Dear All,
Sorry for the wrong pointless file. With this mail i have attached the
pointless run file from the unmerged data. This file also suggests the
C2221 spacegroup.
Appu
On 22 April 2015 at 17:40, Christian Roth <[email protected]
> wrote:
> Hi Appu,
>
> you start already with a fixed spacegroup (scaled merged data) according
> to your pointless log. So you can't get another possible solution from
> pointless.
>
> Cheers
>
>
>
> Am 22.04.2015 um 22:28 schrieb Appu kumar:
>
>> Dear CCP4 Member,
>> I seek your advice on the refinement issues at the low resolution 4A. I
>> am trying to refine a membrane protein structure after getting the
>> phases from MR using the PHASER. The soluble domain structure which
>> comprises of 40% of protein has been used as template (sequence identity
>> 80%) in MR search . The PHASER gave a good solution having TFZ value of
>> about 14.3. I have then created the polyA model for the transmembrane
>> domain from distant homolog which share 30% sequence identity for TM
>> region and try to find the phases for whole TM domain keeping the
>> soluble domain fixed. I got lucky in getting the phases for the whole
>> protein using the PHASER (TFZ=17.6) but the during the refinement, Rwork
>> and Rfree got stalled at the 41 and 44 respectively after several cycle
>> of the refinement in both refmac and phenix. I checked the spacegroup
>> with pointless and it suggests C2221. I have attached the pointless and
>> phenix.xtriage run file with this mail for your evaluation.
>> Phenix.xtriage suggests no major pathologies with the data except the
>> mild psuedomerohedral twining. There are two molecules of protein in
>> ASU. Evaluation of the density maps, suggest reasonable map for the most
>> of protein part. I am wondering why Rwork and Rfree are not coming down
>> despite of the good MR solution and what i am doing wrong with
>> refinement and if there is some pathologies associated with the data
>> which needs to be answered before heading to refinement.
>>
>> Thanks for your help in advance.
>>
>> Appu
>>
>>
#CCP4I VERSION CCP4Interface 2.2.1
#CCP4I SCRIPT LOG pointless
#CCP4I DATE 22 Apr 2015 17:39:30
#CCP4I USER appu
#CCP4I PROJECT AS015crv6ctd2nq
#CCP4I JOB_ID 119
#CCP4I SCRATCH /tmp/appu
#CCP4I HOSTNAME sasha
#CCP4I PID 47982
###############################################################
###############################################################
###############################################################
### CCP4 6.4: POINTLESS version 1.9.16 : 21/08/14##
###############################################################
User: appu Run date: 22/ 4/2015 Run time: 17:39:30
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 <<<<<
HKLIN /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/AS115c_1_0001.mtz
HKLOUT /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/refine/AS115c_1_0001_pointless1.mtz
## This script run with the command ##########
# /home/appu/Downloads/ccp4-6.4.0/bin/pointless
################################################
>>>>> End of input <<<<<
OS type: linux
Release Date: 21st August2014
******************************************************
* *
* POINTLESS *
* 1.9.16 *
* *
* 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: /home/appu/Downloads/ccp4-6.4.0/lib/data/syminfo.lib
Reflection list generated from file:
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/AS115c_1_0001.mtz
Title: Untitled
Space group from HKLIN file : C 2 2 21
Cell: 130.42 213.36 160.80 90.00 90.00 90.00
Resolution range in file: 65.21 3.75
Time for reading file(s): 2.190 secs
===============================================================
>*> Summary of test data read in:
Resolution range accepted: 65.21 3.75
Number of reflections = 23371
Number of observations = 150865
Number of parts = 619082
Number of batches in file = 600
Number of datasets = 1
Project: New Crystal: New Dataset: New
Run number: 1 consists of batches 1 to 600
Resolution range for run: 65.21 3.75
Phi range: 0.00 to 180.00 Time range: 0.00 to 180.00
Closest reciprocal axis to spindle: c* (angle 25.6 degrees)
Average unit cell: 130.42 213.36 160.80 90.00 90.00 90.00
