This tutorial requires a DIALS 3 installation.
Please click here to go to the tutorial for DIALS 2.2.

Multi-crystal symmetry analysis and scaling with DIALS

Introduction

Recent additions to DIALS and xia2 have enabled multi-crystal analysis to be performed following integration. These tools are particularly relevant for analysis of many partial-datasets, which may be the only practical way of performing data collections for certain crystals. After integration, the space group symmetry can be investigated by testing for the presence of symmetry operations relating the integrated intensities of groups of reflections - the program to perform this is analysis is dials.symmetry (with algorithms similar to those of the program Pointless). Another thing to consider is that for certain space groups (polar space groups), there is an inherent ambiguity in the way that the diffraction pattern can be indexed. In order to combine multiple datasets from these space groups, one must reindex all data to a consistent setting, which can be done with the program dials.cosym (see Gildea and Winter for details). Finally, the data must be scaled, to correct for experimental effects such as differences in crystal size/illuminated volume and radiation damage - this can be done with the program dials.scale (with algorithms similar to those of the program Aimless). After the data has been scaled, choices can then be made about applying a resolution limit to exclude certain regions of the data which may be negatively affected by radiation damage.

In this tutorial, we shall investigate a multi-crystal dataset collected on the VMXi beamline, Diamond’s automated facility for data collection from crystallisation experiments in-situ. The dataset consists of four repeats of a 60-degree rotation measurement on a crystal of Proteinase K, taken at different locations on the crystal. We shall start with the integrated reflections and experiments files generated by running the automated processing software xia2 with pipeline=dials. Have a look at the Processing in Detail tutorial if you want to know more about the different processing steps up to this point.

Note

To obtain the data for this tutorial you can run dials.data get vmxi_proteinase_k_sweeps. If you are at Diamond Light Source on BAG training then the data are already available. After typing module load bagtraining you’ll be moved to a working folder, with the data already located in the tutorial-data/ccp4/integrated_files subdirectory. The processing in this tutorial will produce quite a few files, so it’s recommended to make an move to new directory:

mkdir multi_crystal
cd multi_crystal

xia2.multiplex

The easiest way to run these tools for a multi-dataset analysis is through the program xia2.multiplex. This runs several DIALS programs, including the programs described above, while producing useful plots and output files.

To run xia2.multiplex, we must provide the path to the input integrated files from dials.integrate:

xia2.multiplex experiments_0.expt experiments_1.expt experiments_2.expt experiments_3.expt reflections_0.refl reflections_1.refl reflections_2.refl reflections_3.refl

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DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:

input {
  experiments = experiments_0.expt
  experiments = experiments_1.expt
  experiments = experiments_2.expt
  experiments = experiments_3.expt
  reflections = reflections_0.refl
  reflections = reflections_1.refl
  reflections = reflections_2.refl
  reflections = reflections_3.refl
}

Selecting 4 experiments with profile-fitted reflections
Selecting 4 experiments with refined reflections
                       Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90)

0 singletons:

Point group    a           b           c          alpha        beta         gamma       

1 cluster:

Cluster_id       N_xtals  Med_a         Med_b         Med_c         Med_alpha    Med_beta     Med_gamma   Delta(deg)
4 in P422.
cluster_1        4        68.36 (0.01 ) 68.36 (0.01 ) 103.95(0.02 ) 90.00 (0.00) 90.00 (0.00) 90.00 (0.00)
     P 4/m m m (No. 123)  68.36         68.36         103.95        90.00        90.00        90.00         0.0   


Standard deviations are in brackets.
Each cluster:
Input lattice count, with integration Bravais setting space group.
Cluster median with Niggli cell parameters (std dev in brackets).
Highest possible metric symmetry and unit cell using LePage (J Appl Cryst 1982, 15:255) method, maximum delta 3deg.
Using all data sets for subsequent analysis
Laue group determined by dials.cosym: P 4 2 2
Resolution limit: 1.78 (cc_half > 0.3)
Space group determined by dials.symmetry: P 41 21 2

Overall merging statistics:
+--------------------+--------------+------------------+-------------------+
|                    | Overall      | Low resolution   | High resolution   |
|--------------------+--------------+------------------+-------------------|
| Resolution (Å)     | 68.37 - 1.78 | 68.42 - 4.83     | 1.81 - 1.78       |
| Observations       | 216749       | 21131            | 137               |
| Unique reflections | 20799        | 1380             | 126               |
| Multiplicity       | 10.4         | 15.3             | 1.1               |
| Completeness       | 85.67%       | 100.00%          | 10.61%            |
| Mean I/σ(I)        | 30.6         | 60.3             | 2.2               |
| Rmerge             | 0.057        | 0.047            | 0.139             |
| Rmeas              | 0.059        | 0.048            | 0.192             |
| Rpim               | 0.016        | 0.012            | 0.132             |
| CC½                | 0.999        | 0.999            | 0.965             |
+--------------------+--------------+------------------+-------------------+

Resolution shells:
+------------------+----------+-------------+----------------+----------------+----------+---------------+----------+---------+--------+---------+--------+---------+
| Resolution (Å)   |   N(obs) |   N(unique) |   Multiplicity |   Completeness |   Mean I |   Mean I/σ(I) |   Rmerge |   Rmeas |   Rpim |   Ranom | CC½    |   CCano |
|------------------+----------+-------------+----------------+----------------+----------+---------------+----------+---------+--------+---------+--------+---------|
| 68.42 - 4.83     |    21131 |        1380 |          15.31 |         100    |    263.5 |          60.3 |    0.047 |   0.048 |  0.012 |   0.025 | 0.999* |  -0.147 |
| 4.83 - 3.84      |    20567 |        1269 |          16.21 |         100    |    386.9 |          64.3 |    0.045 |   0.047 |  0.011 |   0.023 | 0.999* |  -0.124 |
| 3.84 - 3.35      |    20421 |        1258 |          16.23 |         100    |    293.3 |          58.9 |    0.048 |   0.05  |  0.012 |   0.026 | 0.999* |  -0.096 |
| 3.35 - 3.05      |    20516 |        1226 |          16.73 |         100    |    201.8 |          52.8 |    0.054 |   0.056 |  0.013 |   0.028 | 0.999* |   0.005 |
| 3.05 - 2.83      |    20404 |        1221 |          16.71 |         100    |    139   |          45.4 |    0.061 |   0.062 |  0.015 |   0.032 | 0.999* |  -0.097 |
| 2.83 - 2.66      |    20944 |        1230 |          17.03 |         100    |    115.3 |          42.4 |    0.067 |   0.069 |  0.016 |   0.036 | 0.998* |  -0.156 |
| 2.66 - 2.53      |    20248 |        1200 |          16.87 |         100    |     91.2 |          35.7 |    0.075 |   0.077 |  0.019 |   0.039 | 0.998* |   0.017 |
| 2.53 - 2.42      |    16539 |        1212 |          13.65 |         100    |     81.3 |          30.3 |    0.081 |   0.084 |  0.023 |   0.047 | 0.997* |  -0.052 |
| 2.42 - 2.32      |    12324 |        1208 |          10.2  |         100    |     72.7 |          25.6 |    0.083 |   0.087 |  0.027 |   0.06  | 0.996* |   0.007 |
| 2.32 - 2.24      |    10345 |        1209 |           8.56 |         100    |     69.6 |          22.4 |    0.084 |   0.09  |  0.03  |   0.065 | 0.994* |   0.011 |
| 2.24 - 2.17      |     8654 |        1193 |           7.25 |          99.92 |     61.3 |          18.9 |    0.088 |   0.095 |  0.035 |   0.07  | 0.993* |  -0.115 |
| 2.17 - 2.11      |     6964 |        1189 |           5.86 |          99.41 |     52.2 |          14.9 |    0.099 |   0.109 |  0.044 |   0.097 | 0.991* |  -0.087 |
| 2.11 - 2.06      |     5481 |        1148 |           4.77 |          96.15 |     47.3 |          12.4 |    0.099 |   0.111 |  0.048 |   0.109 | 0.991* |   0.016 |
| 2.06 - 2.01      |     4333 |        1108 |           3.91 |          92.72 |     40.8 |          10.2 |    0.112 |   0.129 |  0.061 |   0.13  | 0.983* |  -0.018 |
| 2.01 - 1.96      |     3142 |        1028 |           3.06 |          86.46 |     34.8 |           7.9 |    0.124 |   0.148 |  0.079 |   0.172 | 0.974* |  -0.04  |
| 1.96 - 1.92      |     2119 |         928 |           2.28 |          77.46 |     31.7 |           6.4 |    0.123 |   0.152 |  0.087 |   0.171 | 0.966* |  -0.413 |
| 1.92 - 1.88      |     1174 |         719 |           1.63 |          60.27 |     26.6 |           4.6 |    0.141 |   0.186 |  0.12  |   0.247 | 0.947* |   0.946 |
| 1.88 - 1.84      |      819 |         566 |           1.45 |          49    |     23.4 |           3.9 |    0.163 |   0.221 |  0.148 |   0.371 | 0.936* |   0     |
| 1.84 - 1.81      |      487 |         381 |           1.28 |          31.54 |     21.2 |           3.3 |    0.194 |   0.266 |  0.181 |   0.306 | 0.904* |   0     |
| 1.81 - 1.78      |      137 |         126 |           1.09 |          10.61 |     14.5 |           2.2 |    0.139 |   0.192 |  0.132 |   9.536 | 0.965* |   0     |
+------------------+----------+-------------+----------------+----------------+----------+---------------+----------+---------+--------+---------+--------+---------+

