Dear Eleanor,
Many thanks for you comments.
I have run aimless/pointless with those data sets having unit cell (134/67,
134/67, 183, 90, 90 120) previously integrated with P31 2 1.
Previously, I forced aimless to not determine laue group, to keep the original
SG, and now I let aimless determine the SG.
Both aimless and pointless re-indexed both data sets to the P63 2 2 for both
data sets.
Based on the matthews analysis, it seems impossible to put molecule in to small
cell (67. 67, 183, 90, 90, 120), and truncate analysis for this large cell
indicates both tNCS and twinning. I am confused..how to interpret my data sets.
Does it have both tNCS and twinning?
For curiosity, I have ran the Phaser by turning on/off the tNCS with larger
cell (134, 134, 180, 90, 90, 120), and only the phaser 'without tNCS' gave me
the solution, but still it did not give me the 2 molecules/ASU which should be,
and just 1mol/ASU.
Again for curiosity, I ran Refmac but results were like below.
-> Refmac without twin: 0.51/0.56 (work/free)
-> Refmac with twin: 0.52/0.59
I am also attached the log file of pointless for both cells.
Going back to the previous post, I am very open to accept that my C2 refinement
is wrong, happy to learn. But, based on L-test, H-test and dropping R-values
and model with density, I guess this is quite convincing but as you commented
maybe I am misleading. Please let me know if you have more comments.
Best wishes,
Donghyuk
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#CCP4I VERSION CCP4Interface 7.0.051
#CCP4I SCRIPT LOG pointless
#CCP4I DATE 15 Jan 2019 13:42:04
#CCP4I USER user
#CCP4I PROJECT donghyuk_d011_x024
#CCP4I JOB_ID 135
#CCP4I SCRATCH /tmp/user
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 30946
###############################################################
###############################################################
###############################################################
### CCP4 7.0.051: POINTLESS version 1.11.8 : 19/12/17##
###############################################################
User: user Run date: 15/ 1/2019 Run time: 13:42:04
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
==== Input command lines ====
XDSIN /home/user/Donghyuk/d011_x024/process_donghyuk/xds_016/XDS_ASCII.HKL
HKLOUT /home/user/Donghyuk/d011_x024/ccp4/XDS_016_pointless.mtz
## This script run with the command ##########
# /home/user/Downloads/destination/ccp4-7.0/bin/pointless
################################################
==== End of input ====
Release Date: 19th December 2017
******************************************************
* *
* POINTLESS *
* 1.11.8 *
* *
* Determine Laue group from unmerged intensities *
* Phil Evans MRC LMB, Cambridge *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
* *
******************************************************
Reading XDS ascii file from file /home/user/Donghyuk/d011_x024/process_donghyuk/xds_016/XDS_ASCII.HKL
Header lines:
!FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=FALSE
!OUTPUT_FILE=XDS_ASCII.HKL DATE=11-Jan-2019
!Generated by CORRECT (VERSION Jan 26, 2018 BUILT=20180808)
!PROFILE_FITTING= TRUE
!NAME_TEMPLATE_OF_DATA_FRAMES=/home/user/Donghyuk/d011_x024/x024_C11_1_??????.h5 GENERIC
!DATA_RANGE= 1 900
!ROTATION_AXIS= 0.999999 0.001086 -0.000195
!OSCILLATION_RANGE= 0.150000
!STARTING_ANGLE= 0.000
!STARTING_FRAME= 1
!INCLUDE_RESOLUTION_RANGE= 50.000 1.582
!SPACE_GROUP_NUMBER= 152
!UNIT_CELL_CONSTANTS= 134.222 134.222 182.665 90.000 90.000 120.000
!UNIT_CELL_A-AXIS= -9.656 -13.195 133.223
!UNIT_CELL_B-AXIS= 36.958 117.512 -53.297
!UNIT_CELL_C-AXIS= -175.056 51.620 -7.575
!REFLECTING_RANGE_E.S.D.= 0.163
!BEAM_DIVERGENCE_E.S.D.= 0.029
!X-RAY_WAVELENGTH= 0.999987
!INCIDENT_BEAM_DIRECTION= -0.002009 -0.001292 1.000010
!FRACTION_OF_POLARIZATION= 0.990
!POLARIZATION_PLANE_NORMAL= 0.000000 1.000000 0.000000
!AIR= 0.000339
!SILICON= 3.942720
!SENSOR_THICKNESS= 0.450000
!DETECTOR=EIGER
!OVERLOAD= 3000000
!NX= 4150 NY= 4371 QX= 0.075000 QY= 0.075000
!ORGX= 2066.92 ORGY= 2186.64
!DETECTOR_DISTANCE= 260.894
!DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
!DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
!VARIANCE_MODEL= 1.139E+00 8.445E-03
!NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD=12
!ITEM_H=1
!ITEM_K=2
!ITEM_L=3
!ITEM_IOBS=4
!ITEM_SIGMA(IOBS)=5
!ITEM_XD=6
!ITEM_YD=7
!ITEM_ZD=8
!ITEM_RLP=9
!ITEM_PEAK=10
!ITEM_CORR=11
!ITEM_PSI=12
!END_OF_HEADER
Matrix to transform XDS axis system to CCP4 frame:
| 0.0001964, -0.00129, 1|
| 0.001086, -1, -0.00129|
| 1, 0.001086, -0.000195|
Matrix to transform XDS detector coordinates to CCP4 frame:
| 0.0001964, -0.00129, 1|
| 0.001086, -1, -0.00129|
| 1, 0.001086, -0.000195|
Rotation axis in CCP4 frame: ( 0.000 0.000 1.000)
Incident beam in CCP4 frame: ( 1.000 0.000 -0.002)
1649296 observations accepted
Resolution range 49.034 1.582
165938 accepted incomplete observations with PART < 0.98, minimum 0.75
59415 observations flagged as MISFITS in XDS: KEEP MISFIT in Aimless to accept
