The logfile is composed of output from the following programs:
CCP4i: ************************** Running SHELX C/D/E **************************
CCP4i: Running SHELXC to prepare data for heavy atom search
Current view: summary only [Show full logfile] [Hide logfile]
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXC - Create input files for SHELXD and SHELXE - Version 2006/3 +
+ Copyright (C) George M. Sheldrick 2003-6 +
+ SHELX_56_shelxc Started at 14:30:07 on 21 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 <t
which would read the instructions from the file t, or (under most UNIX
systems) by a simple shell script that includes the instructions, e.g.
shelxc xx <t
which would read the instructions from the file t, or (under most UNIX
systems) by a simple shell script that includes the instructions, e.g.
shelxc xx <t
which would read the instructions from the file t, or (under most UNIX
systems) by a simple shell script that includes the instructions, e.g.
shelxc xx EOF
CELL 49.70 57.90 74.17 90 90 90
SPAG P212121
SAD elastase.sca
FIND 12
<t
which would read the instructions from the file t, or (under most UNIX
systems) by a simple shell script that includes the instructions, e.g.
shelxc xx EOF
CELL 49.70 57.90 74.17 90 90 90
SPAG P212121
SAD elastase.sca
FIND 12
<t
which would read the instructions from the file t, or (under most UNIX
systems) by a simple shell script that includes the instructions, e.g.
shelxc xx EOF
CELL 49.70 57.90 74.17 90 90 90
SPAG P212121
SAD elastase.sca
FIND 12
EOF
shelxd xx_fa
shelxe xx xx_fa -s0.37 -m20 -h -b
shelxe xx xx_fa -s0.37 -m20 -h -b -i
which would also run shelxd to locate the sulfur atoms and shelxe (for
both substructure enantiomers) to solve elastase by sulfur-SAD phasing.
This script would read data from the .sca file and write the files xx.hkl
(h,k,l,I,sig(I) in SHELX HKLF4 format for density modification by SHELXE)
xx_fa.ins (cell, symmetry etc. for heavy atoms location by SHELXD) and
xx_fa.hkl (h,k,l,FA,sig(FA),alpha for both SHELXD and SHELXE). The starting
phases for density modification are estimated as (alpha + heavy-atom phase)
in the simplified approach used by SHELXE.
For SIR or SIRAS, two input reflections files are specified by the keywords
NAT and SIR or SIRA; for MAD at least two of the reflection files HREM,
LREM, PEAK and INFL are required and NAT may also be given if higher
resolution native data are available (e.g. SMet for SeMet MAD). Reflection
data should be in SHELX .hkl or SCALEPACK .sca format; many other programs,
including SCALA and XPREP, can output .sca format too. The keywords CELL,
SPAG (space group) SPAG (space group) and FIND (number of heavy atoms) are
always required, SFAC, MIND, NTRY, SHEL, ESEL and DSUL may be given and will
be written to the file xx_fa.ins for SHELXD. MAXM can be used to reserve
memory in units of 1M reflections. For RIP phasing, NAT (or BEFORE) denotes
the file before radiation damage and RIP (or AFTER) the data after radiation
damage. For RIPAS the 'after' file must be called 'RIPA' and a keyword RIPW
(default 0.6) gives the weight w to be assigned to the 'NAT' data in the
estimation of the anomalous signal (a weight of 1-w is applied to the 'RIPA'
data). Finally DSCA (default 0.98) gives the factor to multiply the native
data for SIR and SIRAS or the 'after' data for RIP after the data have been
put on the same scale (this allows for the extra scattering power of the
heavy atoms etc.); this can be critical for RIP phasing.
