#CCP4I VERSION CCP4Interface 1.4.4 #CCP4I SCRIPT LOG shelx_cde #CCP4I DATE 10 Apr 2006 09:18:59 #CCP4I USER pjx #CCP4I PROJECT SHELX_TEST #CCP4I JOB_ID 17 #CCP4I SCRATCH /tmp/pjx #CCP4I HOSTNAME ccp4t.dl.ac.uk #CCP4I PID 14129 *************************************************************************** * Information from CCP4Interface script *************************************************************************** ************************** Running SHELX C/D/E ************************** *************************************************************************** SHELXD References: * Uson & Sheldrick (1999) Curr. Opin. Struct. Biol. 9 643-648 * Sheldrick, Hauptman, Weeks, Miller & Uson (2001) International Tables for Crystallography Vol. F, eds. Arnold & Rossmann, pp. 333-351 * Schneider & Sheldrick (2002) Acta Cryst. D58 1772-1779 SHELXE References: * Sheldrick (2002) Z. Kristallogr. 217 644-650 *************************************************************************** * Information from CCP4Interface script *************************************************************************** Running SHELXC to prepare data for heavy atom search *************************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXC - Create input files for SHELXD and SHELXE - Version 2006/3 + + Copyright (C) George M. Sheldrick 2003-6 + + SHELX_TEST_17_shelxc Started at 09:18:59 on 10 Apr 2006 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SHELXC reads a filename stem (denoted here by 'xx') on the command line plus some instructions from 'standard input'. It writes some statistics to 'standard output' and prepares the three files needed to run SHELXD and SHELXE. SHELXC can be called from a GUI by a command line such as: shelxc xx 101.0 103.6 112.9 110.8 143.1 142.9 108.4 85.1 61.4 44.1 23.0 %Complete 93.8 98.6 99.1 99.4 99.3 99.7 99.8 99.8 99.8 99.9 99.6 2.81 2.89 2.00 1.53 1.67 1.72 1.56 1.38 1.13 1.03 0.89 38458 Reflections written to file SHELX_TEST_17_shelxc.hkl for input to SHELXE 27946 Reflections read from SIRA file /home/pjx/SHELX/CCP4i_TEST/DATA/thau-iod.hkl 15823 Unique reflections, highest resolution 2.000 Angstroms Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.5 - 3.0 - 2.8 - 2.6 - 2.4 - 2.2 - 2.00 N(data) 352 432 532 1167 1145 2021 1237 1656 2209 2824 2248 40.0 36.4 42.6 50.0 45.8 36.0 26.2 21.2 16.7 9.8 7.6 %Complete 94.4 98.6 99.1 99.5 99.5 99.7 99.8 99.8 99.7 90.7 51.0 4.07 3.72 3.77 2.97 2.20 1.95 1.68 1.45 1.20 0.96 0.93 21.44 20.53 20.19 18.74 18.91 15.75 12.19 10.83 8.29 4.92 4.15 R(isom) 0.402 0.533 0.411 0.332 0.367 0.392 0.424 0.469 0.451 0.431 0.473 For zero signal and should be about 0.80 15305 Reflections written to file SHELX_TEST_17_shelxc_fa.hkl for input to SHELXD/E File SHELX_TEST_17_shelxc_fa.ins written for input to SHELXD: TITL SHELX_TEST_17_shelxc_fa.ins SIRAS in P41212 CELL 0.98000 58.04 58.04 151.29 90.00 90.00 90.00 LATT -1 SYMM 1/2-Y, 1/2+X, 1/4+Z SYMM -X, -Y, 1/2+Z SYMM 1/2+Y, 1/2-X, 3/4+Z SYMM 1/2-X, 1/2+Y, 1/4-Z SYMM Y, X, -Z SYMM 1/2+X, 1/2-Y, 3/4-Z SYMM -Y, -X, 1/2-Z SFAC SE UNIT 544 SHEL 999 2.3 PATS FIND 17 MIND -3.5 -0.1 NTRY 10 SEED 1 HKLF 3 END ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXC for SHELX_TEST_17_shelxc finished at 09:19:00 on 10 Apr 200 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *************************************************************************** * Information from CCP4Interface script *************************************************************************** $TABLE :SHELXC Analysis of , completeness, : $GRAPHS : vs Resolution :A:1,3,4 : : %Completeness vs Resolution :A:1,5,6 : : vs