Intensity correlation clustering summary:
=========  ==============  ==========  ========  ==============  ==============
  Cluster    No. datasets  Datasets      Height    Multiplicity    Completeness
=========  ==============  ==========  ========  ==============  ==============
        1               2  0 3           0.0021             3.3            0.68
        2               2  1 2           0.0029             5.6            0.79
        3               4  0 1 2 3       0.0038             8.1            0.83
=========  ==============  ==========  ========  ==============  ==============

Cos(angle) clustering summary:
=========  ==============  ==========  ========  ==============  ==============
  Cluster    No. datasets  Datasets      Height    Multiplicity    Completeness
=========  ==============  ==========  ========  ==============  ==============
        1               2  1 2          9.6e-06             5.6            0.79
        2               3  1 2 3        0.0092              5.6            0.79
        3               4  0 1 2 3      0.032               8.1            0.83
=========  ==============  ==========  ========  ==============  ==============

This runs dials.cosym to analyse the Laue symmetry and reindex all datasets consistently, scales the data with dials.scale, calculates a resolution limit with dials.resolutionizer and reruns dials.scale with the determined resolution cutoff. The final dataset is exported to an unmerged mtz and a HTML report is generated. The easiest way to see the results is to open the HTML report in your browser of choice e.g.:

firefox xia2.multiplex.html

Provided is a summary of the merging statistics as well as several plots, please explore these for a few minutes now! This dataset results in good merging statistics, however if you navigate to the “Analysis by batch” tab in “All data”, you will see that the fourth dataset has poorer statistics compared to the others. Let’s repeat the processing manually to explore the different steps and address this issue.

Manual reprocessing

The first step is Laue/Patterson group analysis using dials.cosym:

dials.cosym experiments_0.expt experiments_1.expt experiments_2.expt experiments_3.expt reflections_0.refl reflections_1.refl reflections_2.refl reflections_3.refl
Scoring all possible sub-groups
+-------------------+-----+--------------+----------+--------+--------+---------+--------------------+
| Patterson group   |     |   Likelihood |   NetZcc |   Zcc+ |   Zcc- |   delta | Reindex operator   |
|-------------------+-----+--------------+----------+--------+--------+---------+--------------------|
| P 4/m m m         | *** |            1 |     9.86 |   9.86 |   0    |       0 | -a,b,-c            |
| C m m m           |     |            0 |     0.01 |   9.86 |   9.85 |       0 | a+b,-a+b,c         |
| P m m m           |     |            0 |     0    |   9.86 |   9.85 |       0 | -a,b,-c            |
| P 4/m             |     |            0 |    -0.01 |   9.85 |   9.86 |       0 | -a,b,-c            |
| P 1 2/m 1         |     |            0 |     0.04 |   9.89 |   9.85 |       0 | -a,b,-c            |
| C 1 2/m 1         |     |            0 |     0.03 |   9.88 |   9.85 |       0 | a-b,a+b,c          |
| P 1 2/m 1         |     |            0 |     0    |   9.86 |   9.86 |       0 | b,c,a              |
| C 1 2/m 1         |     |            0 |    -0.02 |   9.84 |   9.86 |       0 | a+b,-a+b,c         |
| P 1 2/m 1         |     |            0 |    -0.03 |   9.83 |   9.86 |       0 | -b,-a,-c           |
| P -1              |     |            0 |    -9.86 |   0    |   9.86 |       0 | -a,b,-c            |
+-------------------+-----+--------------+----------+--------+--------+---------+--------------------+
Best solution: P 4/m m m
Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90)
Reindex operator: -a,b,-c
Laue group probability: 1.000
Laue group confidence: 1.000
Space groups:
P 4 2 2
[0, 1, 2, 3]
Reindexing operators:
x,y,z
[0, 1, 2, 3]

Show/Hide Log

DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:

input {
  experiments = experiments_0.expt
  experiments = experiments_1.expt
  experiments = experiments_2.expt
  experiments = experiments_3.expt
  reflections = reflections_0.refl
  reflections = reflections_1.refl
  reflections = reflections_2.refl
  reflections = reflections_3.refl
}

Hierarchical clustering of unit cells
Using Andrews-Bernstein distance from Andrews & Bernstein J Appl Cryst 47:346 (2014)
Distances have been calculated
                       Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90)

0 singletons:

Point group    a           b           c          alpha        beta         gamma       

1 cluster:

Cluster_id       N_xtals  Med_a         Med_b         Med_c         Med_alpha    Med_beta     Med_gamma   Delta(deg)
4 in P422.
cluster_1        4        68.36 (0.01 ) 68.36 (0.01 ) 103.95(0.02 ) 90.00 (0.00) 90.00 (0.00) 90.00 (0.00)
     P 4/m m m (No. 123)  68.36         68.36         103.95        90.00        90.00        90.00         0.0   


Standard deviations are in brackets.
Each cluster:
Input lattice count, with integration Bravais setting space group.
Cluster median with Niggli cell parameters (std dev in brackets).
Highest possible metric symmetry and unit cell using LePage (J Appl Cryst 1982, 15:255) method, maximum delta 3deg.
Filtering reflections for dataset 0
Read 76079 predicted reflections
Selected 54367 reflections integrated by profile and summation methods
Combined 1127 partial reflections with other partial reflections
Removed 20 reflections below partiality threshold
Removed 0 intensity.sum.value reflections with I/Sig(I) < -5
Removed 14 intensity.prf.value reflections with I/Sig(I) < -5
Filtering reflections for dataset 1
Read 75607 predicted reflections
Selected 54845 reflections integrated by profile and summation methods
Combined 1284 partial reflections with other partial reflections
Removed 50 reflections below partiality threshold
Removed 0 intensity.sum.value reflections with I/Sig(I) < -5
Removed 14 intensity.prf.value reflections with I/Sig(I) < -5
Filtering reflections for dataset 2
Read 77983 predicted reflections
Selected 54461 reflections integrated by profile and summation methods
Combined 1404 partial reflections with other partial reflections
Removed 38 reflections below partiality threshold
Removed 0 intensity.sum.value reflections with I/Sig(I) < -5
Removed 8 intensity.prf.value reflections with I/Sig(I) < -5
Filtering reflections for dataset 3
Read 76468 predicted reflections
Selected 53877 reflections integrated by profile and summation methods
Combined 1062 partial reflections with other partial reflections
Removed 8 reflections below partiality threshold
Removed 0 intensity.sum.value reflections with I/Sig(I) < -5
Removed 5 intensity.prf.value reflections with I/Sig(I) < -5
Patterson group: P 4/m m m

--------------------------------------------------------------------------------

Normalising intensities for dataset 1

ML estimate of overall B value:
   13.46 A**2
ML estimate of  -log of scale factor:
  -3.04

--------------------------------------------------------------------------------

Normalising intensities for dataset 2

ML estimate of overall B value:
   11.05 A**2
ML estimate of  -log of scale factor:
  -3.50

--------------------------------------------------------------------------------

Normalising intensities for dataset 3

ML estimate of overall B value:
   11.44 A**2
ML estimate of  -log of scale factor:
  -2.96

--------------------------------------------------------------------------------

Normalising intensities for dataset 4

ML estimate of overall B value:
   12.14 A**2
ML estimate of  -log of scale factor:
  -2.67

--------------------------------------------------------------------------------

Estimation of resolution for Laue group analysis

Resolution estimate from <I>/<σ(I)> > 4.0 : 2.12
Resolution estimate from CC½ > 0.60: 1.83
High resolution limit set to: 1.83
Selecting 190318 reflections with d > 1.83
================================================================================

Automatic determination of number of dimensions for analysis
+--------------+--------------+
|   Dimensions |   Functional |
|--------------+--------------|
|            1 |      14.4189 |
|            2 |      15.5305 |
|            3 |      14.5025 |
|            4 |      14.9418 |
|            5 |      14.8184 |
|            6 |      14.6554 |
|            7 |      14.731  |
|            8 |      14.7    |
+--------------+--------------+
Best number of dimensions: 3
Using 3 dimensions for analysis
Principal component analysis:
Explained variance: 0.0078, 0.0051, 5.1e-05
Explained variance ratio: 0.6, 0.39, 0.004
Scoring individual symmetry elements
+--------------+--------+------+-----+-----------------+
|   likelihood |   Z-CC |   CC |     | Operator        |
|--------------+--------+------+-----+-----------------|
|        0.943 |   9.85 | 0.98 | *** | 4 |(0, 0, 1)    |
|        0.943 |   9.85 | 0.99 | *** | 4^-1 |(0, 0, 1) |
|        0.942 |   9.83 | 0.98 | *** | 2 |(1, 0, 0)    |
|        0.945 |   9.89 | 0.99 | *** | 2 |(0, 1, 0)    |
|        0.943 |   9.86 | 0.99 | *** | 2 |(0, 0, 1)    |
|        0.945 |   9.88 | 0.99 | *** | 2 |(1, 1, 0)    |
|        0.942 |   9.84 | 0.98 | *** | 2 |(-1, 1, 0)   |
+--------------+--------+------+-----+-----------------+
Scoring all possible sub-groups
+-------------------+-----+--------------+----------+--------+--------+---------+--------------------+
| Patterson group   |     |   Likelihood |   NetZcc |   Zcc+ |   Zcc- |   delta | Reindex operator   |
|-------------------+-----+--------------+----------+--------+--------+---------+--------------------|
| P 4/m m m         | *** |            1 |     9.86 |   9.86 |   0    |       0 | -a,b,-c            |
| C m m m           |     |            0 |     0.01 |   9.86 |   9.85 |       0 | a+b,-a+b,c         |
| P m m m           |     |            0 |     0    |   9.86 |   9.85 |       0 | -a,b,-c            |
| P 4/m             |     |            0 |    -0.01 |   9.85 |   9.86 |       0 | -a,b,-c            |
| P 1 2/m 1         |     |            0 |     0.04 |   9.89 |   9.85 |       0 | -a,b,-c            |
| C 1 2/m 1         |     |            0 |     0.03 |   9.88 |   9.85 |       0 | a-b,a+b,c          |
| P 1 2/m 1         |     |            0 |     0    |   9.86 |   9.86 |       0 | b,c,a              |
| C 1 2/m 1         |     |            0 |    -0.02 |   9.84 |   9.86 |       0 | a+b,-a+b,c         |
| P 1 2/m 1         |     |            0 |    -0.03 |   9.83 |   9.86 |       0 | -b,-a,-c           |
| P -1              |     |            0 |    -9.86 |   0    |   9.86 |       0 | -a,b,-c            |
+-------------------+-----+--------------+----------+--------+--------+---------+--------------------+
Best solution: P 4/m m m
Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90)
Reindex operator: -a,b,-c
Laue group probability: 1.000
Laue group confidence: 1.000
Space groups:
P 4 2 2
[0, 1, 2, 3]
Reindexing operators:
x,y,z
[0, 1, 2, 3]
Writing html report to: dials.cosym.html
Writing json to: dials.cosym.json
Saving reindexed experiments to symmetrized.expt
Saving reindexed reflections to symmetrized.refl