==============================================================================
74884 Reflections read from NAT file /home/pjx/SHELX/cde-data/jia_nat.hkl
74884 Unique reflections, highest resolution 1.902 Angstroms
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.5 - 3.0 - 2.7 - 2.5 - 2.3 - 2.1 - 1.90
N(data) 1014 1435 1821 3996 4031 7128 7151 6825 9373 13264 18846
26.1 34.2 38.0 41.6 36.8 25.1 16.4 12.8 10.5 8.0 4.8
%Complete 89.6 99.4 99.6 99.7 99.8 99.9 99.8 99.9 99.9 99.8 98.2
74884 Reflections written to file SHELX_56_shelxc.hkl for input to SHELXE
64131 Reflections read from LREM file /home/pjx/SHELX/cde-data/jia_lrem.sca
33521 Unique reflections, highest resolution 2.497 Angstroms
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.7 - 3.5 - 3.3 - 3.1 - 2.9 - 2.7 - 2.50
N(data) 1005 1437 1824 4002 2176 1862 2362 2983 3877 5069 6924
58.8 51.8 51.1 51.7 45.4 39.1 33.5 28.5 22.6 18.1 13.4
%Complete 88.8 99.6 99.8 99.8 100.0 99.9 100.0 99.9 99.9 100.0 99.4
1.00 0.98 0.90 0.78 0.75 0.76 0.78 0.78 0.78 0.81 0.81
63856 Reflections read from HREM file /home/pjx/SHELX/cde-data/jia_hrem.sca
33409 Unique reflections, highest resolution 2.498 Angstroms
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.7 - 3.5 - 3.3 - 3.1 - 2.9 - 2.7 - 2.50
N(data) 971 1436 1821 3985 2176 1862 2361 2983 3877 5069 6868
54.7 52.0 51.8 49.1 44.1 38.3 33.5 29.4 24.1 18.7 14.0
%Complete 85.8 99.5 99.6 99.4 100.0 99.9 99.9 99.9 99.9 100.0 99.6
3.36 3.16 2.60 1.80 1.58 1.39 1.37 1.28 1.22 1.16 1.06
63743 Reflections read from PEAK file /home/pjx/SHELX/cde-data/jia_peak.sca
33375 Unique reflections, highest resolution 2.498 Angstroms
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.7 - 3.5 - 3.3 - 3.1 - 2.9 - 2.7 - 2.50
N(data) 954 1434 1820 3972 2176 1862 2359 2983 3876 5069 6870
54.9 49.4 47.2 47.3 42.8 37.4 34.4 29.9 22.8 19.3 14.6
%Complete 84.3 99.4 99.6 99.1 100.0 99.9 99.8 99.9 99.9 100.0 99.2
4.06 3.74 2.98 2.14 1.86 1.67 1.66 1.55 1.42 1.33 1.22
63655 Reflections read from INFL file /home/pjx/SHELX/cde-data/jia_infl.sca
33317 Unique reflections, highest resolution 2.502 Angstroms
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.7 - 3.5 - 3.3 - 3.1 - 2.9 - 2.7 - 2.50
N(data) 989 1435 1824 3995 2175 1861 2360 2983 3877 5068 6750
52.7 47.6 46.9 45.3 42.1 36.7 32.2 28.0 20.9 18.3 13.8
%Complete 87.4 99.4 99.8 99.6 99.9 99.8 99.9 99.9 99.9 99.9 99.7
2.28 2.18 1.83 1.32 1.19 1.11 1.10 1.08 1.02 1.01 0.95
Correlation coefficients (%) between signed anomalous differences
Resl. Inf - 8.0 - 6.0 - 5.0 - 4.0 - 3.7 - 3.5 - 3.3 - 3.1 - 2.9 - 2.7 - 2.50
LREM/HREM 64.2 57.2 48.8 40.3 31.7 27.7 27.3 21.3 15.7 12.0 6.6
LREM/PEAK 62.5 56.1 48.6 42.5 30.3 27.1 26.9 24.8 17.9 14.3 12.7
LREM/INFL 62.4 54.4 49.4 40.3 28.6 26.0 25.4 22.8 17.1 8.9 7.6
HREM/PEAK 95.9 95.7 93.3 88.7 83.7 80.7 77.1 70.9 63.8 54.5 47.3
HREM/INFL 92.0 89.8 86.8 77.9 72.3 67.0 62.8 53.4 47.4 41.7 31.6
PEAK/INFL 93.0 91.3 88.9 82.7 74.4 72.6 67.1 59.2 53.1 45.9 38.1
For zero signal and should be about 0.80
29328 Reflections written to file SHELX_56_shelxc_fa.hkl for input to SHELXD/E
File SHELX_56_shelxc_fa.ins written for input to SHELXD:
TITL SHELX_56_shelxc_fa.ins MAD in C2221
CELL 0.98000 96.00 120.00 166.13 90.00 90.00 90.00
LATT -7
SYMM -X, -Y, 1/2+Z
SYMM -X, Y, 1/2-Z
SYMM X, -Y, -Z
SFAC Se
UNIT 256
SHEL 999 3.0
PATS
FIND 8
MIND -1.5 -0.1
NTRY 5
SEED 1
HKLF 3
END