Reconstructing orientation matrix [U] from 199 observations
Orientation matrix [U]:
| 0.9163, -0.3982, -0.04201|
| -0.3931, -0.8747, -0.2837|
| 0.07621, 0.2765, -0.958|
Determinant = 1.000
Time for reading file(s): 4.270 secs
===============================================================
>*> Summary of test data read in:
Resolution range accepted: 49.03 1.58
Number of reflections = 239042
Number of observations = 1649296
Number of parts = 1649296
Number of batches in file = 900
Number of datasets = 1
Project: XDSproject Crystal: XDScrystal Dataset: XDSdataset
Run number: 1 consists of batches 1 - 900
Resolution range for run: 49.03 1.58
Phi range: 0.00 to 135.00 Time range: 0.00 to 135.00
Closest reciprocal axis to spindle: c* (angle 16.7 degrees)
Unit cell for dataset: 134.22 134.22 182.66 90.00 90.00 120.00
Wavelength: 0.99999
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 0.000 0.000
PKratio too large 0 0 0.000 0.000
Negative < 5sigma 0 0
Gradient too large 0 0 0.000 0.000
Profile-fitted overloads 0 0
Spots on edge 0 0
XDS misfits (outliers) 59415 0
===============================================================
Number of reflections = 239042
Number of observations = 1649296
Average multiplicity = 6.9
Resolution range in list: 49.03 -> 1.58
Intensity normalisation: B-factor = -19.3 + -0.0026 * time (final B -19.7)
Estimation of useful resolution for point group determination:
--------------------------------------------------------------
Point group correlation statistics are not reliable for very weak data,
so a high resolution cutoff (for this purpose only) is estimated either
from CC(1/2) using P1 (Friedel) symmetry (limit 0.60), or
from Mean(I/sigma(I)) (limit 2.06), if there are sufficient data
High-resolution estimate from CC(1/2): 2.45
High-resolution estimate from <I/sig(I)>: 2.81
High resolution limit reset to 2.45 using CC(1/2) cutoff (in P1)
$TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution:
$GRAPHS:Resolution estimate 2.45A:0.000415921|0.399381x0|1:2,4,6,7,9:
$$
N 1/d^2 Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ $$
1 0.0071 11.90 0.998 3264 0.998 8.50 7951 0.850
2 0.0204 7.01 0.997 6546 0.997 6.87 16243 0.687
3 0.0337 5.45 0.993 8420 0.995 6.29 21565 0.629
4 0.0470 4.61 0.991 10668 0.991 6.46 27431 0.646
5 0.0603 4.07 0.988 9061 0.986 6.02 23298 0.602
6 0.0736 3.69 0.983 7828 0.978 5.03 19849 0.503
7 0.0869 3.39 0.970 10030 0.964 3.84 25311 0.384
8 0.1002 3.16 0.953 15132 0.943 3.15 38729 0.315
9 0.1135 2.97 0.928 18578 0.911 2.59 45058 0.259
10 0.1268 2.81 0.857 20108 0.864 2.15 47338 0.215
11 0.1401 2.67 0.793 13574 0.796 1.77 30517 0.177
12 0.1534 2.55 0.685 22762 0.707 1.51 49567 0.151
13 0.1667 2.45 0.598 24120 0.597 1.35 50486 0.135
14 0.1800 2.36 0.466 24751 0.478 1.17 50078 0.117
15 0.1932 2.27 0.386 14253 0.361 1.07 29113 0.107
16 0.2065 2.20 0.282 22703 0.258 0.93 43990 0.093
17 0.2198 2.13 0.164 24923 0.176 0.84 45128 0.084
18 0.2331 2.07 0.104 16282 0.117 0.78 28260 0.078
19 0.2464 2.01 0.060 27037 0.075 0.74 45441 0.074
20 0.2597 1.96 0.052 17268 0.048 0.71 27924 0.071
21 0.2730 1.91 0.045 12978 0.030 0.66 20105 0.066
22 0.2863 1.87 0.018 22762 0.019 0.59 32714 0.059
23 0.2996 1.83 0.000 28209 0.012 0.48 35644 0.048
24 0.3129 1.79 0.011 22050 0.007 0.37 22535 0.037
25 0.3262 1.75 -0.014 18065 0.004 0.23 12249 0.023
26 0.3395 1.72 -0.040 8602 0.003 0.11 2916 0.011
27 0.3528 1.68 -0.063 12143 0.002 0.09 3276 0.009
28 0.3661 1.65 -0.100 9454 0.001 0.12 3632 0.012
29 0.3794 1.62 -0.068 7471 0.001 0.20 4613 0.020
30 0.3927 1.60 -0.149 1946 0.000 0.25 2364 0.025
$$
Checking for possible twinning
L-test for twinning (acentrics only) to maximum resolution 2.452
Neighbouring reflections for test are +- 2 on h,k,l
$TABLE: L-test for twinning, twin fraction 0.127:
$GRAPHS:Cumulative distribution of |L|, estimated fraction 0.127:N:1,2,3,4:
$$
|L| N(|L|) Untwinned Twinned $$ $$
0.0000 0.0000 0.0000 0.0000
0.0500 0.0645 0.0500 0.0749
0.1000 0.1286 0.1000 0.1495
0.1500 0.1918 0.1500 0.2233
0.2000 0.2544 0.2000 0.2960
0.2500 0.3159 0.2500 0.3672
0.3000 0.3763 0.3000 0.4365
0.3500 0.4353 0.3500 0.5036
0.4000 0.4930 0.4000 0.5680
0.4500 0.5490 0.4500 0.6294
0.5000 0.6031 0.5000 0.6875
0.5500 0.6555 0.5500 0.7418
0.6000 0.7060 0.6000 0.7920
0.6500 0.7541 0.6500 0.8377
0.7000 0.7998 0.7000 0.8785
0.7500 0.8425 0.7500 0.9141
0.8000 0.8822 0.8000 0.9440
0.8500 0.9184 0.8500 0.9679
0.9000 0.9508 0.9000 0.9855
0.9500 0.9784 0.9500 0.9963
1.0000 1.0000 1.0000 1.0000
$$
Estimated twin fraction alpha from cumulative N(|L|) plot 0.139 (+/-0.022)
< |L| >: 0.430 (0.5 untwinned, 0.375 perfect twin)
Estimated twin fraction alpha from < |L| > 0.127
< L^2 >: 0.258 (0.333 untwinned, 0.2 perfect twin)
Estimated twin fraction alpha from < L^2 > 0.114
WARNING: the L-test suggests that the data may be twinned,
so the indicated Laue symmetry may be too high
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
Time for twinning test 4.740 secs