As you can see, the \(P\,4/m\,m\,m\) Patterson group is found with the highest confidence. For the corresponding space group, the mirror symmetries are removed to give \(P\,4\,2\,2\), as the chiral nature of macromolecules means we have a restricted choice of space groups. In this example, all datasets were indexed consistently, but this is not the case in general.

Next, the data can be scaled:

dials.scale symmetrized.expt symmetrized.refl

From the merging statistics it is clear that the data quality is good out to the furthest resolution (\(CC_{1/2} > 0.3\)), which can be confirmed by a resolution analysis:

dials.resolutionizer scaled.expt scaled.refl
Resolution cc_half:      1.78

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The following parameters have been modified:

input {
  experiments = scaled.expt
  reflections = scaled.refl
}

DIALS 3.dev.124-g3812ecd3e
Detected existence of a multi-dataset reflection table 
containing 4 datasets. 

Read 74952 predicted reflections
Selected 54381 scaled reflections
Combined 2 partial reflections with other partial reflections
Read 74323 predicted reflections
Selected 54542 scaled reflections
Combined 3 partial reflections with other partial reflections
Read 76579 predicted reflections
Selected 54072 scaled reflections
Combined 4 partial reflections with other partial reflections
Read 75406 predicted reflections
Selected 54020 scaled reflections
Combined 2 partial reflections with other partial reflections
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)
Resolution cc_half:      1.78
Resolution I/sig:        1.78
Resolution Mn(I/sig):    1.78

If the resolution limit was lower than the extent of the data, scaling would be rerun with a new resolution limit, for example:

dials.scale scaled.expt scaled.refl d_min=1.78

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DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:
cut_data {
  d_min = 1.78
}
input {
  experiments = scaled.expt
  reflections = scaled.refl
}

Checking for the existence of a reflection table 
containing multiple datasets 

Detected existence of a multi-dataset reflection table 
containing 4 datasets. 

Found 4 reflection tables & 4 experiments in total.

Dataset ids are: 0,1,2,3 

Space group being used during scaling is P 4 2 2
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)

Scaling models have been initialised for all experiments.

================================================================================

The experiment id for this dataset is 0.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 20037/74952 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 12546
criterion: excluded for scaling, reflections: 20037

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 1.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 19172/74323 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 11927
criterion: excluded for scaling, reflections: 19172

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 2.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 21795/76579 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 14121
criterion: excluded for scaling, reflections: 21795

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 3.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 20789/75406 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 12917
criterion: excluded for scaling, reflections: 20789

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

Configuring a MultiScaler to handle the individual Scalers. 

Determining symmetry equivalent reflections across datasets.


Using quasi-random reflection selection. Selecting from 17132 symmetry groups
with <I/sI> > 1.0 (203702 reflections)). Selection target of 716.56 reflections
from each dataset, with a total number between 11465.02 and 13758.03.

Summary of cross-dataset reflection groups chosen (1277 groups, 13392 reflections):
+---------------+------------+----------+-----+-----+-----+-----+
| d-range       |   n_groups |   n_refl |   0 |   1 |   2 |   3 |
|---------------+------------+----------+-----+-----+-----+-----|
| 68.43 - 7.961 |         42 |      689 | 105 | 203 | 178 | 203 |
| 7.961 - 5.649 |         31 |      727 |  70 | 241 | 199 | 217 |
| 5.649 - 4.617 |         33 |      831 |  72 | 277 | 231 | 251 |
| 4.617 - 4.001 |         34 |      912 |  70 | 304 | 262 | 276 |
| 4.001 - 3.58  |         37 |      982 |  72 | 324 | 285 | 301 |
| 3.58 - 3.269  |         31 |      885 |  72 | 296 | 242 | 275 |
| 3.269 - 3.027 |         34 |      846 |  70 | 277 | 228 | 271 |
| 3.027 - 2.832 |         31 |      775 |  70 | 253 | 209 | 243 |
| 2.832 - 2.67  |         34 |      818 |  71 | 263 | 220 | 264 |
| 2.67 - 2.533  |         34 |      773 |  71 | 248 | 207 | 247 |
| 2.533 - 2.415 |         31 |      560 |  70 | 197 | 190 | 103 |
| 2.415 - 2.313 |         38 |      551 | 104 | 177 | 200 |  70 |
| 2.313 - 2.222 |         41 |      523 | 121 | 165 | 167 |  70 |
| 2.222 - 2.141 |         46 |      505 | 133 | 164 | 137 |  71 |
| 2.141 - 2.069 |         77 |      594 | 153 | 176 | 105 | 160 |
| 2.069 - 2.003 |        104 |      582 | 150 | 150 | 105 | 177 |
| 2.003 - 1.943 |        137 |      657 | 159 | 217 | 141 | 140 |
| 1.943 - 1.889 |        205 |      614 | 141 | 172 | 161 | 140 |
| 1.889 - 1.838 |        213 |      474 |  83 | 125 | 132 | 134 |
| 1.838 - 1.792 |         44 |       94 |  19 |  28 |  32 |  15 |
+---------------+------------+----------+-----+-----+-----+-----+
Summary of reflections chosen for minimisation from each dataset (52727 total):
+--------------+------------------+----------------------+----------------------+--------------------+
| Dataset id   |     reflections  |   randomly selected  |   randomly selected  |   combined number  |
|              |    connected to  |         reflections  |         reflections  |     of reflections |
|              |   other datasets |       within dataset |      across datasets |                    |
|--------------+------------------+----------------------+----------------------+--------------------|
| 0            |             1876 |                 4603 |                 6250 |              11840 |
| 1            |             4257 |                 4759 |                 6416 |              13937 |
| 2            |             3631 |                 4673 |                 6395 |              13354 |
| 3            |             3628 |                 4801 |                 6405 |              13596 |
| total        |            13392 |                18836 |                25466 |              52727 |
+--------------+------------------+----------------------+----------------------+--------------------+
Completed configuration of MultiScaler. 

================================================================================

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with an LBFGS minimizer. 

Time taken for refinement 5.56

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  52727 |   2.4379 |
|      1 |  52727 |   2.4303 |
|      2 |  52727 |   2.422  |
|      3 |  52727 |   2.4143 |
|      4 |  52727 |   2.409  |
|      5 |  52727 |   2.4053 |
|      6 |  52727 |   2.402  |
|      7 |  52727 |   2.4    |
|      8 |  52727 |   2.3986 |
|      9 |  52727 |   2.397  |
|     10 |  52727 |   2.3965 |
|     11 |  52727 |   2.3956 |
|     12 |  52727 |   2.3945 |
|     13 |  52727 |   2.393  |
|     14 |  52727 |   2.3916 |
|     15 |  52727 |   2.3907 |
|     16 |  52727 |   2.3903 |
|     17 |  52727 |   2.3887 |
|     18 |  52727 |   2.3879 |
|     19 |  52727 |   2.3865 |
|     20 |  52727 |   2.3847 |
|     21 |  52727 |   2.3839 |
|     22 |  52727 |   2.3826 |
|     23 |  52727 |   2.3818 |
|     24 |  52727 |   2.3805 |
|     25 |  52727 |   2.3798 |
|     26 |  52727 |   2.3788 |
|     27 |  52727 |   2.3785 |
|     28 |  52727 |   2.3783 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

================================================================================

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
3346 outliers have been identified. 

Performing multi-dataset profile/summation intensity optimisation.
+-----------------+---------+---------+
| Combination     |   CC1/2 |   Rmeas |
|-----------------+---------+---------|
| prf only        | 0.99924 | 0.05535 |
| sum only        | 0.99898 | 0.06169 |
| Imid = 847.27   | 0.99561 | 0.17683 |
| Imid = 27607.83 | 0.86966 | 0.25308 |
| Imid = 2760.78  | 0.98509 | 0.28965 |
| Imid = 276.08   | 0.99825 | 0.09902 |
+-----------------+---------+---------+
Profile intensities determined to be best for scaling. 

Combined outlier rejection has been performed across multiple datasets, 
3346 outliers have been identified. 

