SARS-CoV-2 main protease (Mpro)

Introduction

DIALS processing may be performed by either running the individual tools (spot finding, indexing, refinement, integration, symmetry, scaling, exporting to MTZ) or you can run xia2 pipeline=dials, which makes informed choices for you at each stage. In this tutorial we will run through each of the steps in turn, checking the output as we go. We will also enforce the correct lattice symmetry.

Tutorial data

The following example uses raw diffraction data for SARS-CoV-2 main protease in complex with PCM-0102340 collected as part of an XChem crystallographic fragment screening campaign on beamline I04-1 at Diamond Light Source (ID: mpro-x0692 / PDB: 5REL). Images are available for download from https://doi.org/10.5281/zenodo.3730940.

Hint

The data can be found under the directory /dls/i04/data/2020/mx27124-1/Mpro-x0692 on the Diamond computer system. Make a new directory under /dls/i04/data/2020/mx27124-1/processing in which to run processing commands

The data is otherwise available for download from mpro_x0692.

Import

The first stage of step-by-step DIALS processing is to import the data - all that happens here is that metadata are read for all the images, and a file describing their contents (imported.expt) is written:

dials.import /dls/i04/data/2020/mx27124-1/Mpro-x0692/Mpro-x0692_1_0*.cbf

The output just describes what the software understands of the images it was passed, in this case one sequence of data containing 400 images:

DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

input {
  experiments = <image files>
}

--------------------------------------------------------------------------------
  format: <class 'dxtbx.format.FormatCBFMiniPilatus.FormatCBFMiniPilatus'>
  num images: 400
  sequences:
    still:    0
    sweep:    1
  num stills: 0
--------------------------------------------------------------------------------
Writing experiments to imported.expt

Now is a good point to take a first look at the data using the dials.image_viewer, both to check that the data is sensible and to anticipate any problems in processing:

dials.image_viewer imported.expt

You will be presented with the main image viewer screen:

https://dials.github.io/images/mpro_x0692/image_viewer.png

Play with the brightness slider (①) a little until you can clearly see the spots on the first image (something in the range 10-20 should make the spots obvious). You can also change the colour scheme (sometimes spots can be easier to identify in ‘inverted’ mode) , toggle various information markers like beam center, and try different configurations for the spot finding (②).

Find Spots

The first “real” task in any processing using DIALS is the spot finding. Since this is looking for spots on every image in the dataset, this process can take some time, so we request multiple processors (nproc=4) to speed this up:

dials.find_spots imported.expt nproc=4

Show/Hide Log

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

spotfinder {
  mp {
    nproc = 4
  }
}
input {
  experiments = imported.expt
}

Setting spotfinder.filter.min_spot_size=3
Configuring spot finder from input parameters
--------------------------------------------------------------------------------
Finding strong spots in imageset 0
--------------------------------------------------------------------------------


Finding spots in image 1 to 400...
Setting chunksize=20
Extracting strong pixels from images
 Using multiprocessing with 4 parallel job(s)

Found 1424 strong pixels on image 1
Found 1578 strong pixels on image 2
Found 1555 strong pixels on image 3
Found 1634 strong pixels on image 4
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Found 1287 strong pixels on image 400

Extracted 30376 spots
Removed 7811 spots with size < 3 pixels
Removed 3 spots with size > 1000 pixels
Calculated 22562 spot centroids
Calculated 22562 spot intensities
Filtered 21740 of 22562 spots by peak-centroid distance

Histogram of per-image spot count for imageset 0:
21740 spots found on 400 images (max 491 / bin)
**                                                          
*******           * *  * ****    *                          
*********      ** ******************* *                     
********* *  * ***************************** *              
****************************************************       *
************************************************************
************************************************************
************************************************************
************************************************************
************************************************************
1                         image                          400

--------------------------------------------------------------------------------
Saved 21740 reflections to strong.refl

Once this has completed, a new reflection filestrong.refl’ is written, containing a record of every spot found. Having found strong spots open the image viewer again, but giving it the newly found reflection list:

dials.image_viewer imported.expt strong.refl

Adjust the brightness so that you can see the spots, then zoom in so that you can see the clustered individual pixels of a single spot. Pixels determined to be part of a spot’s peak are marked with green dots. The blue outline shows the three-dimensional shoebox - the extents over detector x, y and image number z of a all peak pixels in a single spot. The single highest value pixel for any spot is marked with a pink circle, and the centre of mass is marked with a red cross.

The spot centre-of-mass is usually close to the peak pixel, but slightly offset as the algorithm allows calculation of the spot centre at a better precision than the pixel size and image angular ‘width’.

https://dials.github.io/images/mpro_x0692/image_viewer_spot.png

The default parameters for spot finding usually do a good job for Pilatus images, such as these. However they may not be optimal for data from other detector types, such as CCDs or image plates. Issues with incorrectly set gain might, for example, lead to background noise being extracted as spots. You can use the image mode buttons (③) to preview how the parameters affect the spot finding algorithm. The final image, ‘threshold’ is the one on which spots were found, so ensuring this produces peaks at real diffraction spot positions will give the best chance of success.

Another very powerful tool for investigating problems with strong spot positions is dials.reciprocal_lattice_viewer. This displays the strong spots in 3D, after mapping them from their detector positions to reciprocal space. In a favourable case you should be able to see the crystal’s reciprocal lattice by eye in the strong spot positions. Some practice may be needed in rotating the lattice to an orientation that shows off the periodicity in reciprocal lattice positions:

dials.reciprocal_lattice_viewer imported.expt strong.refl
https://dials.github.io/images/mpro_x0692/reciprocal_lattice_strong.png

Although the reciprocal spacing is visible, in this data, there are clearly some systematic distortions. These will be solved in the indexing.

Indexing

The next step will be indexing of the strong spots by dials.index, which by default uses a 3D FFT algorithm (although the 1D FFT algorithm can be selected, using the parameter indexing.method=fft1d). We pass in all the strong spots found in the dataset:

dials.index imported.expt strong.refl

If known, the space group and unit cell can be provided at this stage using the space_group and unit_cell parameters, and will be used to constrain the lattice during refinement, but otherwise indexing and refinement will be carried out in the primitive lattice using space group P1.

Show/Hide Log

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

input {
  experiments = imported.expt
  reflections = strong.refl
}

Found max_cell: 73.7 Angstrom
Setting d_min: 1.56
FFT gridding: (256,256,256)
Number of centroids used: 20836
Candidate solutions:
+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
| unit_cell                          |   volume |   volume score |   #indexed |   % indexed |   % indexed score |   rmsd_xy |   rmsd_xy score |   overall score |
|------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------|
| 44.74 53.39 62.63 115.1 102.0 90.2 |   131784 |           0.01 |      21005 |          97 |              0    |      0.13 |            0    |            0.01 |
| 44.60 53.25 62.49 115.1 101.8 90.2 |   130920 |           0    |      20874 |          96 |              0.01 |      0.13 |            0.01 |            0.02 |
| 44.60 53.25 62.58 115.0 101.7 90.2 |   131244 |           0.01 |      20815 |          96 |              0.01 |      0.13 |            0.01 |            0.03 |
| 44.60 53.25 62.49 115.0 101.8 90.2 |   130947 |           0    |      20903 |          96 |              0.01 |      0.14 |            0.03 |            0.04 |
| 44.54 53.34 62.54 115.1 101.8 90.2 |   130988 |           0    |      20817 |          96 |              0.01 |      0.14 |            0.04 |            0.06 |
| 44.60 53.25 62.71 115.1 101.8 90.2 |   131302 |           0.01 |      20905 |          96 |              0.01 |      0.14 |            0.05 |            0.06 |
| 44.60 53.41 62.49 115.1 101.8 90.1 |   131333 |           0.01 |      20942 |          96 |              0.01 |      0.14 |            0.05 |            0.06 |
| 44.69 53.41 62.58 64.8 78.1 89.9   |   131615 |           0.01 |      20979 |          97 |              0    |      0.14 |            0.07 |            0.08 |
| 44.74 53.40 62.62 115.1 102.0 90.1 |   131757 |           0.01 |      20988 |          97 |              0    |      0.14 |            0.07 |            0.08 |
| 44.64 53.41 62.55 64.8 78.1 89.9   |   131478 |           0.01 |      20971 |          96 |              0    |      0.14 |            0.07 |            0.08 |
| 44.66 53.34 62.71 64.9 78.1 90.0   |   131699 |           0.01 |      20934 |          96 |              0.01 |      0.14 |            0.07 |            0.09 |
| 44.60 53.17 62.49 115.0 101.8 90.2 |   130748 |           0    |      20887 |          96 |              0.01 |      0.14 |            0.09 |            0.1  |
| 44.60 53.43 62.53 115.0 101.7 90.2 |   131505 |           0.01 |      20977 |          96 |              0    |      0.14 |            0.09 |            0.1  |
| 44.60 53.29 62.49 114.9 101.8 90.2 |   131181 |           0    |      20949 |          96 |              0.01 |      0.14 |            0.1  |            0.11 |
| 44.60 53.41 62.68 115.1 101.8 90.1 |   131653 |           0.01 |      20929 |          96 |              0.01 |      0.14 |            0.1  |            0.12 |
| 44.61 53.34 62.45 115.1 101.7 90.1 |   131143 |           0    |      20978 |          96 |              0    |      0.14 |            0.11 |            0.12 |
| 44.60 53.25 62.47 115.1 101.8 90.2 |   130878 |           0    |      20942 |          96 |              0.01 |      0.14 |            0.12 |            0.13 |
| 44.60 53.40 62.62 64.9 78.1 89.9   |   131446 |           0.01 |      21005 |          97 |              0    |      0.14 |            0.12 |            0.13 |
| 44.69 53.41 62.71 64.9 78.1 89.9   |   131949 |           0.01 |      20942 |          96 |              0.01 |      0.14 |            0.11 |            0.13 |
| 44.74 53.41 62.71 64.9 77.9 89.9   |   132001 |           0.01 |      20924 |          96 |              0.01 |      0.14 |            0.12 |            0.14 |
| 44.60 53.41 62.57 115.2 101.9 90.1 |   131286 |           0.01 |      20982 |          97 |              0    |      0.15 |            0.13 |            0.14 |
| 44.58 53.29 62.53 65.0 78.2 90.0   |   131102 |           0    |      20975 |          96 |              0    |      0.15 |            0.14 |            0.14 |
| 44.60 53.43 62.49 114.9 101.8 90.2 |   131553 |           0.01 |      20964 |          96 |              0    |      0.15 |            0.13 |            0.15 |
| 44.74 53.41 62.57 64.8 78.1 89.9   |   131729 |           0.01 |      20986 |          97 |              0    |      0.15 |            0.13 |            0.15 |
| 44.49 53.41 62.33 115.2 101.5 90.0 |   130749 |           0    |      20972 |          96 |              0    |      0.15 |            0.15 |            0.15 |
| 44.60 53.41 62.71 115.1 101.8 90.1 |   131689 |           0.01 |      20935 |          96 |              0.01 |      0.15 |            0.14 |            0.16 |
| 44.59 53.29 62.39 115.0 101.6 90.1 |   130961 |           0    |      20990 |          97 |              0    |      0.15 |            0.15 |            0.16 |
| 44.74 53.29 62.71 65.0 77.9 90.0   |   131849 |           0.01 |      20950 |          96 |              0.01 |      0.15 |            0.14 |            0.16 |
| 44.59 53.41 62.65 64.8 78.2 90.0   |   131547 |           0.01 |      20966 |          96 |              0    |      0.15 |            0.15 |            0.16 |
| 44.60 53.43 62.71 114.9 101.8 90.2 |   131909 |           0.01 |      20958 |          96 |              0    |      0.15 |            0.15 |            0.16 |
| 44.68 53.40 62.62 115.1 102.0 90.1 |   131574 |           0.01 |      20984 |          97 |              0    |      0.15 |            0.15 |            0.17 |
| 44.60 53.41 62.60 64.8 78.1 89.9   |   131360 |           0.01 |      21022 |          97 |              0    |      0.15 |            0.16 |            0.17 |
| 44.65 53.29 62.37 115.0 101.7 90.1 |   131075 |           0    |      21001 |          97 |              0    |      0.15 |            0.17 |            0.17 |
| 44.69 53.41 62.71 115.1 101.9 90.1 |   131936 |           0.01 |      21025 |          97 |              0    |      0.15 |            0.16 |            0.17 |
| 44.65 53.40 62.53 115.2 101.6 90.2 |   131503 |           0.01 |      20944 |          96 |              0.01 |      0.15 |            0.17 |            0.19 |
| 44.54 53.41 62.57 64.8 78.0 90.0   |   131107 |           0    |      20976 |          96 |              0    |      0.15 |            0.18 |            0.19 |
| 44.60 53.41 62.63 115.0 101.8 90.1 |   131689 |           0.01 |      20899 |          96 |              0.01 |      0.15 |            0.17 |            0.19 |
| 44.61 53.41 62.57 64.8 78.2 89.9   |   131398 |           0.01 |      20985 |          97 |              0    |      0.15 |            0.2  |            0.21 |
| 44.64 53.41 62.71 115.1 101.9 90.0 |   131818 |           0.01 |      20938 |          96 |              0.01 |      0.15 |            0.19 |            0.21 |
| 44.65 53.28 62.36 115.0 101.7 90.1 |   131032 |           0    |      21000 |          97 |              0    |      0.15 |            0.21 |            0.21 |
| 44.60 53.43 62.71 115.2 101.8 90.0 |   131708 |           0.01 |      20936 |          96 |              0.01 |      0.15 |            0.2  |            0.22 |
| 44.49 53.41 62.53 115.2 101.6 90.0 |   131069 |           0    |      20967 |          96 |              0    |      0.15 |            0.21 |            0.22 |
| 44.60 53.43 62.41 115.1 101.8 90.2 |   131138 |           0    |      20999 |          97 |              0    |      0.15 |            0.22 |            0.22 |
| 44.69 53.41 62.57 64.8 78.0 89.9   |   131546 |           0.01 |      20986 |          97 |              0    |      0.15 |            0.21 |            0.22 |
| 44.74 53.29 62.71 114.8 102.1 90.1 |   132052 |           0.01 |      20961 |          96 |              0    |      0.15 |            0.22 |            0.24 |
| 44.65 53.41 62.57 115.2 101.7 90.0 |   131547 |           0.01 |      20990 |          97 |              0    |      0.16 |            0.23 |            0.24 |
| 44.49 53.41 62.71 115.1 101.7 90.0 |   131474 |           0.01 |      20941 |          96 |              0.01 |      0.16 |            0.24 |            0.25 |
| 44.49 53.41 62.57 115.2 101.7 90.0 |   131072 |           0    |      20983 |          97 |              0    |      0.16 |            0.25 |            0.26 |
| 44.49 53.40 62.62 64.9 78.5 90.0   |   131363 |           0.01 |      21005 |          97 |              0    |      0.16 |            0.26 |            0.27 |
| 44.65 53.40 62.62 64.9 78.3 90.0   |   131706 |           0.01 |      21012 |          97 |              0    |      0.16 |            0.27 |            0.29 |
+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
Using d_min_step 0.0