Resolution :A:1,7 : : vs Resolution :A:1,8 : $$ M(4SSQ/LL) Resolution NAT SIRA NAT SIRA SIRA SIRA $$ $$ 0.01562 8.0 101.0 40.0 93.8 94.4 21.44 4.07 0.02778 6.0 103.6 36.4 98.6 98.6 20.53 3.72 0.04000 5.0 112.9 42.6 99.1 99.1 20.19 3.77 0.06250 4.0 110.8 50.0 99.4 99.5 18.74 2.97 0.08163 3.5 143.1 45.8 99.3 99.5 18.91 2.20 0.11111 3.0 142.9 36.0 99.7 99.7 15.75 1.95 0.12755 2.8 * 26.2 * 99.8 12.19 1.68 0.14793 2.6 * 21.2 * 99.8 10.83 1.45 0.16000 2.5 108.4 * 99.8 * * * 0.17361 2.4 * 16.7 * 99.7 8.29 1.20 0.20661 2.2 85.1 9.8 99.8 90.7 4.92 0.96 0.25000 2.00 * 7.6 * 51.0 4.15 0.93 0.30864 1.8 44.1 * 99.9 * * * 0.41623 1.55 23.0 * 99.6 * * * $$ *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Running SHELXD to determine heavy atom substructure *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Parameters being sent to SHELXD: TITL SHELX_TEST_17_shelxc_fa.ins SIRAS in P41212 CELL 0.98000 58.04 58.04 151.29 90.00 90.00 90.00 LATT -1 SYMM 1/2-Y, 1/2+X, 1/4+Z SYMM -X, -Y, 1/2+Z SYMM 1/2+Y, 1/2-X, 3/4+Z SYMM 1/2-X, 1/2+Y, 1/4-Z SYMM Y, X, -Z SYMM 1/2+X, 1/2-Y, 3/4-Z SYMM -Y, -X, 1/2-Z SFAC SE UNIT 544 SHEL 999 2.3 PATS FIND 17 MIND -3.5 -0.1 NTRY 10 SEED 1 HKLF 3 END *************************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXD-2006/3 - MACROMOLECULAR DIRECT METHODS - FORTRAN-95 VERSION + + Copyright (C) George M. Sheldrick 2000-2006 + + SHELX_TEST_17_shelxd_fa started at 09:19:00 on 10 Apr 2006 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Read instructions and process reflection data 11890 unique data; R(int) = 0.000; R(sigma) = 0.252; Mean|E^2-1| = 0.709 ============================================================================= SHEL dmax 999.00 dmin 2.30 MIND mdis -3.500 mdeq -0.100 FRES res 2.5 SEED nrand 1 PATS np 100 npt 99999 nf 5 PSMF pres 2.5 psfac 0.340 FIND na 17 ncy 20 DSUL nss 0 dss 2.060 TANG ftan -0.900 fex 0.400 NTPR ntpr 100 SKIP min2 0.0 ESEL Emin 1.500 dlim 1.000 WEED fro 0.000 TEST CCmin 10.00 delCC 99.00 CCWT g 0.000 NTRY ntry 10 ============================================================================= 1307 E > 1.500, average of 99.2 TPR for each phase, = 0.312 ----------------------------------------------------------------------------- Fourier grid = 64 x 64 x 23 -0.006 <= z <= 0.131 PSUM 9.59 PSMF Peaks: 96 91 66 66 63 62 59 56 54 53 53 51 46 45 42 40 40 40 Try 1:20 Peaks 99 82 69 61 59 55 55 51 48 45 40 35 35 34 33 32 32 32 30 29 R = 0.426, Min.fun. = 0.526, = 0.145, Ra = 0.589 Try 1, CC All/Weak 18.51 / 5.35, best 18.51 / 5.35, best PATFOM 0.00 PATFOM 0.24 ----------------------------------------------------------------------------- PSUM 82.90 PSMF Peaks: 97 93 54 52 45 40 37 29 29 26 25 24 23 23 22 19 19 Try 2:20 Peaks 99 82 61 51 49 47 44 42 42 36 33 31 31 29 29 27 26 23 22 19 R = 0.274, Min.fun. = 0.403, = 0.417, Ra = 0.298 Try 2, CC All/Weak 54.88 / 35.18, best 54.88 / 35.18, best PATFOM 0.24 PATFOM 3.54 ----------------------------------------------------------------------------- PSUM 17.04 PSMF Peaks: 224 137 109 68 52 51 50 48 45 42 42 39 33 32 30 25 Try 3:20 Peaks 99 84 60 53 46 45 45 42 41 38 32 30 30 28 28 28 28 25 23 21 R = 0.276, Min.fun. = 0.402, = 0.417, Ra = 0.297 Try 3, CC All/Weak 54.31 / 32.89, best 54.88 / 35.18, best PATFOM 3.54 PATFOM 3.46 ----------------------------------------------------------------------------- PSUM 13.30 PSMF Peaks: 137 81 58 56 52 42 34 34 33 33 31 29 29 25 24 24 24 Try 4:20 Peaks 99 88 80 75 74 71 66 64 58 54 49 48 46 45 43 42 37 32 31 29 R = 0.415, Min.fun. = 0.465, = 0.289, Ra = 0.446 Try 4, CC All/Weak 37.35 / 21.10, best 54.88 / 35.18, best PATFOM 3.54 PATFOM 