Multi-lattice Tutorial

Introduction

The following example uses semi-synthetic multi-lattice trypsin datasets collected using beamline I04 at Diamond Light Source which is available for download from semisynthetic. This tutorial uses one of the 2-lattice datasets which are contained in the file semisynthetic_multilattice_data_2.tar.bz2.

Import

The first stage of step-by-step DIALS processing is to import the data - all that happens here is that the image headers are read, and a file describing their contents (datablock.json) is written. It’s worth noting that if this file is changed subsequent processing can use this.

dials.import semisynthetic_multilattice_data/2/ag/trp_ag_*.cbf

The output just describes what the software understands of the images it was passed, in this case one sweep of data containing 100 images.

The following parameters have been modified:

input {
  datablock = <image files>
}

--------------------------------------------------------------------------------
DataBlock 0
  format: <class 'dxtbx.format.FormatCBFMiniPilatusDLS6MSN100.FormatCBFMiniPilatusDLS6MSN100'>
  num images: 100
  num sweeps: 1
  num stills: 0
--------------------------------------------------------------------------------
Writing datablocks to datablock.json

Find Spots

The first “real” task in any DIALS processing will be the spot finding. Here we tweak the minimum spot size (min_spot_size=3) and use multiple processors to speed up the spot-finding (nproc=4).

dials.find_spots datablock.json min_spot_size=3 nproc=4

This will just report the number of spots found.

Writing datablocks to datablock.json

The following parameters have been modified:

spotfinder {
  mp {
    nproc = 4
  }
  filter {
    min_spot_size = 3
  }
}
input {
  datablock = datablock.json
}

Configuring spot finder from input parameters
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------

Finding spots in image 0 to 100...
Extracting strong pixels from images (may take a while)
Extracted strong pixels from images
Merging 4 pixel lists
Merged 4 pixel lists with 763338 pixels
Extracting spots
Extracted 68439 spots
Calculating 68439 spot centroids
Calculated 68439 spot centroids
Calculating 68439 spot intensities
Calculated 68439 spot intensities
Filtering 68439 spots by number of pixels
Filtered 40212 spots by number of pixels
Filtering 40212 spots by peak-centroid distance
Filtered 38341 spots by peak-centroid distance

--------------------------------------------------------------------------------
Saving 38341 reflections to strong.pickle
Saved 38341 reflections to strong.pickle

Indexing

The next step will be indexing of the strong spots. By default only one lattice is searched for, but if there are sufficient unindexed reflections remaining after indexing the first lattice, we can switch on indexing of multiple lattices using the parameter max_lattices=2 (e.g.):

dials.index datablock.json strong.pickle \
  max_lattices=2
The following parameters have been modified:

indexing {
  multiple_lattice_search {
    max_lattices = 2
  }
}
input {
  datablock = datablock.json
  reflections = strong.pickle
}

...

RMSDs by experiment
-------------------
----------------------------------------------
| Exp | Nref  | RMSD_X  | RMSD_Y  | RMSD_Z   |
|     |       | (px)    | (px)    | (images) |
----------------------------------------------
| 0   | 16344 | 0.51285 | 0.41374 | 0.79065  |
| 1   | 16594 | 0.37963 | 0.3806  | 0.78624  |
----------------------------------------------
Finish searching for more lattices: 3834 unindexed reflections remaining.
Rotation matrix to transform crystal 1 to crystal 2
{{0.973, -0.159, -0.170},
 {-0.069, -0.895, 0.441},
 {-0.222, -0.417, -0.881}}
Euler angles (xyz): -153.44, -9.77, 9.28

Final refined crystal models:
model 1 (17355 reflections):
Crystal:
    Unit cell: (54.116, 58.294, 66.530, 90.010, 90.036, 90.023)
    Space group: P 1
    U matrix:  {{-0.1871,  0.7625,  0.6194},
                {-0.0431,  0.6235, -0.7806},
                {-0.9814, -0.1727, -0.0838}}
    B matrix:  {{ 0.0185,  0.0000,  0.0000},
                { 0.0000,  0.0172,  0.0000},
                { 0.0000,  0.0000,  0.0150}}
    A = UB:    {{-0.0034,  0.0131,  0.0093},
                {-0.0008,  0.0107, -0.0117},
                {-0.0181, -0.0030, -0.0013}}

model 2 (17758 reflections):
Crystal:
    Unit cell: (54.134, 58.298, 66.538, 89.995, 89.992, 89.969)
    Space group: P 1
    U matrix:  {{-0.0085,  0.6719,  0.7406},
                {-0.3810, -0.6870,  0.6188},
                { 0.9245, -0.2769,  0.2618}}
    B matrix:  {{ 0.0185,  0.0000,  0.0000},
                {-0.0000,  0.0172,  0.0000},
                {-0.0000, -0.0000,  0.0150}}
    A = UB:    {{-0.0002,  0.0115,  0.0111},
                {-0.0070, -0.0118,  0.0093},
                { 0.0171, -0.0048,  0.0039}}

Next we run dials.refine_bravais_settings refining each indexing solution (separately) in all Bravais settings consistent with the indexed unit cell. In this example we would continue processing using bravais_setting_5.json, i.e. solution number 5.

dials.refine_bravais_settings experiments.json indexed.pickle crystal_id=0

dials.refine_bravais_settings experiments.json indexed.pickle crystal_id=1

gives a table containing the metric fit, rmsds (in mm) and unit cell for each Bravais setting...