Indexed crystal models:
model 1 (21005 reflections):
Crystal:
    Unit cell: 44.736, 53.392, 62.630, 115.139, 101.959, 90.175
    Space group: P 1
    U matrix:  {{ 0.9000, -0.4121, -0.1421},
                { 0.2959,  0.8170, -0.4949},
                { 0.3200,  0.4034,  0.8572}}
    B matrix:  {{ 0.0224,  0.0000,  0.0000},
                { 0.0001,  0.0187,  0.0000},
                { 0.0053,  0.0090,  0.0181}}
    A = UB:    {{ 0.0193, -0.0090, -0.0026},
                { 0.0041,  0.0108, -0.0090},
                { 0.0117,  0.0153,  0.0155}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21005 |           734 | 96.6%       |
+------------+-------------+---------------+-------------+

################################################################################
Starting refinement (macro-cycle 1)
################################################################################


Summary statistics for 20952 observations matched to predictions:
+-------------------+--------+---------+---------+---------+-------+
|                   |    Min |      Q1 |     Med |      Q3 |   Max |
|-------------------+--------+---------+---------+---------+-------|
| Xc - Xo (mm)      | -1.703 | -0.6229 | -0.3916 | -0.1449 | 2.562 |
| Yc - Yo (mm)      | -2.013 | -0.2842 | -0.2246 | -0.1743 | 2.016 |
| Phic - Phio (deg) |  -7.52 | -0.1586 | 0.00306 |   0.119 | 4.551 |
| X weights         |  224.2 |   360.3 |   383.5 |   397.1 | 405.6 |
| Y weights         |  199.2 |     349 |   376.3 |   394.1 | 405.6 |
| Phi weights       |  33.85 |   47.23 |   47.77 |      48 |    48 |
+-------------------+--------+---------+---------+---------+-------+

Detecting centroid outliers using the Tukey algorithm
2347 reflections have been flagged as outliers
18605 reflections remain in the manager

Summary statistics for 18605 observations matched to predictions:
+-------------------+---------+---------+----------+---------+--------+
|                   |     Min |      Q1 |      Med |      Q3 |    Max |
|-------------------+---------+---------+----------+---------+--------|
| Xc - Xo (mm)      |  -1.684 |  -0.607 |  -0.3968 | -0.1734 | 0.9907 |
| Yc - Yo (mm)      |  -1.068 | -0.2767 |  -0.2246 | -0.1807 | 0.5715 |
| Phic - Phio (deg) | -0.9351 | -0.1436 | 0.001552 |  0.1063 | 0.7571 |
| X weights         |   224.2 |   362.5 |    384.5 |   397.3 |  405.6 |
| Y weights         |   199.2 |   353.2 |    378.6 |   394.9 |  405.6 |
| Phi weights       |   35.84 |   47.27 |    47.76 |      48 |     48 |
+-------------------+---------+---------+----------+---------+--------+

There are 16 parameters to refine against 18605 reflections in 3 dimensions

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18605 | 0.51841  | 0.26874  |    0.22605 |
|      1 |  18605 | 0.1268   | 0.10007  |    0.23108 |
|      2 |  18605 | 0.097838 | 0.098106 |    0.23331 |
|      3 |  18605 | 0.096656 | 0.096297 |    0.23343 |
|      4 |  18605 | 0.096506 | 0.095677 |    0.23386 |
|      5 |  18605 | 0.096504 | 0.095601 |    0.23402 |
|      6 |  18605 | 0.096504 | 0.095596 |    0.23403 |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  18605 |  0.56107 |  0.55579 |    0.46806 |
+-------+--------+----------+----------+------------+

Refined crystal models:
model 1 (21005 reflections):
Crystal:
    Unit cell: 44.630(5), 53.435(7), 62.738(8), 115.2234(14), 101.7872(13), 90.0002(12)
    Space group: P 1
    U matrix:  {{ 0.8996, -0.4114, -0.1464},
                { 0.2938,  0.8183, -0.4940},
                { 0.3230,  0.4014,  0.8570}}
    B matrix:  {{ 0.0224,  0.0000,  0.0000},
                { 0.0000,  0.0187,  0.0000},
                { 0.0052,  0.0090,  0.0181}}
    A = UB:    {{ 0.0194, -0.0090, -0.0026},
                { 0.0040,  0.0108, -0.0089},
                { 0.0117,  0.0153,  0.0155}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21005 |           735 | 96.6%       |
+------------+-------------+---------------+-------------+

Indexed crystal models:
model 1 (21029 reflections):
Crystal:
    Unit cell: 44.630(5), 53.435(7), 62.738(8), 115.2234(14), 101.7872(13), 90.0002(12)
    Space group: P 1
    U matrix:  {{ 0.8996, -0.4114, -0.1464},
                { 0.2938,  0.8183, -0.4940},
                { 0.3230,  0.4014,  0.8570}}
    B matrix:  {{ 0.0224,  0.0000,  0.0000},
                { 0.0000,  0.0187,  0.0000},
                { 0.0052,  0.0090,  0.0181}}
    A = UB:    {{ 0.0194, -0.0090, -0.0026},
                { 0.0040,  0.0108, -0.0089},
                { 0.0117,  0.0153,  0.0155}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21163 |           577 | 97.3%       |
+------------+-------------+---------------+-------------+

################################################################################
Starting refinement (macro-cycle 2)
################################################################################


Summary statistics for 20975 observations matched to predictions:
+-------------------+---------+----------+----------+---------+--------+
|                   |     Min |       Q1 |      Med |      Q3 |    Max |
|-------------------+---------+----------+----------+---------+--------|
| Xc - Xo (mm)      | -0.9265 | -0.04435 | 0.002579 | 0.05266 | 0.6455 |
| Yc - Yo (mm)      |    -1.8 | -0.04679 | 0.003802 | 0.04913 |   2.53 |
| Phic - Phio (deg) |  -8.051 |  -0.1087 |  0.05362 |  0.1561 |   5.29 |
| X weights         |   224.2 |    360.3 |    383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |    376.3 |   394.1 |  405.6 |
| Phi weights       |   33.85 |    47.23 |    47.77 |      48 |     48 |
+-------------------+---------+----------+----------+---------+--------+

Detecting centroid outliers using the Tukey algorithm
2632 reflections have been flagged as outliers
18343 reflections remain in the manager

Summary statistics for 18343 observations matched to predictions:
+-------------------+---------+----------+----------+---------+--------+
|                   |     Min |       Q1 |      Med |      Q3 |    Max |
|-------------------+---------+----------+----------+---------+--------|
| Xc - Xo (mm)      | -0.3699 | -0.03984 | 0.003241 | 0.05068 |  0.344 |
| Yc - Yo (mm)      | -0.3939 | -0.03613 | 0.005551 | 0.04528 | 0.4172 |
| Phic - Phio (deg) | -0.8813 | -0.08308 |  0.05629 |  0.1488 | 0.6562 |
| X weights         |   224.2 |    364.4 |    385.5 |   397.6 |  405.6 |
| Y weights         |   199.2 |    355.6 |      380 |   395.3 |  405.6 |
| Phi weights       |   38.65 |    47.25 |    47.74 |      48 |     48 |
+-------------------+---------+----------+----------+---------+--------+

There are 16 parameters to refine against 18343 reflections in 3 dimensions

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18343 | 0.080738 | 0.083417 |    0.21845 |
|      1 |  18343 | 0.079354 | 0.082036 |    0.22074 |
|      2 |  18343 | 0.07875  | 0.082035 |    0.2202  |
|      3 |  18343 | 0.078446 | 0.082152 |    0.21934 |
|      4 |  18343 | 0.078361 | 0.08228  |    0.21896 |
|      5 |  18343 | 0.078348 | 0.082315 |    0.21889 |
|      6 |  18343 | 0.078347 | 0.082318 |    0.21889 |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  18343 |  0.45551 |  0.47859 |    0.43778 |
+-------+--------+----------+----------+------------+

Refined crystal models:
model 1 (21029 reflections):
Crystal:
    Unit cell: 44.499(5), 53.267(6), 62.550(7), 115.2255(12), 101.7863(11), 89.9931(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2937,  0.8184, -0.4940},
                { 0.3230,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0181}}
    A = UB:    {{ 0.0195, -0.0090, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0155}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21029 |           710 | 96.7%       |
+------------+-------------+---------------+-------------+

Indexed crystal models:
model 1 (21028 reflections):
Crystal:
    Unit cell: 44.499(5), 53.267(6), 62.550(7), 115.2255(12), 101.7863(11), 89.9931(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2937,  0.8184, -0.4940},
                { 0.3230,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0181}}
    A = UB:    {{ 0.0195, -0.0090, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0155}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21054 |           685 | 96.8%       |
+------------+-------------+---------------+-------------+

################################################################################
Starting refinement (macro-cycle 3)
################################################################################


Summary statistics for 20974 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.8873 | -0.04424 |   0.00171 | 0.04794 | 0.6379 |
| Yc - Yo (mm)      |  -1.717 | -0.05087 | -0.001016 | 0.04519 |  2.886 |
| Phic - Phio (deg) |  -8.105 |  -0.1071 |   0.05102 |  0.1496 |  7.001 |
| X weights         |   224.2 |    360.3 |     383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |     376.3 |   394.1 |  405.6 |
| Phi weights       |   33.85 |    47.23 |     47.77 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

Detecting centroid outliers using the Tukey algorithm
2728 reflections have been flagged as outliers
18246 reflections remain in the manager

Summary statistics for 18246 observations matched to predictions:
+-------------------+---------+----------+----------+---------+--------+
|                   |     Min |       Q1 |      Med |      Q3 |    Max |
|-------------------+---------+----------+----------+---------+--------|
| Xc - Xo (mm)      | -0.3408 | -0.03953 | 0.002804 | 0.04673 |  0.307 |
| Yc - Yo (mm)      | -0.3899 | -0.04049 | 0.001011 | 0.04132 |  0.412 |
| Phic - Phio (deg) | -0.8957 | -0.08015 |  0.05445 |  0.1428 | 0.6317 |
| X weights         |   224.2 |    364.5 |    385.5 |   397.6 |  405.6 |
| Y weights         |   199.2 |    355.7 |      380 |   395.4 |  405.6 |
| Phi weights       |   38.65 |    47.25 |    47.74 |      48 |     48 |
+-------------------+---------+----------+----------+---------+--------+

There are 16 parameters to refine against 18246 reflections in 3 dimensions

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18246 | 0.0772   | 0.081515 |    0.21713 |
|      1 |  18246 | 0.076915 | 0.081075 |    0.21844 |
|      2 |  18246 | 0.076743 | 0.081138 |    0.2184  |
|      3 |  18246 | 0.076641 | 0.081227 |    0.21821 |
|      4 |  18246 | 0.076606 | 0.081288 |    0.21809 |
|      5 |  18246 | 0.0766   | 0.081303 |    0.21806 |
|      6 |  18246 | 0.0766   | 0.081305 |    0.21806 |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  18246 |  0.44535 |   0.4727 |    0.43612 |
+-------+--------+----------+----------+------------+

Refined crystal models:
model 1 (21028 reflections):
Crystal:
    Unit cell: 44.444(5), 53.198(6), 62.470(7), 115.2252(12), 101.7854(11), 89.9907(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2936,  0.8184, -0.4940},
                { 0.3229,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0182}}
    A = UB:    {{ 0.0195, -0.0091, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0156}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21028 |           711 | 96.7%       |
+------------+-------------+---------------+-------------+

Indexed crystal models:
model 1 (21028 reflections):
Crystal:
    Unit cell: 44.444(5), 53.198(6), 62.470(7), 115.2252(12), 101.7854(11), 89.9907(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2936,  0.8184, -0.4940},
                { 0.3229,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0182}}
    A = UB:    {{ 0.0195, -0.0091, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0156}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21039 |           700 | 96.8%       |
+------------+-------------+---------------+-------------+

################################################################################
Starting refinement (macro-cycle 4)
################################################################################


Summary statistics for 20974 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.8997 | -0.04434 |  0.001314 | 0.04642 | 0.6643 |
| Yc - Yo (mm)      |   -1.72 |  -0.0511 | -0.001655 | 0.04466 |   3.05 |
| Phic - Phio (deg) |   -8.12 |  -0.1074 |   0.04974 |  0.1479 |  7.662 |
| X weights         |   224.2 |    360.3 |     383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |     376.3 |   394.1 |  405.6 |
| Phi weights       |   31.78 |    47.23 |     47.77 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

Detecting centroid outliers using the Tukey algorithm
2689 reflections have been flagged as outliers
18285 reflections remain in the manager

Summary statistics for 18285 observations matched to predictions:
+-------------------+---------+----------+------------+---------+--------+
|                   |     Min |       Q1 |        Med |      Q3 |    Max |
|-------------------+---------+----------+------------+---------+--------|
| Xc - Xo (mm)      | -0.3321 | -0.03982 |   0.002306 | 0.04524 | 0.3082 |
| Yc - Yo (mm)      | -0.3898 | -0.04183 | -9.738e-05 | 0.04119 | 0.4075 |
| Phic - Phio (deg) | -0.9054 | -0.08134 |    0.05293 |  0.1411 | 0.6249 |
| X weights         |   224.2 |    364.5 |      385.5 |   397.6 |  405.6 |
| Y weights         |   199.2 |    355.6 |        380 |   395.4 |  405.6 |
| Phi weights       |   38.65 |    47.25 |      47.74 |      48 |     48 |
+-------------------+---------+----------+------------+---------+--------+