Numbers of observations marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category
Flagged Accepted Maximum MaxAccepted
BGratio too large 0 0 2.000 0.000
PKratio too large 0 0 0.000 0.000
Negative < 5sigma 3 0
Gradient too large 0 0 0.159 0.000
Profile-fitted overloads 0 0
Spots on edge 14294 0
===============================================================
Checking for possible twinning
L-test for twinning (acentrics only) to maximum resolution 6.474
using Mn(I/sigmaI) cutoff 8.0
Neighbouring reflections for test are +- 2 on h,k,l
$TABLE: L-test for twinning, twin fraction 0.000:
$GRAPHS:Cumulative distribution of |L|, estimated fraction 0.000:N:1,2,3,4:
$$
|L| N(|L|) Untwinned Twinned $$ $$
0.0000 0.0000 0.0000 0.0000
0.0500 0.0531 0.0500 0.0749
0.1000 0.1035 0.1000 0.1495
0.1500 0.1542 0.1500 0.2233
0.2000 0.2033 0.2000 0.2960
0.2500 0.2527 0.2500 0.3672
0.3000 0.3024 0.3000 0.4365
0.3500 0.3520 0.3500 0.5036
0.4000 0.4016 0.4000 0.5680
0.4500 0.4513 0.4500 0.6294
0.5000 0.5008 0.5000 0.6875
0.5500 0.5513 0.5500 0.7418
0.6000 0.6025 0.6000 0.7920
0.6500 0.6542 0.6500 0.8377
0.7000 0.7045 0.7000 0.8785
0.7500 0.7562 0.7500 0.9141
0.8000 0.8082 0.8000 0.9440
0.8500 0.8598 0.8500 0.9679
0.9000 0.9100 0.9000 0.9855
0.9500 0.9596 0.9500 0.9963
1.0000 1.0000 1.0000 1.0000
$$
Estimated twin fraction alpha from cumulative N(|L|) plot 0.003 (+/-0.002)
< |L| >: 0.496 (0.5 untwinned, 0.375 perfect twin)
Estimated twin fraction alpha from < |L| > 0.000
< L^2 >: 0.328 (0.333 untwinned, 0.2 perfect twin)
Estimated twin fraction alpha from < L^2 > 0.000
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 tests need knowledge of
the point group and the twin operator, which are not available here
Also these statistics come from possibly unscaled (and unmerged) data,
so may be inaccurate for that reason
Time for twinning test 0.300 secs
======================================================================
Model for expectation(CC) = E(m) if symmetry is absent P(m;!S) = (1-m^k)^(1/k) with k = 2.0
Lattice symmetry == HKLIN symmetry
Unit cell (from HKLIN file) used to derive lattice symmetry with tolerance 2.0 degrees
130.42 213.36 160.80 90.00 90.00 90.00
Tolerance (and delta) is the maximum deviation from the
expected angle between two-fold axes in the lattice group
Lattice point group: C 2 2 2
Number of reflections = 23371
Number of observations = 150865
Number of scaled observations = 1611
Average multiplicity = 6.5
Resolution range in list: 65.21 -> 3.75
Intensity normalisation: B-factor = -62.7 + -0.2446 * time (final B -106.8)
Resolution range reset to 65.21 to 6.18
using Mn(I/sigmaI) cutoff 6.0
16 pairs rejected for E^2 too large
Overall CC for 15313 unrelated pairs: 0.089 N= 15313
Estimated expectation value of true correlation coefficient E(CC) = 0.983
Estimated sd(CC) = 1.335 / Sqrt(N)
Estimated E(CC) of true correlation coefficient from identity = 0.972
*******************************************
Analysing rotational symmetry in lattice group C m m m
----------------------------------------------
<!--SUMMARY_BEGIN-->
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell)
1 0.943 9.69 0.97 14273 0.067 identity
2 0.904 9.20 0.92 23532 0.158 *** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.895 9.13 0.91 23697 0.161 ** 2-fold k ( 0 1 0) {-h,k,-l}
4 0.899 9.17 0.92 23557 0.134 ** 2-fold h ( 1 0 0) {h,-k,-l}
<!--SUMMARY_END-->
Time to determine pointgroup: 0.590 secs
Acceptable Laue groups have scores above 0.19
Scores for all possible Laue groups which are sub-groups of lattice group
-------------------------------------------------------------------------
Note that correlation coefficients are from intensities approximately normalised
by resolution, so will be worse than the usual values
Rmeas is the multiplicity weighted R-factor
Lklhd is a likelihood measure, a probability used in the ranking of space groups
Z-scores are from combined scores for all symmetry elements
in the sub-group (Z+) or not in sub-group (Z-)
NetZ = Z+ - Z-
Net Z-scores are calculated for correlation coefficients (cc)
The point-group Z-scores Zc are calculated
