Result:
Best Solution: space group C 2 2 21
| Reindex operator: | [h,k,l] |
|---|---|
| Laue group probability: | 1.000 |
| Systematic absence probability: | 0.993 |
| Total probability: | 0.993 |
| Space group confidence: | 0.989 |
| Laue group confidence | 0.000 |
Unit cell: 83.09 96.79 57.95 90 90 90
42.66 to 1.90 - Resolution range selected on input
Number of batches in file: 1800
The data do not appear to be twinned, from the L-test
The following warnings were issued:
|
The following tables were found in the logfile: |
L-test for twinning, twin fraction 0.024 Axial reflections, axis c (lattice frame) screw axis 2(1) |
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###############################################################
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### CCP4 6.4: POINTLESS version 1.9.2 : 06/03/14##
###############################################################
User: unknown Run date: 15/ 5/2014 Run time: 03:34:00
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.
>>>>> Input command lines <<<<<
lauegroup hklin
setting symmetry-based
>>>>> End of input <<<<<
$TEXT:Warning:$$ $$
WARNING: In LAUEGROUP command:
Rhombohedral group name HKLIN will be used in the hexagonal [H] setting H KLIN
$$
$TEXT:Warning:$$ $$
WARNING: In LAUEGROUP command:
Rhombohedral group name HKLIN will be used in the hexagonal [H] setting H KLIN
$$
Release Date: 6th March 2014
******************************************************
* *
* POINTLESS *
* 1.9.2 *
* *
* Determine Laue group from unmerged intensities *
* Phil Evans MRC LMB, Cambridge *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
* *
******************************************************
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /dls_sw/apps/ccp4/x86_64/6.4.0/8apr2014/ccp4-6.4.0/lib/data/syminfo.lib
Reflection list generated from file:
/dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2
BAx8281/scale/SCALED_SAD_SWEEP1.mtz
Title: From XDS file SCALED_SAD_SWEEP1.HKL, XDS run on 15-May-2014 from image
Space group from HKLIN file : C 2 2 2
Cell: 83.09 96.79 57.95 90.00 90.00 90.00
Resolution range in file: 42.66 1.90
Time for reading file(s): 0.440 secs
===============================================================
>*> Summary of test data read in:
Resolution range accepted: 42.66 1.90
Number of reflections = 18788
Number of observations = 125173
Number of parts = 125173
Number of batches in file = 1800
Number of datasets = 1
Project: nt5073v16 Crystal: xBAZ2BAx8281 Dataset: SAD
Run number: 1 consists of batches 1 to 1800
Phi range: 0.00 to 0.00 Time range: 0.00 to 0.00
Closest reciprocal axis to spindle: a* (angle nan degrees)
Average unit cell: 83.09 96.79 57.95 90.00 90.00 90.00
===============================================================
Checking for possible twinning
L-test for twinning (acentrics only) to maximum resolution 2.522
using Mn(I/sigmaI) cutoff 8.0
Neighbouring reflections for test are +- 2 on h,k,l
$TABLE: L-test for twinning, twin fraction 0.024:
$GRAPHS:Cumulative distribution of |L|, estimated fraction 0.024:N:1,2,3,4:
$$
|L| N(|L|) Untwinned Twinned $$ $$
0.0000 0.0000 0.0000 0.0000
0.0500 0.0569 0.0500 0.0749
0.1000 0.1091 0.1000 0.1495
0.1500 0.1615 0.1500 0.2233
0.2000 0.2135 0.2000 0.2960
0.2500 0.2653 0.2500 0.3672
0.3000 0.3168 0.3000 0.4365
0.3500 0.3693 0.3500 0.5036
0.4000 0.4210 0.4000 0.5680
0.4500 0.4725 0.4500 0.6294
0.5000 0.5251 0.5000 0.6875
0.5500 0.5769 0.5500 0.7418
0.6000 0.6280 0.6000 0.7920
0.6500 0.6782 0.6500 0.8377
0.7000 0.7273 0.7000 0.8785
0.7500 0.7763 0.7500 0.9141
0.8000 0.8255 0.8000 0.9440
0.8500 0.8738 0.8500 0.9679
0.9000 0.9209 0.9000 0.9855
0.9500 0.9649 0.9500 0.9963
1.0000 1.0000 1.0000 1.0000
$$
Estimated twin fraction alpha from cumulative N(|L|) plot 0.027 (+/-0.004)
<|L|>: 0.481 (0.5 untwinned, 0.375 perfect twin)
Estimated twin fraction alpha from <|L|> 0.024
: 0.312 (0.333 untwinned, 0.2 perfect twin)
Estimated twin fraction alpha from 0.021
The L-test suggests that the data are not twinned
Note that the estimate of the twin fraction from the L-test is not very accurate,
particularly for high twin fractions. Better estimates from other test need knowledge of
the point group and the twin operator, which are not available here
Also these statistics come from unscaled (and unmerged) data, so may be inaccurate for that reason
Time for twinning test 0.560 secs
======================================================================
Model for expectation(CC) = E(m) if symmetry is absent P(m;!S) = (1-m^k)^(1/k) with k = 2.3
Reindexing or changing symmetry to selected Laue group C m m m
Reindex operator from input cell to given Lauegroup: [h,k,l]