1.31 ----------------------------------------------------------------------------- PSUM 28.96 PSMF Peaks: 114 87 68 65 64 53 45 36 34 30 28 26 22 19 19 18 17 Try 5:20 Peaks 99 78 62 45 44 43 41 41 34 34 34 30 30 30 26 26 25 23 22 19 R = 0.282, Min.fun. = 0.403, = 0.415, Ra = 0.299 Try 5, CC All/Weak 53.02 / 33.74, best 54.88 / 35.18, best PATFOM 3.54 PATFOM 3.57 ----------------------------------------------------------------------------- PSUM 8.69 PSMF Peaks: 146 92 75 64 62 62 54 53 51 45 45 43 40 39 38 38 35 Try 6:20 Peaks 99 95 93 83 74 72 67 62 62 61 59 59 57 48 48 47 44 37 35 33 R = 0.426, Min.fun. = 0.485, = 0.246, Ra = 0.500 Try 6, CC All/Weak 41.30 / 22.40, best 54.88 / 35.18, best PATFOM 3.57 PATFOM 0.72 ----------------------------------------------------------------------------- PSUM 23.75 PSMF Peaks: 113 87 66 59 59 51 47 43 41 28 28 28 26 24 20 20 19 Try 7:20 Peaks 99 82 61 51 49 47 44 42 42 37 33 32 31 30 29 27 25 23 22 19 R = 0.274, Min.fun. = 0.403, = 0.417, Ra = 0.298 Try 7, CC All/Weak 54.83 / 35.18, best 54.88 / 35.18, best PATFOM 3.57 PATFOM 3.63 ----------------------------------------------------------------------------- PSUM 54.29 PSMF Peaks: 140 119 91 56 53 38 37 36 32 29 27 26 24 23 22 21 20 Try 8:20 Peaks 99 84 60 53 46 46 45 42 40 38 32 30 30 28 28 28 28 25 23 21 R = 0.277, Min.fun. = 0.402, = 0.416, Ra = 0.300 Try 8, CC All/Weak 54.33 / 32.95, best 54.88 / 35.18, best PATFOM 3.63 PATFOM 3.48 ----------------------------------------------------------------------------- PSUM 19.15 PSMF Peaks: 138 94 87 63 57 48 42 35 33 32 30 30 28 27 27 26 26 Try 9:20 Peaks 99 84 60 53 46 46 45 42 41 38 32 30 30 28 28 28 28 25 23 21 R = 0.277, Min.fun. = 0.402, = 0.416, Ra = 0.300 Try 9, CC All/Weak 54.32 / 32.90, best 54.88 / 35.18, best PATFOM 3.63 PATFOM 3.44 ----------------------------------------------------------------------------- PSUM 30.69 PSMF Peaks: 129 125 66 58 48 46 45 43 38 34 28 25 22 21 21 21 20 Try 10:20 Peaks 99 84 60 53 46 45 45 42 41 38 32 30 30 28 28 28 28 25 23 21 R = 0.277, Min.fun. = 0.402, = 0.416, Ra = 0.300 Try 10, CC All/Weak 54.32 / 32.90, best 54.88 / 35.18, best PATFOM 3.63 PATFOM 3.44 ============================================================================== CPU times required in seconds ----------------------------- 0.3 - Data input and E-values 0.3 - Generate TPR 9.5 - PATS 3.5 - Full symmetry PSMF 5.9 - FIND 0.0 - PLOP 0.0 - GROP 3.3 - All FFTs 0.8 - All peak-searches 0.0 - Rest ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXD finished at 09:19:25 Total time: 23.72 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *************************************************************************** * Information from CCP4Interface script *************************************************************************** $TABLE :SHELXD Occupancy for each site : $GRAPHS : Occupancy for each site :A:1,2 : $$ Site Occupancy$$ $$ 1 1.0000 2 0.8259 3 0.6159 4 0.5176 5 0.4985 6 0.4749 7 0.4507 8 0.4282 9 0.4247 10 0.3715 11 0.3359 12 0.3207 13 0.3180 14 0.3015 15 0.2986 16 0.2730 17 0.2653 18 0.2346 19 0.2256 20 0.1927 21 0.1890 22 0.1602 23 0.1310 24 0.1052 $$ *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** $TABLE :SHELXD CC All/Weak for each try : $SCATTER : CC All/Weak per Try :A:1,2,3 : $$ NTry CC_all CC_weak$$ $$ 1 18.51 5.35 2 54.88 35.18 3 54.31 32.89 4 37.35 21.10 5 53.02 33.74 6 41.30 22.40 7 54.83 35.18 8 54.33 32.95 9 54.32 32.90 10 54.32 32.90 $$ *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Running SHELXE to phase from heavy atom substructure *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Phasing