======================================================================
- - - - Checking for possible non-primitive lattice absences in a primitive lattice
Resolution range used in test: 49.0 to 2.45
For each lattice centering type, divide reflections into systematically present
and systematically absent groups
Systematic absences expected for different lattice centering types
A k+l = 2n (unconventional setting, usually C)
B h+l = 2n (unconventional setting, usually C)
C h+k = 2n
I h+k+l = 2n
F h,k,l all = 2n or h,k,l all != 2n
R:H -h+k+l = 3n (hexagonal axes)
Key to table:
N number of putative 'absent' observations in that lattice
< I >present mean intensity for 'present' reflections
< I >absent mean intensity for 'absent' reflections
< E^2 >present mean I/sig(I) for 'present' reflections
< E^2 >absent mean I/sig(I) for 'absent' reflections, usually = 1.0, ~=0 if centered
Since the lattice could possibly be rhombohedral, test for obverse/reverse twin:
there are 4 classes of reflections defined by combinations of 2 tests:
O = (-h+k+l == 3n) and V = (h-k+l == 3n)
Then the classes are:
1. O && notV reflection in domain 1 only, l not= 3n, 2/9 of total (O, V present)
2. notO && V reflection in domain 2 only, l not= 3n, 2/9 of total (O, V absent)
3. O && V reflection from both domains, l = 3n, 1/9 of total (O&&V present)
4. notO && notV absent in both domains, any l, 4/9 of total (O&&V absent)
LatticeType Overall A B C I F R O, V O&&V
N 518580 259250 259420 254168 259148 386419 345767 115281 230486
< I >present 71 72 72 109 72 109 72 73 72
< I >absent 71 71 33 71 58 71 72 70
< E^2 >present 1.04 1.04 1.04 1.47 1.04 1.48 1.04 1.05 1.04
< E^2 >absent 1.03 1.03 0.58 1.03 0.89 1.03 1.04 1.03
Centering probability 0.00 0.00 0.34 0.00 0.00 0.00
No extra lattice symmetry found
- - - -
Time for lattice absence test 0.110 secs
Model for expectation(CC) = E(m) if symmetry is absent P(m;!S) = (1-m^k)^(1/k) with k = 3.3
Unit cell (from HKLIN file) used to derive lattice symmetry with tolerance 2.0 degrees
134.22 134.22 182.66 90.00 90.00 120.00
Tolerance (and delta) is the maximum deviation from the
expected angle between two-fold axes in the lattice group
Lattice point group: P 6 2 2
Reindexing or changing symmetry
Reindex operator from input cell to lattice cell: [h,k,l]
h' = ( h k l ) ( 1 0 0 )
( 0 1 0 )
( 0 0 1 )
Lattice unit cell after reindexing: deviation 0.00 degrees
134.22 134.22 182.66 90.00 90.00 120.00
179 pairs rejected for E^2 too large
Overall CC for 20000 unrelated pairs: 0.034 N= 20000, high resolution limit 2.45
Estimated expectation value of true correlation coefficient E(CC) = 0.686
Estimated sd(CC) = 1.104 / Sqrt(N)
Estimated E(CC) of true correlation coefficient from identity = 0.854
*******************************************
Analysing rotational symmetry in lattice group P 6/m m m
----------------------------------------------
<!--SUMMARY_BEGIN-->
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell)
1 0.907 9.22 0.92 175685 0.132 identity
2 0.905 9.26 0.93 342965 0.134 *** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.910 9.15 0.92 313340 0.154 *** 2-fold k ( 0 1 0) {-h,h+k,-l}
4 0.916 8.99 0.90 261193 0.174 *** 2-fold h ( 1 0 0) {h+k,-k,-l}
5 0.917 8.94 0.89 303748 0.181 *** 2-fold ( 1-1 0) {-k,-h,-l}
6 0.909 9.18 0.92 312708 0.150 *** 2-fold ( 2-1 0) {h,-h-k,-l}
7 0.916 8.97 0.90 259154 0.173 *** 2-fold (-1 2 0) {-h-k,k,-l}
8 0.917 8.93 0.89 298909 0.179 *** 2-fold ( 1 1 0) {k,h,-l}
9 0.914 9.02 0.90 535448 0.169 *** 3-fold l ( 0 0 1) {k,-h-k,l}{-h-k,h,l}
10 0.915 9.00 0.90 537218 0.170 *** 6-fold l ( 0 0 1) {h+k,-h,l}{-k,h+k,l}
<!--SUMMARY_END-->
Time to determine pointgroup: 9.090 secs
Acceptable Laue groups have scores above 0.20
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 P 6/m m m *** 1.000 9.06 9.06 0.00 0.91 0.00 0.16 0.00 0.0 [h,k,l]
2 P -3 1 m 0.000 -0.01 9.06 9.07 0.91 0.91 0.16 0.16 0.0 [h,k,l]
- 3 P -3 m 1 0.000 -0.00 9.06 9.07 0.91 0.91 0.16 0.16 0.0 [h,k,l]
4 C m m m 0.000 0.04 9.09 9.05 0.91 0.90 0.16 0.17 0.0 [h+k,-h+k,l]
5 C m m m 0.000 0.08 9.12 9.03 0.91 0.90 0.15 0.17 0.0 [-k,2h+k,l]
6 P 6/m 0.000 0.09 9.12 9.03 0.91 0.90 0.15 0.17 0.0 [h,k,l]
7 C m m m 0.000 0.23 9.21 8.98 0.92 0.90 0.14 0.17 0.0 [h,h+2k,l]
8 C 1 2/m 1 0.000 0.01 9.07 9.06 0.91 0.91 0.15 0.16 0.0 [h-k,h+k,l]
9 C 1 2/m 1 0.000 0.01 9.07 9.06 0.91 0.91 0.16 0.16 0.0 [h+k,-h+k,l]
10 C 1 2/m 1 0.000 0.04 9.10 9.06 0.91 0.91 0.15 0.16 0.0 [2h+k,k,l]
11 C 1 2/m 1 0.000 0.05 9.10 9.06 0.91 0.91 0.15 0.16 0.0 [-k,2h+k,l]
12 P -3 0.000 0.06 9.11 9.05 0.91 0.91 0.15 0.16 0.0 [h,k,l]
13 C 1 2/m 1 0.000 0.15 9.19 9.04 0.92 0.90 0.14 0.17 0.0 [h,h+2k,l]
14 C 1 2/m 1 0.000 0.17 9.20 9.03 0.92 0.90 0.14 0.17 0.0 [h+2k,-h,l]
15 P 1 2/m 1 0.000 0.22 9.24 9.02 0.92 0.90 0.13 0.17 0.0 [k,l,h]
16 P -1 0.000 0.18 9.22 9.05 0.92 0.90 0.13 0.16 0.0 [-h,-k,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 6(3):
$GRAPHS:I/sigI vs. index, axis c, screw axis 6(3):N:1,4,5:
:I vs. index, axis c, screw axis 6(3):N:1,2:
$$
Index I sigI I/sigI I'/sigI $$ $$
4 1 3 0.43 0.43
5 -0 2 -0.14 0.00
6 2682 186 14.42 14.42
7 1 2 0.56 0.00
8 1 1 0.68 0.66
9 -1 1 -0.53 0.00
10 1 1 0.70 0.68
11 1 2 0.90 0.47
12 31 3 11.57 11.55
13 2 2 1.14 0.70
14 3 2 1.91 1.89
15 -2 2 -0.88 0.00
16 23 3 6.75 6.75
17 -3 3 -1.36 0.00
18 208 21 9.99 9.99
19 -1 3 -0.21 0.00
20 66 7 9.08 9.08
21 -0 3 -0.13 0.00
22 22 4 5.88 5.87
23 3 3 1.13 0.00
24 3501 344 10.19 10.19
25 -2 3 -0.62 0.00
26 56 7 8.47 8.46
27 1 3 0.40 0.04
28 2 3 0.58 0.54
29 6 3 1.66 0.00
30 858 85 10.15 10.15
31 2 4 0.69 0.00
32 73 8 8.68 8.67
33 1 4 0.33 0.00
34 120 13 9.37 9.37
35 -4 4 -0.93 0.00
36 182 19 9.71 9.71
37 -3 4 -0.82 0.00
38 62 8 7.92 7.92
39 -2 4 -0.37 0.00
40 82 10 8.57 8.56
41 4 5 0.93 0.48
42 20 5 3.79 3.77
43 -2 5 -0.40 0.00
44 93 11 8.54 8.54
45 -3 5 -0.58 0.00
46 290 30 9.84 9.83
47 8 6 1.35 0.00
48 1451 143 10.15 10.15
49 6 6 1.01 0.00
50 43 7 5.82 5.81
51 -1 6 -0.21 0.00
52 238 25 9.68 9.67
53 13 6 2.07 1.00
54 93 11 8.18 8.16
56 280 29 9.77 9.76
57 8 6 1.31 0.33
58 14 6 2.29 2.25
59 6 6 0.99 0.31
60 190 20 9.48 9.47
61 -1 6 -0.14 0.00
62 188 20 9.47 9.47
63 0 5 0.05 0.00
64 37 7 5.44 5.44
65 -5 5 -0.97 0.00
66 74 10 7.80 7.80
67 -4 5 -0.82 0.00
68 5 5 0.97 0.95
69 5 5 0.85 0.84
70 -0 6 -0.07 0.00
71 -5 5 -0.84 0.00
72 52 8 6.61 6.61
73 1 5 0.11 0.00
74 -0 5 -0.00 0.00
75 0 5 0.04 0.00
76 10 5 1.91 1.91
77 -1 5 -0.26 0.00
78 542 54 10.03 10.03
79 -2 5 -0.45 0.00
80 4 5 0.70 0.70
81 -5 5 -0.94 0.00
82 46 7 6.21 6.21
83 -5 5 -0.98 0.00
84 7 5 1.27 1.26
85 1 5 0.19 0.10
86 19 4 4.55 4.53
87 4 4 1.03 0.92
88 2 4 0.41 1.17
89 -0 4 -0.03 0.00
90 418 30 14.05 14.05
91 -0 4 -0.02 0.00
92 7 4 1.96 1.95
93 1 3 0.23 0.21
94 6 3 1.84 1.83
95 1 3 0.32 0.37
96 1 3 0.27 0.57
97 -7 3 -2.27 0.00
$$
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 P 6/m m m
1 screw axis 6(3) [c] 115 0.957 0.095 *** 1.000 00l: l=2n
1 screw axis 6(2) [c] 115 0.248 0.068 0.000 00l: l=3n
1 screw axis 6(1) [c] 115 0.244 0.069 0.000 00l: l=6n
<!--SUMMARY_END-->
Time for systematic absence tests: 0.650 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
P 63 2 2 (182) 1.000 1.000 00l: l=2n (zone 1)
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 1.00
Laue group confidence (= Sqrt(Score * (Score - NextBestScore))) = 1.00
Selecting space group P 63 2 2 as there is a single space group with the highest score
<!--SUMMARY_BEGIN--> $TEXT:Result: $$ $$
Best Solution: space group P 63 2 2
Reindex operator: [h,k,l]
Laue group probability: 1.000
Systematic absence probability: 1.000
Total probability: 1.000
Space group confidence: 1.000
Laue group confidence 1.000
Unit cell: 134.22 134.22 182.66 90.00 90.00 120.00
49.03 to 2.45 - Resolution range used for Laue group search
49.03 to 1.58 - Resolution range in file, used for systematic absence check
Number of batches in file: 900
WARNING: the L-test suggests that the data may be twinned,
so the indicated Laue symmetry may be too high
Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.139 +/-(0.022)
Rough estimated twin fraction alpha from < |L| > 0.127
Rough estimated twin fraction alpha from < L^2 > 0.114
$$ <!--SUMMARY_END-->
HKLIN spacegroup: P 31 2 1 primitive trigonal
Filename:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Writing unmerged data to file /home/user/Donghyuk/d011_x024/ccp4/XDS_016_pointless.mtz in space group P 63 2 2
Reindexing operator [h,k,l]
Real space transformation (x,y,z)
* Title:
From XDS file XDS_ASCII.HKL, XDS run on 11-Jan-2019 from images /home/
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 XDSproject
XDScrystal
XDSdataset
134.2220 134.2220 182.6650 90.0000 90.0000 120.0000
0.99999
* Number of Columns = 13
* Number of Reflections = 1649296
* Missing value set to NaN in input mtz file
* Number of Batches = 900
* Column Labels :
H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP FLAG
* Column Types :
H H H Y B J Q R R R R R I
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
134.2220 134.2220 182.6650 90.0000 90.0000 120.0000
* Resolution Range :
0.00042 0.39938 ( 49.034 - 1.582 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P 63 2 2' (number 182)
(spacegroup is known)
$TEXT:Reference: $$ 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 15 Jan 2019 13:42:21
#CCP4I MESSAGE Task completed successfully
#CCP4I VERSION CCP4Interface 7.0.051
#CCP4I SCRIPT LOG pointless
#CCP4I DATE 15 Jan 2019 13:42:14
#CCP4I USER user
#CCP4I PROJECT donghyuk_d011_x024
#CCP4I JOB_ID 136
#CCP4I SCRATCH /tmp/user
#CCP4I HOSTNAME localhost.localdomain
#CCP4I PID 31683
###############################################################
###############################################################
###############################################################
### CCP4 7.0.051: POINTLESS version 1.11.8 : 19/12/17##
###############################################################
User: user Run date: 15/ 1/2019 Run time: 13:42:14
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.