There are 16 parameters to refine against 18285 reflections in 3 dimensions

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18285 | 0.076424 | 0.081591 |    0.21765 |
|      1 |  18285 | 0.076361 | 0.081373 |    0.21833 |
|      2 |  18285 | 0.076313 | 0.081403 |    0.21832 |
|      3 |  18285 | 0.076281 | 0.081442 |    0.21826 |
|      4 |  18285 | 0.076268 | 0.081466 |    0.21822 |
|      5 |  18285 | 0.076266 | 0.081471 |    0.21821 |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  18285 |  0.44341 |  0.47367 |    0.43642 |
+-------+--------+----------+----------+------------+

Refined crystal models:
model 1 (21028 reflections):
Crystal:
    Unit cell: 44.421(5), 53.170(6), 62.437(7), 115.2250(12), 101.7844(11), 89.9899(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2936,  0.8184, -0.4940},
                { 0.3229,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0182}}
    A = UB:    {{ 0.0195, -0.0091, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0156}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21028 |           711 | 96.7%       |
+------------+-------------+---------------+-------------+

Indexed crystal models:
model 1 (21027 reflections):
Crystal:
    Unit cell: 44.421(5), 53.170(6), 62.437(7), 115.2250(12), 101.7844(11), 89.9899(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2936,  0.8184, -0.4940},
                { 0.3229,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0182}}
    A = UB:    {{ 0.0195, -0.0091, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0156}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21033 |           706 | 96.8%       |
+------------+-------------+---------------+-------------+

################################################################################
Starting refinement (macro-cycle 5)
################################################################################


Summary statistics for 20973 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.9039 | -0.04434 |  0.001238 | 0.04604 | 0.6737 |
| Yc - Yo (mm)      |  -1.721 | -0.05114 | -0.001455 | 0.04477 |  3.104 |
| Phic - Phio (deg) |  -8.136 |  -0.1071 |   0.05018 |  0.1486 |  7.955 |
| X weights         |   224.2 |    360.3 |     383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |     376.3 |   394.1 |  405.6 |
| Phi weights       |   31.78 |    47.23 |     47.77 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

Detecting centroid outliers using the Tukey algorithm
2679 reflections have been flagged as outliers
18294 reflections remain in the manager

Summary statistics for 18294 observations matched to predictions:
+-------------------+---------+----------+------------+---------+--------+
|                   |     Min |       Q1 |        Med |      Q3 |    Max |
|-------------------+---------+----------+------------+---------+--------|
| Xc - Xo (mm)      | -0.3319 | -0.03988 |   0.002168 | 0.04478 | 0.3091 |
| Yc - Yo (mm)      | -0.3894 | -0.04171 | -1.155e-05 | 0.04124 | 0.4076 |
| Phic - Phio (deg) | -0.9195 | -0.08125 |    0.05369 |  0.1407 | 0.6192 |
| X weights         |   224.2 |    364.4 |      385.4 |   397.6 |  405.6 |
| Y weights         |   199.2 |    355.6 |        380 |   395.3 |  405.6 |
| Phi weights       |   38.65 |    47.25 |      47.75 |      48 |     48 |
+-------------------+---------+----------+------------+---------+--------+

There are 16 parameters to refine against 18294 reflections in 3 dimensions

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18294 | 0.076338 | 0.081412 |    0.21795 |
|      1 |  18294 | 0.076296 | 0.081315 |    0.2183  |
|      2 |  18294 | 0.076268 | 0.081329 |    0.21833 |
|      3 |  18294 | 0.076252 | 0.081346 |    0.21832 |
|      4 |  18294 | 0.076246 | 0.081356 |    0.21831 |
|      5 |  18294 | 0.076245 | 0.081358 |    0.2183  |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  18294 |  0.44329 |  0.47301 |    0.43661 |
+-------+--------+----------+----------+------------+

Refined crystal models:
model 1 (21027 reflections):
Crystal:
    Unit cell: 44.412(5), 53.159(6), 62.424(7), 115.2251(12), 101.7837(11), 89.9895(10)
    Space group: P 1
    U matrix:  {{ 0.8997, -0.4112, -0.1464},
                { 0.2936,  0.8184, -0.4940},
                { 0.3229,  0.4015,  0.8570}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0052,  0.0091,  0.0182}}
    A = UB:    {{ 0.0195, -0.0091, -0.0027},
                { 0.0040,  0.0109, -0.0090},
                { 0.0117,  0.0153,  0.0156}}
+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21027 |           712 | 96.7%       |
+------------+-------------+---------------+-------------+
Saving refined experiments to indexed.expt
Saving refined reflections to indexed.refl

If successful, dials.index writes two output data files - an indexed.expt containing the tuned experimental model and determined parameters, and a indexed.refl reflection file, including index data from the best fit.

It is worth reading through this output to understand what the indexing program has done. Note that this log is automatically captured in the file dials.index.log. A more verbose debug log can be generated by adding the ‘-v’ option to a dials command line program, but this is probably only helpful if something has gone wrong and you are trying to track down why.

Inspecting the beginning of the log shows that the indexing step is done at a resolution lower than the full dataset; 1.56 Å:

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Found max_cell: 73.7 Angstrom
Setting d_min: 1.56
FFT gridding: (256,256,256)

The resolution limit of data that can be used in indexing is determined by the size of the 3D FFT grid, and the likely maximum cell dimension. Here we used the default 256³ grid points. These are used to make an initial estimate for the unit cell parameters.

What then follows are ‘macro-cycles’ of refinement where the experimental model is first tuned to get the best possible fit from the data, and then the resolution limit is reduced to cover more data than the previous cycle. 16 parameters of the diffraction geometry are tuned - 6 for the detector, one for beam angle, 3 crystal orientation angles and the 6 triclinic cell parameters.

We see that the first macrocycle of refinement makes a big improvement in the positional RMSDs:

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+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  18605 | 0.51841  | 0.26874  |    0.22605 |
|      1 |  18605 | 0.1268   | 0.10007  |    0.23108 |
|      2 |  18605 | 0.097838 | 0.098106 |    0.23331 |
|      3 |  18605 | 0.096656 | 0.096297 |    0.23343 |
|      4 |  18605 | 0.096506 | 0.095677 |    0.23386 |
|      5 |  18605 | 0.096504 | 0.095601 |    0.23402 |
|      6 |  18605 | 0.096504 | 0.095596 |    0.23403 |
+--------+--------+----------+----------+------------+

Second and subsequent macrocycles are refined using the same number of reflections, but after extending to higher resolution. The RMSDs at the start of each cycle start off worse than at the end of the previous cycle, because the best fit model for lower resolution data is being applied to higher resolution reflections. As long as each macrocyle shows a reduction in RMSDs then refinement is doing its job of extending the applicability of the model out to a new resolution limit, until eventually the highest resolution strong spots have been included. The final macrocycle includes data out to 1.55 Å and produces a final model with RMSDs of 0.076 mm in X, 0.081 mm in Y and 0.218° in φ, corresponding to 0.44 pixels in X, 0.47 pixels in Y and 0.44 image widths in φ.

We also notice from the log that at each macrocycle there were some outliers identified and removed from refinement as resolution increases. Large outliers can dominate refinement using a least squares target, so it is important to be able to remove these. More about this is discussed below in Refinement. It’s also worth checking the total number of reflections that were unable to be assigned an index:

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+------------+-------------+---------------+-------------+
|   Imageset |   # indexed |   # unindexed | % indexed   |
|------------+-------------+---------------+-------------|
|          0 |       21027 |           712 | 96.7%       |
+------------+-------------+---------------+-------------+

because this can be an indication of poor data quality or a sign that more care needs to be taken in selecting the strategy used by dials.index.

After indexing it can be useful to inspect the reciprocal lattice again:

dials.reciprocal_lattice_viewer indexed.expt indexed.refl

Now indexed/unindexed spots are differentiated by colour, and it is possible to see which spots were marked by dials.refine as outliers. If you have a dataset with multiple lattices present, it may be possible to spot them in the unindexed reflections.

In this case, we can see that the refinement has clearly resolved whatever systematic error was causing distortions in the reciprocal space view, and the determined reciprocal unit cell fits the data well:

https://dials.github.io/images/mpro_x0692/reciprocal_lattice_indexed.png

Bravais Lattice Refinement

Since we didn’t know the Bravais lattice before indexing, we can now use dials.refine_bravais_settings to determine likely candidates. This takes the results of the P1 autoindexing and runs refinement with all of the possible Bravais settings applied, allowing you to choose your preferred solution:

dials.refine_bravais_settings indexed.expt indexed.refl

giving a table containing scoring data and unit cell for each Bravais setting:

Chiral space groups corresponding to each Bravais lattice:
aP: P1
mC: C2
+------------+--------------+--------+--------------+----------+-----------+------------------------------------------+----------+---------------+
|   Solution |   Metric fit |   rmsd | min/max cc   |   #spots | lattice   | unit_cell                                |   volume | cb_op         |
|------------+--------------+--------+--------------+----------+-----------+------------------------------------------+----------+---------------|
|   *      2 |       0.0252 |  0.112 | 0.743/0.743  |    18270 | mC        | 44.39  53.14 111.61  90.00  99.76  90.00 |   259466 | a,-b,-a-b-2*c |
|   *      1 |       0      |  0.111 | -/-          |    18292 | aP        | 44.41  53.16  62.42 115.23 101.78  89.99 |   129876 | a,b,c         |
+------------+--------------+--------+--------------+----------+-----------+------------------------------------------+----------+---------------+
* = recommended solution

Saving summary as bravais_summary.json
Saving solution 2 as bravais_setting_2.expt
Saving solution 1 as bravais_setting_1.expt

The scores include the metric fit (in degrees), RMSDs (in mm), and the best and worse correlation coefficients for data related by symmetry elements implied by the lowest symmetry space group from the Bravais setting. This uses the raw spot intensity measurement from the spot- finding procedure (uncorrected and unscaled) but provides a very useful check to see if the data does appear to adhere to the proposed symmetry operators.

A separate bravais_setting_N.expt experiments file is written for each plausible lattice type, corresponding to the solution index. In this example there is only one option other than P1. We choose to continue processing with bravais_setting_2.expt, the C2 solution.

In cases where the change of basis operator to the chosen setting is the identity operator (a,b,c) we can proceed directly to further refinement. However, we notice that the change of basis operator for our chosen solution is a,-b,-a-b-2*c, so it is necessary to reindex the indexed.refl file output by using dials.reindex:

dials.reindex indexed.refl change_of_basis_op=a,-b,-a-b-2*c

This outputs the file reindexed.refl which we now use as input to downstream programs, in place of the original indexed.refl.

Refinement

The model is already refined during indexing, but we can also add explicit refinement steps using dials.refine in here, to use all reflections in refinement rather than a subset and to fit a scan-varying model of the crystal. There are many options to refinement - to show all the options up to and including expert_level=1 use this command:

dials.refine -c -e 1

and descriptions of each of the options can be included by adding -a1 to the command. All of the main DIALS tools have equivalent command-line options to list available options.

To automatically refine a scan-static model followed by a scan-varying model for the crystal we would use the command dials.refine bravais_setting_2.expt reindexed.refl. However to explore the steps in more detail here we will run each stage separately.

To refine a static model including the monoclinic constraints from dials.refine_bravais_settings run:

dials.refine bravais_setting_2.expt reindexed.refl scan_varying=false

Show/Hide Log

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

refinement {
  parameterisation {
    scan_varying = False
  }
}
input {
  experiments = bravais_setting_2.expt
  reflections = reindexed.refl
}

Configuring refiner

Summary statistics for 20973 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.9033 | -0.04466 |  0.001136 | 0.04684 | 0.6841 |
| Yc - Yo (mm)      |  -1.746 | -0.05035 | -0.000477 | 0.04411 |  3.105 |
| Phic - Phio (deg) |  -8.283 |  -0.1058 |   0.05333 |  0.1476 |   8.03 |
| X weights         |   224.2 |    360.3 |     383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |     376.3 |   394.1 |  405.6 |
| Phi weights       |   31.78 |    47.23 |     47.77 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

Detecting centroid outliers using the MCD algorithm
4003 reflections have been flagged as outliers
16970 reflections remain in the manager

Summary statistics for 16970 observations matched to predictions:
+-------------------+---------+----------+----------+---------+--------+
|                   |     Min |       Q1 |      Med |      Q3 |    Max |
|-------------------+---------+----------+----------+---------+--------|
| Xc - Xo (mm)      | -0.3565 | -0.03722 | 0.002704 | 0.04449 | 0.3007 |
| Yc - Yo (mm)      | -0.4479 | -0.03615 | 0.001418 | 0.03843 | 0.4335 |
| Phic - Phio (deg) | -0.8576 | -0.06506 |  0.05966 |  0.1383 | 0.5737 |
| X weights         |   224.2 |    366.5 |    386.7 |     398 |  405.6 |
| Y weights         |   199.2 |    358.1 |    381.8 |     396 |  405.6 |
| Phi weights       |   38.65 |    47.26 |    47.73 |      48 |     48 |
+-------------------+---------+----------+----------+---------+--------+

There are 14 parameters to refine against 16970 reflections in 3 dimensions
Performing refinement of a single Experiment...