using original heavy atom enantiomorph *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Running SHELXE command: shelxe SHELX_TEST_17_shelxe SHELX_TEST_17_shelxe_fa -s0.5 -m20 *************************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2006/3 + + Copyright (C) George M. Sheldrick 2001-6 + + Started at 09:19:25 on 10 Apr 2006 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SHELXE has following modes of action (xx and yy are filename stems): shelxe xx [reads xx.hkl and xx.ins, phases from atoms] shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res] shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins] shelxe xx.fcf [reads only xx.fcf] shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl] shelxe xx.fcf yy [reads xx.fcf, yy.hkl, yy.res] xx.hkl contains native data, yy.hkl contains FA and alpha and should have been created using SHELXC or XPREP. xx.phi has .phs format but only the starting phases are read from it; if a .phi file is read, the cell and symmetry are read from xx.ins and the native F-values are read from xx.hkl. xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and starting phases. The output phases are written to xx.phs, the log file is written to xx.lst and, if -b is set, improved substructure phases are output to xx.pha and revised heavy atoms to xx.hat. The first two modes provide density modification starting from atoms or phases, the third and fourth modes are for phase extension, the fifth is an inverse cross-Fourier for finding heavy atoms for a second derivative with the same origin as the first, and the last mode is useful to confirm the heavy atom substructure from the final refined phases. For these last two modes, the phases for the inverse Fourier are phi(nat)-alpha, where phi(nat) may be refined (-m etc.) and alpha is taken from yy.hkl. SHELXE normally requires a few command line switches, e.g. shelxe xx yy -m20 -s0.45 -h8 -b would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file assuming that they are also present in the native structure (-h8) and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel. The new switch -e may be used to extrapolate the data to the specified resolution (the 'free lunch algorithm'); -e1.0 can produce spectacular results, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable, it is best to establish the substructure enantiomorph without -e first. The current values of all parameters are output at the start of the shelxe output, the default values will rarely need changing. Please cite: G.M. Sheldrick (2002), "Macromolecular phasing with SHELXE", Z. Kristallogr. 217, 644-650 whenever SHELXE proves useful. ============================================================================== Cell, symmetry and heavy atoms from: SHELX_TEST_17_shelxe_fa.res DelF from: SHELX_TEST_17_shelxe_fa.hkl Native data from: SHELX_TEST_17_shelxe.hkl Listing file: SHELX_TEST_17_shelxe.lst Phase output file: SHELX_TEST_17_shelxe.phs Summary of parameters to be employed: -f NOT SET: read intensity not F from native .hkl file -i NOT SET: no structure inversion -n NOT SET: resolve 2-fold ambiguity if SAD or SIR -h NOT SET: heavy atoms not present in native -b NOT SET: do not output revised heavy atom sites and phases -z NOT SET: sharpen density maps -e NOT SET: fill in missing data up to maximum resolution + 0.2 Angstroms -d 0.000 high resolution limit to be applied to input data -m 20 cycles of density modification -j 5 output pseudo-free CC before every Nth cycle -s 0.500 solvent fraction -c 0.400 fraction of pixels in crossover region -g 1.100 solvent gamma flipping factor -v 