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXC for SHELX_56_shelxc finished at 14:30:11 on 21 Apr 2006 +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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|
The following tables were found in the logfile: |
SHELXC Analysis of <I/sig>, completeness, <d"/sig> SHELXC Anomalous CC analysis |
CCP4i: Running SHELXD to determine heavy atom substructure
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXD-2006/3 - MACROMOLECULAR DIRECT METHODS - FORTRAN-95 VERSION +
+ Copyright (C) George M. Sheldrick 2000-2006 +
+ SHELX_56_shelxd_fa started at 14:30:11 on 21 Apr 2006 +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Read instructions and process reflection data
17436 unique data; R(int) = 0.000; R(sigma) = 0.427; Mean|E^2-1| = 0.865
=============================================================================
SHEL dmax 999.00 dmin 3.00
MIND mdis -1.500 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 8 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 5
=============================================================================
2249 E > 1.500, average of 98.8 TPR for each phase, = 0.600
-----------------------------------------------------------------------------
Fourier grid = 128 x 128 x 37 -0.007 <= z <= 0.257
PSUM 30.97 PSMF Peaks: 84 80 76 73 69 63 58 48 34 25 24 23 23 23 22 22
Try 1:20 Peaks 99 97 93 87 87 84 84 80 11 9 6
R = 0.302, Min.fun. = 0.340, = 0.526, Ra = 0.269
Try 1, CC All/Weak 54.60 / 39.19, best 54.60 / 39.19, best PATFOM 0.00
PATFOM 27.27
-----------------------------------------------------------------------------
PSUM 38.38 PSMF Peaks: 86 86 79 66 66 64 62 55 31 31 30 29 27 25 25 24
Try 2:20 Peaks 99 97 93 87 87 84 84 80 11 9 6
R = 0.302, Min.fun. = 0.340, = 0.526, Ra = 0.269
Try 2, CC All/Weak 54.60 / 39.19, best 54.60 / 39.19, best PATFOM 27.27
PATFOM 27.27
-----------------------------------------------------------------------------
PSUM 40.52 PSMF Peaks: 84 77 75 69 65 63 53 47 44 42 29 26 25 25 24 24
Try 3:20 Peaks 99 98 93 88 87 84 83 81 18 11 6
R = 0.302, Min.fun. = 0.340, = 0.526, Ra = 0.269
Try 3, CC All/Weak 54.75 / 39.32, best 54.75 / 39.32, best PATFOM 27.27
PATFOM 27.27
-----------------------------------------------------------------------------
PSUM 33.91 PSMF Peaks: 124 86 73 59 51 40 39 37 33 32 30 30 30 29 28 26
Try 4:20 Peaks 99 92 91 90 86 83 68 48 44 39 36
R = 0.416, Min.fun. = 0.432, = 0.428, Ra = 0.354
Try 4, CC All/Weak 38.38 / 21.69, best 54.75 / 39.32, best PATFOM 27.27
PATFOM 9.08
-----------------------------------------------------------------------------
PSUM 22.84 PSMF Peaks: 101 39 39 36 35 34 34 33 32 31 30 30 30 30 30 30
Try 5:20 Peaks 99 87 61 60 51 49 48 47 44 39 34
R = 0.412, Min.fun. = 0.492, = 0.364, Ra = 0.418
Try 5, CC All/Weak 40.91 / 27.36, best 54.75 / 39.32, best PATFOM 27.27
PATFOM 6.61
==============================================================================
CPU times required in seconds
-----------------------------
0.2 - Data input and E-values
0.5 - Generate TPR
2.6 - PATS
5.6 - Full symmetry PSMF
1.5 - FIND
0.0 - PLOP
0.0 - GROP
10.8 - All FFTs
2.2 - All peak-searches
0.0 - Rest
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXD finished at 14:30:36 Total time: 23.43 secs +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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|
The following tables were found in the logfile: |
SHELXD Occupancy for each site SHELXD CC All/Weak for each try |
CCP4i: Running SHELXE to phase from heavy atom substructure