------------------------------------------------------------------------------------------------------------
Solution Metric fit  rmsd #spots  crystal_system                                 unit_cell volume      cb_op
------------------------------------------------------------------------------------------------------------
       9  4.2577 dg 1.988   1000   tetragonal tP  60.17  60.17  69.10  90.00  90.00  90.00 250161      a,b,c
       8  4.2577 dg 1.982   1000 orthorhombic oC  84.45  85.33  69.01  90.00  90.00  90.00 497254 a+b,-a+b,c
       7  4.2577 dg 1.950   1000   monoclinic mC  85.47  84.17  68.98  90.00  89.85  90.00 496214  a-b,a+b,c
       6  4.2576 dg 1.948   1000   monoclinic mC  84.43  85.30  68.99  90.00  89.97  90.00 496845 a+b,-a+b,c
       5  0.0432 dg 0.135   1000 orthorhombic oP  54.16  58.30  66.54  90.00  90.00  90.00 210119      a,b,c
       4  0.0432 dg 0.135   1000   monoclinic mP  58.31  54.16  66.54  90.00  90.01  90.00 210136   -b,-a,-c
       3  0.0376 dg 0.135   1000   monoclinic mP  54.16  66.54  58.30  90.00  90.03  90.00 210093   -a,-c,-b
       2  0.0255 dg 0.136   1000   monoclinic mP  54.15  58.30  66.52  90.00  90.06  90.00 209989      a,b,c
       1  0.0000 dg 0.134   1000    triclinic aP  54.15  58.29  66.52  90.02  90.07  90.04 209985      a,b,c
------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------
Solution Metric fit  rmsd #spots  crystal_system                                 unit_cell volume      cb_op
------------------------------------------------------------------------------------------------------------
       9  4.2423 dg 2.228   1000   tetragonal tP  59.39  59.39  68.39  90.00  90.00  90.00 241196      a,b,c
       8  4.2423 dg 2.208   1000 orthorhombic oC  84.64  83.94  68.47  90.00  90.00  90.00 486463  a-b,a+b,c
       7  4.2423 dg 1.930   1000   monoclinic mC  82.03  83.17  67.01  90.00  91.78  90.00 456951  a-b,a+b,c
       6  4.2423 dg 1.797   1000   monoclinic mC  83.47  82.31  67.96  90.00  88.86  90.00 466784 a+b,-a+b,c
       5  0.0317 dg 0.133   1000 orthorhombic oP  54.09  58.32  66.53  90.00  90.00  90.00 209871      a,b,c
       4  0.0317 dg 0.133   1000   monoclinic mP  58.32  54.09  66.53  90.00  90.00  90.00 209868   -b,-a,-c
       3  0.0311 dg 0.133   1000   monoclinic mP  54.07  58.31  66.50  90.00  90.06  90.00 209664      a,b,c
       2  0.0093 dg 0.136   1000   monoclinic mP  54.11  66.54  58.33  90.00  90.04  90.00 210020   -a,-c,-b
       1  0.0000 dg 0.138   1000    triclinic aP  54.09  58.33  66.50  89.99  90.07  90.05 209814      a,b,c
------------------------------------------------------------------------------------------------------------

Now we re-run the indexing, this time imposing the lattice constraints for the chosen Bravais setting, in this case number 5, i.e. oP, or point group P222.

dials.index datablock.json strong.pickle \
  max_lattices=2 \
  space_group=P222
The following parameters have been modified:

indexing {
  known_symmetry {
    space_group = P222
  }
  multiple_lattice_search {
    max_lattices = 2
  }
}
input {
  datablock = datablock.json
  reflections = strong.pickle
}

...

RMSDs by experiment
-------------------
----------------------------------------------
| Exp | Nref  | RMSD_X  | RMSD_Y  | RMSD_Z   |
|     |       | (px)    | (px)    | (images) |
----------------------------------------------
| 0   | 17030 | 0.52795 | 0.42652 | 0.78267  |
| 1   | 17351 | 0.41002 | 0.39527 | 0.79255  |
----------------------------------------------
Finish searching for more lattices: 3834 unindexed reflections remaining.
Rotation matrix to transform crystal 1 to crystal 2
{{0.052, 0.997, -0.063},
 {-0.978, 0.038, -0.204},
 {-0.201, 0.072, 0.977}}
Euler angles (xyz): 11.79, -3.60, -87.01

Final refined crystal models:
model 1 (17356 reflections):
Crystal:
    Unit cell: (54.115, 58.298, 66.535, 90.000, 90.000, 90.000)
    Space group: P 2 2 2
    U matrix:  {{-0.1865,  0.7626,  0.6193},
                {-0.0431,  0.6234, -0.7807},
                {-0.9815, -0.1723, -0.0834}}
    B matrix:  {{ 0.0185,  0.0000,  0.0000},
                {-0.0000,  0.0172,  0.0000},
                {-0.0000,  0.0000,  0.0150}}
    A = UB:    {{-0.0034,  0.0131,  0.0093},
                {-0.0008,  0.0107, -0.0117},
                {-0.0181, -0.0030, -0.0013}}

model 2 (17757 reflections):
Crystal:
    Unit cell: (54.133, 58.311, 66.533, 90.000, 90.000, 90.000)
    Space group: P 2 2 2
    U matrix:  {{-0.0090,  0.6719,  0.7406},
                {-0.3809, -0.6871,  0.6187},
                { 0.9246, -0.2766,  0.2621}}
    B matrix:  {{ 0.0185,  0.0000,  0.0000},
                {-0.0000,  0.0171,  0.0000},
                {-0.0000,  0.0000,  0.0150}}
    A = UB:    {{-0.0002,  0.0115,  0.0111},
                {-0.0070, -0.0118,  0.0093},
                { 0.0171, -0.0047,  0.0039}}

Refinement

Although the models are already refined in indexing we can also add a refinement step in here to allow e.g. scan varying refinement.

dials.refine experiments.json indexed.pickle \
  scan_varying=True \
  outlier.algorithm=tukey
The following parameters have been modified:

refinement {
  parameterisation {
    crystal {
      scan_varying = True
    }
  }
  reflections {
    outlier {
      algorithm = null *tukey
    }
  }
}
input {
  experiments = experiments.json
  reflections = indexed.pickle
}

Configuring refiner

Summary statistics for observations matched to predictions:
-------------------------------------------------------------------------
|                   | Min     | Q1       | Med       | Q3      | Max    |
-------------------------------------------------------------------------
| Xc - Xo (mm)      | -0.9823 | -0.0517  | 0.002165  | 0.04972 | 0.6267 |
| Yc - Yo (mm)      | -2.051  | -0.03828 | 0.0007268 | 0.03696 | 2.383  |
| Phic - Phio (deg) | -4.79   | -0.01656 | 0.002315  | 0.0159  | 4.187  |
| X weights         | 126.2   | 134.4    | 134.9     | 135.1   | 135.2  |
| Y weights         | 125.4   | 134.5    | 135       | 135.2   | 135.2  |
| Phi weights       | 379.4   | 398.9    | 399.6     | 399.9   | 400    |
-------------------------------------------------------------------------


Summary statistics for observations matched to predictions:
--------------------------------------------------------------------------
|                   | Min      | Q1       | Med      | Q3      | Max     |
--------------------------------------------------------------------------
| Xc - Xo (mm)      | -0.2037  | -0.04754 | 0.003321 | 0.04794 | 0.2018  |
| Yc - Yo (mm)      | -0.1511  | -0.03304 | 0.002045 | 0.03517 | 0.1497  |
| Phic - Phio (deg) | -0.06525 | -0.01247 | 0.002878 | 0.01467 | 0.06455 |
| X weights         | 126.5    | 134.5    | 134.9    | 135.1   | 135.2   |
| Y weights         | 125.4    | 134.6    | 135      | 135.2   | 135.2   |
| Phi weights       | 381.1    | 399      | 399.6    | 399.9   | 400     |
--------------------------------------------------------------------------