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  16970 | 0.069884 | 0.0763   |    0.2106  |
|      1 |  16970 | 0.069813 | 0.075927 |    0.21154 |
|      2 |  16970 | 0.06974  | 0.075885 |    0.21167 |
|      3 |  16970 | 0.069601 | 0.075855 |    0.21191 |
|      4 |  16970 | 0.069488 | 0.075838 |    0.21213 |
|      5 |  16970 | 0.06945  | 0.075835 |    0.2122  |
|      6 |  16970 | 0.069444 | 0.075837 |    0.2122  |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  16970 |  0.40374 |  0.44091 |     0.4244 |
+-------+--------+----------+----------+------------+
Updating predictions for indexed reflections

Final refined crystal model:
Crystal:
    Unit cell: 44.389(5), 53.129(6), 111.588(12), 90.0, 99.7643(11), 90.0
    Space group: C 1 2 1
    U matrix:  {{ 0.8998,  0.4111,  0.1463},
                { 0.2935, -0.8183,  0.4943},
                { 0.3229, -0.4018, -0.8569}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                { 0.0000,  0.0188,  0.0000},
                { 0.0039,  0.0000,  0.0091}}
    A = UB:    {{ 0.0208,  0.0077,  0.0013},
                { 0.0085, -0.0154,  0.0045},
                { 0.0040, -0.0076, -0.0078}}
Saving refined experiments to refined.expt
Saving reflections with updated predictions to refined.refl

This uses all reflections in refinement rather than a subset and provided a small reduction in RMSDs, writing the results out to refined.expt and refined.refl.

However, the refined model is still static over the whole dataset. We may want to do an additional refinement job to fit a more sophisticated model for the crystal, allowing small misset rotations to occur over the course of the scan. There are usually even small changes to the cell dimensions (typically resulting in a net increase in cell volume) caused by exposure to radiation during data collection. To account for both of these effects we can extend our parameterisation to obtain a smoothed scan-varying model for both the crystal orientation and unit cell. This means running a further refinement job starting from the output of the previous job:

dials.refine refined.expt refined.refl scan_varying=true

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

refinement {
  parameterisation {
    scan_varying = True
  }
}
input {
  experiments = refined.expt
  reflections = refined.refl
}

Configuring refiner

Summary statistics for 20972 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.9123 | -0.04532 | 0.0003223 | 0.04463 | 0.6947 |
| Yc - Yo (mm)      |  -1.721 | -0.05091 | -0.001733 | 0.04276 |   2.52 |
| Phic - Phio (deg) |  -8.112 |  -0.1061 |    0.0507 |  0.1453 |  8.366 |
| X weights         |   224.2 |    360.3 |     383.6 |   397.1 |  405.6 |
| Y weights         |   199.2 |    349.1 |     376.3 |   394.1 |  405.6 |
| Phi weights       |   31.78 |    47.23 |     47.77 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

Detecting centroid outliers using the MCD algorithm
4016 reflections have been flagged as outliers
16956 reflections remain in the manager

Summary statistics for 16956 observations matched to predictions:
+-------------------+---------+----------+-----------+---------+--------+
|                   |     Min |       Q1 |       Med |      Q3 |    Max |
|-------------------+---------+----------+-----------+---------+--------|
| Xc - Xo (mm)      | -0.3626 | -0.03764 |  0.002133 | 0.04217 | 0.3164 |
| Yc - Yo (mm)      | -0.4412 | -0.03715 | 0.0001863 | 0.03678 | 0.4934 |
| Phic - Phio (deg) | -0.8769 | -0.06585 |    0.0575 |  0.1367 | 0.5653 |
| X weights         |   224.2 |    366.5 |     386.7 |     398 |  405.6 |
| Y weights         |   222.4 |    358.2 |     381.8 |     396 |  405.6 |
| Phi weights       |   38.65 |    47.26 |     47.73 |      48 |     48 |
+-------------------+---------+----------+-----------+---------+--------+

There are 56 parameters to refine against 16956 reflections in 3 dimensions
Performing refinement of a single Experiment...

Refinement steps:
+--------+--------+----------+----------+------------+
|   Step |   Nref |   RMSD_X |   RMSD_Y |   RMSD_Phi |
|        |        |     (mm) |     (mm) |      (deg) |
|--------+--------+----------+----------+------------|
|      0 |  16956 | 0.069491 | 0.075515 |    0.21224 |
|      1 |  16956 | 0.063336 | 0.061462 |    0.18593 |
|      2 |  16956 | 0.061679 | 0.061136 |    0.17525 |
|      3 |  16956 | 0.058619 | 0.06067  |    0.16096 |
|      4 |  16956 | 0.054825 | 0.05995  |    0.13797 |
|      5 |  16956 | 0.051804 | 0.059035 |    0.11663 |
|      6 |  16956 | 0.050298 | 0.058368 |    0.10889 |
|      7 |  16956 | 0.0497   | 0.058003 |    0.10702 |
|      8 |  16956 | 0.049539 | 0.057894 |    0.10632 |
|      9 |  16956 | 0.049433 | 0.057867 |    0.10621 |
|     10 |  16956 | 0.049326 | 0.05786  |    0.10626 |
|     11 |  16956 | 0.049252 | 0.057867 |    0.10638 |
|     12 |  16956 | 0.049229 | 0.057871 |    0.10645 |
|     13 |  16956 | 0.049228 | 0.05787  |    0.10645 |
+--------+--------+----------+----------+------------+
RMSD no longer decreasing

RMSDs by experiment:
+-------+--------+----------+----------+------------+
|   Exp |   Nref |   RMSD_X |   RMSD_Y |     RMSD_Z |
|    id |        |     (px) |     (px) |   (images) |
|-------+--------+----------+----------+------------|
|     0 |  16956 |  0.28621 |  0.33645 |    0.21291 |
+-------+--------+----------+----------+------------+
Updating predictions for indexed reflections

Final refined crystal model:
Crystal:
    Unit cell: 44.389(5), 53.129(6), 111.588(12), 90.0, 99.7643(11), 90.0
    Space group: C 1 2 1
    U matrix:  {{ 0.8998,  0.4111,  0.1463},
                { 0.2935, -0.8183,  0.4943},
                { 0.3229, -0.4018, -0.8569}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0039, -0.0000,  0.0091}}
    A = UB:    {{ 0.0208,  0.0077,  0.0013},
                { 0.0085, -0.0154,  0.0045},
                { 0.0040, -0.0076, -0.0078}}
    A sampled at 401 scan points
Saving refined experiments to refined.expt
Saving reflections with updated predictions to refined.refl

which writes over the refined.expt and refined.refl from the previous refinement step. By default the scan-varying refinement looks for smooth changes over an interval of 36° intervals, to avoid fitting unphysical models to noise, though this parameter can be tuned. We can use the HTML report, described shortly, to view the results of fitting to smoothly varying crystal cell parameters:

https://dials.github.io/images/mpro_x0692/scan_varying.png

In this tutorial, we see no overall increase in all three cell parameters. If significant cell volume increases had been observed that might be indicative of radiation damage. However we can’t yet conclude that there is no radiation damage from the lack of considerable change observed.

Integration

After the refinement is done the next step is integration, which is performed by the program dials.integrate. Mostly, the default parameters are fine for Pilatus data, which will perform XDS-like 3D profile fitting while using a generalized linear model in order to fit a Poisson-distributed background model. We will also increase the number of processors used to speed the job up.

dials.integrate refined.expt refined.refl nproc=4

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:
integration {
  mp {
    nproc = 4
  }
}
input {
  experiments = refined.expt
  reflections = refined.refl
}


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

Experiments

Models for experiment 0

Beam:
    wavelength: 0.9126
    sample to source direction : {0.00194855,-0,0.999998}
    divergence: 0
    sigma divergence: 0
    polarization normal: {0,1,0}
    polarization fraction: 0.999

Detector:
Panel:
  name: Panel
  type: SENSOR_PAD
  identifier: 
  pixel_size:{0.172,0.172}
  image_size: {2463,2527}
  trusted_range: {-1,94172}
  thickness: 0.32
  material: Si
  mu: 3.21947
  gain: 1
  pedestal: 0
  fast_axis: {0.999994,0.00344821,-0.000187617}
  slow_axis: {0.00344841,-0.999993,0.00105475}
  origin: {-214.209,250.872,-324.763}
  distance: 324.537
  pixel to millimeter strategy: ParallaxCorrectedPxMmStrategy
    mu: 3.21947
    t0: 0.32

Goniometer:
    Rotation axis:   {1,0,0}
    Fixed rotation:  {1,0,0,0,1,0,0,0,1}
    Setting rotation:{1,0,0,0,1,0,0,0,1}

Scan:
    image range:   {1,400}
    oscillation:   {216,0.5}
    exposure time: 0.04

Crystal:
    Unit cell: 44.389(5), 53.129(6), 111.588(12), 90.0, 99.7643(11), 90.0
    Space group: C 1 2 1
    U matrix:  {{ 0.8998,  0.4111,  0.1463},
                { 0.2935, -0.8183,  0.4943},
                { 0.3229, -0.4018, -0.8569}}
    B matrix:  {{ 0.0225,  0.0000,  0.0000},
                {-0.0000,  0.0188,  0.0000},
                { 0.0039, -0.0000,  0.0091}}
    A = UB:    {{ 0.0208,  0.0077,  0.0013},
                { 0.0085, -0.0154,  0.0045},
                { 0.0040, -0.0076, -0.0078}}
    A sampled at 401 scan points

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

Initialising
Processing reference reflections
 read 21740 strong spots
 removing 713 unindexed reflections
 removing 4071 reflections marked as bad for refinement
 using 16956 indexed reflections
 found 4784 junk reflections
 masked neighbouring pixels in 704 shoeboxes

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

Predicting reflections
Prediction type: scan varying crystal prediction
Predicted 198737 reflections
Matching reference spots with predicted reflections
 16956 observed reflections input
 198737 reflections predicted
 8384 reflections matched
 8384 reflections accepted

********************************************************************************
Warning: 8572 reference spots were not matched to predictions
********************************************************************************

Using 8384 / 8384 reflections for sigma calculation
Calculating E.S.D Beam Divergence.
Calculating E.S.D Reflecting Range (mosaicity).
 sigma b: 0.039451 degrees
 sigma m: 0.327789 degrees
================================================================================

Processing reflections

 Processing the following experiments:

 Experiments: 1
 Beams:       1
 Detectors:   1
 Goniometers: 1
 Scans:       1
 Crystals:    1
 Imagesets:   1

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

Modelling reflection profiles

 Split 185 reflections overlapping job boundaries

Memory situation report:
  Available system memory (excluding swap)          : 29.2 GB
  Available swap memory                             :  1.1 GB
  Available system memory (including swap)          : 30.3 GB
  Maximum memory for processing (including swap)    : 27.3 GB
  Maximum memory for processing (excluding swap)    : 26.3 GB
  Memory required per process                       :  0.0 GB
  no memory ulimit set

Processing reflections in the following blocks of images:

 block_size: 20 frames

+-----+---------+--------------+------------+--------------+------------+-----------------+
|   # |   Group |   Frame From |   Frame To |   Angle From |   Angle To |   # Reflections |
|-----+---------+--------------+------------+--------------+------------+-----------------|
|   0 |       0 |            1 |         20 |          216 |        226 |             430 |
|   1 |       0 |           11 |         30 |          221 |        231 |             278 |
|   2 |       0 |           21 |         40 |          226 |        236 |             247 |
|   3 |       0 |           31 |         50 |          231 |        241 |             234 |
|   4 |       0 |           41 |         60 |          236 |        246 |             237 |
|   5 |       0 |           51 |         70 |          241 |        251 |             178 |
|   6 |       0 |           61 |         80 |          246 |        256 |             194 |
|   7 |       0 |           71 |         90 |          251 |        261 |             161 |
|   8 |       0 |           81 |        100 |          256 |        266 |             196 |
|   9 |       0 |           91 |        110 |          261 |        271 |             240 |
|  10 |       0 |          101 |        120 |          266 |        276 |             237 |
|  11 |       0 |          111 |        130 |          271 |        281 |             226 |
|  12 |       0 |          121 |        140 |          276 |        286 |             240 |
|  13 |       0 |          131 |        150 |          281 |        291 |             251 |
|  14 |       0 |          141 |        160 |          286 |        296 |             248 |
|  15 |       0 |          151 |        170 |          291 |        301 |             250 |
|  16 |       0 |          161 |        180 |          296 |        306 |             263 |
|  17 |       0 |          171 |        190 |          301 |        311 |             237 |
|  18 |       0 |          181 |        200 |          306 |        316 |             290 |
|  19 |       0 |          191 |        210 |          311 |        321 |             283 |
|  20 |       0 |          201 |        220 |          316 |        326 |             279 |
|  21 |       0 |          211 |        230 |          321 |        331 |             244 |
|  22 |       0 |          221 |        240 |          326 |        336 |             273 |
|  23 |       0 |          231 |        250 |          331 |        341 |             248 |
|  24 |       0 |          241 |        260 |          336 |        346 |             227 |
|  25 |       0 |          251 |        270 |          341 |        351 |             212 |
|  26 |       0 |          261 |        280 |          346 |        356 |             210 |
|  27 |       0 |          271 |        290 |          351 |        361 |             216 |
|  28 |       0 |          281 |        300 |          356 |        366 |             192 |
|  29 |       0 |          291 |        310 |          361 |        371 |             203 |
|  30 |       0 |          301 |        320 |          366 |        376 |             177 |
|  31 |       0 |          311 |        330 |          371 |        381 |             180 |
|  32 |       0 |          321 |        340 |          376 |        386 |             172 |
|  33 |       0 |          331 |        350 |          381 |        391 |             161 |
|  34 |       0 |          341 |        360 |          386 |        396 |             133 |
|  35 |       0 |          351 |        370 |          391 |        401 |             131 |
|  36 |       0 |          361 |        380 |          396 |        406 |             121 |
|  37 |       0 |          371 |        390 |          401 |        411 |             131 |
|  38 |       0 |          381 |        400 |          406 |        416 |             139 |
+-----+---------+--------------+------------+--------------+------------+-----------------+

 Using multiprocessing with 4 parallel job(s)


 Frames: 1 -> 20

 Number of reflections
  Partial:     79
  Full:        351
  In ice ring: 0
  Total:       430


 Frames: 11 -> 30

 Number of reflections
  Partial:     5
  Full:        273
  In ice ring: 0
  Total:       278


 Frames: 21 -> 40

 Number of reflections
  Partial:     12
  Full:        235
  In ice ring: 0
  Total:       247


 Frames: 31 -> 50

 Number of reflections
  Partial:     21
  Full:        213
  In ice ring: 0
  Total:       234


 Frames: 41 -> 60

 Number of reflections
  Partial:     16
  Full:        221
  In ice ring: 0
  Total:       237