CCP4i: Phasing using original heavy atom enantiomorph
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXE - PHASING AND DENSITY MODIFICATION - Version 2006/3 +
+ Copyright (C) George M. Sheldrick 2001-6 +
+ Started at 14:30:36 on 21 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_56_shelxe_fa.res
DelF from: SHELX_56_shelxe_fa.hkl
Native data from: SHELX_56_shelxe.hkl
Listing file: SHELX_56_shelxe.lst
Phase output file: SHELX_56_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 0.600 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
11 heavy atoms read from .res file
29328 reflections read from file SHELX_56_shelxe_fa.hkl
74884 reflections read from file SHELX_56_shelxe.hkl
Maximum resolution of native data = 1.902 Angstroms
186 reflections with d > 2.102 and 0 in range 2.102 > d > 2.102 added
Fourier grid = 256 x 256 x 66 0.000 <= z <= 0.250
92 point spherical net set up with radius 2.42A
8 extra Fourier layers will be generated
Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 39.02%
= 0.167 for initial phases
= 0.206, Contrast = 0.072, Connect. = 0.829 for dens.mod. cycle 1
= 0.247, Contrast = 0.247, Connect. = 0.881 for dens.mod. cycle 2
= 0.299, Contrast = 0.449, Connect. = 0.906 for dens.mod. cycle 3
= 0.300, Contrast = 0.576, Connect. = 0.919 for dens.mod. cycle 4
Pseudo-free CC = 61.25 %
= 0.300, Contrast = 0.698, Connect. = 0.931 for dens.mod. cycle 5
= 0.300, Contrast = 0.771, Connect. = 0.938 for dens.mod. cycle 6
= 0.300, Contrast = 0.824, Connect. = 0.943 for dens.mod. cycle 7
= 0.300, Contrast = 0.860, Connect. = 0.946 for dens.mod. cycle 8
= 0.300, Contrast = 0.888, Connect. = 0.949 for dens.mod. cycle 9
Pseudo-free CC = 69.90 %
= 0.300, Contrast = 0.907, Connect. = 0.951 for dens.mod. cycle 10
= 0.300, Contrast = 0.923, Connect. = 0.952 for dens.mod. cycle 11
= 0.300, Contrast = 0.935, Connect. = 0.953 for dens.mod. cycle 12
= 0.300, Contrast = 0.944, Connect. = 0.953 for dens.mod. cycle 13
= 0.300, Contrast = 0.951, Connect. = 0.954 for dens.mod. cycle 14
Pseudo-free CC = 73.53 %
= 0.300, Contrast = 0.957, Connect. = 0.954 for dens.mod. cycle 15
= 0.300, Contrast = 0.962, Connect. = 0.954 for dens.mod. cycle 16
= 0.300, Contrast = 0.967, Connect. = 0.954 for dens.mod. cycle 17
= 0.300, Contrast = 0.971, Connect. = 0.954 for dens.mod. cycle 18
= 0.300, Contrast = 0.974, Connect. = 0.954 for dens.mod. cycle 19
= 0.300, Contrast = 0.977, Connect. = 0.954 for dens.mod. cycle 20
Mean weight and estimated mapCC as a function of resolution
d inf - 4.14 - 3.28 - 2.86 - 2.60 - 2.41 - 2.27 - 2.15 - 2.06 - 1.98 - 1.91
0.711 0.732 0.718 0.717 0.718 0.714 0.707 0.682 0.669 0.632
0.890 0.903 0.901 0.910 0.921 0.920 0.915 0.905 0.909 0.881
N 7536 7537 7569 7444 7564 7387 7930 7214 7483 7220
Pseudo-free CC = 75.63 %
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SHELXE finished at 14:34:01 Total time: 198.15 secs +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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The following warnings were issued:
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############################################################### ############################################################### ############################################################### ### CCP4 6.0: f2mtz version 6.0 : 06/09/05## ############################################################### User: pjx Run date: 21/ 4/2006 Run time: 14:34:01 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.