==== Input command lines ====
XDSIN /home/user/Donghyuk/d011_x024/process_donghyuk/xds_018/XDS_ASCII.HKL
HKLOUT /home/user/Donghyuk/d011_x024/ccp4/XDS_018_pointless.mtz
## This script run with the command ##########
# /home/user/Downloads/destination/ccp4-7.0/bin/pointless
################################################
==== End of input ====
Release Date: 19th December 2017
******************************************************
* *
* POINTLESS *
* 1.11.8 *
* *
* Determine Laue group from unmerged intensities *
* Phil Evans MRC LMB, Cambridge *
* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
* *
******************************************************
Reading XDS ascii file from file /home/user/Donghyuk/d011_x024/process_donghyuk/xds_018/XDS_ASCII.HKL
Header lines:
!FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=FALSE
!OUTPUT_FILE=XDS_ASCII.HKL DATE=11-Jan-2019
!Generated by CORRECT (VERSION Jan 26, 2018 BUILT=20180808)
!PROFILE_FITTING= TRUE
!NAME_TEMPLATE_OF_DATA_FRAMES=/home/user/Donghyuk/d011_x024/x024_C11_1_??????.h5 GENERIC
!DATA_RANGE= 1 900
!ROTATION_AXIS= 0.999999 0.001139 -0.000341
!OSCILLATION_RANGE= 0.150000
!STARTING_ANGLE= 0.000
!STARTING_FRAME= 1
!INCLUDE_RESOLUTION_RANGE= 50.000 1.584
!SPACE_GROUP_NUMBER= 152
!UNIT_CELL_CONSTANTS= 67.149 67.149 182.749 90.000 90.000 120.000
!UNIT_CELL_A-AXIS= -4.819 -6.577 66.652
!UNIT_CELL_B-AXIS= 18.484 58.780 -26.688
!UNIT_CELL_C-AXIS= -175.139 51.637 -7.567
!REFLECTING_RANGE_E.S.D.= 0.148
!BEAM_DIVERGENCE_E.S.D.= 0.031
!X-RAY_WAVELENGTH= 0.999987
!INCIDENT_BEAM_DIRECTION= -0.001905 -0.001169 1.000010
!FRACTION_OF_POLARIZATION= 0.990
!POLARIZATION_PLANE_NORMAL= 0.000000 1.000000 0.000000
!AIR= 0.000339
!SILICON= 3.942720
!SENSOR_THICKNESS= 0.450000
!DETECTOR=EIGER
!OVERLOAD= 3000000
!NX= 4150 NY= 4371 QX= 0.075000 QY= 0.075000
!ORGX= 2066.53 ORGY= 2186.22
!DETECTOR_DISTANCE= 261.027
!DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
!DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
!VARIANCE_MODEL= 1.377E+00 4.333E-03
!NUMBER_OF_ITEMS_IN_EACH_DATA_RECORD=12
!ITEM_H=1
!ITEM_K=2
!ITEM_L=3
!ITEM_IOBS=4
!ITEM_SIGMA(IOBS)=5
!ITEM_XD=6
!ITEM_YD=7
!ITEM_ZD=8
!ITEM_RLP=9
!ITEM_PEAK=10
!ITEM_CORR=11
!ITEM_PSI=12
!END_OF_HEADER
Matrix to transform XDS axis system to CCP4 frame:
| 0.0003423, -0.001166, 1|
| 0.001139, -1, -0.001167|
| 1, 0.001139, -0.000341|
Matrix to transform XDS detector coordinates to CCP4 frame:
| 0.0003423, -0.001166, 1|
| 0.001139, -1, -0.001167|
| 1, 0.001139, -0.000341|
Rotation axis in CCP4 frame: ( 0.000 0.000 1.000)
Incident beam in CCP4 frame: ( 1.000 0.000 -0.002)
412568 observations accepted
Resolution range 49.060 1.584
17820 accepted incomplete observations with PART < 0.98, minimum 0.75
6679 observations flagged as MISFITS in XDS: KEEP MISFIT in Aimless to accept
Reconstructing orientation matrix [U] from 199 observations
Orientation matrix [U]:
| 0.9163, -0.3984, -0.04202|
| -0.3933, -0.8746, -0.2837|
| 0.07625, 0.2764, -0.958|
Determinant = 1.000
Time for reading file(s): 1.080 secs
===============================================================
>*> Summary of test data read in:
Resolution range accepted: 49.06 1.58
Number of reflections = 61295
Number of observations = 412568
Number of parts = 412568
Number of batches in file = 900
Number of datasets = 1
Project: XDSproject Crystal: XDScrystal Dataset: XDSdataset
Run number: 1 consists of batches 1 - 900
Resolution range for run: 49.06 1.58
Phi range: 0.00 to 135.00 Time range: 0.00 to 135.00
Closest reciprocal axis to spindle: c* (angle 16.7 degrees)
Unit cell for dataset: 67.15 67.15 182.75 90.00 90.00 120.00
Wavelength: 0.99999
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 0.000 0.000
PKratio too large 0 0 0.000 0.000
Negative < 5sigma 0 0
Gradient too large 0 0 0.000 0.000
Profile-fitted overloads 0 0
Spots on edge 0 0
XDS misfits (outliers) 6679 0
===============================================================
Number of reflections = 61295
Number of observations = 412568
Average multiplicity = 6.7
Resolution range in list: 49.06 -> 1.58
Intensity normalisation: B-factor = -18.5 + -0.0050 * time (final B -19.2)
Estimation of useful resolution for point group determination:
--------------------------------------------------------------