 Frames: 51 -> 70

 Number of reflections
  Partial:     8
  Full:        170
  In ice ring: 0
  Total:       178


 Frames: 61 -> 80

 Number of reflections
  Partial:     4
  Full:        190
  In ice ring: 0
  Total:       194


 Frames: 71 -> 90

 Number of reflections
  Partial:     2
  Full:        159
  In ice ring: 0
  Total:       161


 Frames: 81 -> 100

 Number of reflections
  Partial:     4
  Full:        192
  In ice ring: 0
  Total:       196


 Frames: 91 -> 110

 Number of reflections
  Partial:     12
  Full:        228
  In ice ring: 0
  Total:       240


 Frames: 101 -> 120

 Number of reflections
  Partial:     10
  Full:        227
  In ice ring: 0
  Total:       237


 Frames: 111 -> 130

 Number of reflections
  Partial:     11
  Full:        215
  In ice ring: 0
  Total:       226


 Frames: 121 -> 140

 Number of reflections
  Partial:     7
  Full:        233
  In ice ring: 0
  Total:       240


 Frames: 131 -> 150

 Number of reflections
  Partial:     8
  Full:        243
  In ice ring: 0
  Total:       251


 Frames: 141 -> 160

 Number of reflections
  Partial:     13
  Full:        235
  In ice ring: 0
  Total:       248


 Frames: 151 -> 170

 Number of reflections
  Partial:     11
  Full:        239
  In ice ring: 0
  Total:       250


 Frames: 161 -> 180

 Number of reflections
  Partial:     7
  Full:        256
  In ice ring: 0
  Total:       263


 Frames: 171 -> 190

 Number of reflections
  Partial:     6
  Full:        231
  In ice ring: 0
  Total:       237


 Frames: 181 -> 200

 Number of reflections
  Partial:     24
  Full:        266
  In ice ring: 0
  Total:       290


 Frames: 191 -> 210

 Number of reflections
  Partial:     21
  Full:        262
  In ice ring: 0
  Total:       283


 Frames: 201 -> 220

 Number of reflections
  Partial:     13
  Full:        266
  In ice ring: 0
  Total:       279


 Frames: 211 -> 230

 Number of reflections
  Partial:     5
  Full:        239
  In ice ring: 0
  Total:       244


 Frames: 221 -> 240

 Number of reflections
  Partial:     4
  Full:        269
  In ice ring: 0
  Total:       273


 Frames: 231 -> 250

 Number of reflections
  Partial:     1
  Full:        247
  In ice ring: 0
  Total:       248


 Frames: 241 -> 260

 Number of reflections
  Partial:     1
  Full:        226
  In ice ring: 0
  Total:       227


 Frames: 251 -> 270

 Number of reflections
  Partial:     3
  Full:        209
  In ice ring: 0
  Total:       212


 Frames: 261 -> 280

 Number of reflections
  Partial:     2
  Full:        208
  In ice ring: 0
  Total:       210


 Frames: 271 -> 290

 Number of reflections
  Partial:     4
  Full:        212
  In ice ring: 0
  Total:       216


 Frames: 281 -> 300

 Number of reflections
  Partial:     2
  Full:        190
  In ice ring: 0
  Total:       192


 Frames: 291 -> 310

 Number of reflections
  Partial:     4
  Full:        199
  In ice ring: 0
  Total:       203


 Frames: 301 -> 320

 Number of reflections
  Partial:     12
  Full:        165
  In ice ring: 0
  Total:       177


 Frames: 311 -> 330

 Number of reflections
  Partial:     5
  Full:        175
  In ice ring: 0
  Total:       180


 Frames: 321 -> 340

 Number of reflections
  Partial:     7
  Full:        165
  In ice ring: 0
  Total:       172


 Frames: 331 -> 350

 Number of reflections
  Partial:     5
  Full:        156
  In ice ring: 0
  Total:       161


 Frames: 341 -> 360

 Number of reflections
  Partial:     1
  Full:        132
  In ice ring: 0
  Total:       133


 Frames: 351 -> 370

 Number of reflections
  Partial:     0
  Full:        131
  In ice ring: 0
  Total:       131


 Frames: 361 -> 380

 Number of reflections
  Partial:     0
  Full:        121
  In ice ring: 0
  Total:       121


 Frames: 371 -> 390

 Number of reflections
  Partial:     0
  Full:        131
  In ice ring: 0
  Total:       131


 Frames: 381 -> 400

 Number of reflections
  Partial:     20
  Full:        119
  In ice ring: 0
  Total:       139