Maximum number of columns in this version: 80 Data line--- TITLE Phase information from SHELXE Data line--- SYMMETRY c2221 Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib Data line--- CELL 96.000 120.000 166.130 90.000 90.000 90.000 Data line--- FORMAT '(3f4.0,f9.2,f8.4,f8.1,f8.2)'
$TEXT:Warning: $$ comment $$ WARNING: Format I replaced with F $$
Data line--- LABOUT H K L F_ori FOM_ori PHI_ori SIGF_ori Number of columns to be read in: 7 Data line--- CTYPOUT H H H F W P Q Data line--- NAME PROJECT SHELXE CRYSTAL Unknown DATASET original Data line--- END FORMATTED OLD file opened on unit 1
Logical name: HKLIN, Filename: SHELX_56_shelxe.phs
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/pjx/PROJECTS/SHELX/jia_infl_shelx_phs3.mtz
* Title:
Phase information from SHELXE
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 SHELXE
Unknown
original
96.0000 120.0000 166.1300 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 7
* Number of Reflections = 75070
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
From f2mtz 21/ 4/2006 14:34:01
* Column Labels, Types, Ranges [and Dataset IDs] :
H H 0.0000 50.0000 0
K H 0.0000 63.0000 0
L H 0.0000 87.0000 0
F_ori F 0.0000 9999.0000 1
FOM_ori W 0.0000 1.0000 1
PHI_ori P 0.0000 360.0000 1
SIGF_ori Q 6.3600 756.7100 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
96.0000 120.0000 166.1300 90.0000 90.0000 90.0000
* Resolution Range :
0.00014 0.27648 ( 83.065 - 1.902 A )
* Sort Order :
0 0 0 0 0
* Number of Symmetry Operations = 8
* Number of Primitive Operations = 4
* Space Group = 20 'C 2 2 21'
* Lattice Type = C
* Point Group Name = PG222
* Symmetry Operations :
Symmetry 1 X, Y, Z
1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 2 -X, -Y, Z+1/2
-1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 3 X, -Y, -Z
1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 4 -X, Y, -Z+1/2
-1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 5 X+1/2, Y+1/2, Z
1.00 0.00 0.00 0.50
0.00 1.00 0.00 0.50
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 6 -X+1/2, -Y+1/2, Z+1/2
-1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.50
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 7 X+1/2, -Y+1/2, -Z
1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.50
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 8 -X+1/2, Y+1/2, -Z+1/2
-1.00 0.00 0.00 0.50
0.00 1.00 0.00 0.50
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
75070 input reflections processed
f2mtz: Normal termination Times: User: 2.1s System: 0.0s Elapsed: 0:02
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CCP4i: Phasing using inverted heavy atom enantiomorph
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+ SHELXE - PHASING AND DENSITY MODIFICATION - Version 2006/3 +
+ Copyright (C) George M. Sheldrick 2001-6 +
+ Started at 14:34:03 on 21 Apr 2006 +
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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_56_shelxe_fa.res
DelF from: SHELX_56_shelxe_fa.hkl
Native data from: SHELX_56_shelxe.hkl
Listing file: SHELX_56_shelxe_i.lst
Phase output file: SHELX_56_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 0.600 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
11 heavy atoms read from .res file
29328 reflections read from file SHELX_56_shelxe_fa.hkl
74884 reflections read from file SHELX_56_shelxe.hkl
Maximum resolution of native data = 1.902 Angstroms
186 reflections with d > 2.102 and 0 in range 2.102 > d > 2.102 added
Fourier grid = 256 x 256 x 66 0.000 <= z <= 0.250
92 point spherical net set up with radius 2.42A
8 extra Fourier layers will be generated
Overall CC between Eobs (from delF) and Ecalc (from heavy atoms) = 39.02%
= 0.167 for initial phases
= 0.199, Contrast = 0.047, Connect. = 0.763 for dens.mod. cycle 1
= 0.222, Contrast = 0.144, Connect. = 0.831 for dens.mod. cycle 2
= 0.239, Contrast = 0.167, Connect. = 0.839 for dens.mod. cycle 3
= 0.249, Contrast = 0.178, Connect. = 0.843 for dens.mod. cycle 4
Pseudo-free CC = 39.60 %
= 0.258, Contrast = 0.223, Connect. = 0.855 for dens.mod. cycle 5
= 0.273, Contrast = 0.243, Connect. = 0.861 for dens.mod. cycle 6
= 0.294, Contrast = 0.295, Connect. = 0.871 for dens.mod. cycle 7
= 0.299, Contrast = 0.347, Connect. = 0.880 for dens.mod. cycle 8
= 0.300, Contrast = 0.401, Connect. = 0.888 for dens.mod. cycle 9
Pseudo-free CC = 52.18 %
= 0.300, Contrast = 0.449, Connect. = 0.894 for dens.mod. cycle 10