1.500 low density reduction factor -w 0.200 weight for retained experimental phases -r 3.00 map resolution (multiplies maximum indices) -l 2 space for 2000000 reflections 24 heavy atoms read from .res file 15305 reflections read from file SHELX_TEST_17_shelxe_fa.hkl 38458 reflections read from file SHELX_TEST_17_shelxe.hkl Maximum resolution of native data = 1.550 Angstroms 8 reflections with d > 1.750 and 0 in range 1.750 > d > 1.750 added Fourier grid = 128 x 128 x 37 0.000 <= z <= 0.125 92 point spherical net set up with radius 2.42A 10 extra Fourier layers will be generated Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 44.66% = 0.205 for initial phases = 0.208, Contrast = 0.073, Connect. = 0.861 for dens.mod. cycle 1 = 0.254, Contrast = 0.190, Connect. = 0.880 for dens.mod. cycle 2 = 0.300, Contrast = 0.359, Connect. = 0.905 for dens.mod. cycle 3 = 0.300, Contrast = 0.462, Connect. = 0.914 for dens.mod. cycle 4 Pseudo-free CC = 71.46 % = 0.300, Contrast = 0.550, Connect. = 0.921 for dens.mod. cycle 5 = 0.300, Contrast = 0.603, Connect. = 0.924 for dens.mod. cycle 6 = 0.300, Contrast = 0.636, Connect. = 0.926 for dens.mod. cycle 7 = 0.300, Contrast = 0.654, Connect. = 0.927 for dens.mod. cycle 8 = 0.300, Contrast = 0.666, Connect. = 0.928 for dens.mod. cycle 9 Pseudo-free CC = 80.24 % = 0.300, Contrast = 0.673, Connect. = 0.928 for dens.mod. cycle 10 = 0.300, Contrast = 0.679, Connect. = 0.929 for dens.mod. cycle 11 = 0.300, Contrast = 0.682, Connect. = 0.929 for dens.mod. cycle 12 = 0.300, Contrast = 0.685, Connect. = 0.929 for dens.mod. cycle 13 = 0.300, Contrast = 0.687, Connect. = 0.930 for dens.mod. cycle 14 Pseudo-free CC = 81.76 % = 0.300, Contrast = 0.688, Connect. = 0.930 for dens.mod. cycle 15 = 0.300, Contrast = 0.689, Connect. = 0.930 for dens.mod. cycle 16 = 0.300, Contrast = 0.690, Connect. = 0.930 for dens.mod. cycle 17 = 0.300, Contrast = 0.691, Connect. = 0.930 for dens.mod. cycle 18 = 0.300, Contrast = 0.692, Connect. = 0.930 for dens.mod. cycle 19 = 0.300, Contrast = 0.692, Connect. = 0.931 for dens.mod. cycle 20 Mean weight and estimated mapCC as a function of resolution d inf - 3.43 - 2.70 - 2.35 - 2.13 - 1.97 - 1.85 - 1.76 - 1.68 - 1.61 - 1.56 0.729 0.749 0.782 0.792 0.822 0.811 0.808 0.803 0.805 0.770 0.897 0.886 0.911 0.918 0.954 0.957 0.948 0.946 0.960 0.942 N 3859 3875 3846 3845 3955 3945 3661 3961 4152 3359 Pseudo-free CC = 82.05 % ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 09:20:17 Total time: 51.45 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *************************************************************************** * Information from CCP4Interface script *************************************************************************** Phasing using inverted heavy atom enantiomorph *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Running SHELXE command: shelxe SHELX_TEST_17_shelxe SHELX_TEST_17_shelxe_fa -s0.5 -m20 -i *************************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE - PHASING AND DENSITY MODIFICATION - Version 2006/3 + + Copyright (C) George M. Sheldrick 2001-6 + + Started at 09:20:17 on 10 Apr 2006 + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SHELXE has following modes of action (xx and yy are filename stems): shelxe xx [reads xx.hkl and xx.ins, phases from atoms] shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res] shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins] shelxe xx.fcf [reads only xx.fcf] shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl] shelxe xx.fcf yy [reads xx.fcf, yy.hkl, yy.res] xx.hkl contains native data, yy.hkl contains FA and