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with an LBFGS minimizer. 

Time taken for refinement 3.27

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51871 |   1.3313 |
|      1 |  51871 |   1.3275 |
|      2 |  51871 |   1.3232 |
|      3 |  51871 |   1.3215 |
|      4 |  51871 |   1.32   |
|      5 |  51871 |   1.3189 |
|      6 |  51871 |   1.3181 |
|      7 |  51871 |   1.3168 |
|      8 |  51871 |   1.3163 |
|      9 |  51871 |   1.316  |
|     10 |  51871 |   1.3158 |
|     11 |  51871 |   1.3156 |
|     12 |  51871 |   1.3153 |
|     13 |  51871 |   1.3151 |
|     14 |  51871 |   1.3149 |
|     15 |  51871 |   1.3148 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

================================================================================

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
3188 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 1.04470, b = 0.02586
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 37.022

Results of error model refinement. Uncorrected and corrected variances
of normalised intensity deviations for given intensity ranges. Variances
are expected to be ~1.0 for reliable errors (sigmas).
+--------------------------+----------+------------------------+----------------------+
| Intensity range (<Ih>)   |   n_refl |   Uncorrected variance |   Corrected variance |
|--------------------------+----------+------------------------+----------------------|
| 9962.36 - 1722.63        |     1407 |                  5.592 |                0.741 |
| 1722.63 - 1323.39        |     1407 |                  5.144 |                1.012 |
| 1323.39 - 1114.88        |     1407 |                  4.866 |                1.158 |
| 1114.88 - 908.23         |     2257 |                  4.462 |                1.193 |
| 908.23 - 499.06          |    11838 |                  3.669 |                1.341 |
| 499.06 - 274.23          |    20482 |                  2.752 |                1.39  |
| 274.23 - 150.69          |    28659 |                  1.985 |                1.277 |
| 150.69 - 82.80           |    31238 |                  1.433 |                1.07  |
| 82.80 - 45.50            |    25893 |                  1.136 |                0.919 |
| 45.50 - 24.99            |    16172 |                  0.868 |                0.741 |
+--------------------------+----------+------------------------+----------------------+

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with a Levenberg-Marquardt minimizer.

Time taken for refinement 12.35

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51900 |  1.0029  |
|      1 |  51900 |  0.99855 |
|      2 |  51900 |  0.99795 |
|      3 |  51900 |  0.99755 |
|      4 |  51900 |  0.9974  |
|      5 |  51900 |  0.9973  |
+--------+--------+----------+
RMSD no longer decreasing

================================================================================

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with a Levenberg-Marquardt minimizer.

Time taken for refinement 4.02

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51900 |   0.9973 |
|      1 |  51900 |   0.9973 |
+--------+--------+----------+
RMSD no longer decreasing

================================================================================

Calculating error estimates of inverse scale factors. 

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
883 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 0.90997, b = 0.04540
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 24.208

Results of error model refinement. Uncorrected and corrected variances
of normalised intensity deviations for given intensity ranges. Variances
are expected to be ~1.0 for reliable errors (sigmas).
+--------------------------+----------+------------------------+----------------------+
| Intensity range (<Ih>)   |   n_refl |   Uncorrected variance |   Corrected variance |
|--------------------------+----------+------------------------+----------------------|
| 10299.63 - 1829.55       |     1430 |                 17.547 |                0.882 |
| 1829.55 - 1396.62        |     1430 |                 12.237 |                0.988 |
| 1396.62 - 1177.84        |     1430 |                 10.193 |                1.04  |
| 1177.84 - 926.57         |     2691 |                  9.249 |                1.129 |
| 926.57 - 507.45          |    12191 |                  6.144 |                1.15  |
| 507.45 - 277.91          |    20922 |                  3.825 |                1.215 |
| 277.91 - 152.20          |    28897 |                  2.408 |                1.233 |
| 152.20 - 83.36           |    31604 |                  1.615 |                1.148 |
| 83.36 - 45.65            |    26161 |                  1.211 |                1.067 |
| 45.65 - 24.99            |    16300 |                  0.907 |                0.909 |
+--------------------------+----------+------------------------+----------------------+


The reflection table variances have been adjusted to account for the
uncertainty in the scaling models for all datasets
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)

Total time taken: 34.0184s 

================================================================================

Warning: Over half (51.19%) of model parameters have signficant
uncertainty (sigma/abs(parameter) > 0.5), which could indicate a
poorly-determined scaling problem or overparameterisation.

Summary of dataset partialities
+------------------+----------+
| Partiality (p)   |   n_refl |
|------------------+----------|
| all reflections  |   301260 |
| p > 0.99         |   246904 |
| 0.5 < p < 0.99   |     2533 |
| 0.01 < p < 0.5   |     5463 |
| p < 0.01         |    46360 |
+------------------+----------+

Reflections below a partiality_cutoff of 0.4 are not considered for any
part of the scaling analysis or for the reporting of merging statistics.
Additionally, if applicable, only reflections with a min_partiality > 0.95
were considered for use when refining the scaling model.


            ----------Merging statistics by resolution bin----------           

 d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   r_anom   cc1/2   cc_ano
 68.41   4.83  21293   1380   15.43 100.00     274.2    60.8    0.046    0.048    0.012    0.024   0.999*  -0.096
  4.83   3.84  20813   1271   16.38 100.00     402.1    64.8    0.045    0.046    0.011    0.023   0.999*  -0.172
  3.84   3.35  20603   1256   16.40 100.00     305.9    59.6    0.048    0.050    0.012    0.027   0.999*  -0.028
  3.35   3.05  20755   1226   16.93 100.00     210.5    53.4    0.054    0.056    0.013    0.029   0.999*  -0.020
  3.05   2.83  20652   1221   16.91 100.00     145.1    45.9    0.061    0.063    0.015    0.032   0.999*  -0.075
  2.83   2.66  21263   1233   17.24 100.00     120.5    43.0    0.067    0.069    0.016    0.038   0.998*  -0.081
  2.66   2.53  20380   1197   17.03 100.00      95.3    36.0    0.075    0.077    0.018    0.042   0.999*  -0.037
  2.53   2.42  16646   1212   13.73 100.00      85.0    30.4    0.080    0.083    0.022    0.049   0.998*  -0.007
  2.42   2.32  12505   1213   10.31  99.92      76.7    25.9    0.082    0.087    0.027    0.062   0.996*   0.073
  2.32   2.24  10395   1207    8.61  99.92      72.3    22.4    0.084    0.089    0.030    0.067   0.996*  -0.038
  2.24   2.17   8635   1191    7.25  99.75      64.5    18.7    0.087    0.093    0.034    0.069   0.993*  -0.183
  2.17   2.11   6956   1189    5.85  99.33      54.8    14.7    0.097    0.106    0.043    0.094   0.991*  -0.101
  2.11   2.06   5477   1147    4.78  95.98      49.7    12.2    0.097    0.109    0.048    0.107   0.992*  -0.028
  2.06   2.01   4340   1110    3.91  92.65      42.9    10.0    0.109    0.125    0.059    0.127   0.986*  -0.010
  2.01   1.96   3144   1029    3.06  86.40      36.8     7.8    0.120    0.143    0.076    0.168   0.976*  -0.055
  1.96   1.92   2115    929    2.28  77.35      33.2     6.3    0.121    0.150    0.086    0.167   0.967*  -0.335
  1.92   1.88   1171    716    1.64  60.17      28.1     4.5    0.137    0.182    0.118    0.248   0.950*   0.945
  1.88   1.84    816    564    1.45  48.83      24.7     3.9    0.156    0.213    0.143    0.364   0.941*   0.000
  1.84   1.81    489    383    1.28  31.63      22.2     3.3    0.182    0.250    0.170    0.288   0.911*   0.000
  1.81   1.78    136    125    1.09  10.52      15.4     2.2    0.139    0.193    0.133    9.301   0.962*   0.000
 68.36   1.78 218584  20799   10.51  85.44     125.7    30.7    0.056    0.059    0.016    0.040   0.999*  -0.064



            -------------Summary of merging statistics--------------           

                                             Overall    Low     High
High resolution limit                           1.78    4.83    1.78
Low resolution limit                           68.36   68.41    1.81
Completeness                                   85.4   100.0    10.5
Multiplicity                                   10.5    15.4     1.1
I/sigma                                        30.7    60.8     2.2
Rmerge(I)                                     0.056   0.046   0.139
Rmerge(I+/-)                                  0.055   0.045   0.115
Rmeas(I)                                      0.059   0.048   0.193
Rmeas(I+/-)                                   0.059   0.048   0.159
Rpim(I)                                       0.016   0.012   0.133
Rpim(I+/-)                                    0.021   0.016   0.109
CC half                                       0.999   0.999   0.962
Anomalous completeness                         69.3   100.0     0.1
Anomalous multiplicity                          6.2     9.4     1.1
Anomalous correlation                        -0.064  -0.096   0.000
Anomalous slope                               0.972
dF/F                                          0.037
dI/s(dI)                                      0.831
Total observations                           218584   21293     136
Total unique                                  20799    1380     125

Writing html report to dials.scale.html
Saving the scaled experiments to scaled.expt
Saving the scaled reflections to scaled.refl
See dials.github.io/dials_scale_user_guide.html for more info on scaling options

For exploring the scaling results, a wide variety of scaling and merging plots can be found in the dials.scale.html report generated by dials.scale.

