X-dVal: X-ray Data Validation

phenix.xtriage / Matthew's Coefficient / Twinning Detection / CRYST Record analysis

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Job 53 (Mar 25th, 2013 [02:09 PM])   → twinning detected

Your X-dVal Results

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Section
Summary
Completeness Plot
CRYST1 Record Search
Twin Detection Plot
Anisotropicity analyses
Twinning Analyses
Patterson analyses
Systematic absences
Wilson ratio and moments
L test for acentric data
Twinning and intensity statistics summary
L test for acentric data

using difference vectors (dh,dk,dl) of the form:
(2hp,2kp,2lp)
where hp, kp, and lp are random signed integers such that
2 <= |dh| + |dk| + |dl| <= 8

Mean |L|   :0.516  (untwinned: 0.500; perfect twin: 0.375)
Mean  L^2  :0.358  (untwinned: 0.333; perfect twin: 0.200)

The distribution of |L| values indicates a twin fraction of
0.00. Note that this estimate is not as reliable as obtained
via a Britton plot or H-test if twin laws are available.



---------------------------------------------
Analysing possible twin law :  l,-k,h
---------------------------------------------


Results of the H-test on acentric data:

(Only 50.0% of the strongest twin pairs were used)

mean |H| : 0.489   (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.333   (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.011
Estimation of twin fraction via cum. dist. of H: 0.021



Britton analyses

Extrapolation performed on  0.00 < alpha < 0.495
Estimated twin fraction: -0.020
Correlation: 0.9996

R vs R statistic:
R_abs_twin = <|I1-I2|>/<|I1+I2|>
Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

R_abs_twin observed data   : 0.535

R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data    : 0.380
No calculated data available.
R_twin for calculated data not determined.


Maximum Likelihood twin fraction determination
Zwart, Read, Grosse-Kunstleve & Adams, to be published.


The estimated twin fraction is equal to 0.022



Exploring higher metric symmetry

The point group of data as dictated by the space group is P 2 3
The point group in the niggli setting is P 2 3
The point group of the lattice is P 4 3 2
A summary of R values for various possible point groups follow.

----------------------------------------------------------------------------------------------
| Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC       | choice |
----------------------------------------------------------------------------------------------
| P 4 3 2     | 0.535       | 0.535      | None          | None         | 3.199e+06 |        |
| P 2 3       | None        | None       | 0.535         | 0.535        | 6.451e+04 | <---   |
----------------------------------------------------------------------------------------------

R_used: mean and maximum R value for symmetry operators *used* in this point group
R_unused: mean and minimum R value for symmetry operators *not used* in this point group
An automated point group suggestion is made on the basis of the BIC (Bayesian information criterion).


The likely point group of the data is: P 2 3

Possible space groups in this point group are:
Unit cell: (150.28, 150.28, 150.28, 90, 90, 90)
Space group: P 2 3 (No. 195)

Unit cell: (150.28, 150.28, 150.28, 90, 90, 90)
Space group: P 21 3 (No. 198)


Note that this analysis does not take into account the effects of twinning.
If the data are (almost) perfectly twinned, the symmetry will appear to be
higher than it actually is.



-----------------------------------------------------------------------------------------------------------------
Merging in *highest possible* point group P 4 3 2.
***** THIS MIGHT NOT BE THE BEST POINT GROUP SYMMETRY *****
-----------------------------------------------------------------------------------------------------------------

R-linear = sum(abs(data - mean(data))) / sum(abs(data))
R-square = sum((data - mean(data))**2) / sum(data**2)
In these sums single measurements are excluded.
Redundancy       Mean      Mean
Min  Max   Mean  R-linear  R-square
unused:        - 9.9965
bin  1: 9.9965 - 6.7635    1    2  1.798    0.5277    0.3309
bin  2: 6.7635 - 5.6778    1    2  1.817    0.5183    0.2808
bin  3: 5.6778 - 5.0653    1    2  1.831    0.5329    0.2896
bin  4: 5.0653 - 4.6532    1    2  1.832    0.5120    0.2668
bin  5: 4.6532 - 4.3491    1    2  1.851    0.5396    0.2915
bin  6: 4.3491 - 4.1115    1    2  1.839    0.5304    0.2787
bin  7: 4.1115 - 3.9186    1    2  1.848    0.5375    0.2778
bin  8: 3.9186 - 3.7575    1    2  1.848    0.5534    0.2905
bin  9: 3.7575 - 3.6199    1    2  1.874    0.5445    0.2777
bin 10: 3.6199 - 3.5006    1    2  1.863    0.5564    0.2849
unused: 3.5006 -

Suggesting various space group choices on the basis of systematic absence analyses


Analyses of the absences table indicates a number of likely space group
candidates, which are listed below. For each space group, the number of
absent violations are listed under the '+++' column. The number of present
violations (weak reflections) are listed under '---'. The last column is a
likelihood based score for the particular space group.  Note that
enantiomorphic spacegroups will have equal scores. Also, if absences were
removed while processing the data, they will be regarded as missing
information, rather then as enforcing that absence in the space group choices.


------------------------------------------------------------------------------------
| space group | n absent | _absent | _absent | +++ | ---  | score       |
------------------------------------------------------------------------------------
| P 4 3 2     | 0        |     0.00   |     0.00        |  0  |  12  |  0.000e+00  |
| P 42 3 2    | 13       |     0.07   |     3.30        |  0  |  12  |  0.000e+00  |
| P 43 3 2    | 20       |     0.67   |    11.95        |  2  |  1   |  7.646e-01  |
| P 41 3 2    | 20       |     0.67   |    11.95        |  2  |  1   |  7.646e-01  |
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