as the Zcc-scores recalculated for all symmetry elements for or against,
CC- and R- are the correlation coefficients and R-factors for symmetry elements not in the group
Delta is maximum angular difference (degrees) between original cell
and cell with symmetry constraints imposed
The reindex operator converts original index scheme into the conventional
scheme for sub-group
Accepted Laue groups are marked '>'
The HKLIN Laue group is marked '=' if accepted, '-' if rejected
<!--SUMMARY_BEGIN-->
Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta ReindexOperator
= 1 C m m m *** 0.963 9.27 9.27 0.00 0.93 0.00 0.13 0.00 0.0 [h,k,l]
2 P 1 2/m 1 0.013 0.25 9.40 9.15 0.94 0.91 0.11 0.15 0.0 [-1/2h-1/2k,l,-1/2h+1/2k]
3 C 1 2/m 1 0.012 0.30 9.43 9.13 0.94 0.91 0.10 0.16 0.0 [-k,h,l]
4 C 1 2/m 1 0.011 0.27 9.42 9.14 0.94 0.91 0.11 0.15 0.0 [h,k,l]
5 P -1 0.001 0.55 9.69 9.13 0.97 0.91 0.07 0.15 0.0 [1/2h+1/2k,-1/2h+1/2k,l]
<!--SUMMARY_END-->
********************************************************
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:
$$
Index I sigI I/sigI I'/sigI $$ $$
3 15 2 9.86 0.00
4 3963 5 820.78 820.59
5 29 2 17.21 0.00
6 34591 17 2060.90 2060.86
7 4 2 2.04 0.00
8 3692 9 396.04 396.03
9 1 2 0.56 0.00
10 10491 12 863.53 863.52
11 2 3 0.87 0.00
12 15767 23 683.11 683.09
13 18 3 5.57 0.00
14 1159 6 199.40 199.34
15 -1 4 -0.21 0.00
19 13 5 2.43 0.00
20 881 8 115.04 115.01
21 -12 9 -1.37 0.00
22 37 9 4.07 4.07
23 -2 9 -0.17 0.00
24 1910 13 146.05 146.04
25 5 10 0.50 0.00
26 -10 10 -1.03 0.00
27 -17 16 -1.05 0.00
28 107 11 9.60 9.60
29 -3 11 -0.24 0.22
30 58 13 4.53 4.51
31 9 18 0.52 0.36
32 88 13 6.80 6.77
33 15 22 0.69 0.61
36 -20 16 -1.31 0.00
37 -4 13 -0.29 0.18
38 -14 14 -1.00 0.00
39 14 16 0.88 0.88
40 -1 16 -0.06 0.60
41 22 17 1.29 1.27
42 18 17 1.04 1.02
$$
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
<!--SUMMARY_BEGIN-->
Zone Number PeakHeight SD Probability ReflectionCondition
Zones for Laue group C m m m
1 screw axis 2(1) [c] 64 0.999 0.263 *** 0.922 00l: l=2n
<!--SUMMARY_END-->
Time for systematic absence tests: 0.210 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) 0.887 0.922 00l: l=2n (zone 1)
..........
C 2 2 2 ( 21) 0.075 0.078
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.85
Laue group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.96
Selecting space group C 2 2 21 as there is a single space group with the highest score
<!--SUMMARY_BEGIN--> $TEXT:Result: $$ $$
Best Solution: space group C 2 2 21
Reindex operator: [h,k,l]
Laue group probability: 0.963
Systematic absence probability: 0.922
Total probability: 0.887
Space group confidence: 0.848
Laue group confidence 0.956
Unit cell: 130.42 213.36 160.80 90.00 90.00 90.00
65.21 to 6.18 - Resolution range used for Laue group search
65.21 to 3.75 - Resolution range in file, used for systematic absence check
Number of batches in file: 600
The data do not appear to be twinned, from the L-test
$$ <!--SUMMARY_END-->
HKLIN spacegroup: C 2 2 21 C-centred orthorhombic
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/AS115c_1_0001.mtz
Filename: /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/AS115c_1_0001.mtz
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Writing unmerged data to file
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/refine/AS115c_1_0001_pointless1.mtz in space group C 2 2 21
Reindexing operator [h,k,l]
Real space transformation (x,y,z)
* Title:
Untitled
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 New
New
New
130.4194 213.3596 160.7990 90.0000 90.0000 90.0000
0.97919
* Number of Columns = 18
* Number of Reflections = 619082
* Missing value set to NaN in input mtz file
* Number of Batches = 600
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS
* Column Types :
H H H Y B J Q J Q R R R R R R I I R
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
130.4194 213.3596 160.7990 90.0000 90.0000 90.0000
* Resolution Range :
0.00024 0.07111 ( 65.210 - 3.750 A )
* Sort Order :
1 2 3 4 5
* Space group = 'C 2 2 21' (number 20)
(spacegroup is known)
$TEXT:Reference: $$ Please cite $$
P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst. D62, 72-82 (2006).