Performing refinement

Running refinement
------------------
0 1 2 3 4 5 6

Refinement steps
----------------
-------------------------------------------------
| Step | Nref  | RMSD_X   | RMSD_Y   | RMSD_Phi |
|      |       | (mm)     | (mm)     | (deg)    |
-------------------------------------------------
| 0    | 30214 | 0.07155  | 0.051119 | 0.022657 |
| 1    | 30214 | 0.07135  | 0.050939 | 0.022084 |
| 2    | 30214 | 0.071261 | 0.050932 | 0.021906 |
| 3    | 30214 | 0.071173 | 0.050916 | 0.021827 |
| 4    | 30214 | 0.071139 | 0.05092  | 0.02178  |
| 5    | 30214 | 0.071134 | 0.050924 | 0.02177  |
| 6    | 30214 | 0.071133 | 0.050925 | 0.021769 |
-------------------------------------------------
RMSD no longer decreasing

RMSDs by experiment
-------------------
----------------------------------------------
| Exp | Nref  | RMSD_X  | RMSD_Y  | RMSD_Z   |
|     |       | (px)    | (px)    | (images) |
----------------------------------------------
| 0   | 14739 | 0.46827 | 0.28366 | 0.22357  |
| 1   | 15475 | 0.35367 | 0.30743 | 0.21195  |
----------------------------------------------
Saving refined experiments to refined_experiments.json

Integration

After the refinement is done the next step is integration, which is performed by the program dials.integrate.

dials.integrate refined_experiments.json refined.pickle

This program outputs a lot of information as integration progresses, concluding with a summary of the integration results.