Point group correlation statistics are not reliable for very weak data,
so a high resolution cutoff (for this purpose only) is estimated either
from CC(1/2) using P1 (Friedel) symmetry (limit 0.60), or
from Mean(I/sigma(I)) (limit 4.20), if there are sufficient data
High-resolution estimate from CC(1/2): 2.33
High-resolution estimate from <I/sig(I)>: 2.97
High resolution limit reset to 2.33 using CC(1/2) cutoff (in P1)
$TABLE: Mn(I/sigI) and CC(1/2) [in P1] vs. resolution:
$GRAPHS:Resolution estimate 2.33A:0.000415476|0.398716x0|1:2,4,6,7,9:
$$
N 1/d^2 Dmid CC(1/2) N_CC CCfit Mn(I/sigI) N (I/sigI)/10 $$ $$
1 0.0071 11.91 0.999 840 0.999 12.56 1833 1.256
2 0.0203 7.01 0.998 1618 0.998 11.64 3763 1.164
3 0.0336 5.45 0.993 2070 0.996 11.20 5127 1.120
4 0.0469 4.62 0.991 2527 0.994 11.24 6387 1.124
5 0.0602 4.08 0.988 2224 0.991 10.98 5606 1.098
6 0.0734 3.69 0.982 1700 0.986 9.92 4297 0.992
7 0.0867 3.40 0.976 2334 0.978 7.77 6069 0.777
8 0.1000 3.16 0.975 3530 0.966 6.30 9361 0.630
9 0.1133 2.97 0.953 4376 0.947 5.09 11368 0.509
10 0.1265 2.81 0.902 4721 0.918 4.03 12230 0.403
11 0.1398 2.67 0.874 3082 0.876 3.17 7876 0.317
12 0.1531 2.56 0.794 5357 0.817 2.57 13775 0.257
13 0.1664 2.45 0.727 5742 0.737 2.16 14427 0.216
14 0.1797 2.36 0.612 5911 0.639 1.75 14568 0.175
15 0.1929 2.28 0.574 3628 0.527 1.53 9033 0.153
16 0.2062 2.20 0.466 5316 0.413 1.29 12743 0.129
17 0.2195 2.13 0.283 6041 0.307 1.05 13256 0.105
18 0.2328 2.07 0.208 3750 0.219 0.94 7831 0.094
19 0.2460 2.02 0.120 6605 0.150 0.81 13102 0.081
20 0.2593 1.96 0.089 4092 0.100 0.79 7768 0.079
21 0.2726 1.92 0.070 3451 0.066 0.72 6202 0.072
22 0.2859 1.87 0.034 5204 0.042 0.67 8864 0.067
23 0.2991 1.83 0.017 6852 0.027 0.63 11378 0.063
24 0.3124 1.79 0.039 5453 0.017 0.61 9038 0.061
25 0.3257 1.75 0.003 4496 0.011 0.57 7095 0.057
26 0.3390 1.72 0.009 2381 0.007 0.40 2857 0.040
27 0.3522 1.68 0.005 3359 0.004 0.41 4234 0.041
28 0.3655 1.65 -0.021 2800 0.003 0.31 2746 0.031
29 0.3788 1.62 0.002 2302 0.002 0.21 1601 0.021
30 0.3921 1.60 -0.060 635 0.001 0.30 933 0.030
$$
Checking for possible twinning
L-test for twinning (acentrics only) to maximum resolution 2.329
Neighbouring reflections for test are +- 2 on h,k,l
$TABLE: L-test for twinning, twin fraction 0.279:
$GRAPHS:Cumulative distribution of |L|, estimated fraction 0.279:N:1,2,3,4:
$$
|L| N(|L|) Untwinned Twinned $$ $$
0.0000 0.0000 0.0000 0.0000
0.0500 0.0728 0.0500 0.0749
0.1000 0.1447 0.1000 0.1495
0.1500 0.2151 0.1500 0.2233
0.2000 0.2845 0.2000 0.2960
0.2500 0.3523 0.2500 0.3672
0.3000 0.4179 0.3000 0.4365
0.3500 0.4818 0.3500 0.5036
0.4000 0.5436 0.4000 0.5680
0.4500 0.6030 0.4500 0.6294
0.5000 0.6598 0.5000 0.6875
0.5500 0.7138 0.5500 0.7418
0.6000 0.7641 0.6000 0.7920
0.6500 0.8110 0.6500 0.8377
0.7000 0.8538 0.7000 0.8785
0.7500 0.8915 0.7500 0.9141
0.8000 0.9244 0.8000 0.9440
0.8500 0.9525 0.8500 0.9679
0.9000 0.9744 0.9000 0.9855
0.9500 0.9902 0.9500 0.9963
1.0000 1.0000 1.0000 1.0000
$$
Estimated twin fraction alpha from cumulative N(|L|) plot 0.286 (+/-0.025)
< |L| >: 0.392 (0.5 untwinned, 0.375 perfect twin)
Estimated twin fraction alpha from < |L| > 0.279
< L^2 >: 0.219 (0.333 untwinned, 0.2 perfect twin)
Estimated twin fraction alpha from < L^2 > 0.263
WARNING: the L-test suggests that the data may be twinned,
so the indicated Laue symmetry may be too high
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
Time for twinning test 1.400 secs
======================================================================
- - - - Checking for possible non-primitive lattice absences in a primitive lattice
Resolution range used in test: 49.1 to 2.33
For each lattice centering type, divide reflections into systematically present
and systematically absent groups
Systematic absences expected for different lattice centering types
A k+l = 2n (unconventional setting, usually C)
B h+l = 2n (unconventional setting, usually C)
C h+k = 2n
I h+k+l = 2n
F h,k,l all = 2n or h,k,l all != 2n
R:H -h+k+l = 3n (hexagonal axes)
Key to table:
N number of putative 'absent' observations in that lattice
< I >present mean intensity for 'present' reflections
< I >absent mean intensity for 'absent' reflections
< E^2 >present mean I/sig(I) for 'present' reflections
< E^2 >absent mean I/sig(I) for 'absent' reflections, usually = 1.0, ~=0 if centered