<a href="http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html";>
<b>PDF</b></a>
P.R.Evans, 'An introduction to data reduction: space-group determination, scaling and intensity
statistics' Acta Cryst. D67, 282-292 (2011)
<a href="http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html";>
<b>PDF</b></a>
$$
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 22 Apr 2015 17:39:35
#CCP4I MESSAGE Task completed successfully
#CCP4I VERSION CCP4Interface 2.2.1
#CCP4I SCRIPT LOG pointless
#CCP4I DATE 22 Apr 2015 17:40:45
#CCP4I USER appu
#CCP4I PROJECT AS015crv6ctd2nq
#CCP4I JOB_ID 120
#CCP4I SCRATCH /tmp/appu
#CCP4I HOSTNAME sasha
#CCP4I PID 48006
###############################################################
###############################################################
###############################################################
### CCP4 6.4: POINTLESS version 1.9.16 : 21/08/14##
###############################################################
User: appu Run date: 22/ 4/2015 Run time: 17:40:45
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 <<<<<
HKLIN /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/pointless_AS115c_1_0001.mtz
HKLOUT /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/refine/pointless_AS115c_1_0001_pointless1.mtz
## This script run with the command ##########
# /home/appu/Downloads/ccp4-6.4.0/bin/pointless
################################################
>>>>> End of input <<<<<
OS type: linux
Release Date: 21st August2014
******************************************************
* *
* POINTLESS *
* 1.9.16 *
* *
* 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: /home/appu/Downloads/ccp4-6.4.0/lib/data/syminfo.lib
Reflection list generated from file:
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/pointless_AS115c_1_0001.mtz
Title: Untitled
Space group from HKLIN file : C 2 2 21
Cell: 130.42 213.36 160.80 90.00 90.00 90.00
Resolution range in file: 65.21 3.75
Time for reading file(s): 1.730 secs
===============================================================
>*> Summary of test data read in:
Resolution range accepted: 65.21 3.75
Number of reflections = 23371
Number of observations = 150865
Number of parts = 619082
Number of batches in file = 600
Number of datasets = 1
Project: New Crystal: New Dataset: New
Run number: 1 consists of batches 1 to 600
Resolution range for run: 65.21 3.75
Phi range: 0.00 to 180.00 Time range: 0.00 to 180.00
Closest reciprocal axis to spindle: c* (angle 25.6 degrees)
Average unit cell: 130.42 213.36 160.80 90.00 90.00 90.00
Numbers of observations marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category
Flagged Accepted Maximum MaxAccepted
BGratio too large 0 0 2.000 0.000
PKratio too large 0 0 0.000 0.000
Negative < 5sigma 3 0
Gradient too large 0 0 0.159 0.000
Profile-fitted overloads 0 0
Spots on edge 14294 0
===============================================================
Checking for possible twinning
L-test for twinning (acentrics only) to maximum resolution 6.474
using Mn(I/sigmaI) cutoff 8.0
Neighbouring reflections for test are +- 2 on h,k,l
$TABLE: L-test for twinning, twin fraction 0.000:
$GRAPHS:Cumulative distribution of |L|, estimated fraction 0.000:N:1,2,3,4:
$$
|L| N(|L|) Untwinned Twinned $$ $$
0.0000 0.0000 0.0000 0.0000
0.0500 0.0531 0.0500 0.0749
0.1000 0.1035 0.1000 0.1495
0.1500 0.1542 0.1500 0.2233
0.2000 0.2033 0.2000 0.2960
0.2500 0.2527 0.2500 0.3672
0.3000 0.3024 0.3000 0.4365
0.3500 0.3520 0.3500 0.5036
0.4000 0.4016 0.4000 0.5680
0.4500 0.4513 0.4500 0.6294
0.5000 0.5008 0.5000 0.6875
0.5500 0.5513 0.5500 0.7418
0.6000 0.6025 0.6000 0.7920
0.6500 0.6542 0.6500 0.8377
0.7000 0.7045 0.7000 0.8785
0.7500 0.7562 0.7500 0.9141
0.8000 0.8082 0.8000 0.9440
0.8500 0.8598 0.8500 0.9679