= 0.300, Contrast = 0.492, Connect. = 0.900 for dens.mod. cycle 11
= 0.300, Contrast = 0.528, Connect. = 0.905 for dens.mod. cycle 12
= 0.300, Contrast = 0.558, Connect. = 0.909 for dens.mod. cycle 13
= 0.300, Contrast = 0.581, Connect. = 0.911 for dens.mod. cycle 14
Pseudo-free CC = 58.12 %
= 0.300, Contrast = 0.602, Connect. = 0.914 for dens.mod. cycle 15
= 0.300, Contrast = 0.618, Connect. = 0.915 for dens.mod. cycle 16
= 0.300, Contrast = 0.632, Connect. = 0.917 for dens.mod. cycle 17
= 0.300, Contrast = 0.643, Connect. = 0.918 for dens.mod. cycle 18
= 0.300, Contrast = 0.653, Connect. = 0.919 for dens.mod. cycle 19
= 0.300, Contrast = 0.662, Connect. = 0.921 for dens.mod. cycle 20
Mean weight and estimated mapCC as a function of resolution
d inf - 4.14 - 3.28 - 2.86 - 2.60 - 2.41 - 2.27 - 2.15 - 2.06 - 1.98 - 1.91
0.502 0.550 0.558 0.557 0.558 0.579 0.570 0.534 0.528 0.514
0.729 0.767 0.782 0.792 0.810 0.837 0.824 0.797 0.796 0.783
N 7536 7537 7569 7444 7564 7387 7930 7214 7483 7220
Pseudo-free CC = 60.07 %
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+ SHELXE finished at 14:37:27 Total time: 198.54 secs +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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############################################################### ############################################################### ############################################################### ### CCP4 6.0: f2mtz version 6.0 : 06/09/05## ############################################################### User: pjx Run date: 21/ 4/2006 Run time: 14:37:27 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.
Maximum number of columns in this version: 80 Data line--- TITLE Phase information from SHELXE Data line--- SYMMETRY c2221 Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib Data line--- CELL 96.000 120.000 166.130 90.000 90.000 90.000 Data line--- FORMAT '(3f4.0,f9.2,f8.4,f8.1,f8.2)'
$TEXT:Warning: $$ comment $$ WARNING: Format I replaced with F $$
Data line--- LABOUT H K L F_inv FOM_inv PHI_inv SIGF_inv Number of columns to be read in: 7 Data line--- CTYPOUT H H H F W P Q Data line--- NAME PROJECT SHELXE CRYSTAL Unknown DATASET inverted Data line--- END FORMATTED OLD file opened on unit 1
Logical name: HKLIN, Filename: SHELX_56_shelxe_i.phs
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/pjx/PROJECTS/SHELX/jia_infl_shelx_phs_i3.mtz
* Title:
Phase information from SHELXE
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 SHELXE
Unknown
inverted
96.0000 120.0000 166.1300 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 7
* Number of Reflections = 75070
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
From f2mtz 21/ 4/2006 14:37:27
* Column Labels, Types, Ranges [and Dataset IDs] :
H H 0.0000 50.0000 0
K H 0.0000 63.0000 0
L H 0.0000 87.0000 0
F_inv F 0.0000 9999.0000 1
FOM_inv W 0.0000 1.0000 1
PHI_inv P 0.0000 360.0000 1
SIGF_inv Q 6.3600 756.2200 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
96.0000 120.0000 166.1300 90.0000 90.0000 90.0000
* Resolution Range :
0.00014 0.27648 ( 83.065 - 1.902 A )
* Sort Order :
0 0 0 0 0
* Number of Symmetry Operations = 8
* Number of Primitive Operations = 4
* Space Group = 20 'C 2 2 21'
* Lattice Type = C
* Point Group Name = PG222
* Symmetry Operations :
Symmetry 1 X, Y, Z
1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 2 -X, -Y, Z+1/2
-1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 3 X, -Y, -Z
1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 4 -X, Y, -Z+1/2
-1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 5 X+1/2, Y+1/2, Z
1.00 0.00 0.00 0.50
0.00 1.00 0.00 0.50
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 6 -X+1/2, -Y+1/2, Z+1/2
-1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.50
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 7 X+1/2, -Y+1/2, -Z
1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.50
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 8 -X+1/2, Y+1/2, -Z+1/2
-1.00 0.00 0.00 0.50
0.00 1.00 0.00 0.50
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
75070 input reflections processed
f2mtz: Normal termination Times: User: 2.1s System: 0.0s Elapsed: 0:02
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The following tables were found in the logfile: |
SHELXE Contrast and Connectivity SHELXE Estimated CC(map) |
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