Since the lattice could possibly be rhombohedral, test for obverse/reverse twin:
there are 4 classes of reflections defined by combinations of 2 tests:
O = (-h+k+l == 3n) and V = (h-k+l == 3n)
Then the classes are:
1. O && notV reflection in domain 1 only, l not= 3n, 2/9 of total (O, V present)
2. notO && V reflection in domain 2 only, l not= 3n, 2/9 of total (O, V absent)
3. O && V reflection from both domains, l = 3n, 1/9 of total (O&&V present)
4. notO && notV absent in both domains, any l, 4/9 of total (O&&V absent)
LatticeType Overall A B C I F R O, V O&&V
N 154989 77588 77526 77490 77529 116302 103322 34430 68892
< I >present 167 167 167 166 167 166 168 168 168
< I >absent 167 166 167 166 167 166 170 164
< E^2 >present 1.00 1.01 1.01 1.00 1.00 1.01 1.01 1.01 1.01
< E^2 >absent 1.00 1.00 1.01 1.00 1.00 1.00 1.01 0.99
Centering probability 0.00 0.00 0.00 0.00 0.00 0.00
No extra lattice symmetry found
- - - -
Time for lattice absence test 0.030 secs
Model for expectation(CC) = E(m) if symmetry is absent P(m;!S) = (1-m^k)^(1/k) with k = 4.2
Unit cell (from HKLIN file) used to derive lattice symmetry with tolerance 2.0 degrees
67.15 67.15 182.75 90.00 90.00 120.00
Tolerance (and delta) is the maximum deviation from the
expected angle between two-fold axes in the lattice group
Lattice point group: P 6 2 2
Reindexing or changing symmetry
Reindex operator from input cell to lattice cell: [h,k,l]
h' = ( h k l ) ( 1 0 0 )
( 0 1 0 )
( 0 0 1 )
Lattice unit cell after reindexing: deviation 0.00 degrees
67.15 67.15 182.75 90.00 90.00 120.00
1 pairs rejected for E^2 too large
Overall CC for 20000 unrelated pairs: -0.002 N= 20000, high resolution limit 2.33
Estimated expectation value of true correlation coefficient E(CC) = 0.659
Estimated sd(CC) = 1.030 / Sqrt(N)
Estimated E(CC) of true correlation coefficient from identity = 0.823
*******************************************
Analysing rotational symmetry in lattice group P 6/m m m
----------------------------------------------
<!--SUMMARY_BEGIN-->
Scores for each symmetry element
Nelmt Lklhd Z-cc CC N Rmeas Symmetry & operator (in Lattice Cell)
1 0.889 9.01 0.90 58380 0.071 identity
2 0.885 9.08 0.91 115275 0.073 ** 2-fold l ( 0 0 1) {-h,-k,l}
3 0.891 8.98 0.90 104855 0.089 ** 2-fold k ( 0 1 0) {-h,h+k,-l}
4 0.899 8.85 0.88 88548 0.097 ** 2-fold h ( 1 0 0) {h+k,-k,-l}
5 0.903 8.78 0.88 103746 0.101 *** 2-fold ( 1-1 0) {-k,-h,-l}
6 0.890 9.00 0.90 103885 0.087 ** 2-fold ( 2-1 0) {h,-h-k,-l}
7 0.900 8.82 0.88 87518 0.097 *** 2-fold (-1 2 0) {-h-k,k,-l}
8 0.903 8.77 0.88 101551 0.101 *** 2-fold ( 1 1 0) {k,h,-l}
9 0.897 8.88 0.89 182326 0.093 ** 3-fold l ( 0 0 1) {k,-h-k,l}{-h-k,h,l}
10 0.897 8.88 0.89 182892 0.092 ** 6-fold l ( 0 0 1) {h+k,-h,l}{-k,h+k,l}
<!--SUMMARY_END-->
Time to determine pointgroup: 2.890 secs
Acceptable Laue groups have scores above 0.20
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 P 6/m m m *** 1.000 8.90 8.90 0.00 0.89 0.00 0.09 0.00 0.0 [h,k,l]
- 2 P -3 m 1 0.000 -0.02 8.89 8.91 0.89 0.89 0.09 0.09 0.0 [h,k,l]
3 P -3 1 m 0.000 -0.02 8.89 8.91 0.89 0.89 0.09 0.09 0.0 [h,k,l]
4 C m m m 0.000 0.01 8.91 8.90 0.89 0.89 0.09 0.09 0.0 [h+k,-h+k,l]
5 C m m m 0.000 0.06 8.94 8.88 0.89 0.89 0.08 0.09 0.0 [-k,2h+k,l]
6 P 6/m 0.000 0.09 8.95 8.86 0.90 0.89 0.08 0.10 0.0 [h,k,l]
7 C m m m 0.000 0.19 9.02 8.83 0.90 0.88 0.08 0.10 0.0 [h,h+2k,l]
8 C 1 2/m 1 0.000 -0.02 8.88 8.91 0.89 0.89 0.09 0.09 0.0 [h-k,h+k,l]
9 C 1 2/m 1 0.000 -0.02 8.88 8.91 0.89 0.89 0.09 0.09 0.0 [h+k,-h+k,l]
10 C 1 2/m 1 0.000 0.01 8.91 8.90 0.89 0.89 0.08 0.09 0.0 [2h+k,k,l]
11 C 1 2/m 1 0.000 0.03 8.92 8.90 0.89 0.89 0.08 0.09 0.0 [-k,2h+k,l]
12 P -3 0.000 0.04 8.94 8.89 0.89 0.89 0.08 0.09 0.0 [h,k,l]
13 C 1 2/m 1 0.000 0.11 8.99 8.88 0.90 0.89 0.08 0.09 0.0 [h,h+2k,l]
14 C 1 2/m 1 0.000 0.12 9.00 8.88 0.90 0.89 0.08 0.09 0.0 [h+2k,-h,l]
15 P 1 2/m 1 0.000 0.18 9.05 8.87 0.90 0.89 0.07 0.09 0.0 [k,l,h]
16 P -1 0.000 0.12 9.01 8.89 0.90 0.89 0.07 0.09 0.0 [-h,-k,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 6(3):
$GRAPHS:I/sigI vs. index, axis c, screw axis 6(3):N:1,4,5:
:I vs. index, axis c, screw axis 6(3):N:1,2:
$$
Index I sigI I/sigI I'/sigI $$ $$
4 1 5 0.24 0.24
5 -0 3 -0.03 0.00
6 2345 128 18.27 18.27
7 1 2 0.45 0.00
8 1 2 0.47 0.46
