at 10:28:24 04-Jun-04