0.9000 0.9100 0.9000 0.9855
0.9500 0.9596 0.9500 0.9963
1.0000 1.0000 1.0000 1.0000
$$
Estimated twin fraction alpha from cumulative N(|L|) plot 0.003 (+/-0.002)
< |L| >: 0.496 (0.5 untwinned, 0.375 perfect twin)
Estimated twin fraction alpha from < |L| > 0.000
< L^2 >: 0.328 (0.333 untwinned, 0.2 perfect twin)
Estimated twin fraction alpha from < L^2 > 0.000
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 tests need knowledge of
the point group and the twin operator, which are not available here
Also these statistics come from possibly unscaled (and unmerged) data,
so may be inaccurate for that reason
Time for twinning test 0.290 secs
======================================================================
Model for expectation(CC) = E(m) if symmetry is absent P(m;!S) = (1-m^k)^(1/k) with k = 2.0
Lattice symmetry == HKLIN symmetry
Unit cell (from HKLIN file) used to derive lattice symmetry with tolerance 2.0 degrees
130.42 213.36 160.80 90.00 90.00 90.00
Tolerance (and delta) is the maximum deviation from the
expected angle between two-fold axes in the lattice group
Lattice point group: C 2 2 2
Number of reflections = 23371
Number of observations = 150865
Number of scaled observations = 1611
Average multiplicity = 6.5
Resolution range in list: 65.21 -> 3.75
Intensity normalisation: B-factor = -62.8 + -0.2443 * time (final B -106.7)
Resolution range reset to 65.21 to 6.18
using Mn(I/sigmaI) cutoff 6.0
16 pairs rejected for E^2 too large
Overall CC for 15313 unrelated pairs: 0.092 N= 15313
Estimated expectation value of true correlation coefficient E(CC) = 0.983
Estimated sd(CC) = 1.360 / Sqrt(N)
Estimated E(CC) of true correlation coefficient from identity = 0.971
*******************************************
Analysing rotational symmetry in lattice group C m m m
----------------------------------------------
<!--SUMMARY_BEGIN-->
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell)
1 0.942 9.68 0.97 14273 0.067 identity
2 0.903 9.20 0.92 23532 0.158 *** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.912 9.28 0.93 23697 0.161 *** 2-fold k ( 0 1 0) {-h,k,-l}
4 0.918 9.34 0.93 23557 0.134 *** 2-fold h ( 1 0 0) {h,-k,-l}
<!--SUMMARY_END-->
Time to determine pointgroup: 0.590 secs
Acceptable Laue groups have scores above 0.19
Scores for all possible Laue groups which are sub-groups of lattice group
-------------------------------------------------------------------------
Note that correlation coefficients are from intensities approximately normalised
by resolution, so will be worse than the usual values
Rmeas is the multiplicity weighted R-factor
Lklhd is a likelihood measure, a probability used in the ranking of space groups
Z-scores are from combined scores for all symmetry elements
in the sub-group (Z+) or not in sub-group (Z-)
NetZ = Z+ - Z-
Net Z-scores are calculated for correlation coefficients (cc)
The point-group Z-scores Zc are calculated
as the Zcc-scores recalculated for all symmetry elements for or against,
CC- and R- are the correlation coefficients and R-factors for symmetry elements not in the group
Delta is maximum angular difference (degrees) between original cell
and cell with symmetry constraints imposed
The reindex operator converts original index scheme into the conventional
scheme for sub-group
Accepted Laue groups are marked '>'
The HKLIN Laue group is marked '=' if accepted, '-' if rejected
<!--SUMMARY_BEGIN-->
Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta ReindexOperator
= 1 C m m m *** 0.972 9.27 9.27 0.00 0.93 0.00 0.13 0.00 0.0 [h,k,l]
2 C 1 2/m 1 0.010 0.25 9.49 9.24 0.95 0.92 0.10 0.16 0.0 [-k,h,l]
3 C 1 2/m 1 0.009 0.33 9.44 9.11 0.94 0.91 0.11 0.15 0.0 [h,k,l]
4 P 1 2/m 1 0.008 0.25 9.40 9.15 0.94 0.91 0.11 0.15 0.0 [-1/2h-1/2k,l,-1/2h+1/2k]