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

Summary of integration results for experiment 0

 Summary of integration results as a function of image number
 --------------------------------------------------------------------------------
 Image | # full | # part | # sum | # prf | <Ibg> | <I/sigI> | <I/sigI> | <CC prf>
       |        |        |       |       |       |    (sum) |    (prf) |
 --------------------------------------------------------------------------------
     0 |    315 |   1202 |  1517 |  1047 | 18.20 |    35.81 |    53.38 |     0.64
     1 |    563 |   1204 |  1767 |  1282 | 18.18 |    35.19 |    51.10 |     0.65
     2 |    791 |   1204 |  1995 |  1496 | 18.22 |    34.96 |    49.89 |     0.65
     3 |   1010 |   1205 |  2215 |  1696 | 18.16 |    34.05 |    48.05 |     0.65
     4 |   1245 |   1182 |  2427 |  1898 | 18.12 |    33.80 |    47.20 |     0.66
     5 |   1464 |   1042 |  2506 |  2037 | 18.11 |    33.91 |    46.42 |     0.66
     6 |   1691 |    887 |  2578 |  2164 | 18.01 |    33.83 |    45.41 |     0.66
     7 |   1975 |    689 |  2664 |  2288 | 18.02 |    34.25 |    45.32 |     0.66
     8 |   2105 |    560 |  2665 |  2325 | 17.99 |    34.15 |    44.75 |     0.66
     9 |   2193 |    456 |  2649 |  2323 | 17.88 |    34.12 |    44.60 |     0.66
    10 |   2250 |    396 |  2646 |  2332 | 17.69 |    33.83 |    44.03 |     0.65
    11 |   2306 |    350 |  2656 |  2357 | 17.68 |    33.45 |    43.46 |     0.65
    12 |   2379 |    306 |  2685 |  2394 | 17.77 |    33.58 |    43.53 |     0.65
    13 |   2381 |    283 |  2664 |  2385 | 17.83 |    34.23 |    44.21 |     0.65
    14 |   2425 |    263 |  2688 |  2424 | 17.98 |    35.23 |    45.06 |     0.65
    15 |   2415 |    244 |  2659 |  2400 | 17.91 |    34.84 |    44.68 |     0.65
    16 |   2422 |    231 |  2653 |  2390 | 17.83 |    34.75 |    44.49 |     0.65
    17 |   2436 |    217 |  2653 |  2401 | 17.77 |    33.49 |    42.78 |     0.64
    18 |   2471 |    199 |  2670 |  2425 | 17.74 |    33.79 |    42.96 |     0.64
    19 |   2492 |    195 |  2687 |  2452 | 17.79 |    34.27 |    43.41 |     0.64
    20 |   2495 |    182 |  2677 |  2444 | 17.91 |    34.67 |    43.83 |     0.65
    21 |   2533 |    171 |  2704 |  2478 | 17.98 |    34.48 |    43.66 |     0.64
    22 |   2553 |    162 |  2715 |  2483 | 17.97 |    34.32 |    43.48 |     0.64
    23 |   2614 |    151 |  2765 |  2537 | 17.90 |    33.70 |    42.91 |     0.65
    24 |   2608 |    144 |  2752 |  2528 | 17.84 |    33.06 |    42.21 |     0.65
    25 |   2620 |    140 |  2760 |  2535 | 17.83 |    33.67 |    42.84 |     0.65
    26 |   2605 |    143 |  2748 |  2525 | 17.68 |    33.45 |    42.54 |     0.64
    27 |   2624 |    145 |  2769 |  2552 | 17.79 |    34.59 |    43.82 |     0.65
    28 |   2594 |    140 |  2734 |  2521 | 17.81 |    34.78 |    44.06 |     0.65
    29 |   2585 |    142 |  2727 |  2511 | 17.75 |    34.76 |    44.08 |     0.65
    30 |   2560 |    134 |  2694 |  2483 | 17.86 |    35.42 |    44.76 |     0.64
    31 |   2557 |    140 |  2697 |  2487 | 17.88 |    35.90 |    45.39 |     0.64
    32 |   2589 |    142 |  2731 |  2516 | 17.79 |    35.91 |    45.40 |     0.64
    33 |   2590 |    147 |  2737 |  2522 | 17.76 |    35.86 |    45.29 |     0.64
    34 |   2627 |    145 |  2772 |  2553 | 17.94 |    36.56 |    46.03 |     0.64
    35 |   2605 |    143 |  2748 |  2534 | 17.96 |    36.88 |    46.36 |     0.64
    36 |   2618 |    140 |  2758 |  2541 | 17.98 |    37.18 |    46.66 |     0.64
    37 |   2648 |    136 |  2784 |  2570 | 17.80 |    36.17 |    45.55 |     0.63
    38 |   2649 |    133 |  2782 |  2561 | 17.84 |    36.68 |    46.28 |     0.63
    39 |   2637 |    131 |  2768 |  2546 | 17.69 |    35.89 |    45.31 |     0.63
    40 |   2624 |    129 |  2753 |  2537 | 17.75 |    36.46 |    45.98 |     0.63
    41 |   2647 |    128 |  2775 |  2562 | 17.75 |    36.41 |    45.89 |     0.64
    42 |   2616 |    126 |  2742 |  2535 | 17.68 |    36.67 |    46.19 |     0.63
    43 |   2622 |    126 |  2748 |  2542 | 17.75 |    37.47 |    47.11 |     0.63
    44 |   2619 |    123 |  2742 |  2532 | 17.86 |    37.15 |    46.89 |     0.64
    45 |   2637 |    120 |  2757 |  2549 | 17.95 |    37.63 |    47.43 |     0.64
    46 |   2632 |    121 |  2753 |  2548 | 17.96 |    37.85 |    47.64 |     0.64
    47 |   2603 |    121 |  2724 |  2517 | 18.15 |    38.82 |    48.72 |     0.64
    48 |   2623 |    122 |  2745 |  2538 | 18.14 |    38.62 |    48.28 |     0.64
    49 |   2644 |    121 |  2765 |  2556 | 18.10 |    38.03 |    47.79 |     0.64
    50 |   2653 |    121 |  2774 |  2567 | 18.04 |    37.25 |    46.84 |     0.64
    51 |   2657 |    121 |  2778 |  2574 | 18.04 |    37.28 |    46.82 |     0.64
    52 |   2664 |    121 |  2785 |  2578 | 17.91 |    37.54 |    47.13 |     0.64
    53 |   2643 |    121 |  2764 |  2553 | 17.85 |    37.33 |    46.84 |     0.64
    54 |   2631 |    122 |  2753 |  2546 | 17.88 |    37.62 |    47.16 |     0.64
    55 |   2642 |    122 |  2764 |  2556 | 17.87 |    38.09 |    47.70 |     0.64
    56 |   2651 |    122 |  2773 |  2557 | 17.95 |    37.98 |    47.73 |     0.64
    57 |   2667 |    125 |  2792 |  2576 | 18.07 |    38.70 |    48.56 |     0.64
    58 |   2665 |    128 |  2793 |  2572 | 18.05 |    39.47 |    49.44 |     0.64
    59 |   2655 |    128 |  2783 |  2558 | 18.07 |    39.60 |    49.76 |     0.64
    60 |   2628 |    129 |  2757 |  2539 | 18.23 |    40.19 |    50.45 |     0.64
    61 |   2608 |    131 |  2739 |  2514 | 18.23 |    40.10 |    50.45 |     0.64
    62 |   2630 |    133 |  2763 |  2541 | 18.11 |    39.59 |    49.74 |     0.64
    63 |   2604 |    134 |  2738 |  2519 | 18.03 |    39.25 |    49.43 |     0.64
    64 |   2594 |    134 |  2728 |  2512 | 18.11 |    39.51 |    49.80 |     0.64
    65 |   2596 |    140 |  2736 |  2518 | 17.95 |    39.14 |    49.46 |     0.65
    66 |   2559 |    138 |  2697 |  2480 | 17.85 |    38.71 |    49.00 |     0.64
    67 |   2583 |    140 |  2723 |  2501 | 17.73 |    37.24 |    47.33 |     0.64
    68 |   2604 |    146 |  2750 |  2552 | 17.72 |    35.66 |    44.99 |     0.63
    69 |   2662 |    144 |  2806 |  2609 | 17.81 |    35.98 |    45.27 |     0.63
    70 |   2616 |    149 |  2765 |  2567 | 17.78 |    36.38 |    45.66 |     0.63
    71 |   2587 |    152 |  2739 |  2546 | 17.85 |    36.08 |    45.27 |     0.63
    72 |   2588 |    155 |  2743 |  2547 | 17.93 |    36.68 |    45.91 |     0.63
    73 |   2579 |    156 |  2735 |  2532 | 17.98 |    36.85 |    46.11 |     0.63
    74 |   2583 |    158 |  2741 |  2540 | 17.95 |    37.26 |    46.51 |     0.63
    75 |   2560 |    165 |  2725 |  2521 | 17.99 |    37.35 |    46.76 |     0.63
    76 |   2571 |    167 |  2738 |  2535 | 18.05 |    37.62 |    47.15 |     0.64
    77 |   2531 |    171 |  2702 |  2492 | 17.88 |    37.57 |    47.15 |     0.63
    78 |   2530 |    175 |  2705 |  2479 | 17.77 |    37.02 |    46.63 |     0.63
    79 |   2548 |    180 |  2728 |  2491 | 17.69 |    37.21 |    46.94 |     0.64
    80 |   2572 |    182 |  2754 |  2513 | 17.71 |    36.75 |    46.50 |     0.64
    81 |   2547 |    183 |  2730 |  2485 | 17.70 |    36.76 |    46.64 |     0.64
    82 |   2521 |    188 |  2709 |  2460 | 17.66 |    36.00 |    45.75 |     0.64
    83 |   2533 |    192 |  2725 |  2475 | 17.65 |    35.69 |    45.47 |     0.64
    84 |   2517 |    200 |  2717 |  2460 | 17.70 |    35.44 |    45.42 |     0.64
    85 |   2502 |    217 |  2719 |  2455 | 17.64 |    34.51 |    44.46 |     0.64
    86 |   2483 |    233 |  2716 |  2449 | 17.54 |    34.35 |    44.41 |     0.65
    87 |   2419 |    255 |  2674 |  2415 | 17.59 |    33.79 |    43.82 |     0.65
    88 |   2361 |    300 |  2661 |  2389 | 17.45 |    33.56 |    43.64 |     0.65
    89 |   2305 |    345 |  2650 |  2375 | 17.37 |    32.41 |    42.39 |     0.65
    90 |   2259 |    405 |  2664 |  2371 | 17.36 |    32.19 |    42.34 |     0.65
    91 |   2147 |    489 |  2636 |  2322 | 17.30 |    32.86 |    43.43 |     0.65
    92 |   1984 |    598 |  2582 |  2243 | 17.24 |    33.04 |    44.01 |     0.66
    93 |   1752 |    823 |  2575 |  2166 | 17.16 |    32.66 |    44.45 |     0.65
    94 |   1506 |    997 |  2503 |  2037 | 17.13 |    32.52 |    44.95 |     0.65
    95 |   1253 |   1139 |  2392 |  1879 | 17.11 |    31.90 |    44.96 |     0.65
    96 |   1045 |   1178 |  2223 |  1700 | 17.14 |    31.51 |    45.01 |     0.65
    97 |    805 |   1177 |  1982 |  1477 | 17.11 |    32.27 |    46.79 |     0.65
    98 |    526 |   1176 |  1702 |  1212 | 16.92 |    31.56 |    46.93 |     0.64
    99 |    300 |   1172 |  1472 |   997 | 16.90 |    31.33 |    48.07 |     0.64
 --------------------------------------------------------------------------------