Almost there

As mentioned previously, the fourth dataset is giving significantly higher R-merge values and much lower I/sigma. Therefore the question one must ask is if it is better to exclude this dataset. We can get some useful information about the agreement between datasets by running the program dials.compute_delta_cchalf. This program implements a version of the algorithms described in Assmann et al. :

dials.compute_delta_cchalf scaled.refl scaled.expt
# Datasets: 4
# Groups: 4
# Reflections: 216475
# Unique reflections: 20793
CC 1/2 mean: 99.285
CC 1/2 excluding group 0: 99.334
CC 1/2 excluding group 1: 99.301
CC 1/2 excluding group 2: 99.267
CC 1/2 excluding group 3: 99.192
Dataset: 0, ΔCC½: -0.049
Dataset: 1, ΔCC½: -0.015
Dataset: 2, ΔCC½: 0.018
Dataset: 3, ΔCC½: 0.093

mean delta_cc_half 0.011805181872864834
stddev delta_cc_half 0.052558310545037755
cutoff value: -0.19842806030728619 

Show/Hide Log

Read 301260 predicted reflections
Selected 218584 scaled reflections
Combined 14 partial reflections with other partial reflections
Combined 14 partial reflections with other partial reflections
Combined 14 partial reflections with other partial reflections
Combined 9 partial reflections with other partial reflections
Removed 2058 reflections below partiality threshold
Resolution bins
0: 68.363, 5.616
1: 5.616, 3.978
2: 3.978, 3.250
3: 3.250, 2.815
4: 2.815, 2.518
5: 2.518, 2.299
6: 2.299, 2.129
7: 2.129, 1.991
8: 1.991, 1.878
9: 1.878, 1.781

Summary of input data:
# Datasets: 4
# Groups: 4
# Reflections: 216475
# Unique reflections: 20793
CC 1/2 mean: 99.285
CC 1/2 excluding group 0: 99.334
CC 1/2 excluding group 1: 99.301
CC 1/2 excluding group 2: 99.267
CC 1/2 excluding group 3: 99.192
Dataset: 0, ΔCC½: -0.049
Dataset: 1, ΔCC½: -0.015
Dataset: 2, ΔCC½: 0.018
Dataset: 3, ΔCC½: 0.093

mean delta_cc_half 0.011805181872864834
stddev delta_cc_half 0.052558310545037755
cutoff value: -0.19842806030728619 

Writing table to delta_cchalf.dat
Saving 301260 reflections to filtered.refl
Saving the experiments to filtered.expt
Writing html report to: compute_delta_cchalf.html

It looks like we could get a significantly better \(CC_{1/2}\) by excluding the final dataset - it has a negative \(\Delta CC_{1/2}\). But how bad is too bad that it warrants exclusion? Unfortunately this is a difficult question to answer and it may be the case that one would need to refine several structures with different data excluded to properly address this question. If we had many datasets and only a small fraction had a very large negative \(\Delta CC_{1/2}\) then one could argue that these measurements are not drawn from the same population as the rest of the data and should be excluded.

To see the effect of removing the last dataset (dataset ‘3’), we can rerun dials.scale (note that this will overwrite the previous scaled files):

dials.scale scaled.expt scaled.refl d_min=1.78

Show/Hide Log

DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:
cut_data {
  d_min = 1.78
}
input {
  experiments = scaled.expt
  reflections = scaled.refl
}

Checking for the existence of a reflection table 
containing multiple datasets 

Detected existence of a multi-dataset reflection table 
containing 4 datasets. 

Found 4 reflection tables & 4 experiments in total.

Dataset ids are: 0,1,2,3 

Space group being used during scaling is P 4 2 2
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)

Scaling models have been initialised for all experiments.

================================================================================

The experiment id for this dataset is 0.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 20037/74952 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 12546
criterion: excluded for scaling, reflections: 20037

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 1.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 19172/74323 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 11927
criterion: excluded for scaling, reflections: 19172

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 2.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 21795/76579 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 14121
criterion: excluded for scaling, reflections: 21795

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

The experiment id for this dataset is 3.
The scaling model type being applied is physical. 

Applying filter of min_isigi > -5.0, partiality > 0.4
Excluding 20789/75406 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 12917
criterion: excluded for scaling, reflections: 20789

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             10 |
| decay        |              8 |
| absorption   |             24 |
+--------------+----------------+
Using previously determined optimal intensity choice: profile intensities

Completed preprocessing and initialisation for this dataset.

================================================================================

Configuring a MultiScaler to handle the individual Scalers. 

Determining symmetry equivalent reflections across datasets.


Using quasi-random reflection selection. Selecting from 17132 symmetry groups
with <I/sI> > 1.0 (203702 reflections)). Selection target of 716.56 reflections
from each dataset, with a total number between 11465.02 and 13758.03.

Summary of cross-dataset reflection groups chosen (1277 groups, 13392 reflections):
+---------------+------------+----------+-----+-----+-----+-----+
| d-range       |   n_groups |   n_refl |   0 |   1 |   2 |   3 |
|---------------+------------+----------+-----+-----+-----+-----|
| 68.43 - 7.961 |         42 |      689 | 105 | 203 | 178 | 203 |
| 7.961 - 5.649 |         31 |      727 |  70 | 241 | 199 | 217 |
| 5.649 - 4.617 |         33 |      831 |  72 | 277 | 231 | 251 |
| 4.617 - 4.001 |         34 |      912 |  70 | 304 | 262 | 276 |
| 4.001 - 3.58  |         37 |      982 |  72 | 324 | 285 | 301 |
| 3.58 - 3.269  |         31 |      885 |  72 | 296 | 242 | 275 |
| 3.269 - 3.027 |         34 |      846 |  70 | 277 | 228 | 271 |
| 3.027 - 2.832 |         31 |      775 |  70 | 253 | 209 | 243 |
| 2.832 - 2.67  |         34 |      818 |  71 | 263 | 220 | 264 |
| 2.67 - 2.533  |         34 |      773 |  71 | 248 | 207 | 247 |
| 2.533 - 2.415 |         31 |      560 |  70 | 197 | 190 | 103 |
| 2.415 - 2.313 |         38 |      551 | 104 | 177 | 200 |  70 |
| 2.313 - 2.222 |         41 |      523 | 121 | 165 | 167 |  70 |
| 2.222 - 2.141 |         46 |      505 | 133 | 164 | 137 |  71 |
| 2.141 - 2.069 |         77 |      594 | 153 | 176 | 105 | 160 |
| 2.069 - 2.003 |        104 |      582 | 150 | 150 | 105 | 177 |
| 2.003 - 1.943 |        137 |      657 | 159 | 217 | 141 | 140 |
| 1.943 - 1.889 |        205 |      614 | 141 | 172 | 161 | 140 |
| 1.889 - 1.838 |        213 |      474 |  83 | 125 | 132 | 134 |
| 1.838 - 1.792 |         44 |       94 |  19 |  28 |  32 |  15 |
+---------------+------------+----------+-----+-----+-----+-----+
Summary of reflections chosen for minimisation from each dataset (52727 total):
+--------------+------------------+----------------------+----------------------+--------------------+
| Dataset id   |     reflections  |   randomly selected  |   randomly selected  |   combined number  |
|              |    connected to  |         reflections  |         reflections  |     of reflections |
|              |   other datasets |       within dataset |      across datasets |                    |
|--------------+------------------+----------------------+----------------------+--------------------|
| 0            |             1876 |                 4603 |                 6250 |              11840 |
| 1            |             4257 |                 4759 |                 6416 |              13937 |
| 2            |             3631 |                 4673 |                 6395 |              13354 |
| 3            |             3628 |                 4801 |                 6405 |              13596 |
| total        |            13392 |                18836 |                25466 |              52727 |
+--------------+------------------+----------------------+----------------------+--------------------+
Completed configuration of MultiScaler. 

================================================================================

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with an LBFGS minimizer. 

Time taken for refinement 2.43

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  52727 |   2.401  |
|      1 |  52727 |   2.3969 |
|      2 |  52727 |   2.3919 |
|      3 |  52727 |   2.3904 |
|      4 |  52727 |   2.3883 |
|      5 |  52727 |   2.3876 |
|      6 |  52727 |   2.3868 |
|      7 |  52727 |   2.3856 |
|      8 |  52727 |   2.3851 |
|      9 |  52727 |   2.3846 |
|     10 |  52727 |   2.3844 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

================================================================================

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
3326 outliers have been identified. 

Performing multi-dataset profile/summation intensity optimisation.
+-----------------+---------+---------+
| Combination     |   CC1/2 |   Rmeas |
|-----------------+---------+---------|
| prf only        | 0.99921 | 0.05534 |
| sum only        | 0.99898 | 0.06158 |
| Imid = 847.67   | 0.99567 | 0.17728 |
| Imid = 27607.83 | 0.88287 | 0.25356 |
| Imid = 2760.78  | 0.9849  | 0.29009 |
| Imid = 276.08   | 0.99818 | 0.0994  |
+-----------------+---------+---------+
Profile intensities determined to be best for scaling. 

Combined outlier rejection has been performed across multiple datasets, 
3326 outliers have been identified. 

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with an LBFGS minimizer. 