h' = ( h k l ) ( 1 0 0 )
( 0 1 0 )
( 0 0 1 )
Unit cell after reindexing: 83.09 96.79 57.95 90.00 90.00 90.00
Number of reflections = 18788
Number of observations = 125173
Average multiplicity = 6.7
Resolution range in list: 42.66 -> 1.90
Intensity normalisation: B-factor = -19.2 + -0.0002 * time (final B -19.6)
Resolution range reset to 42.66 to 2.39
using Mn(I/sigmaI) cutoff 6.0
********************************************************
Testing Lauegroups for systematic absences
------------------------------------------
I' is intensity adjusted by subtraction of a small fraction (0.02, NEIGHBOUR)
of the neighbouring intensities, to allow for possible overlap
$TABLE: Axial reflections, axis c (lattice frame) screw axis 2(1):
$GRAPHS:I/sigI vs. index, axis c, screw axis 2(1):N:1,4,5:
:I vs. index, axis c, screw axis 2(1):N:1,2:
$$
Index I sigI I/sigI I'/sigI $$ $$
2 888 26 33.54 33.54
3 -1 3 -0.19 0.00
4 10643 314 33.88 33.88
5 -1 2 -0.24 0.00
7 -1 2 -0.43 0.00
8 2969 88 33.58 33.58
9 -1 2 -0.44 0.00
10 801 25 32.33 32.33
11 -1 2 -0.62 0.00
12 1000 31 32.40 32.40
14 125 6 22.29 22.29
15 0 3 0.14 0.00
16 632 21 30.69 30.68
17 2 3 0.59 0.00
18 713 23 31.02 31.01
19 1 3 0.50 0.00
20 409 14 28.67 28.66
21 1 3 0.42 0.00
22 31 3 9.01 9.01
23 -0 3 -0.18 0.00
24 42 4 10.81 10.81
26 124 7 18.11 18.11
27 -1 3 -0.39 0.00
28 305 12 25.03 25.03
29 3 4 0.68 0.00
30 8 5 1.58 1.57
$$
Each 'zone' (axis or plane) in which some reflections may be systematically absent
are scored by Fourier analysis of I'/sigma(I). 'PeakHeight' is the value
in Fourier space at the relevent point (eg at 1/2 for a 2(1) axis)
relative to the origin. This has an ideal value of 1.0 if the corresponding
symmetry element is present. Zone directions (a,b,c) shown here are in the
lattice group frame
'Probability' is an estimate of how likely the element is to be present
Zone Number PeakHeight SD Probability ReflectionCondition Zones for Laue group C m m m 1 screw axis 2(1) [c] 50 1.000 0.079 *** 0.993 00l: l=2n
Time for systematic absence tests: 0.890 secs
Possible spacegroups:
--------------------
Indistinguishable space groups are grouped together on successive lines
'Reindex' is the operator to convert from the input hklin frame to the standard spacegroup frame.
'TotProb' is a total probability estimate (unnormalised)
'SysAbsProb' is an estimate of the probability of the space group based on
the observed systematic absences.
'Conditions' are the reflection conditions (absences)
Spacegroup TotProb SysAbsProb Reindex Conditions
<C 2 2 21> ( 20) 0.993 0.993 00l: l=2n (zone 1)
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.99
Laue group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.00
Selecting space group C 2 2 21 as there is a single space group with the highest score
$TEXT:Result: $$ $$ Best Solution: space group C 2 2 21 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.993 Total probability: 0.993 Space group confidence: 0.989 Laue group confidence 0.000 Unit cell: 83.09 96.79 57.95 90 90 90 42.66 to 1.90 - Resolution range selected on input Number of batches in file: 1800 The data do not appear to be twinned, from the L-test $$
HKLIN spacegroup: C 2 2 2 C-centred orthorhombic
/dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2BAx8281/scale/SCALED_SAD_SWEEP1.mtz
Filename:
/dls/i04-1/data/2014/nt5073-16/tmp/BAZ2BA/BAZ2BA-x828/BAZ2BA-x828_1_/xia2-3daii-run/1400120766/xBAZ2
BAx8281/scale/SCALED_SAD_SWEEP1.mtz
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Writing unmerged data to file pointless.mtz in space group C 2 2 21
Reindexing operator [h,k,l]
Real space transformation (x,y,z)
* Title:
From XDS file SCALED_SAD_SWEEP1.HKL, XDS run on 15-May-2014 from image
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 nt5073v16
xBAZ2BAx8281
SAD
83.0900 96.7900 57.9500 90.0000 90.0000 90.0000
0.92001
* Number of Columns = 11
* Number of Reflections = 125173
* Missing value set to NaN in input mtz file
* Number of Batches = 1800
* Column Labels :
H K L M/ISYM BATCH I SIGI XDET YDET ROT FLAG
* Column Types :
H H H Y B J Q R R R I
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
83.0900 96.7900 57.9500 90.0000 90.0000 90.0000
* Resolution Range :
0.00055 0.27701 ( 42.665 - 1.900 A )
* Sort Order :
1 2 3 4 5
* Space group = 'C 2 2 21' (number 20)
(spacegroup is known)
$TEXT:Reference: $$ Please cite $$
P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst. D62, 72-82 (2006).
PDF
P.R.Evans, 'An introduction to data reduction: space-group determination, scaling and intensity
statistics' Acta Cryst. D67, 282-292 (2011)
PDF
$$
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