 Summary of integration results binned by resolution
 ---------------------------------------------------------------------------------------------------------
 d min | d max | # full | # part | # over | # ice | # sum | # prf | <Ibg> | <I/sigI> | <I/sigI> | <CC prf>
       |       |        |        |        |       |       |       |       |    (sum) |    (prf) |
 ---------------------------------------------------------------------------------------------------------
  1.06 |  1.08 |     31 |      3 |      0 |     0 |    34 |    18 |  4.43 |     2.05 |     3.65 |     0.34
  1.08 |  1.10 |    124 |     18 |      0 |     0 |   142 |   110 |  4.81 |     2.18 |     3.55 |     0.35
  1.10 |  1.12 |    204 |     18 |      0 |     0 |   222 |   180 |  5.32 |     2.27 |     3.66 |     0.34
  1.12 |  1.14 |    326 |     30 |      0 |     0 |   356 |   295 |  5.84 |     2.79 |     4.69 |     0.41
  1.14 |  1.17 |    433 |     39 |      0 |     0 |   472 |   396 |  6.37 |     3.18 |     5.66 |     0.45
  1.17 |  1.20 |    578 |     65 |      0 |     0 |   643 |   548 |  7.00 |     3.48 |     5.70 |     0.45
  1.20 |  1.23 |    779 |     82 |      0 |     0 |   861 |   732 |  7.70 |     3.89 |     6.33 |     0.48
  1.23 |  1.26 |   1071 |    105 |      0 |     0 |  1176 |  1026 |  8.52 |     4.31 |     7.20 |     0.51
  1.26 |  1.30 |   1334 |    148 |      0 |     0 |  1482 |  1311 |  9.21 |     4.75 |     7.60 |     0.52
  1.30 |  1.34 |   1496 |    166 |      0 |     0 |  1662 |  1470 | 10.02 |     5.06 |     8.22 |     0.54
  1.34 |  1.39 |   1411 |    177 |      0 |     0 |  1588 |  1450 | 10.76 |     5.98 |     9.40 |     0.57
  1.39 |  1.44 |   1475 |    189 |      0 |     0 |  1664 |  1499 | 11.72 |     7.15 |    11.24 |     0.61
  1.44 |  1.51 |   1478 |    188 |      0 |     0 |  1666 |  1507 | 12.84 |     9.47 |    14.62 |     0.66
  1.51 |  1.59 |   1484 |    181 |      0 |     0 |  1665 |  1508 | 14.05 |    12.22 |    18.01 |     0.70
  1.59 |  1.69 |   1495 |    182 |      0 |     0 |  1677 |  1558 | 15.63 |    17.15 |    24.11 |     0.73
  1.69 |  1.82 |   1495 |    173 |      0 |     0 |  1668 |  1539 | 17.86 |    22.56 |    31.01 |     0.76
  1.82 |  2.00 |   1503 |    203 |      0 |     0 |  1706 |  1549 | 22.59 |    33.97 |    45.28 |     0.79
  2.00 |  2.29 |   1539 |    197 |      0 |     0 |  1736 |  1589 | 29.55 |    52.79 |    67.63 |     0.80
  2.29 |  2.88 |   1554 |    181 |      0 |     0 |  1735 |  1630 | 32.68 |    80.83 |    98.92 |     0.80
  2.88 | 28.90 |   1572 |    179 |      1 |     0 |  1751 |  1693 | 52.36 |   186.21 |   210.33 |     0.79
 ---------------------------------------------------------------------------------------------------------

 Summary of integration results for the whole dataset
 ---------------------------------------------
 Number fully recorded                 | 24911
 Number partially recorded             | 3031
 Number with overloaded pixels         | 5
 Number in powder rings                | 0
 Number processed with summation       | 23906
 Number processed with profile fitting | 21608
 <Ibg>                                 | 18.16
 <I/sigI> (summation)                  | 32.18
 <I/sigI> (profile fitting)            | 41.74
 <CC prf>                              | 0.51
 ---------------------------------------------