alpha and should have been created using SHELXC or XPREP. xx.phi has .phs format but only the starting phases are read from it; if a .phi file is read, the cell and symmetry are read from xx.ins and the native F-values are read from xx.hkl. xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and starting phases. The output phases are written to xx.phs, the log file is written to xx.lst and, if -b is set, improved substructure phases are output to xx.pha and revised heavy atoms to xx.hat. The first two modes provide density modification starting from atoms or phases, the third and fourth modes are for phase extension, the fifth is an inverse cross-Fourier for finding heavy atoms for a second derivative with the same origin as the first, and the last mode is useful to confirm the heavy atom substructure from the final refined phases. For these last two modes, the phases for the inverse Fourier are phi(nat)-alpha, where phi(nat) may be refined (-m etc.) and alpha is taken from yy.hkl. SHELXE normally requires a few command line switches, e.g. shelxe xx yy -m20 -s0.45 -h8 -b would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file assuming that they are also present in the native structure (-h8) and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel. The new switch -e may be used to extrapolate the data to the specified resolution (the 'free lunch algorithm'); -e1.0 can produce spectacular results, but since a large number of cycles is required (-m400) and the 'contrast' and 'connectivity' become unreliable, it is best to establish the substructure enantiomorph without -e first. The current values of all parameters are output at the start of the shelxe output, the default values will rarely need changing. Please cite: G.M. Sheldrick (2002), "Macromolecular phasing with SHELXE", Z. Kristallogr. 217, 644-650 whenever SHELXE proves useful. ============================================================================== Cell, symmetry and heavy atoms from: SHELX_TEST_17_shelxe_fa.res DelF from: SHELX_TEST_17_shelxe_fa.hkl Native data from: SHELX_TEST_17_shelxe.hkl Listing file: SHELX_TEST_17_shelxe_i.lst Phase output file: SHELX_TEST_17_shelxe.phs Summary of parameters to be employed: -f NOT SET: read intensity not F from native .hkl file -i invert HA structure (and space group) -n NOT SET: resolve 2-fold ambiguity if SAD or SIR -h NOT SET: heavy atoms not present in native -b NOT SET: do not output revised heavy atom sites and phases -z NOT SET: sharpen density maps -e NOT SET: fill in missing data up to maximum resolution + 0.2 Angstroms -d 0.000 high resolution limit to be applied to input data -m 20 cycles of density modification -j 5 output pseudo-free CC before every Nth cycle -s 0.500 solvent fraction -c 0.400 fraction of pixels in crossover region -g 1.100 solvent gamma flipping factor -v 1.500 low density reduction factor -w 0.200 weight for retained experimental phases -r 3.00 map resolution (multiplies maximum indices) -l 2 space for 2000000 reflections 24 heavy atoms read from .res file 15305 reflections read from file SHELX_TEST_17_shelxe_fa.hkl 38458 reflections read from file SHELX_TEST_17_shelxe.hkl Maximum resolution of native data = 1.550 Angstroms 8 reflections with d > 1.750 and 0 in range 1.750 > d > 1.750 added Fourier grid = 128 x 128 x 37 0.000 <= z <= 0.125 92 point spherical net set up with radius 2.42A 10 extra Fourier layers will be generated ** Space group converted to enantiomorph ** Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 44.66% = 0.205 for initial phases = 0.172, Contrast = 0.014, Connect. = 0.556 for dens.mod. cycle 1 = 