Time taken for refinement 2.40

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51874 |   1.3273 |
|      1 |  51874 |   1.3232 |
|      2 |  51874 |   1.3178 |
|      3 |  51874 |   1.3157 |
|      4 |  51874 |   1.3137 |
|      5 |  51874 |   1.3127 |
|      6 |  51874 |   1.312  |
|      7 |  51874 |   1.3109 |
|      8 |  51874 |   1.3105 |
|      9 |  51874 |   1.3102 |
|     10 |  51874 |   1.3102 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

================================================================================

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
3177 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 1.04105, b = 0.02610
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 36.810

Results of error model refinement. Uncorrected and corrected variances
of normalised intensity deviations for given intensity ranges. Variances
are expected to be ~1.0 for reliable errors (sigmas).
+--------------------------+----------+------------------------+----------------------+
| Intensity range (<Ih>)   |   n_refl |   Uncorrected variance |   Corrected variance |
|--------------------------+----------+------------------------+----------------------|
| 10006.52 - 1720.92       |     1408 |                  5.668 |                0.745 |
| 1720.92 - 1322.15        |     1408 |                  5.087 |                0.988 |
| 1322.15 - 1114.13        |     1408 |                  5.048 |                1.184 |
| 1114.13 - 910.64         |     2217 |                  4.435 |                1.184 |
| 910.64 - 500.16          |    11834 |                  3.696 |                1.341 |
| 500.16 - 274.71          |    20494 |                  2.752 |                1.391 |
| 274.71 - 150.88          |    28648 |                  1.969 |                1.27  |
| 150.88 - 82.87           |    31300 |                  1.424 |                1.068 |
| 82.87 - 45.52            |    25962 |                  1.133 |                0.922 |
| 45.52 - 24.99            |    16170 |                  0.861 |                0.74  |
+--------------------------+----------+------------------------+----------------------+

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with a Levenberg-Marquardt minimizer.

Time taken for refinement 6.12

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51904 |  1.0009  |
|      1 |  51904 |  0.99771 |
|      2 |  51904 |  0.99765 |
+--------+--------+----------+
RMSD no longer decreasing

================================================================================

Components to be refined in this cycle for all datasets: scale, decay, absorption
Performing a round of scaling with a Levenberg-Marquardt minimizer.

Time taken for refinement 4.01

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  51904 |  0.99765 |
|      1 |  51904 |  0.99765 |
+--------+--------+----------+
RMSD no longer decreasing

================================================================================

Calculating error estimates of inverse scale factors. 

Scale factors determined during minimisation have now been
applied to all datasets.

Combined outlier rejection has been performed across multiple datasets, 
869 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 0.91105, b = 0.04535
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 24.203

Results of error model refinement. Uncorrected and corrected variances
of normalised intensity deviations for given intensity ranges. Variances
are expected to be ~1.0 for reliable errors (sigmas).
+--------------------------+----------+------------------------+----------------------+
| Intensity range (<Ih>)   |   n_refl |   Uncorrected variance |   Corrected variance |
|--------------------------+----------+------------------------+----------------------|
| 10314.23 - 1827.11       |     1430 |                 17.492 |                0.877 |
| 1827.11 - 1396.51        |     1430 |                 12.194 |                0.987 |
| 1396.51 - 1176.92        |     1430 |                 10.222 |                1.04  |
| 1176.92 - 927.35         |     2666 |                  9.332 |                1.137 |
| 927.35 - 507.80          |    12193 |                  6.205 |                1.158 |
| 507.80 - 278.07          |    20934 |                  3.849 |                1.218 |
| 278.07 - 152.26          |    28905 |                  2.422 |                1.235 |
| 152.26 - 83.38           |    31618 |                  1.615 |                1.147 |
| 83.38 - 45.66            |    26169 |                  1.211 |                1.066 |
| 45.66 - 24.99            |    16311 |                  0.907 |                0.907 |
+--------------------------+----------+------------------------+----------------------+


The reflection table variances have been adjusted to account for the
uncertainty in the scaling models for all datasets
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)

Total time taken: 23.6294s 

================================================================================

Warning: Over half (51.19%) of model parameters have signficant
uncertainty (sigma/abs(parameter) > 0.5), which could indicate a
poorly-determined scaling problem or overparameterisation.

Summary of dataset partialities
+------------------+----------+
| Partiality (p)   |   n_refl |
|------------------+----------|
| all reflections  |   301260 |
| p > 0.99         |   246904 |
| 0.5 < p < 0.99   |     2533 |
| 0.01 < p < 0.5   |     5463 |
| p < 0.01         |    46360 |
+------------------+----------+

Reflections below a partiality_cutoff of 0.4 are not considered for any
part of the scaling analysis or for the reporting of merging statistics.
Additionally, if applicable, only reflections with a min_partiality > 0.95
were considered for use when refining the scaling model.


            ----------Merging statistics by resolution bin----------           

 d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   r_anom   cc1/2   cc_ano
 68.41   4.83  21294   1380   15.43 100.00     273.6    60.8    0.046    0.048    0.012    0.024   0.999*  -0.080
  4.83   3.84  20818   1271   16.38 100.00     401.4    64.8    0.045    0.046    0.011    0.023   0.999*  -0.182
  3.84   3.35  20603   1256   16.40 100.00     305.3    59.5    0.048    0.050    0.012    0.027   0.999*  -0.027
  3.35   3.05  20758   1226   16.93 100.00     210.1    53.3    0.054    0.056    0.013    0.029   0.999*  -0.024
  3.05   2.83  20654   1221   16.92 100.00     144.8    45.9    0.061    0.063    0.015    0.032   0.999*  -0.076
  2.83   2.66  21264   1233   17.25 100.00     120.2    43.0    0.067    0.069    0.016    0.038   0.998*  -0.075
  2.66   2.53  20381   1197   17.03 100.00      95.1    36.0    0.075    0.077    0.018    0.042   0.998*  -0.041
  2.53   2.42  16647   1212   13.74 100.00      84.9    30.4    0.080    0.083    0.022    0.048   0.998*   0.050
  2.42   2.32  12505   1213   10.31  99.92      76.5    25.9    0.082    0.087    0.027    0.062   0.996*   0.073
  2.32   2.24  10395   1207    8.61  99.92      72.2    22.3    0.084    0.089    0.030    0.067   0.996*  -0.036
  2.24   2.17   8635   1191    7.25  99.75      64.4    18.7    0.087    0.093    0.034    0.069   0.993*  -0.183
  2.17   2.11   6956   1189    5.85  99.33      54.7    14.7    0.097    0.106    0.043    0.094   0.991*  -0.101
  2.11   2.06   5477   1147    4.78  95.98      49.6    12.2    0.097    0.109    0.048    0.107   0.992*  -0.025
  2.06   2.01   4340   1110    3.91  92.65      42.8    10.0    0.109    0.125    0.059    0.127   0.986*  -0.011
  2.01   1.96   3144   1029    3.06  86.40      36.7     7.8    0.120    0.143    0.076    0.168   0.976*  -0.054
  1.96   1.92   2115    929    2.28  77.35      33.1     6.3    0.121    0.150    0.086    0.167   0.967*  -0.334
  1.92   1.88   1171    716    1.64  60.17      28.0     4.5    0.137    0.182    0.117    0.248   0.950*   0.944
  1.88   1.84    816    564    1.45  48.83      24.7     3.9    0.156    0.213    0.143    0.364   0.941*   0.000
  1.84   1.81    489    383    1.28  31.63      22.2     3.3    0.182    0.250    0.170    0.288   0.911*   0.000
  1.81   1.78    136    125    1.09  10.52      15.4     2.2    0.139    0.192    0.133    9.297   0.962*   0.000
 68.36   1.78 218598  20799   10.51  85.44     125.5    30.7    0.056    0.059    0.016    0.040   0.999*  -0.039



            -------------Summary of merging statistics--------------           

                                             Overall    Low     High
High resolution limit                           1.78    4.83    1.78
Low resolution limit                           68.36   68.41    1.81
Completeness                                   85.4   100.0    10.5
Multiplicity                                   10.5    15.4     1.1
I/sigma                                        30.7    60.8     2.2
Rmerge(I)                                     0.056   0.046   0.139
Rmerge(I+/-)                                  0.055   0.045   0.115
Rmeas(I)                                      0.059   0.048   0.192
Rmeas(I+/-)                                   0.059   0.048   0.159
Rpim(I)                                       0.016   0.012   0.133
Rpim(I+/-)                                    0.021   0.016   0.109
CC half                                       0.999   0.999   0.962
Anomalous completeness                         69.3   100.0     0.1
Anomalous multiplicity                          6.2     9.4     1.1
Anomalous correlation                        -0.039  -0.080   0.000
Anomalous slope                               0.971
dF/F                                          0.037
dI/s(dI)                                      0.830
Total observations                           218598   21294     136
Total unique                                  20799    1380     125

Writing html report to dials.scale.html
Saving the scaled experiments to scaled.expt
Saving the scaled reflections to scaled.refl
See dials.github.io/dials_scale_user_guide.html for more info on scaling options

The overall merging statistics look significantly improved and therefore one would probably proceed with the first three datasets:

Resolution:         68.40 - 1.78  > 68.40 - 1.79
Observations:       222563        > 166095
Unique reflections: 16534         > 16285
Redundancy:         13.5          > 10.2
Completeness:       68.18%        > 67.56%
Mean intensity:     45.3          > 46.0
Mean I/sigma(I):    25.0          > 26.1
R-merge:            0.132         > 0.059
R-meas:             0.136         > 0.062
R-pim:              0.033         > 0.017

We could have also excluded a subset of images, for example using the option exclude_images=3:301:600 to exclude the last 300 images of dataset 3. This option could be used to exclude the end of a dataset that was showing sigificant radiation damage, or if the crystal had moved out of the beam part-way through the measurement.