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

Summary of integration results for experiment 1

 Summary of integration results as a function of image number
 --------------------------------------------------------------------------------
 Image | # full | # part | # sum | # prf | <Ibg> | <I/sigI> | <I/sigI> | <CC prf>
       |        |        |       |       |       |    (sum) |    (prf) |
 --------------------------------------------------------------------------------
     0 |    287 |   1329 |  1616 |  1100 | 18.51 |    32.45 |    50.08 |     0.67
     1 |    532 |   1331 |  1863 |  1330 | 18.52 |    32.34 |    48.37 |     0.67
     2 |    767 |   1333 |  2100 |  1549 | 18.60 |    32.59 |    47.70 |     0.67
     3 |   1003 |   1335 |  2338 |  1760 | 18.81 |    32.58 |    46.99 |     0.67
     4 |   1233 |   1331 |  2564 |  1964 | 18.59 |    32.06 |    45.79 |     0.67
     5 |   1481 |   1216 |  2697 |  2117 | 18.42 |    31.95 |    45.18 |     0.67
     6 |   1742 |   1056 |  2798 |  2261 | 18.27 |    31.91 |    44.27 |     0.67
     7 |   1971 |    850 |  2821 |  2351 | 18.28 |    31.78 |    43.24 |     0.67
     8 |   2187 |    655 |  2842 |  2411 | 18.11 |    31.31 |    42.14 |     0.67
     9 |   2348 |    528 |  2876 |  2482 | 18.15 |    31.04 |    41.42 |     0.67
    10 |   2445 |    447 |  2892 |  2513 | 18.19 |    30.91 |    41.13 |     0.67
    11 |   2495 |    390 |  2885 |  2515 | 18.04 |    30.85 |    40.91 |     0.67
    12 |   2561 |    350 |  2911 |  2553 | 17.89 |    30.35 |    40.22 |     0.67
    13 |   2590 |    317 |  2907 |  2552 | 17.94 |    30.76 |    40.68 |     0.67
    14 |   2625 |    289 |  2914 |  2565 | 18.04 |    31.46 |    41.44 |     0.67
    15 |   2609 |    274 |  2883 |  2540 | 17.97 |    31.71 |    41.71 |     0.66
    16 |   2621 |    262 |  2883 |  2542 | 17.85 |    31.82 |    41.80 |     0.66
    17 |   2640 |    250 |  2890 |  2547 | 17.84 |    31.83 |    41.92 |     0.66
    18 |   2657 |    237 |  2894 |  2550 | 17.71 |    31.52 |    41.38 |     0.66
    19 |   2697 |    219 |  2916 |  2575 | 17.69 |    31.17 |    41.02 |     0.67
    20 |   2701 |    208 |  2909 |  2572 | 17.71 |    31.41 |    41.26 |     0.67
    21 |   2752 |    196 |  2948 |  2612 | 17.79 |    32.25 |    42.26 |     0.67
    22 |   2761 |    186 |  2947 |  2607 | 17.85 |    32.39 |    42.50 |     0.66
    23 |   2819 |    182 |  3001 |  2662 | 17.91 |    32.49 |    42.64 |     0.67
    24 |   2837 |    182 |  3019 |  2682 | 17.97 |    33.04 |    43.22 |     0.67
    25 |   2810 |    176 |  2986 |  2660 | 18.14 |    33.63 |    43.94 |     0.67
    26 |   2834 |    169 |  3003 |  2666 | 18.26 |    33.99 |    44.39 |     0.67
    27 |   2833 |    165 |  2998 |  2662 | 18.28 |    34.47 |    45.00 |     0.67
    28 |   2856 |    162 |  3018 |  2680 | 18.20 |    34.88 |    45.31 |     0.67
    29 |   2869 |    160 |  3029 |  2699 | 18.20 |    34.98 |    45.30 |     0.67
    30 |   2849 |    161 |  3010 |  2680 | 18.12 |    34.48 |    44.70 |     0.67
    31 |   2844 |    160 |  3004 |  2673 | 18.06 |    34.60 |    44.86 |     0.66
    32 |   2818 |    162 |  2980 |  2652 | 17.94 |    34.45 |    44.57 |     0.66
    33 |   2831 |    163 |  2994 |  2662 | 17.92 |    34.48 |    44.54 |     0.66
    34 |   2846 |    159 |  3005 |  2686 | 18.02 |    34.94 |    44.97 |     0.66
    35 |   2839 |    159 |  2998 |  2667 | 17.86 |    34.12 |    44.11 |     0.66
    36 |   2835 |    158 |  2993 |  2660 | 17.81 |    34.17 |    44.06 |     0.66
    37 |   2822 |    156 |  2978 |  2642 | 17.67 |    33.51 |    43.30 |     0.66
    38 |   2800 |    155 |  2955 |  2629 | 17.76 |    33.32 |    43.04 |     0.66
    39 |   2836 |    154 |  2990 |  2669 | 17.74 |    33.38 |    42.99 |     0.66
    40 |   2832 |    152 |  2984 |  2666 | 17.65 |    33.54 |    43.03 |     0.66
    41 |   2866 |    154 |  3020 |  2692 | 17.57 |    33.17 |    42.77 |     0.66
    42 |   2872 |    155 |  3027 |  2704 | 17.58 |    33.38 |    42.99 |     0.66
    43 |   2853 |    154 |  3007 |  2684 | 17.58 |    33.92 |    43.53 |     0.66
    44 |   2870 |    155 |  3025 |  2704 | 17.70 |    34.33 |    43.98 |     0.65
    45 |   2891 |    155 |  3046 |  2730 | 17.71 |    33.87 |    43.35 |     0.65
    46 |   2915 |    147 |  3062 |  2743 | 17.83 |    34.23 |    43.83 |     0.66
    47 |   2913 |    148 |  3061 |  2745 | 17.74 |    33.24 |    42.59 |     0.65
    48 |   2899 |    146 |  3045 |  2735 | 17.83 |    33.87 |    43.29 |     0.65
    49 |   2915 |    145 |  3060 |  2743 | 18.09 |    34.86 |    44.50 |     0.66
    50 |   2919 |    145 |  3064 |  2750 | 18.14 |    34.72 |    44.22 |     0.66
    51 |   2874 |    144 |  3018 |  2711 | 18.08 |    34.65 |    44.14 |     0.66
    52 |   2894 |    146 |  3040 |  2734 | 18.07 |    34.25 |    43.63 |     0.65
    53 |   2896 |    147 |  3043 |  2737 | 18.04 |    34.02 |    43.32 |     0.66
    54 |   2900 |    145 |  3045 |  2731 | 17.87 |    33.77 |    43.05 |     0.65
    55 |   2896 |    146 |  3042 |  2726 | 17.97 |    33.94 |    43.33 |     0.66
    56 |   2855 |    147 |  3002 |  2684 | 17.89 |    33.85 |    43.26 |     0.66
    57 |   2831 |    146 |  2977 |  2669 | 17.78 |    33.78 |    43.04 |     0.65
    58 |   2818 |    144 |  2962 |  2649 | 17.73 |    33.27 |    42.35 |     0.65
    59 |   2813 |    146 |  2959 |  2638 | 17.72 |    32.37 |    41.42 |     0.65
    60 |   2796 |    150 |  2946 |  2618 | 17.75 |    32.36 |    41.51 |     0.66
    61 |   2792 |    155 |  2947 |  2610 | 17.79 |    33.39 |    42.80 |     0.65
    62 |   2760 |    155 |  2915 |  2578 | 17.73 |    33.19 |    42.66 |     0.66
    63 |   2735 |    156 |  2891 |  2548 | 17.67 |    33.34 |    42.94 |     0.66
    64 |   2740 |    158 |  2898 |  2556 | 17.63 |    33.08 |    42.63 |     0.66
    65 |   2754 |    160 |  2914 |  2563 | 17.64 |    32.25 |    41.85 |     0.66
    66 |   2747 |    162 |  2909 |  2545 | 17.62 |    31.48 |    41.14 |     0.65
    67 |   2762 |    166 |  2928 |  2563 | 17.73 |    31.86 |    41.58 |     0.65
    68 |   2772 |    168 |  2940 |  2603 | 17.72 |    30.59 |    39.60 |     0.64
    69 |   2783 |    165 |  2948 |  2615 | 17.87 |    31.21 |    40.38 |     0.64
    70 |   2784 |    161 |  2945 |  2626 | 18.05 |    31.93 |    41.01 |     0.64
    71 |   2792 |    163 |  2955 |  2632 | 18.03 |    31.86 |    40.98 |     0.64
    72 |   2807 |    169 |  2976 |  2653 | 18.06 |    31.86 |    41.00 |     0.65
    73 |   2801 |    172 |  2973 |  2671 | 17.74 |    31.13 |    40.02 |     0.65
    74 |   2772 |    180 |  2952 |  2640 | 17.68 |    30.81 |    39.75 |     0.65
    75 |   2767 |    185 |  2952 |  2643 | 17.51 |    30.38 |    39.15 |     0.65
    76 |   2794 |    194 |  2988 |  2654 | 17.42 |    30.69 |    39.75 |     0.65
    77 |   2777 |    199 |  2976 |  2639 | 17.42 |    31.01 |    40.14 |     0.65
    78 |   2753 |    209 |  2962 |  2620 | 17.24 |    30.84 |    39.98 |     0.65
    79 |   2733 |    226 |  2959 |  2607 | 17.18 |    30.81 |    40.04 |     0.65
    80 |   2699 |    235 |  2934 |  2567 | 17.10 |    30.15 |    39.50 |     0.65
    81 |   2620 |    244 |  2864 |  2489 | 17.08 |    30.48 |    40.12 |     0.66
    82 |   2629 |    253 |  2882 |  2504 | 17.25 |    31.24 |    41.06 |     0.66
    83 |   2606 |    269 |  2875 |  2500 | 17.18 |    31.45 |    41.35 |     0.66
    84 |   2629 |    282 |  2911 |  2532 | 17.26 |    31.75 |    41.72 |     0.66
    85 |   2601 |    302 |  2903 |  2512 | 17.22 |    31.80 |    41.92 |     0.66
    86 |   2562 |    332 |  2894 |  2493 | 17.19 |    31.71 |    41.99 |     0.66
    87 |   2550 |    365 |  2915 |  2512 | 17.15 |    31.02 |    41.15 |     0.66
    88 |   2489 |    413 |  2902 |  2488 | 17.25 |    31.07 |    41.40 |     0.66
    89 |   2437 |    467 |  2904 |  2486 | 17.25 |    30.44 |    40.61 |     0.66
    90 |   2358 |    548 |  2906 |  2477 | 17.23 |    30.44 |    40.72 |     0.66
    91 |   2234 |    668 |  2902 |  2457 | 17.25 |    30.41 |    40.81 |     0.66
    92 |   2017 |    837 |  2854 |  2378 | 17.25 |    30.28 |    41.14 |     0.67
    93 |   1744 |   1022 |  2766 |  2249 | 17.15 |    29.87 |    41.14 |     0.67
    94 |   1510 |   1180 |  2690 |  2124 | 17.23 |    29.72 |    41.72 |     0.67
    95 |   1253 |   1295 |  2548 |  1956 | 17.31 |    29.49 |    41.98 |     0.66
    96 |   1018 |   1299 |  2317 |  1744 | 17.18 |    29.22 |    41.95 |     0.66
    97 |    804 |   1298 |  2102 |  1550 | 17.10 |    29.30 |    42.50 |     0.65
    98 |    577 |   1298 |  1875 |  1349 | 16.95 |    28.98 |    42.41 |     0.65
    99 |    315 |   1297 |  1612 |  1108 | 17.00 |    30.02 |    45.06 |     0.65
 --------------------------------------------------------------------------------