0.182, Contrast = 0.029, Connect. = 0.613 for dens.mod. cycle 2 = 0.191, Contrast = 0.033, Connect. = 0.629 for dens.mod. cycle 3 = 0.201, Contrast = 0.037, Connect. = 0.640 for dens.mod. cycle 4 Pseudo-free CC = 17.51 % = 0.211, Contrast = 0.041, Connect. = 0.648 for dens.mod. cycle 5 = 0.221, Contrast = 0.045, Connect. = 0.654 for dens.mod. cycle 6 = 0.231, Contrast = 0.048, Connect. = 0.659 for dens.mod. cycle 7 = 0.240, Contrast = 0.051, Connect. = 0.664 for dens.mod. cycle 8 = 0.250, Contrast = 0.054, Connect. = 0.668 for dens.mod. cycle 9 Pseudo-free CC = 27.36 % = 0.259, Contrast = 0.057, Connect. = 0.672 for dens.mod. cycle 10 = 0.267, Contrast = 0.061, Connect. = 0.678 for dens.mod. cycle 11 = 0.275, Contrast = 0.063, Connect. = 0.681 for dens.mod. cycle 12 = 0.282, Contrast = 0.068, Connect. = 0.688 for dens.mod. cycle 13 = 0.289, Contrast = 0.069, Connect. = 0.691 for dens.mod. cycle 14 Pseudo-free CC = 33.39 % = 0.296, Contrast = 0.076, Connect. = 0.699 for dens.mod. cycle 15 = 0.300, Contrast = 0.078, Connect. = 0.703 for dens.mod. cycle 16 = 0.300, Contrast = 0.082, Connect. = 0.708 for dens.mod. cycle 17 = 0.300, Contrast = 0.084, Connect. = 0.711 for dens.mod. cycle 18 = 0.300, Contrast = 0.087, Connect. = 0.716 for dens.mod. cycle 19 = 0.300, Contrast = 0.089, Connect. = 0.720 for dens.mod. cycle 20 Mean weight and estimated mapCC as a function of resolution d inf - 3.43 - 2.70 - 2.35 - 2.13 - 1.97 - 1.85 - 1.76 - 1.68 - 1.61 - 1.56 0.337 0.213 0.256 0.292 0.346 0.305 0.321 0.335 0.395 0.406 0.450 0.259 0.317 0.408 0.521 0.481 0.495 0.518 0.597 0.613 N 3859 3875 3846 3845 3955 3945 3661 3961 4152 3359 Pseudo-free CC = 37.12 % ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXE finished at 09:21:09 Total time: 51.84 secs + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *************************************************************************** * Information from CCP4Interface script *************************************************************************** WARNING SHELXE converted space group to enantiomorph (P43212) *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** $TABLE :SHELXE Contrast and Connectivity : $GRAPHS : Contrast versus Cycle :A:1,2,4 : : Connectivity versus Cycle :A:1,3,5 : $$ Cycle Original Original Inverted Inverted$$ $$ 1 0.073 0.861 0.014 0.556 2 0.190 0.880 0.029 0.613 3 0.359 0.905 0.033 0.629 4 0.462 0.914 0.037 0.640 5 0.550 0.921 0.041 0.648 6 0.603 0.924 0.045 0.654 7 0.636 0.926 0.048 0.659 8 0.654 0.927 0.051 0.664 9 0.666 0.928 0.054 0.668 10 0.673 0.928 0.057 0.672 11 0.679 0.929 0.061 0.678 12 0.682 0.929 0.063 0.681 13 0.685 0.929 0.068 0.688 14 0.687 0.930 0.069 0.691 15 0.688 0.930 0.076 0.699 16 0.689 0.930 0.078 0.703 17 0.690 0.930 0.082 0.708 18 0.691 0.930 0.084 0.711 19 0.692 0.930 0.087 0.716 20 0.692 0.931 0.089 0.720 $$ *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** $TABLE :SHELXE Estimated CC(map) : $GRAPHS : Estimated CC(map) vs Resolution :A:1,3,4 : $$ M(4SSQ/LL) Resolution Original Inverted$$ $$ 0.08500 3.43 0.897 0.450 0.13717 2.70 0.886 0.259 0.18108 2.35 0.911 0.317 0.22041 2.13 0.918 0.408 0.25767 1.97 0.954 0.521 0.29218 1.85 0.957 0.481 0.32283 1.76 0.948 0.495 0.35431 1.68 0.946 0.518 0.38579 1.61 0.960 0.597 0.41091 1.56 0.942 0.613 $$ *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 10 Apr 2006 09:21:09 #CCP4I TERMINATION OUTPUT_FILES SHELX_TEST_17_shelxc_fa.ins SHELX_TEST SHELX_TEST_17_shelxd_fa.lst SHELX_TEST SHELX_TEST_17_shelxd_fa.res SHELX_TEST SHELX_TEST_17_shelxe.lst SHELX_TEST SHELX_TEST_17_shelxe_i.lst SHELX_TEST #CCP4I MESSAGE Task completed successfully