 Summary of profile model
+------+-----------+-----------+----------+----------+----------+-----------------+
|   ID |   Profile | Created   |   X (px) |   Y (px) |   Z (im) |   # reflections |
|------+-----------+-----------+----------+----------+----------+-----------------|
|    0 |         0 | True      |    410.5 |   421.17 |        5 |             236 |
|    0 |         1 | True      |   1231.5 |   421.17 |        5 |             269 |
|    0 |         2 | True      |   2052.5 |   421.17 |        5 |             257 |
|    0 |         3 | True      |    410.5 |  1263.5  |        5 |             451 |
|    0 |         4 | True      |   1231.5 |  1263.5  |        5 |             493 |
|    0 |         5 | True      |   2052.5 |  1263.5  |        5 |             450 |
|    0 |         6 | True      |    410.5 |  2105.83 |        5 |             432 |
|    0 |         7 | True      |   1231.5 |  2105.83 |        5 |             472 |
|    0 |         8 | True      |   2052.5 |  2105.83 |        5 |             429 |
|    0 |         9 | True      |    410.5 |   421.17 |       15 |             366 |
|    0 |        10 | True      |   1231.5 |   421.17 |       15 |             415 |
|    0 |        11 | True      |   2052.5 |   421.17 |       15 |             391 |
|    0 |        12 | True      |    410.5 |  1263.5  |       15 |             667 |
|    0 |        13 | True      |   1231.5 |  1263.5  |       15 |             735 |
|    0 |        14 | True      |   2052.5 |  1263.5  |       15 |             674 |
|    0 |        15 | True      |    410.5 |  2105.83 |       15 |             637 |
|    0 |        16 | True      |   1231.5 |  2105.83 |       15 |             701 |
|    0 |        17 | True      |   2052.5 |  2105.83 |       15 |             640 |
|    0 |        18 | True      |    410.5 |   421.17 |       25 |             386 |
|    0 |        19 | True      |   1231.5 |   421.17 |       25 |             438 |
|    0 |        20 | True      |   2052.5 |   421.17 |       25 |             412 |
|    0 |        21 | True      |    410.5 |  1263.5  |       25 |             655 |
|    0 |        22 | True      |   1231.5 |  1263.5  |       25 |             725 |
|    0 |        23 | True      |   2052.5 |  1263.5  |       25 |             670 |
|    0 |        24 | True      |    410.5 |  2105.83 |       25 |             622 |
|    0 |        25 | True      |   1231.5 |  2105.83 |       25 |             690 |
|    0 |        26 | True      |   2052.5 |  2105.83 |       25 |             636 |
|    0 |        27 | True      |    410.5 |   421.17 |       35 |             387 |
|    0 |        28 | True      |   1231.5 |   421.17 |       35 |             436 |
|    0 |        29 | True      |   2052.5 |   421.17 |       35 |             408 |
|    0 |        30 | True      |    410.5 |  1263.5  |       35 |             599 |
|    0 |        31 | True      |   1231.5 |  1263.5  |       35 |             665 |
|    0 |        32 | True      |   2052.5 |  1263.5  |       35 |             617 |
|    0 |        33 | True      |    410.5 |  2105.83 |       35 |             571 |
|    0 |        34 | True      |   1231.5 |  2105.83 |       35 |             634 |
|    0 |        35 | True      |   2052.5 |  2105.83 |       35 |             587 |
|    0 |        36 | True      |    410.5 |   421.17 |       45 |             371 |
|    0 |        37 | True      |   1231.5 |   421.17 |       45 |             415 |
|    0 |        38 | True      |   2052.5 |   421.17 |       45 |             390 |
|    0 |        39 | True      |    410.5 |  1263.5  |       45 |             568 |
|    0 |        40 | True      |   1231.5 |  1263.5  |       45 |             621 |
|    0 |        41 | True      |   2052.5 |  1263.5  |       45 |             576 |
|    0 |        42 | True      |    410.5 |  2105.83 |       45 |             545 |
|    0 |        43 | True      |   1231.5 |  2105.83 |       45 |             597 |
|    0 |        44 | True      |   2052.5 |  2105.83 |       45 |             553 |
|    0 |        45 | True      |    410.5 |   421.17 |       55 |             325 |
|    0 |        46 | True      |   1231.5 |   421.17 |       55 |             369 |
|    0 |        47 | True      |   2052.5 |   421.17 |       55 |             346 |
|    0 |        48 | True      |    410.5 |  1263.5  |       55 |             535 |
|    0 |        49 | True      |   1231.5 |  1263.5  |       55 |             589 |
|    0 |        50 | True      |   2052.5 |  1263.5  |       55 |             544 |
|    0 |        51 | True      |    410.5 |  2105.83 |       55 |             522 |
|    0 |        52 | True      |   1231.5 |  2105.83 |       55 |             575 |
|    0 |        53 | True      |   2052.5 |  2105.83 |       55 |             530 |
|    0 |        54 | True      |    410.5 |   421.17 |       65 |             273 |
|    0 |        55 | True      |   1231.5 |   421.17 |       65 |             305 |
|    0 |        56 | True      |   2052.5 |   421.17 |       65 |             287 |
|    0 |        57 | True      |    410.5 |  1263.5  |       65 |             489 |
|    0 |        58 | True      |   1231.5 |  1263.5  |       65 |             527 |
|    0 |        59 | True      |   2052.5 |  1263.5  |       65 |             484 |
|    0 |        60 | True      |    410.5 |  2105.83 |       65 |             479 |
|    0 |        61 | True      |   1231.5 |  2105.83 |       65 |             517 |
|    0 |        62 | True      |   2052.5 |  2105.83 |       65 |             474 |
|    0 |        63 | True      |    410.5 |   421.17 |       75 |             233 |
|    0 |        64 | True      |   1231.5 |   421.17 |       75 |             263 |
|    0 |        65 | True      |   2052.5 |   421.17 |       75 |             251 |
|    0 |        66 | True      |    410.5 |  1263.5  |       75 |             460 |
|    0 |        67 | True      |   1231.5 |  1263.5  |       75 |             497 |
|    0 |        68 | True      |   2052.5 |  1263.5  |       75 |             457 |
|    0 |        69 | True      |    410.5 |  2105.83 |       75 |             454 |
|    0 |        70 | True      |   1231.5 |  2105.83 |       75 |             491 |
|    0 |        71 | True      |   2052.5 |  2105.83 |       75 |             451 |
|    0 |        72 | True      |    410.5 |   421.17 |       85 |             242 |
|    0 |        73 | True      |   1231.5 |   421.17 |       85 |             263 |
|    0 |        74 | True      |   2052.5 |   421.17 |       85 |             252 |
|    0 |        75 | True      |    410.5 |  1263.5  |       85 |             495 |
|    0 |        76 | True      |   1231.5 |  1263.5  |       85 |             524 |
|    0 |        77 | True      |   2052.5 |  1263.5  |       85 |             488 |
|    0 |        78 | True      |    410.5 |  2105.83 |       85 |             488 |
|    0 |        79 | True      |   1231.5 |  2105.83 |       85 |             517 |
|    0 |        80 | True      |   2052.5 |  2105.83 |       85 |             481 |
|    0 |        81 | True      |    410.5 |   421.17 |       95 |             267 |
|    0 |        82 | True      |   1231.5 |   421.17 |       95 |             287 |
|    0 |        83 | True      |   2052.5 |   421.17 |       95 |             278 |
|    0 |        84 | True      |    410.5 |  1263.5  |       95 |             565 |
|    0 |        85 | True      |   1231.5 |  1263.5  |       95 |             599 |
|    0 |        86 | True      |   2052.5 |  1263.5  |       95 |             556 |
|    0 |        87 | True      |    410.5 |  2105.83 |       95 |             557 |
|    0 |        88 | True      |   1231.5 |  2105.83 |       95 |             591 |
|    0 |        89 | True      |   2052.5 |  2105.83 |       95 |             548 |
|    0 |        90 | True      |    410.5 |   421.17 |      105 |             276 |
|    0 |        91 | True      |   1231.5 |   421.17 |      105 |             295 |
|    0 |        92 | True      |   2052.5 |   421.17 |      105 |             287 |
|    0 |        93 | True      |    410.5 |  1263.5  |      105 |             603 |
|    0 |        94 | True      |   1231.5 |  1263.5  |      105 |             637 |
|    0 |        95 | True      |   2052.5 |  1263.5  |      105 |             591 |
|    0 |        96 | True      |    410.5 |  2105.83 |      105 |             593 |
|    0 |        97 | True      |   1231.5 |  2105.83 |      105 |             627 |
|    0 |        98 | True      |   2052.5 |  2105.83 |      105 |             581 |
|    0 |        99 | True      |    410.5 |   421.17 |      115 |             289 |
|    0 |       100 | True      |   1231.5 |   421.17 |      115 |             310 |
|    0 |       101 | True      |   2052.5 |   421.17 |      115 |             305 |
|    0 |       102 | True      |    410.5 |  1263.5  |      115 |             627 |
|    0 |       103 | True      |   1231.5 |  1263.5  |      115 |             662 |
|    0 |       104 | True      |   2052.5 |  1263.5  |      115 |             614 |
|    0 |       105 | True      |    410.5 |  2105.83 |      115 |             618 |
|    0 |       106 | True      |   1231.5 |  2105.83 |      115 |             653 |
|    0 |       107 | True      |   2052.5 |  2105.83 |      115 |             605 |
|    0 |       108 | True      |    410.5 |   421.17 |      125 |             288 |
|    0 |       109 | True      |   1231.5 |   421.17 |      125 |             313 |
|    0 |       110 | True      |   2052.5 |   421.17 |      125 |             306 |
|    0 |       111 | True      |    410.5 |  1263.5  |      125 |             631 |
|    0 |       112 | True      |   1231.5 |  1263.5  |      125 |             668 |
|    0 |       113 | True      |   2052.5 |  1263.5  |      125 |             619 |
|    0 |       114 | True      |    410.5 |  2105.83 |      125 |             620 |
|    0 |       115 | True      |   1231.5 |  2105.83 |      125 |             657 |
|    0 |       116 | True      |   2052.5 |  2105.83 |      125 |             608 |
|    0 |       117 | True      |    410.5 |   421.17 |      135 |             306 |
|    0 |       118 | True      |   1231.5 |   421.17 |      135 |             326 |
|    0 |       119 | True      |   2052.5 |   421.17 |      135 |             319 |
|    0 |       120 | True      |    410.5 |  1263.5  |      135 |             651 |
|    0 |       121 | True      |   1231.5 |  1263.5  |      135 |             684 |
|    0 |       122 | True      |   2052.5 |  1263.5  |      135 |             636 |
|    0 |       123 | True      |    410.5 |  2105.83 |      135 |             638 |
|    0 |       124 | True      |   1231.5 |  2105.83 |      135 |             671 |
|    0 |       125 | True      |   2052.5 |  2105.83 |      135 |             623 |
|    0 |       126 | True      |    410.5 |   421.17 |      145 |             309 |
|    0 |       127 | True      |   1231.5 |   421.17 |      145 |             331 |
|    0 |       128 | True      |   2052.5 |   421.17 |      145 |             320 |
|    0 |       129 | True      |    410.5 |  1263.5  |      145 |             652 |
|    0 |       130 | True      |   1231.5 |  1263.5  |      145 |             688 |
|    0 |       131 | True      |   2052.5 |  1263.5  |      145 |             637 |
|    0 |       132 | True      |    410.5 |  2105.83 |      145 |             634 |
|    0 |       133 | True      |   1231.5 |  2105.83 |      145 |             670 |
|    0 |       134 | True      |   2052.5 |  2105.83 |      145 |             619 |
|    0 |       135 | True      |    410.5 |   421.17 |      155 |             325 |
|    0 |       136 | True      |   1231.5 |   421.17 |      155 |             342 |
|    0 |       137 | True      |   2052.5 |   421.17 |      155 |             325 |
|    0 |       138 | True      |    410.5 |  1263.5  |      155 |             669 |
|    0 |       139 | True      |   1231.5 |  1263.5  |      155 |             700 |
|    0 |       140 | True      |   2052.5 |  1263.5  |      155 |             640 |
|    0 |       141 | True      |    410.5 |  2105.83 |      155 |             647 |
|    0 |       142 | True      |   1231.5 |  2105.83 |      155 |             678 |
|    0 |       143 | True      |   2052.5 |  2105.83 |      155 |             618 |
|    0 |       144 | True      |    410.5 |   421.17 |      165 |             334 |
|    0 |       145 | True      |   1231.5 |   421.17 |      165 |             354 |
|    0 |       146 | True      |   2052.5 |   421.17 |      165 |             336 |
|    0 |       147 | True      |    410.5 |  1263.5  |      165 |             677 |
|    0 |       148 | True      |   1231.5 |  1263.5  |      165 |             710 |
|    0 |       149 | True      |   2052.5 |  1263.5  |      165 |             649 |
|    0 |       150 | True      |    410.5 |  2105.83 |      165 |             652 |
|    0 |       151 | True      |   1231.5 |  2105.83 |      165 |             685 |
|    0 |       152 | True      |   2052.5 |  2105.83 |      165 |             624 |
|    0 |       153 | True      |    410.5 |   421.17 |      175 |             345 |
|    0 |       154 | True      |   1231.5 |   421.17 |      175 |             360 |
|    0 |       155 | True      |   2052.5 |   421.17 |      175 |             338 |
|    0 |       156 | True      |    410.5 |  1263.5  |      175 |             677 |
|    0 |       157 | True      |   1231.5 |  1263.5  |      175 |             706 |
|    0 |       158 | True      |   2052.5 |  1263.5  |      175 |             641 |
|    0 |       159 | True      |    410.5 |  2105.83 |      175 |             653 |
|    0 |       160 | True      |   1231.5 |  2105.83 |      175 |             682 |
|    0 |       161 | True      |   2052.5 |  2105.83 |      175 |             617 |
|    0 |       162 | True      |    410.5 |   421.17 |      185 |             366 |
|    0 |       163 | True      |   1231.5 |   421.17 |      185 |             385 |
|    0 |       164 | True      |   2052.5 |   421.17 |      185 |             364 |
|    0 |       165 | True      |    410.5 |  1263.5  |      185 |             697 |
|    0 |       166 | True      |   1231.5 |  1263.5  |      185 |             729 |
|    0 |       167 | True      |   2052.5 |  1263.5  |      185 |             669 |
|    0 |       168 | True      |    410.5 |  2105.83 |      185 |             666 |
|    0 |       169 | True      |   1231.5 |  2105.83 |      185 |             698 |
|    0 |       170 | True      |   2052.5 |  2105.83 |      185 |             638 |
|    0 |       171 | True      |    410.5 |   421.17 |      195 |             395 |
|    0 |       172 | True      |   1231.5 |   421.17 |      195 |             425 |
|    0 |       173 | True      |   2052.5 |   421.17 |      195 |             402 |
|    0 |       174 | True      |    410.5 |  1263.5  |      195 |             702 |
|    0 |       175 | True      |   1231.5 |  1263.5  |      195 |             746 |
|    0 |       176 | True      |   2052.5 |  1263.5  |      195 |             684 |
|    0 |       177 | True      |    410.5 |  2105.83 |      195 |             657 |
|    0 |       178 | True      |   1231.5 |  2105.83 |      195 |             699 |
|    0 |       179 | True      |   2052.5 |  2105.83 |      195 |             637 |
|    0 |       180 | True      |    410.5 |   421.17 |      205 |             394 |
|    0 |       181 | True      |   1231.5 |   421.17 |      205 |             433 |
|    0 |       182 | True      |   2052.5 |   421.17 |      205 |             416 |
|    0 |       183 | True      |    410.5 |  1263.5  |      205 |             692 |
|    0 |       184 | True      |   1231.5 |  1263.5  |      205 |             743 |
|    0 |       185 | True      |   2052.5 |  1263.5  |      205 |             691 |
|    0 |       186 | True      |    410.5 |  2105.83 |      205 |             638 |
|    0 |       187 | True      |   1231.5 |  2105.83 |      205 |             684 |
|    0 |       188 | True      |   2052.5 |  2105.83 |      205 |             632 |
|    0 |       189 | True      |    410.5 |   421.17 |      215 |             409 |
|    0 |       190 | True      |   1231.5 |   421.17 |      215 |             455 |
|    0 |       191 | True      |   2052.5 |   421.17 |      215 |             442 |
|    0 |       192 | True      |    410.5 |  1263.5  |      215 |             688 |
|    0 |       193 | True      |   1231.5 |  1263.5  |      215 |             748 |
|    0 |       194 | True      |   2052.5 |  1263.5  |      215 |             707 |
|    0 |       195 | True      |    410.5 |  2105.83 |      215 |             621 |
|    0 |       196 | True      |   1231.5 |  2105.83 |      215 |             673 |
|    0 |       197 | True      |   2052.5 |  2105.83 |      215 |             632 |
|    0 |       198 | True      |    410.5 |   421.17 |      225 |             409 |
|    0 |       199 | True      |   1231.5 |   421.17 |      225 |             453 |
|    0 |       200 | True      |   2052.5 |   421.17 |      225 |             444 |
|    0 |       201 | True      |    410.5 |  1263.5  |      225 |             682 |
|    0 |       202 | True      |   1231.5 |  1263.5  |      225 |             741 |
|    0 |       203 | True      |   2052.5 |  1263.5  |      225 |             711 |
|    0 |       204 | True      |    410.5 |  2105.83 |      225 |             610 |
|    0 |       205 | True      |   1231.5 |  2105.83 |      225 |             660 |
|    0 |       206 | True      |   2052.5 |  2105.83 |      225 |             630 |
|    0 |       207 | True      |    410.5 |   421.17 |      235 |             428 |
|    0 |       208 | True      |   1231.5 |   421.17 |      235 |             469 |
|    0 |       209 | True      |   2052.5 |   421.17 |      235 |             462 |
|    0 |       210 | True      |    410.5 |  1263.5  |      235 |             689 |
|    0 |       211 | True      |   1231.5 |  1263.5  |      235 |             749 |
|    0 |       212 | True      |   2052.5 |  1263.5  |      235 |             722 |
|    0 |       213 | True      |    410.5 |  2105.83 |      235 |             615 |
|    0 |       214 | True      |   1231.5 |  2105.83 |      235 |             666 |
|    0 |       215 | True      |   2052.5 |  2105.83 |      235 |             639 |
|    0 |       216 | True      |    410.5 |   421.17 |      245 |             396 |
|    0 |       217 | True      |   1231.5 |   421.17 |      245 |             438 |
|    0 |       218 | True      |   2052.5 |   421.17 |      245 |             429 |
|    0 |       219 | True      |    410.5 |  1263.5  |      245 |             642 |
|    0 |       220 | True      |   1231.5 |  1263.5  |      245 |             702 |
|    0 |       221 | True      |   2052.5 |  1263.5  |      245 |             678 |
|    0 |       222 | True      |    410.5 |  2105.83 |      245 |             590 |
|    0 |       223 | True      |   1231.5 |  2105.83 |      245 |             643 |
|    0 |       224 | True      |   2052.5 |  2105.83 |      245 |             619 |
|    0 |       225 | True      |    410.5 |   421.17 |      255 |             364 |
|    0 |       226 | True      |   1231.5 |   421.17 |      255 |             400 |
|    0 |       227 | True      |   2052.5 |   421.17 |      255 |             389 |
|    0 |       228 | True      |    410.5 |  1263.5  |      255 |             598 |
|    0 |       229 | True      |   1231.5 |  1263.5  |      255 |             649 |
|    0 |       230 | True      |   2052.5 |  1263.5  |      255 |             625 |
|    0 |       231 | True      |    410.5 |  2105.83 |      255 |             566 |
|    0 |       232 | True      |   1231.5 |  2105.83 |      255 |             611 |
|    0 |       233 | True      |   2052.5 |  2105.83 |      255 |             587 |
|    0 |       234 | True      |    410.5 |   421.17 |      265 |             330 |
|    0 |       235 | True      |   1231.5 |   421.17 |      265 |             371 |
|    0 |       236 | True      |   2052.5 |   421.17 |      265 |             359 |
|    0 |       237 | True      |    410.5 |  1263.5  |      265 |             553 |
|    0 |       238 | True      |   1231.5 |  1263.5  |      265 |             605 |
|    0 |       239 | True      |   2052.5 |  1263.5  |      265 |             583 |
|    0 |       240 | True      |    410.5 |  2105.83 |      265 |             528 |
|    0 |       241 | True      |   1231.5 |  2105.83 |      265 |             577 |
|    0 |       242 | True      |   2052.5 |  2105.83 |      265 |             555 |
|    0 |       243 | True      |    410.5 |   421.17 |      275 |             332 |
|    0 |       244 | True      |   1231.5 |   421.17 |      275 |             366 |
|    0 |       245 | True      |   2052.5 |   421.17 |      275 |             356 |
|    0 |       246 | True      |    410.5 |  1263.5  |      275 |             539 |
|    0 |       247 | True      |   1231.5 |  1263.5  |      275 |             586 |
|    0 |       248 | True      |   2052.5 |  1263.5  |      275 |             568 |
|    0 |       249 | True      |    410.5 |  2105.83 |      275 |             517 |
|    0 |       250 | True      |   1231.5 |  2105.83 |      275 |             562 |
|    0 |       251 | True      |   2052.5 |  2105.83 |      275 |             544 |
|    0 |       252 | True      |    410.5 |   421.17 |      285 |             338 |
|    0 |       253 | True      |   1231.5 |   421.17 |      285 |             376 |
|    0 |       254 | True      |   2052.5 |   421.17 |      285 |             366 |
|    0 |       255 | True      |    410.5 |  1263.5  |      285 |             535 |
|    0 |       256 | True      |   1231.5 |  1263.5  |      285 |             589 |
|    0 |       257 | True      |   2052.5 |  1263.5  |      285 |             573 |
|    0 |       258 | True      |    410.5 |  2105.83 |      285 |             518 |
|    0 |       259 | True      |   1231.5 |  2105.83 |      285 |             570 |
|    0 |       260 | True      |   2052.5 |  2105.83 |      285 |             554 |
|    0 |       261 | True      |    410.5 |   421.17 |      295 |             338 |
|    0 |       262 | True      |   1231.5 |   421.17 |      295 |             371 |
|    0 |       263 | True      |   2052.5 |   421.17 |      295 |             360 |
|    0 |       264 | True      |    410.5 |  1263.5  |      295 |             520 |
|    0 |       265 | True      |   1231.5 |  1263.5  |      295 |             570 |
|    0 |       266 | True      |   2052.5 |  1263.5  |      295 |             554 |
|    0 |       267 | True      |    410.5 |  2105.83 |      295 |             512 |
|    0 |       268 | True      |   1231.5 |  2105.83 |      295 |             560 |
|    0 |       269 | True      |   2052.5 |  2105.83 |      295 |             544 |
|    0 |       270 | True      |    410.5 |   421.17 |      305 |             316 |
|    0 |       271 | True      |   1231.5 |   421.17 |      305 |             348 |
|    0 |       272 | True      |   2052.5 |   421.17 |      305 |             334 |
|    0 |       273 | True      |    410.5 |  1263.5  |      305 |             491 |
|    0 |       274 | True      |   1231.5 |  1263.5  |      305 |             538 |
|    0 |       275 | True      |   2052.5 |  1263.5  |      305 |             519 |
|    0 |       276 | True      |    410.5 |  2105.83 |      305 |             486 |
|    0 |       277 | True      |   1231.5 |  2105.83 |      305 |             531 |
|    0 |       278 | True      |   2052.5 |  2105.83 |      305 |             512 |
|    0 |       279 | True      |    410.5 |   421.17 |      315 |             289 |
|    0 |       280 | True      |   1231.5 |   421.17 |      315 |             320 |
|    0 |       281 | True      |   2052.5 |   421.17 |      315 |             308 |
|    0 |       282 | True      |    410.5 |  1263.5  |      315 |             458 |
|    0 |       283 | True      |   1231.5 |  1263.5  |      315 |             506 |
|    0 |       284 | True      |   2052.5 |  1263.5  |      315 |             489 |
|    0 |       285 | True      |    410.5 |  2105.83 |      315 |             454 |
|    0 |       286 | True      |   1231.5 |  2105.83 |      315 |             502 |
|    0 |       287 | True      |   2052.5 |  2105.83 |      315 |             485 |
|    0 |       288 | True      |    410.5 |   421.17 |      325 |             269 |
|    0 |       289 | True      |   1231.5 |   421.17 |      325 |             297 |
|    0 |       290 | True      |   2052.5 |   421.17 |      325 |             286 |
|    0 |       291 | True      |    410.5 |  1263.5  |      325 |             442 |
|    0 |       292 | True      |   1231.5 |  1263.5  |      325 |             484 |
|    0 |       293 | True      |   2052.5 |  1263.5  |      325 |             468 |
|    0 |       294 | True      |    410.5 |  2105.83 |      325 |             439 |
|    0 |       295 | True      |   1231.5 |  2105.83 |      325 |             481 |
|    0 |       296 | True      |   2052.5 |  2105.83 |      325 |             465 |
|    0 |       297 | True      |    410.5 |   421.17 |      335 |             250 |
|    0 |       298 | True      |   1231.5 |   421.17 |      335 |             274 |
|    0 |       299 | True      |   2052.5 |   421.17 |      335 |             265 |
|    0 |       300 | True      |    410.5 |  1263.5  |      335 |             413 |
|    0 |       301 | True      |   1231.5 |  1263.5  |      335 |             453 |
|    0 |       302 | True      |   2052.5 |  1263.5  |      335 |             440 |
|    0 |       303 | True      |    410.5 |  2105.83 |      335 |             411 |
|    0 |       304 | True      |   1231.5 |  2105.83 |      335 |             451 |
|    0 |       305 | True      |   2052.5 |  2105.83 |      335 |             438 |
|    0 |       306 | True      |    410.5 |   421.17 |      345 |             240 |
|    0 |       307 | True      |   1231.5 |   421.17 |      345 |             256 |
|    0 |       308 | True      |   2052.5 |   421.17 |      345 |             248 |
|    0 |       309 | True      |    410.5 |  1263.5  |      345 |             392 |
|    0 |       310 | True      |   1231.5 |  1263.5  |      345 |             420 |
|    0 |       311 | True      |   2052.5 |  1263.5  |      345 |             409 |
|    0 |       312 | True      |    410.5 |  2105.83 |      345 |             392 |
|    0 |       313 | True      |   1231.5 |  2105.83 |      345 |             420 |
|    0 |       314 | True      |   2052.5 |  2105.83 |      345 |             409 |
|    0 |       315 | True      |    410.5 |   421.17 |      355 |             220 |
|    0 |       316 | True      |   1231.5 |   421.17 |      355 |             233 |
|    0 |       317 | True      |   2052.5 |   421.17 |      355 |             227 |
|    0 |       318 | True      |    410.5 |  1263.5  |      355 |             353 |
|    0 |       319 | True      |   1231.5 |  1263.5  |      355 |             379 |
|    0 |       320 | True      |   2052.5 |  1263.5  |      355 |             373 |
|    0 |       321 | True      |    410.5 |  2105.83 |      355 |             353 |
|    0 |       322 | True      |   1231.5 |  2105.83 |      355 |             379 |
|    0 |       323 | True      |   2052.5 |  2105.83 |      355 |             373 |
|    0 |       324 | True      |    410.5 |   421.17 |      365 |             213 |
|    0 |       325 | True      |   1231.5 |   421.17 |      365 |             226 |
|    0 |       326 | True      |   2052.5 |   421.17 |      365 |             222 |
|    0 |       327 | True      |    410.5 |  1263.5  |      365 |             344 |
|    0 |       328 | True      |   1231.5 |  1263.5  |      365 |             370 |
|    0 |       329 | True      |   2052.5 |  1263.5  |      365 |             366 |
|    0 |       330 | True      |    410.5 |  2105.83 |      365 |             344 |
|    0 |       331 | True      |   1231.5 |  2105.83 |      365 |             370 |
|    0 |       332 | True      |   2052.5 |  2105.83 |      365 |             366 |
|    0 |       333 | True      |    410.5 |   421.17 |      375 |             208 |
|    0 |       334 | True      |   1231.5 |   421.17 |      375 |             217 |
|    0 |       335 | True      |   2052.5 |   421.17 |      375 |             211 |
|    0 |       336 | True      |    410.5 |  1263.5  |      375 |             337 |
|    0 |       337 | True      |   1231.5 |  1263.5  |      375 |             358 |
|    0 |       338 | True      |   2052.5 |  1263.5  |      375 |             352 |
|    0 |       339 | True      |    410.5 |  2105.83 |      375 |             337 |
|    0 |       340 | True      |   1231.5 |  2105.83 |      375 |             358 |
|    0 |       341 | True      |   2052.5 |  2105.83 |      375 |             352 |
|    0 |       342 | True      |    410.5 |   421.17 |      385 |             184 |
|    0 |       343 | True      |   1231.5 |   421.17 |      385 |             191 |
|    0 |       344 | True      |   2052.5 |   421.17 |      385 |             186 |
|    0 |       345 | True      |    410.5 |  1263.5  |      385 |             295 |
|    0 |       346 | True      |   1231.5 |  1263.5  |      385 |             313 |
|    0 |       347 | True      |   2052.5 |  1263.5  |      385 |             308 |
|    0 |       348 | True      |    410.5 |  2105.83 |      385 |             295 |
|    0 |       349 | True      |   1231.5 |  2105.83 |      385 |             313 |
|    0 |       350 | True      |   2052.5 |  2105.83 |      385 |             308 |
|    0 |       351 | True      |    410.5 |   421.17 |      395 |             113 |
|    0 |       352 | True      |   1231.5 |   421.17 |      395 |             115 |
|    0 |       353 | True      |   2052.5 |   421.17 |      395 |             113 |
|    0 |       354 | True      |    410.5 |  1263.5  |      395 |             177 |
|    0 |       355 | True      |   1231.5 |  1263.5  |      395 |             184 |
|    0 |       356 | True      |   2052.5 |  1263.5  |      395 |             182 |
|    0 |       357 | True      |    410.5 |  2105.83 |      395 |             177 |
|    0 |       358 | True      |   1231.5 |  2105.83 |      395 |             184 |
|    0 |       359 | True      |   2052.5 |  2105.83 |      395 |             182 |
+------+-----------+-----------+----------+----------+----------+-----------------+