 Summary of integration results binned by resolution
 ---------------------------------------------------------------------------------------------------------
 d min | d max | # full | # part | # over | # ice | # sum | # prf | <Ibg> | <I/sigI> | <I/sigI> | <CC prf>
       |       |        |        |        |       |       |       |       |    (sum) |    (prf) |
 ---------------------------------------------------------------------------------------------------------
  1.06 |  1.08 |     32 |      1 |      0 |     0 |    33 |    19 |  4.41 |     1.89 |     3.56 |     0.29
  1.08 |  1.10 |    122 |     13 |      0 |     0 |   135 |    91 |  4.79 |     2.21 |     3.75 |     0.36
  1.10 |  1.12 |    201 |     17 |      0 |     0 |   218 |   163 |  5.29 |     2.17 |     3.79 |     0.35
  1.12 |  1.14 |    326 |     45 |      0 |     0 |   371 |   279 |  5.79 |     2.63 |     4.59 |     0.41
  1.14 |  1.17 |    410 |     51 |      0 |     0 |   461 |   387 |  6.35 |     2.91 |     4.86 |     0.42
  1.17 |  1.19 |    561 |     59 |      0 |     0 |   620 |   515 |  6.96 |     3.40 |     5.69 |     0.46
  1.19 |  1.22 |    797 |     80 |      0 |     0 |   877 |   722 |  7.66 |     3.62 |     6.21 |     0.49
  1.22 |  1.26 |   1047 |    108 |      0 |     0 |  1155 |   970 |  8.46 |     4.20 |     7.17 |     0.54
  1.26 |  1.29 |   1327 |    173 |      0 |     0 |  1500 |  1251 |  9.18 |     4.41 |     7.49 |     0.54
  1.29 |  1.34 |   1441 |    197 |      0 |     0 |  1638 |  1410 |  9.95 |     5.06 |     8.35 |     0.57
  1.34 |  1.38 |   1456 |    189 |      0 |     0 |  1645 |  1443 | 10.75 |     5.55 |     9.08 |     0.59
  1.38 |  1.44 |   1449 |    192 |      0 |     0 |  1641 |  1432 | 11.71 |     6.97 |    11.29 |     0.65
  1.44 |  1.50 |   1475 |    220 |      0 |     0 |  1695 |  1512 | 12.84 |     8.67 |    13.80 |     0.68
  1.50 |  1.58 |   1486 |    194 |      0 |     0 |  1680 |  1509 | 13.99 |    11.69 |    17.56 |     0.72
  1.58 |  1.68 |   1491 |    200 |      0 |     0 |  1691 |  1517 | 15.61 |    15.12 |    21.66 |     0.73
  1.68 |  1.81 |   1490 |    196 |      0 |     0 |  1686 |  1480 | 17.79 |    20.17 |    27.99 |     0.76
  1.81 |  2.00 |   1514 |    183 |      0 |     0 |  1697 |  1487 | 22.54 |    30.80 |    40.80 |     0.79
  2.00 |  2.28 |   1501 |    235 |      0 |     0 |  1736 |  1495 | 29.61 |    47.66 |    61.68 |     0.80
  2.28 |  2.88 |   1537 |    202 |      0 |     0 |  1739 |  1586 | 32.65 |    70.58 |    88.11 |     0.80
  2.88 | 25.50 |   1513 |    211 |      0 |     0 |  1724 |  1676 | 52.68 |   171.78 |   193.58 |     0.80
 ---------------------------------------------------------------------------------------------------------

 Summary of integration results for the whole dataset
 ---------------------------------------------
 Number fully recorded                 | 24420
 Number partially recorded             | 3307
 Number with overloaded pixels         | 3
 Number in powder rings                | 0
 Number processed with summation       | 23942
 Number processed with profile fitting | 20944
 <Ibg>                                 | 18.11
 <I/sigI> (summation)                  | 29.09
 <I/sigI> (profile fitting)            | 38.57
 <CC prf>                              | 0.51
 ---------------------------------------------

Exporting as MTZ

The final step of dials processing is to export the integrated results to mtz format, suitable for input to downstream processing programs such as pointless and aimless. Currently dials.export only supports one experiment at a time, therefore it is necessary to first split the integrated_experiments.json and integrated.pickle into separate files

dials.split_experiments integrated_experiments.json integrated.pickle \
  experiments_prefix=integrated_experiments reflections_prefix=integrated
Saving experiment 0 to integrated_experiments_0.json
Saving reflections for experiment 0 to integrated_0.pickle
Saving experiment 1 to integrated_experiments_1.json
Saving reflections for experiment 1 to integrated_1.pickle

Now we are ready to run dials.export on the individual .pickle and .json files output for each experiment.

dials.export integrated_0.pickle integrated_experiments_0.json mtz.hklout=integrated_0.mtz
dials.export integrated_1.pickle integrated_experiments_1.json mtz.hklout=integrated_1.mtz

And this is the output, showing the reflection file statistics.