9 -1 2 -0.27 0.00
10 1 2 0.37 0.36
11 1 2 0.58 0.30
12 27 2 11.56 11.54
13 1 2 0.72 0.42
14 2 2 1.19 1.18
15 -1 3 -0.43 0.00
16 21 3 6.53 6.53
17 -3 3 -0.97 0.00
18 196 16 12.45 12.45
19 0 3 0.07 0.00
20 64 6 10.53 10.53
21 -1 3 -0.23 0.00
22 23 4 6.07 6.06
23 2 3 0.60 0.00
24 3406 264 12.93 12.93
25 -3 3 -0.78 0.00
26 56 6 9.53 9.52
27 1 4 0.33 0.00
28 2 4 0.67 0.64
29 5 4 1.33 0.00
30 850 66 12.83 12.83
31 2 4 0.41 0.00
32 72 7 9.90 9.90
33 0 4 0.11 0.00
34 119 11 11.16 11.16
35 -3 4 -0.60 0.00
36 187 16 11.88 11.88
37 -3 4 -0.75 0.00
38 65 7 8.78 8.78
39 -2 5 -0.34 0.00
40 87 9 9.85 9.84
41 4 5 0.92 0.47
42 22 5 4.08 4.06
43 -3 5 -0.56 0.00
44 96 10 9.75 9.75
45 -1 6 -0.23 0.00
46 300 25 12.15 12.15
47 7 6 1.17 0.00
48 1500 117 12.84 12.84
49 3 6 0.55 0.00
50 47 8 6.16 6.15
51 -1 6 -0.24 0.00
52 248 21 11.84 11.83
53 12 7 1.88 0.82
54 97 11 9.16 9.14
56 297 25 12.03 12.03
57 7 7 1.05 0.10
58 14 7 2.16 2.12
59 6 6 0.85 0.18
60 202 18 11.46 11.45
61 -2 6 -0.36 0.00
62 200 17 11.47 11.47
63 -1 6 -0.14 0.00
64 41 7 5.84 5.84
65 -4 6 -0.78 0.00
66 85 9 9.07 9.07
67 -3 6 -0.50 0.00
68 7 6 1.17 1.16
69 5 6 0.81 0.78
70 1 6 0.15 0.14
71 -4 6 -0.76 0.00
72 54 7 7.15 7.15
73 -1 6 -0.16 0.00
74 0 6 0.02 0.01
75 2 6 0.41 0.36
76 12 6 2.12 2.11
77 -4 6 -0.73 0.00
78 576 46 12.59 12.59
79 -2 6 -0.32 0.00
80 4 6 0.66 0.66
81 -5 6 -0.84 0.00
82 55 8 6.86 6.86
83 -7 6 -1.17 0.00
84 7 6 1.20 1.19
85 2 6 0.43 0.33
86 21 4 4.69 4.67
87 3 4 0.80 0.68
88 4 4 0.98 1.24
89 -2 4 -0.37 0.00
90 444 25 17.54 17.54
91 -2 4 -0.42 0.00
92 6 4 1.68 1.68
93 1 4 0.16 0.13
94 4 4 1.26 1.26
95 0 3 0.06 0.24
96 2 3 0.57 0.56
97 -6 3 -1.77 0.00
$$
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 P 6/m m m
1 screw axis 6(3) [c] 115 0.969 0.054 *** 1.000 00l: l=2n
1 screw axis 6(2) [c] 115 0.279 0.050 0.000 00l: l=3n
1 screw axis 6(1) [c] 115 0.274 0.050 0.000 00l: l=6n
<!--SUMMARY_END-->
Time for systematic absence tests: 0.280 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
P 63 2 2 (182) 1.000 1.000 00l: l=2n (zone 1)
---------------------------------------------------------------
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 1.00
Laue group confidence (= Sqrt(Score * (Score - NextBestScore))) = 1.00
Selecting space group P 63 2 2 as there is a single space group with the highest score
<!--SUMMARY_BEGIN--> $TEXT:Result: $$ $$
Best Solution: space group P 63 2 2
Reindex operator: [h,k,l]
Laue group probability: 1.000
Systematic absence probability: 1.000
Total probability: 1.000
Space group confidence: 1.000
Laue group confidence 1.000
Unit cell: 67.15 67.15 182.75 90.00 90.00 120.00
49.06 to 2.33 - Resolution range used for Laue group search
49.06 to 1.58 - Resolution range in file, used for systematic absence check
Number of batches in file: 900
WARNING: the L-test suggests that the data may be twinned,
so the indicated Laue symmetry may be too high
Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.286 +/-(0.025)
Rough estimated twin fraction alpha from < |L| > 0.279
Rough estimated twin fraction alpha from < L^2 > 0.263
$$ <!--SUMMARY_END-->
HKLIN spacegroup: P 31 2 1 primitive trigonal
Filename:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Writing unmerged data to file /home/user/Donghyuk/d011_x024/ccp4/XDS_018_pointless.mtz in space group P 63 2 2
Reindexing operator [h,k,l]
Real space transformation (x,y,z)
* Title:
From XDS file XDS_ASCII.HKL, XDS run on 11-Jan-2019 from images /home/
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 XDSproject
XDScrystal
XDSdataset
67.1490 67.1490 182.7490 90.0000 90.0000 120.0000
0.99999
* Number of Columns = 13
* Number of Reflections = 412568
* Missing value set to NaN in input mtz file
* Number of Batches = 900
* Column Labels :
H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP FLAG
* Column Types :
H H H Y B J Q R R R R R I
* Associated datasets :
0 0 0 0 0 0 0 0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
67.1490 67.1490 182.7490 90.0000 90.0000 120.0000
* Resolution Range :
0.00042 0.39872 ( 49.060 - 1.584 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P 63 2 2' (number 182)
(spacegroup is known)
$TEXT:Reference: $$ 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 15 Jan 2019 13:42:19
#CCP4I MESSAGE Task completed successfully