Timing information for reference profile formation
+-------------------+---------------+
| Read time         | 60.15 seconds |
| Extract time      | 0.45 seconds  |
| Pre-process time  | 0.02 seconds  |
| Process time      | 8.99 seconds  |
| Post-process time | 0.00 seconds  |
| Total time        | 70.25 seconds |
+-------------------+---------------+

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

Integrating reflections

 Split 11110 reflections overlapping job boundaries

Memory situation report:
  Available system memory (excluding swap)          : 29.2 GB
  Available swap memory                             :  1.1 GB
  Available system memory (including swap)          : 30.3 GB
  Maximum memory for processing (including swap)    : 27.3 GB
  Maximum memory for processing (excluding swap)    : 26.3 GB
  Memory required per process                       :  0.2 GB
  no memory ulimit set

Processing reflections in the following blocks of images:

 block_size: 24 frames

+-----+---------+--------------+------------+--------------+------------+-----------------+
|   # |   Group |   Frame From |   Frame To |   Angle From |   Angle To |   # Reflections |
|-----+---------+--------------+------------+--------------+------------+-----------------|
|   0 |       0 |            1 |         24 |          216 |        228 |           10086 |
|   1 |       0 |           13 |         36 |          222 |        234 |            6194 |
|   2 |       0 |           25 |         48 |          228 |        240 |            6224 |
|   3 |       0 |           37 |         60 |          234 |        246 |            6366 |
|   4 |       0 |           49 |         72 |          240 |        252 |            6148 |
|   5 |       0 |           61 |         84 |          246 |        258 |            6262 |
|   6 |       0 |           73 |         96 |          252 |        264 |            6376 |
|   7 |       0 |           85 |        108 |          258 |        270 |            6109 |
|   8 |       0 |           97 |        120 |          264 |        276 |            6232 |
|   9 |       0 |          109 |        132 |          270 |        282 |            6215 |
|  10 |       0 |          121 |        144 |          276 |        288 |            6157 |
|  11 |       0 |          133 |        156 |          282 |        294 |            6152 |
|  12 |       0 |          145 |        168 |          288 |        300 |            6174 |
|  13 |       0 |          157 |        180 |          294 |        306 |            6150 |
|  14 |       0 |          169 |        192 |          300 |        312 |            6143 |
|  15 |       0 |          181 |        204 |          306 |        318 |            6160 |
|  16 |       0 |          193 |        216 |          312 |        324 |            6194 |
|  17 |       0 |          205 |        228 |          318 |        330 |            6158 |
|  18 |       0 |          217 |        240 |          324 |        336 |            6138 |
|  19 |       0 |          229 |        252 |          330 |        342 |            6172 |
|  20 |       0 |          241 |        264 |          336 |        348 |            6210 |
|  21 |       0 |          253 |        276 |          342 |        354 |            6148 |
|  22 |       0 |          265 |        288 |          348 |        360 |            6204 |
|  23 |       0 |          277 |        300 |          354 |        366 |            6200 |
|  24 |       0 |          289 |        312 |          360 |        372 |            6147 |
|  25 |       0 |          301 |        324 |          366 |        378 |            6199 |
|  26 |       0 |          313 |        336 |          372 |        384 |            6179 |
|  27 |       0 |          325 |        348 |          378 |        390 |            6181 |
|  28 |       0 |          337 |        360 |          384 |        396 |            6161 |
|  29 |       0 |          349 |        372 |          390 |        402 |            6228 |
|  30 |       0 |          361 |        384 |          396 |        408 |            6161 |
|  31 |       0 |          373 |        396 |          402 |        414 |            4973 |
|  32 |       0 |          385 |        400 |          408 |        416 |            7001 |
+-----+---------+--------------+------------+--------------+------------+-----------------+

 Using multiprocessing with 4 parallel job(s)


 Frames: 0 -> 24

 Number of reflections
  Partial:     2500
  Full:        7586
  In ice ring: 0
  Integrate:   10086
  Total:       10086


 Frames: 12 -> 36

 Number of reflections
  Partial:     418
  Full:        5776
  In ice ring: 0
  Integrate:   6194
  Total:       6194


 Frames: 24 -> 48

 Number of reflections
  Partial:     415
  Full:        5809
  In ice ring: 0
  Integrate:   6224
  Total:       6224


 Frames: 36 -> 60

 Number of reflections
  Partial:     465
  Full:        5901
  In ice ring: 0
  Integrate:   6366
  Total:       6366


 Frames: 48 -> 72

 Number of reflections
  Partial:     408
  Full:        5740
  In ice ring: 0
  Integrate:   6148
  Total:       6148


 Frames: 60 -> 84

 Number of reflections
  Partial:     430
  Full:        5832
  In ice ring: 0
  Integrate:   6262
  Total:       6262


 Frames: 72 -> 96

 Number of reflections
  Partial:     419
  Full:        5957
  In ice ring: 0
  Integrate:   6376
  Total:       6376


 Frames: 84 -> 108

 Number of reflections
  Partial:     401
  Full:        5708
  In ice ring: 0
  Integrate:   6109
  Total:       6109


 Frames: 96 -> 120

 Number of reflections
  Partial:     403
  Full:        5829
  In ice ring: 0
  Integrate:   6232
  Total:       6232


 Frames: 108 -> 132

 Number of reflections
  Partial:     399
  Full:        5816
  In ice ring: 0
  Integrate:   6215
  Total:       6215


 Frames: 120 -> 144

 Number of reflections
  Partial:     410
  Full:        5747
  In ice ring: 0
  Integrate:   6157
  Total:       6157


 Frames: 132 -> 156

 Number of reflections
  Partial:     403
  Full:        5749
  In ice ring: 0
  Integrate:   6152
  Total:       6152


 Frames: 144 -> 168

 Number of reflections
  Partial:     426
  Full:        5748
  In ice ring: 0
  Integrate:   6174
  Total:       6174


 Frames: 156 -> 180

 Number of reflections
  Partial:     421
  Full:        5729
  In ice ring: 0
  Integrate:   6150
  Total:       6150


 Frames: 168 -> 192

 Number of reflections
  Partial:     415
  Full:        5728
  In ice ring: 0
  Integrate:   6143
  Total:       6143


 Frames: 180 -> 204

 Number of reflections
  Partial:     397
  Full:        5763
  In ice ring: 0
  Integrate:   6160
  Total:       6160


 Frames: 192 -> 216

 Number of reflections
  Partial:     412
  Full:        5782
  In ice ring: 0
  Integrate:   6194
  Total:       6194


 Frames: 204 -> 228

 Number of reflections
  Partial:     403
  Full:        5755
  In ice ring: 0
  Integrate:   6158
  Total:       6158


 Frames: 216 -> 240

 Number of reflections
  Partial:     366
  Full:        5772
  In ice ring: 0
  Integrate:   6138
  Total:       6138


 Frames: 228 -> 252

 Number of reflections
  Partial:     388
  Full:        5784
  In ice ring: 0
  Integrate:   6172
  Total:       6172


 Frames: 240 -> 264

 Number of reflections
  Partial:     421
  Full:        5789
  In ice ring: 0
  Integrate:   6210
  Total:       6210


 Frames: 252 -> 276

 Number of reflections
  Partial:     387
  Full:        5761
  In ice ring: 0
  Integrate:   6148
  Total:       6148


 Frames: 264 -> 288

 Number of reflections
  Partial:     415
  Full:        5789
  In ice ring: 0
  Integrate:   6204
  Total:       6204