It is also worth checking the assigned space group using dials.symmetry. In dials.cosym, only the Laue/Patterson group was tested to determine a space group of \(P\,4\,2\,2\). However, a number of other MX space groups are possible for the Laue group (due to the possibility of screw-axes), such as \(P\,4\,2_1\,2\), \(P\,4_1\,2\,2\) etc. The screw-axes tests are performed by dials.symmetry, and we can disable the Laue group testing as we are already confident about this:

dials.symmetry scaled.expt scaled.refl laue_group=None
Read 74952 predicted reflections
Selected 54797 scaled reflections
Combined 14 partial reflections with other partial reflections
Read 74323 predicted reflections
Selected 54996 scaled reflections
Combined 15 partial reflections with other partial reflections
Read 76579 predicted reflections
Selected 54523 scaled reflections
Combined 14 partial reflections with other partial reflections
Read 75406 predicted reflections
Selected 54282 scaled reflections
Combined 9 partial reflections with other partial reflections
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)
Resolution estimate from <I>/<σ(I)> > 4.0 : 1.86
Resolution estimate from CC½ > 0.60: 1.78
Performing systematic absence checks on scaled data
Read 301260 predicted reflections
Selected 218598 scaled reflections
Removed 1 reflections with d <= 1.78
Combined 14 partial reflections with other partial reflections
Combined 15 partial reflections with other partial reflections
Combined 14 partial reflections with other partial reflections
Combined 9 partial reflections with other partial reflections
Removed 2060 reflections below partiality threshold
Laue group: P 4/m m m
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
| Screw axis   |   Score |   No. present |   No. absent |   <I> present |   <I> absent |   <I/sig> present |   <I/sig> absent |
|--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------|
| 41c          |       1 |            11 |           34 |       606.032 |        0.051 |            37.209 |            0.408 |
| 21a          |       1 |            14 |           14 |       809.548 |        0.44  |            24.579 |            1.076 |
| 42c          |       1 |            23 |           22 |       289.628 |        0.301 |            18.127 |            0.283 |
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
+---------------+---------+
| Space group   |   score |
|---------------+---------|
| P 4 2 2       |       0 |
| P 4 21 2      |       0 |
| P 41 2 2      |       0 |
| P 42 2 2      |       0 |
| P 41 21 2     |       1 |
| P 42 21 2     |       0 |
+---------------+---------+
Recommended space group: P 41 21 2
Space group with equivalent score (enantiomorphic pair): P 43 21 2

Show/Hide Log

DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:

laue_group = None
input {
  experiments = scaled.expt
  reflections = scaled.refl
}

Detected existence of a multi-dataset reflection table 
containing 4 datasets. 

================================================================================

Analysing systematic absences

Laue group: P 4/m m m
Read 74952 predicted reflections
Selected 54797 scaled reflections
Combined 14 partial reflections with other partial reflections
Read 74323 predicted reflections
Selected 54996 scaled reflections
Combined 15 partial reflections with other partial reflections
Read 76579 predicted reflections
Selected 54523 scaled reflections
Combined 14 partial reflections with other partial reflections
Read 75406 predicted reflections
Selected 54282 scaled reflections
Combined 9 partial reflections with other partial reflections
Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)
Resolution estimate from <I>/<σ(I)> > 4.0 : 1.86
Resolution estimate from CC½ > 0.60: 1.78
Performing systematic absence checks on scaled data
Read 301260 predicted reflections
Selected 218598 scaled reflections
Removed 1 reflections with d <= 1.78
Combined 14 partial reflections with other partial reflections
Combined 15 partial reflections with other partial reflections
Combined 14 partial reflections with other partial reflections
Combined 9 partial reflections with other partial reflections
Removed 2060 reflections below partiality threshold
Laue group: P 4/m m m
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
| Screw axis   |   Score |   No. present |   No. absent |   <I> present |   <I> absent |   <I/sig> present |   <I/sig> absent |
|--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------|
| 41c          |       1 |            11 |           34 |       606.032 |        0.051 |            37.209 |            0.408 |
| 21a          |       1 |            14 |           14 |       809.548 |        0.44  |            24.579 |            1.076 |
| 42c          |       1 |            23 |           22 |       289.628 |        0.301 |            18.127 |            0.283 |
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
+---------------+---------+
| Space group   |   score |
|---------------+---------|
| P 4 2 2       |       0 |
| P 4 21 2      |       0 |
| P 41 2 2      |       0 |
| P 42 2 2      |       0 |
| P 41 21 2     |       1 |
| P 42 21 2     |       0 |
+---------------+---------+
Recommended space group: P 41 21 2
Space group with equivalent score (enantiomorphic pair): P 43 21 2
Saving reindexed experiments to symmetrized.expt in space group P 41 21 2
Saving 301260 reindexed reflections to symmetrized.refl

By analysing the sets of reflections we expect to be present and absent, the existence of the \(4_1\) and \(2_1\) screw axes are confirmed, hence the space group is assigned as \(P\,4_1\,2_1\,2\). Note that we can do this analysis before or after scaling, as we only need to know the Laue group for scaling, however it is preferable to do this after scaling as outliers may have been removed by scaling.

Finally, we must merge the data and produce an MTZ file for downstream structure solution:

dials.merge symmetrized.expt symmetrized.refl

Show/Hide Log

DIALS 3.dev.283-g93b4f28db
The following parameters have been modified:

input {
  experiments = symmetrized.expt
  reflections = symmetrized.refl
}

Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90)

Merging scaled reflection data

Read 301260 predicted reflections
Selected 218598 scaled reflections
Combined 14 partial reflections with other partial reflections
Combined 15 partial reflections with other partial reflections
Combined 14 partial reflections with other partial reflections
Combined 9 partial reflections with other partial reflections
Running systematic absences check
Laue group: P 4/m m m
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
| Screw axis   |   Score |   No. present |   No. absent |   <I> present |   <I> absent |   <I/sig> present |   <I/sig> absent |
|--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------|
| 41c          |       1 |            12 |           34 |       554.969 |        0.081 |            34.492 |            0.417 |
| 21a          |       1 |            14 |           14 |       809.548 |        0.44  |            24.579 |            1.076 |
| 42c          |       1 |            24 |           22 |       277.323 |        0.301 |            17.576 |            0.283 |
+--------------+---------+---------------+--------------+---------------+--------------+-------------------+------------------+
+---------------+---------+
| Space group   |   score |
|---------------+---------|
| P 4 2 2       |       0 |
| P 4 21 2      |       0 |
| P 41 2 2      |       0 |
| P 42 2 2      |       0 |
| P 41 21 2     |       1 |
| P 42 21 2     |       0 |
+---------------+---------+
Recommended space group: P 41 21 2
Space group with equivalent score (enantiomorphic pair): P 43 21 2

Performing French-Wilson treatment of scaled intensities
Total number of rejected intensities 1

===================== Absolute scaling and Wilson analysis ====================


        ----------Maximum likelihood isotropic Wilson scaling----------

 ML estimate of overall B value:
   12.44 A**2
 Estimated -log of scale factor:
   -2.92
 The overall B value ("Wilson B-factor", derived from the Wilson plot) gives
 an isotropic approximation for the falloff of intensity as a function of
 resolution.  Note that this approximation may be misleading for anisotropic
 data (where the crystal is poorly ordered along an axis).  The Wilson B is
 strongly correlated with refined atomic B-factors but these may differ by
 a significant amount, especially if anisotropy is present.

       ----------Maximum likelihood anisotropic Wilson scaling----------

ML estimate of overall B_cart value:
  11.67,  0.00,  0.00
         11.67,  0.00
                13.74

Equivalent representation as U_cif:
   0.15, -0.00, -0.00
          0.15,  0.00
                 0.17

Eigen analyses of B-cart:
  -------------------------------------------------
  | Eigenvector | Value   | Vector                |
  -------------------------------------------------
  | 1           |  13.737 | ( 0.00,  0.00,  1.00) |
  | 2           |  11.673 | (-0.71,  0.71, -0.00) |
  | 3           |  11.673 | ( 0.71,  0.71, -0.00) |
  -------------------------------------------------
ML estimate of  -log of scale factor:
  -2.93

                    ----------Anisotropy analyses----------


 For the resolution shell spanning between 1.93 - 1.78 Angstrom,
 the mean I/sigI is equal to  4.30. 52.5 % of these intensities have
 an I/sigI > 3. When sorting these intensities by their anisotropic
 correction factor and analysing the I/sigI behavior for this ordered
 list, we can gauge the presence of 'anisotropy induced noise amplification'
 in reciprocal space.

 The quarter of Intensities *least* affected by the anisotropy correction show

    <I/sigI>                 :   4.64e+00
    Fraction of I/sigI > 3   :   5.65e-01     ( Z =     1.75 )
  The quarter of Intensities *most* affected by the anisotropy correction show

    <I/sigI>                 :   3.30e+00
    Fraction of I/sigI > 3   :   4.08e-01     ( Z =     5.26 )
 Z-scores are computed on the basis of a Bernoulli model assuming independence
 of weak reflections with respect to anisotropy.

                        ----------Wilson plot----------

 The Wilson plot shows the falloff in intensity as a function in resolution;
 this is used to calculate the overall B-factor ("Wilson B-factor") for the
 data shown above.  The expected plot is calculated based on analysis of
 macromolecule structures in the PDB, and the distinctive appearance is due to
 the non-random arrangement of atoms in the crystal.  Some variation is
 natural, but major deviations from the expected plot may indicate pathological
 data (including ice rings, detector problems, or processing errors).