5 P -1 0.001 0.55 9.68 9.13 0.97 0.91 0.07 0.15 0.0 [1/2h+1/2k,-1/2h+1/2k,l]
<!--SUMMARY_END-->
********************************************************
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:
$$
Index I sigI I/sigI I'/sigI $$ $$
3 15 2 9.86 0.00
4 3963 5 820.78 820.59
5 29 2 17.21 0.00
6 34591 17 2060.90 2060.86
7 4 2 2.04 0.00
8 3692 9 396.04 396.03
9 1 2 0.56 0.00
10 10491 12 863.53 863.52
11 2 3 0.87 0.00
12 15767 23 683.11 683.09
13 18 3 5.57 0.00
14 1159 6 199.40 199.34
15 -1 4 -0.21 0.00
19 13 5 2.43 0.00
20 881 8 115.04 115.01
21 -12 9 -1.37 0.00
22 37 9 4.07 4.07
23 -2 9 -0.17 0.00
24 1910 13 146.05 146.04
25 5 10 0.50 0.00
26 -10 10 -1.03 0.00
27 -17 16 -1.05 0.00
28 107 11 9.60 9.60
29 -3 11 -0.24 0.22
30 58 13 4.53 4.51
31 9 18 0.52 0.36
32 88 13 6.80 6.77
33 15 22 0.69 0.61
36 -20 16 -1.31 0.00
37 -4 13 -0.29 0.18
38 -14 14 -1.00 0.00
39 14 16 0.88 0.88
40 -1 16 -0.06 0.60
41 22 17 1.29 1.27
42 18 17 1.04 1.02
$$
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
<!--SUMMARY_BEGIN-->
Zone Number PeakHeight SD Probability ReflectionCondition
Zones for Laue group C m m m
1 screw axis 2(1) [c] 64 0.999 0.260 *** 0.923 00l: l=2n
<!--SUMMARY_END-->
Time for systematic absence tests: 0.210 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) 0.897 0.923 00l: l=2n (zone 1)
..........
C 2 2 2 ( 21) 0.075 0.077
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.86
Laue group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.97
Selecting space group C 2 2 21 as there is a single space group with the highest score
<!--SUMMARY_BEGIN--> $TEXT:Result: $$ $$
Best Solution: space group C 2 2 21
Reindex operator: [h,k,l]
Laue group probability: 0.972
Systematic absence probability: 0.923
Total probability: 0.897
Space group confidence: 0.859
Laue group confidence 0.967
Unit cell: 130.42 213.36 160.80 90.00 90.00 90.00
65.21 to 6.18 - Resolution range used for Laue group search
65.21 to 3.75 - Resolution range in file, used for systematic absence check
Number of batches in file: 600
The data do not appear to be twinned, from the L-test
$$ <!--SUMMARY_END-->
HKLIN spacegroup: C 2 2 21 C-centred orthorhombic
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/pointless_AS115c_1_0001.mtz
Filename: /home/appu/xtal/2015_04_17_APS_24IDC/AS015c/imosflm/pointless_AS115c_1_0001.mtz
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Writing unmerged data to file
/home/appu/xtal/2015_04_17_APS_24IDC/AS015c/refine/pointless_AS115c_1_0001_pointless1.mtz in space group C 2 2 21
Reindexing operator [h,k,l]
Real space transformation (x,y,z)
* Title:
Untitled
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 New
New
New
130.4194 213.3596 160.7990 90.0000 90.0000 90.0000
0.97919
* Number of Columns = 18
* Number of Reflections = 619082
* Missing value set to NaN in input mtz file
* Number of Batches = 600
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS
* Column Types :
H H H Y B J Q J Q R R R R R R I I R
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
130.4194 213.3596 160.7990 90.0000 90.0000 90.0000
* Resolution Range :
0.00024 0.07111 ( 65.210 - 3.750 A )
* Sort Order :
1 2 3 4 5
* Space group = 'C 2 2 21' (number 20)
(spacegroup is known)
$TEXT:Reference: $$ Please cite $$
P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst. D62, 72-82 (2006).
<a href="http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html";>
<b>PDF</b></a>
P.R.Evans, 'An introduction to data reduction: space-group determination, scaling and intensity
statistics' Acta Cryst. D67, 282-292 (2011)
<a href="http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html";>
<b>PDF</b></a>
$$
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 22 Apr 2015 17:40:50
#CCP4I MESSAGE Task completed successfully