Removing 1277 reflections with negative variance
Removing 5057 profile reflections with negative variance
Removing 1153 incomplete reflections
Title: from dials.export
Space group symbol from file: P222
Space group number from file: 16
Space group from matrices: P 2 2 2 (No. 16)
Point group symbol from file: 222
Number of batches: 100
Number of crystals: 1
Number of Miller indices: 20455
Resolution range: 28.8939 1.06627
History:
Crystal 1:
  Name: XTAL
  Project: DIALS
  Id: 1
  Unit cell: (54.1146, 58.298, 66.5347, 90, 90, 90)
  Number of datasets: 1
  Dataset 1:
    Name: FROMDIALS
    Id: 1
    Wavelength: 0.97949
    Number of columns: 14
    label        #valid  %valid       min       max type
    H             20455 100.00%      0.00     32.00 H: index h,k,l
    K             20455 100.00%      0.00     51.00 H: index h,k,l
    L             20455 100.00%      0.00     59.00 H: index h,k,l
    M_ISYM        20455 100.00%      2.00      8.00 Y: M/ISYM, packed partial/reject flag and symmetry number
    BATCH         20455 100.00%      3.00     98.00 B: BATCH number
    IPR           20455 100.00%  -9311.98 174317.56 J: intensity
    SIGIPR        20455 100.00%     24.17    421.85 Q: standard deviation
    I             20455 100.00% -11542.51 174304.84 J: intensity
    SIGI          20455 100.00%     29.08    424.15 Q: standard deviation
    FRACTIONCALC  20455 100.00%      1.00      1.00 R: real
    XDET          20455 100.00%     11.79   2450.61 R: real
    YDET          20455 100.00%      9.78   2515.63 R: real
    ROT           20455 100.00%      0.18      9.62 R: real
    LP            20455 100.00%      0.01      0.86 R: real


Removing 1465 reflections with negative variance
Removing 5318 profile reflections with negative variance
Removing 1317 incomplete reflections
Title: from dials.export
Space group symbol from file: P222
Space group number from file: 16
Space group from matrices: P 2 2 2 (No. 16)
Point group symbol from file: 222
Number of batches: 100
Number of crystals: 1
Number of Miller indices: 19627
Resolution range: 25.491 1.06429
History:
Crystal 1:
  Name: XTAL
  Project: DIALS
  Id: 1
  Unit cell: (54.133, 58.3114, 66.5333, 90, 90, 90)
  Number of datasets: 1
  Dataset 1:
    Name: FROMDIALS
    Id: 1
    Wavelength: 0.97949
    Number of columns: 14
    label        #valid  %valid       min       max type
    H             19627 100.00%      0.00     37.00 H: index h,k,l
    K             19627 100.00%      0.00     53.00 H: index h,k,l
    L             19627 100.00%      0.00     60.00 H: index h,k,l
    M_ISYM        19627 100.00%      1.00      8.00 Y: M/ISYM, packed partial/reject flag and symmetry number
    BATCH         19627 100.00%      4.00     97.00 B: BATCH number
    IPR           19627 100.00% -11344.32 118159.02 J: intensity
    SIGIPR        19627 100.00%     18.96    348.01 Q: standard deviation
    I             19627 100.00% -14248.27 116392.28 J: intensity
    SIGI          19627 100.00%     23.14    347.57 Q: standard deviation
    FRACTIONCALC  19627 100.00%      1.00      1.00 R: real
    XDET          19627 100.00%     10.39   2451.64 R: real
    YDET          19627 100.00%      8.78   2517.64 R: real
    ROT           19627 100.00%      0.21      9.59 R: real
    LP            19627 100.00%      0.02      0.87 R: real

What to do Next

The following demonstrates how to take the output of dials processing and continue with downstream analysis, first using rebatch to ensure that the reflections for each lattice have different batch numbers, and then using pointless to sort the data and assign the correct symmetry, followed by scaling with aimless and intensity analysis using ctruncate:

rebatch hklin integrated_0.mtz hklout rebatch_0.mtz > rebatch_0.log << EOF
batch add 0
EOF

rebatch hklin integrated_1.mtz hklout rebatch_1.mtz > rebatch_1.log << EOF
batch add 200
EOF

pointless hklin rebatch_0.mtz rebatch_1.mtz hklout sorted.mtz > pointless.log

aimless hklin sorted.mtz hklout scaled.mtz > aimless.log << EOF
anomalous off
EOF

ctruncate -hklin scaled.mtz -hklout truncated.mtz \
-colin '/*/*/[IMEAN,SIGIMEAN]' > ctruncate.log

to get merged data for downstream analysis. The output from this will include the merging statistics which will give some idea of the data quality. Often passing in a sensible resolution limit to aimless is also helpful... this should give you something like:

Summary data for        Project: DIALS Crystal: XTAL Dataset: FROMDIALS

                                           Overall  InnerShell  OuterShell
Low resolution limit                       28.89     28.89      1.08
High resolution limit                       1.06      5.83      1.06

Rmerge  (within I+/I-)                     0.034     0.017     0.000
Rmerge  (all I+ and I-)                    0.037     0.018     0.000
Rmeas (within I+/I-)                       0.047     0.024     0.000
Rmeas (all I+ & I-)                        0.051     0.024     0.000
Rpim (within I+/I-)                        0.033     0.017     0.000
Rpim (all I+ & I-)                         0.035     0.016     0.000
Rmerge in top intensity bin                0.022        -         -
Total number of observations               40064       390        51
Total number unique                        31116       285        50
Mean((I)/sd(I))                              7.1      15.8       2.1
Mn(I) half-set correlation CC(1/2)         0.994     0.999     0.000
Completeness                                33.1      42.8       1.1
Multiplicity                                 1.3       1.4       1.0

Anomalous completeness                       5.1       9.5       0.0
Anomalous multiplicity                       0.2       1.2       1.0
DelAnom correlation between half-sets     -0.001     0.000     0.000
Mid-Slope of Anom Normal Probability       0.582       -         -

Estimates of resolution limits: overall
   from half-dataset correlation CC(1/2) >  0.50: limit =  1.08A
   from Mn(I/sd) >  2.00:                         limit =  1.06A  == maximum resolution

Estimates of resolution limits in reciprocal lattice directions:
  Along k axis
   from half-dataset correlation CC(1/2) >  0.50: limit =  1.12A
   from Mn(I/sd) >  2.00:                         limit =  1.06A  == maximum resolution
  Along l axis
   from half-dataset correlation CC(1/2) >  0.50: limit =  1.14A
   from Mn(I/sd) >  2.00:                         limit =  1.12A

Anisotropic deltaB (i.e. range of principal components), A^2:  2.00

Average unit cell:   54.12   58.30   66.53   90.00   90.00   90.00
Space group: P 2 2 2
Average mosaicity:   0.00