                  ----------Mean intensity analyses----------

 Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59.
 The following resolution shells are worrisome:
  -----------------------------------------------------------------
  | Mean intensity by shell (outliers)                            |
  |---------------------------------------------------------------|
  | d_spacing     | z_score       | completeness  | <Iobs>/<Iexp> |
  |---------------------------------------------------------------|
  |     2.033     |    4.81       |    0.76       |      0.822    |
  -----------------------------------------------------------------

 Possible reasons for the presence of the reported unexpected low or elevated
 mean intensity in a given resolution bin are :
   - missing overloaded or weak reflections
   - suboptimal data processing
   - satellite (ice) crystals
   - NCS
   - translational pseudo symmetry (detected elsewhere)
   - outliers (detected elsewhere)
   - ice rings (detected elsewhere)
   - other problems
 Note that the presence of abnormalities in a certain region of reciprocal
 space might confuse the data validation algorithm throughout a large region
 of reciprocal space, even though the data are acceptable in those areas.



                     ----------Possible outliers----------

  Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764

Acentric reflections:
            None

Centric reflections:
  -----------------------------------------------------------------------------------------------------
  | Centric reflections                                                                               |
  |---------------------------------------------------------------------------------------------------|
  | d_spacing         | H K L             | |E|               | p(wilson)         | p(extreme)        |
  |---------------------------------------------------------------------------------------------------|
  |    2.628          |    26,    0,    1 |   4.18            |  2.93e-05         |   7.87e-02        |
  -----------------------------------------------------------------------------------------------------



 p(wilson)  : 1-(erf[|E|/sqrt(2)])
 p(extreme) : 1-(erf[|E|/sqrt(2)])^(n_acentrics)


 p(wilson) is the probability that an E-value of the specified
 value would be observed when it would selected at random from
 the given data set.
 p(extreme) is the probability that the largest |E| value is
 larger or equal than the observed largest |E| value.

 Both measures can be used for outlier detection. p(extreme)
 takes into account the size of the dataset.


                 ----------Ice ring related problems----------

 The following statistics were obtained from ice-ring insensitive resolution
 ranges:

    mean bin z_score      : 1.41
        ( rms deviation   : 1.14 )
    mean bin completeness : 0.86
        ( rms deviation   : 0.29 )

 The following table shows the Wilson plot Z-scores and completeness for
 observed data in ice-ring sensitive areas.  The expected relative intensity
 is the theoretical intensity of crystalline ice at the given resolution.
 Large z-scores and high completeness in these resolution ranges might
 be a reason to re-assess your data processsing if ice rings were present.

  -------------------------------------------------------------
  | d_spacing | Expected rel. I | Data Z-score | Completeness |
  -------------------------------------------------------------
  |     3.897 |      1.000      |    2.74      |    1.00      |
  |     3.669 |      0.750      |    1.09      |    1.00      |
  |     3.441 |      0.530      |    3.37      |    0.99      |
  |     2.671 |      0.170      |    1.27      |    0.99      |
  |     2.249 |      0.390      |    1.63      |    0.98      |
  |     2.072 |      0.300      |    0.90      |    0.81      |
  |     1.948 |      0.040      |    1.66      |    0.51      |
  |     1.918 |      0.180      |    0.04      |    0.37      |
  |     1.883 |      0.030      |    0.43      |    0.30      |
  -------------------------------------------------------------
 Abnormalities in mean intensity or completeness at resolution ranges with a
 relative ice ring intensity lower than 0.10 will be ignored.
 No ice ring related problems detected.
 If ice rings were present, the data does not look worse at ice ring related
 d_spacings as compared to the rest of the data set.


            ----------Merging statistics by resolution bin----------           

 d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   r_anom   cc1/2   cc_ano
 68.41   4.83  21293   1380   15.43 100.00     273.6    60.8    0.046    0.048    0.012    0.024   0.999*  -0.084
  4.83   3.84  20815   1271   16.38 100.00     401.4    64.8    0.045    0.046    0.011    0.023   0.999*  -0.184
  3.84   3.35  20599   1256   16.40 100.00     305.3    59.5    0.048    0.050    0.012    0.027   0.999*  -0.042
  3.35   3.05  20754   1226   16.93 100.00     210.1    53.3    0.054    0.056    0.013    0.029   0.999*  -0.033
  3.05   2.83  20643   1221   16.91 100.00     144.8    45.9    0.061    0.063    0.015    0.032   0.999*  -0.151
  2.83   2.66  21256   1233   17.24 100.00     120.2    43.0    0.067    0.069    0.016    0.038   0.998*  -0.091
  2.66   2.53  20369   1197   17.02 100.00      95.1    36.0    0.075    0.077    0.018    0.042   0.998*  -0.007
  2.53   2.42  16644   1212   13.73 100.00      84.9    30.4    0.080    0.083    0.022    0.048   0.997*   0.026
  2.42   2.32  12503   1213   10.31 100.00      76.5    25.9    0.082    0.087    0.027    0.062   0.996*   0.070
  2.32   2.24  10391   1207    8.61 100.00      72.2    22.3    0.084    0.089    0.030    0.067   0.995*   0.010
  2.24   2.17   8635   1191    7.25  99.92      64.4    18.7    0.087    0.093    0.034    0.069   0.993*  -0.183
  2.17   2.11   6956   1189    5.85  99.41      54.7    14.7    0.097    0.106    0.043    0.094   0.991*  -0.101
  2.11   2.06   5477   1147    4.78  96.14      49.6    12.2    0.097    0.109    0.048    0.107   0.992*  -0.025
  2.06   2.01   4340   1110    3.91  92.73      42.8    10.0    0.109    0.125    0.059    0.127   0.986*  -0.011
  2.01   1.96   3144   1029    3.06  86.47      36.7     7.8    0.120    0.143    0.076    0.168   0.976*  -0.054
  1.96   1.92   2115    929    2.28  77.48      33.1     6.3    0.121    0.150    0.086    0.167   0.967*  -0.334
  1.92   1.88   1171    716    1.64  60.22      28.0     4.5    0.137    0.182    0.117    0.248   0.950*   0.944
  1.88   1.84    816    564    1.45  48.87      24.7     3.9    0.156    0.213    0.143    0.364   0.941*   0.000
  1.84   1.81    489    383    1.28  31.65      22.2     3.3    0.182    0.250    0.170    0.288   0.911*   0.000
  1.81   1.78    136    125    1.09  10.53      15.4     2.2    0.139    0.192    0.133    9.297   0.962*   0.000
 68.36   1.78 218546  20799   10.51  85.66     125.5    30.7    0.056    0.059    0.016    0.040   0.999*  -0.061


            -------------Summary of merging statistics--------------           

                                             Overall    Low     High
High resolution limit                           1.78    4.83    1.78
Low resolution limit                           68.36   68.41    1.81
Completeness                                   85.7   100.0    10.5
Multiplicity                                   10.5    15.4     1.1
I/sigma                                        30.7    60.8     2.2
Rmerge(I)                                     0.056   0.046   0.139
Rmerge(I+/-)                                  0.055   0.045   0.115
Rmeas(I)                                      0.059   0.048   0.192
Rmeas(I+/-)                                   0.059   0.048   0.159
Rpim(I)                                       0.016   0.012   0.133
Rpim(I+/-)                                    0.021   0.016   0.109
CC half                                       0.999   0.999   0.962
Anomalous completeness                         69.3   100.0     0.1
Anomalous multiplicity                          6.2     9.4     1.1
Anomalous correlation                        -0.061  -0.084   0.000
Anomalous slope                               0.971
dF/F                                          0.037
dI/s(dI)                                      0.830
Total observations                           218546   21293     136
Total unique                                  20799    1380     125


Writing reflections to merged.mtz
Title: From dials.merge
Space group symbol from file: P41212
Space group number from file: 92
Space group from matrices: P 41 21 2 (No. 92)
Point group symbol from file: 422
Number of crystals: 1
Number of Miller indices: 20799
Resolution range: 68.3603 1.78117
History:
  From DIALS 3.dev.283-g93b4f28db, run on 2020-11-21 at 08:16:44 GMT
Crystal 1:
  Name: XTAL
  Project: AUTOMATIC
  Id: 1
  Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90)
  Number of datasets: 1
  Dataset 1:
    Name: NATIVE
    Id: 1
    Wavelength: 0.979493
    Number of columns: 17
    label    #valid  %valid    min     max type
    H         20799 100.00%   0.00   37.00 H: index h,k,l
    K         20799 100.00%   0.00   24.00 H: index h,k,l
    L         20799 100.00%   0.00   56.00 H: index h,k,l
    IMEAN     20799 100.00% -24.86 5274.54 J: intensity
    SIGIMEAN  20799 100.00%   0.13  155.96 Q: standard deviation
    I(+)      20519  98.65% -24.86 5274.54 K: I(+) or I(-)
    SIGI(+)   20519  98.65%   0.13  155.96 M: standard deviation
    I(-)      14677  70.57% -28.67 3453.91 K: I(+) or I(-)
    SIGI(-)   14677  70.57%   0.37   59.94 M: standard deviation
    N(+)      20519  98.65%   2.00    8.00 I: integer
    N(-)      14677  70.57%   8.00    8.00 I: integer
    F         20798 100.00%   0.28   72.39 F: amplitude
    SIGF      20798 100.00%   0.04    1.84 Q: standard deviation
    F(+)      20519  98.65%   0.28   72.39 G: F(+) or F(-)
    SIGF(+)   20519  98.65%   0.04    1.49 L: standard deviation
    F(-)      14676  70.56%   0.40   58.74 G: F(+) or F(-)
    SIGF(-)   14676  70.56%   0.05    1.44 L: standard deviation

This merges the data and performs a truncation procedure, to give a merged MTZ file containing intensities and strictly-positive structure factors (Fs).