 Frames: 276 -> 300

 Number of reflections
  Partial:     410
  Full:        5790
  In ice ring: 0
  Integrate:   6200
  Total:       6200


 Frames: 288 -> 312

 Number of reflections
  Partial:     398
  Full:        5749
  In ice ring: 0
  Integrate:   6147
  Total:       6147


 Frames: 300 -> 324

 Number of reflections
  Partial:     406
  Full:        5793
  In ice ring: 0
  Integrate:   6199
  Total:       6199


 Frames: 312 -> 336

 Number of reflections
  Partial:     420
  Full:        5759
  In ice ring: 0
  Integrate:   6179
  Total:       6179


 Frames: 324 -> 348

 Number of reflections
  Partial:     406
  Full:        5775
  In ice ring: 0
  Integrate:   6181
  Total:       6181


 Frames: 336 -> 360

 Number of reflections
  Partial:     421
  Full:        5740
  In ice ring: 0
  Integrate:   6161
  Total:       6161


 Frames: 348 -> 372

 Number of reflections
  Partial:     440
  Full:        5788
  In ice ring: 0
  Integrate:   6228
  Total:       6228


 Frames: 360 -> 384

 Number of reflections
  Partial:     402
  Full:        5759
  In ice ring: 0
  Integrate:   6161
  Total:       6161


 Frames: 372 -> 396

 Number of reflections
  Partial:     190
  Full:        4783
  In ice ring: 0
  Integrate:   4973
  Total:       4973


 Frames: 384 -> 400

 Number of reflections
  Partial:     2606
  Full:        4395
  In ice ring: 0
  Integrate:   7001
  Total:       7001


 Summary vs image number
+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
|   ID |   Image |   # full |   # part |   # over |   # ice |   # sum |   # prf |   Ibg |   I/sigI |   I/sigI |   CC prf |   RMSD XY |
|      |         |          |          |          |         |         |         |       |    (sum) |    (prf) |          |           |
|------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------|
|    0 |       1 |        0 |     1530 |        0 |       0 |    1287 |     376 |  0.2  |     0.58 |     1.96 |     0.54 |      0.65 |
|    0 |       2 |        8 |      466 |        0 |       0 |     385 |     383 |  0.22 |     1.56 |     1.73 |     0.54 |      0.44 |
|    0 |       3 |      301 |      193 |        0 |       0 |     427 |     421 |  0.2  |     1.73 |     1.84 |     0.54 |      0.4  |
|    0 |       4 |      389 |       86 |        0 |       0 |     396 |     388 |  0.21 |     1.71 |     1.74 |     0.54 |      0.39 |
|    0 |       5 |      448 |       35 |        0 |       0 |     406 |     402 |  0.2  |     1.76 |     1.73 |     0.53 |      0.39 |
|    0 |       6 |      507 |       24 |        0 |       0 |     449 |     446 |  0.21 |     1.74 |     1.8  |     0.54 |      0.38 |
|    0 |       7 |      487 |       30 |        0 |       0 |     427 |     417 |  0.19 |     1.5  |     1.56 |     0.53 |      0.4  |
|    0 |       8 |      547 |       16 |        0 |       0 |     463 |     458 |  0.2  |     1.45 |     1.43 |     0.54 |      0.38 |
|    0 |       9 |      495 |       24 |        0 |       0 |     422 |     412 |  0.22 |     1.8  |     1.83 |     0.56 |      0.37 |
|    0 |      10 |      430 |        9 |        0 |       0 |     366 |     359 |  0.22 |     2.03 |     2.13 |     0.56 |      0.38 |
|    0 |      11 |      450 |        6 |        0 |       0 |     387 |     376 |  0.2  |     0.91 |     1.02 |     0.53 |      0.38 |
|    0 |      12 |      496 |        4 |        0 |       0 |     436 |     423 |  0.21 |     1.8  |     1.96 |     0.54 |      0.39 |
|    0 |      13 |      504 |       18 |        0 |       0 |     447 |     437 |  0.2  |     1.53 |     1.59 |     0.54 |      0.36 |
|    0 |      14 |      491 |       19 |        0 |       0 |     442 |     433 |  0.22 |     1.95 |     1.99 |     0.56 |      0.38 |
|    0 |      15 |      451 |       20 |        0 |       0 |     403 |     388 |  0.21 |     1.43 |     1.6  |     0.55 |      0.38 |
|    0 |      16 |      473 |       28 |        0 |       0 |     426 |     410 |  0.22 |     2.09 |     2.22 |     0.54 |      0.38 |
|    0 |      17 |      510 |       18 |        0 |       0 |     448 |     435 |  0.23 |     1.98 |     2.04 |     0.56 |      0.37 |
|    0 |      18 |      501 |       33 |        0 |       0 |     423 |     411 |  0.21 |     1.6  |     1.67 |     0.54 |      0.37 |
|    0 |      19 |      494 |       42 |        0 |       0 |     431 |     420 |  0.21 |     1.5  |     1.65 |     0.54 |      0.37 |
|    0 |      20 |      510 |       40 |        0 |       0 |     488 |     471 |  0.22 |     2.06 |     2.25 |     0.56 |      0.38 |
|    0 |      21 |      488 |       30 |        0 |       0 |     447 |     436 |  0.23 |     1.93 |     2.27 |     0.56 |      0.37 |
|    0 |      22 |      475 |       29 |        0 |       0 |     414 |     407 |  0.21 |     1.84 |     1.88 |     0.55 |      0.38 |
|    0 |      23 |      471 |       29 |        0 |       0 |     422 |     410 |  0.22 |     1.89 |     1.99 |     0.55 |      0.39 |
|    0 |      24 |      469 |       14 |        0 |       0 |     399 |     391 |  0.2  |     1.84 |     1.9  |     0.54 |      0.4  |
|    0 |      25 |      494 |       19 |        0 |       0 |     440 |     427 |  0.21 |     1.96 |     2    |     0.54 |      0.39 |
|    0 |      26 |      498 |       15 |        0 |       0 |     435 |     427 |  0.21 |     2.43 |     2.56 |     0.55 |      0.37 |
|    0 |      27 |      468 |       25 |        0 |       0 |     421 |     413 |  0.22 |     2    |     1.99 |     0.55 |      0.42 |
|    0 |      28 |      469 |       53 |        0 |       0 |     416 |     394 |  0.21 |     1.73 |     2.03 |     0.55 |      0.4  |
|    0 |      29 |      470 |       35 |        0 |       0 |     423 |     408 |  0.21 |     1.82 |     2.04 |     0.55 |      0.4  |
|    0 |      30 |      474 |       64 |        0 |       0 |     449 |     428 |  0.22 |     1.85 |     2.18 |     0.55 |      0.38 |
|    0 |      31 |      450 |       73 |        0 |       0 |     460 |     434 |  0.21 |     1.63 |     1.75 |     0.55 |      0.4  |
|    0 |      32 |      473 |       39 |        0 |       0 |     444 |     431 |  0.2  |     1.47 |     1.45 |     0.54 |      0.41 |
|    0 |      33 |      520 |       36 |        0 |       0 |     461 |     445 |  0.22 |     2.63 |     2.85 |     0.55 |      0.39 |
|    0 |      34 |      487 |       36 |        0 |       0 |     431 |     419 |  0.21 |     1.78 |     1.97 |     0.55 |      0.41 |
|    0 |      35 |      511 |       17 |        0 |       0 |     449 |     438 |  0.21 |     2.01 |     2.19 |     0.53 |      0.39 |
|    0 |      36 |      491 |       22 |        0 |       0 |     427 |     418 |  0.21 |     2.63 |     2.74 |     0.54 |      0.39 |
|    0 |      37 |      485 |       30 |        0 |       0 |     425 |     411 |  0.2  |     1.54 |     1.65 |     0.53 |      0.4  |
|    0 |      38 |      469 |       33 |        0 |       0 |     430 |     414 |  0.2  |     1.43 |     1.55 |     0.53 |      0.41 |
|    0 |      39 |      488 |       55 |        0 |       0 |     446 |     428 |  0.2  |     1.6  |     1.78 |     0.54 |      0.4  |
|    0 |      40 |      486 |       29 |        0 |       0 |     437 |     423 |  0.2  |     2.1  |     2.22 |     0.54 |      0.39 |
|    0 |      41 |      474 |       50 |        0 |       0 |     453 |     429 |  0.19 |     1.41 |     1.42 |     0.53 |      0.39 |
|    0 |      42 |      474 |       76 |        0 |       0 |     421 |     411 |  0.2  |     2.21 |     2.7  |     0.53 |      0.39 |
|    0 |      43 |      486 |       62 |        0 |       0 |     466 |     439 |  0.19 |     1.4  |     1.52 |     0.53 |      0.41 |
|    0 |      44 |      489 |       51 |        0 |       0 |     439 |     417 |  0.2  |     2.3  |     2.6  |     0.54 |      0.4  |
|    0 |      45 |      504 |       47 |        0 |       0 |     429 |     415 |  0.19 |     1.83 |     2.09 |     0.53 |      0.4  |
|    0 |      46 |      487 |       26 |        0 |       0 |     417 |     404 |  0.19 |     1.66 |     1.72 |     0.53 |      0.41 |
|    0 |      47 |      488 |       23 |        0 |       0 |     436 |     424 |  0.2  |     2.53 |     2.67 |     0.53 |      0.39 |
|    0 |      48 |      504 |       62 |        0 |       0 |     455 |     437 |  0.19 |     1.81 |     1.99 |     0.53 |      0.39 |
|    0 |      49 |      504 |       33 |        0 |       0 |     445 |     430 |  0.19 |     2.08 |     2.16 |     0.52 |      0.41 |
|    0 |      50 |      495 |       21 |        0 |       0 |     446 |     426 |  0.19 |     1.57 |     1.52 |     0.52 |      0.4  |
|    0 |      51 |      475 |        7 |        0 |       0 |     414 |     405 |  0.19 |     2.18 |     2.35 |     0.52 |      0.43 |
|    0 |      52 |      495 |       38 |        0 |       0 |     462 |     442 |  0.18 |     1.5  |     1.64 |     0.52 |      0.41 |
|    0 |      53 |      495 |       64 |        0 |       0 |     471 |     449 |  0.18 |     1.28 |     1.44 |     0.52 |      0.44 |
|    0 |      54 |      477 |       70 |        0 |       0 |     463 |     445 |  0.19 |     1.92 |     2.15 |     0.53 |      0.42 |
|    0 |      55 |      465 |       74 |        0 |       0 |     459 |     427 |  0.18 |     1.42 |     1.43 |     0.51 |      0.44 |
|    0 |      56 |      504 |       57 |        0 |       0 |     473 |     448 |  0.19 |     1.88 |     2.16 |     0.52 |      0.42 |
|    0 |      57 |      483 |       69 |        0 |       0 |     469 |     440 |  0.18 |     1.06 |     1.3  |     0.52 |      0.43 |
|    0 |      58 |      461 |       69 |        0 |       0 |     455 |     427 |  0.18 |     1.86 |     2.15 |     0.52 |      0.45 |
|    0 |      59 |      501 |       38 |        0 |       0 |     463 |     437 |  0.17 |     1.45 |     1.56 |     0.51 |      0.44 |
|    0 |      60 |      489 |       21 |        0 |       0 |     428 |     413 |  0.17 |     1.38 |     1.63 |     0.5  |      0.43 |
|    0 |      61 |      497 |       43 |        0 |       0 |     449 |     424 |  0.17 |     1.58 |     1.73 |     0.51 |      0.43 |
|    0 |      62 |      463 |       32 |        0 |       0 |     431 |     410 |  0.17 |     1.35 |     1.54 |     0.51 |      0.43 |
|    0 |      63 |      462 |       26 |        0 |       0 |     422 |     413 |  0.17 |     1.2  |     1.18 |     0.5  |      0.43 |
|    0 |      64 |      498 |       80 |        0 |       0 |     474 |     447 |  0.17 |     1.43 |     1.71 |     0.51 |      0.47 |
|    0 |      65 |      460 |       28 |        0 |       0 |     412 |     396 |  0.16 |     0.89 |     0.89 |     0.49 |      0.46 |
|    0 |      66 |      465 |       37 |        0 |       0 |     424 |     404 |  0.17 |     1.26 |     1.49 |     0.5  |      0.44 |
|    0 |      67 |      480 |       60 |        0 |       0 |     442 |     419 |  0.17 |     1.47 |     1.51 |     0.51 |      0.43 |
|    0 |      68 |      513 |       26 |        0 |       0 |     464 |     454 |  0.19 |     1.92 |     2.31 |     0.52 |      0.41 |
|    0 |      69 |      499 |       49 |        0 |       0 |     454 |     444 |  0.18 |     1.66 |     1.81 |     0.51 |      0.44 |
|    0 |      70 |      528 |       35 |        0 |       0 |     474 |     458 |  0.18 |     1.48 |     1.65 |     0.51 |      0.43 |
|    0 |      71 |      506 |       28 |        0 |       0 |     444 |     424 |  0.17 |     1.75 |     1.8  |     0.51 |      0.43 |
|    0 |      72 |      476 |       32 |        0 |       0 |     439 |     423 |  0.17 |     1.17 |     1.23 |     0.5  |      0.43 |
|    0 |      73 |      478 |       19 |        0 |       0 |     407 |     400 |  0.16 |     1.55 |     1.63 |     0.49 |      0.44 |
|    0 |      74 |      496 |       28 |        0 |       0 |     450 |     441 |  0.16 |     1.43 |     1.49 |     0.49 |      0.44 |
|    0 |      75 |      482 |       22 |        0 |       0 |     441 |     428 |  0.17 |     1.24 |     1.35 |     0.49 |      0.45 |
|    0 |      76 |      458 |       27 |        0 |       0 |     422 |     403 |  0.18 |     1.99 |     2.29 |     0.5  |      0.45 |
|    0 |      77 |      485 |       59 |        0 |       0 |     428 |     410 |  0.17 |     1.64 |     1.93 |     0.5  |      0.45 |
|    0 |      78 |      448 |       68 |        0 |       0 |     436 |     389 |  0.16 |     1.41 |     1.65 |     0.49 |      0.5  |
|    0 |      79 |      500 |       71 |        0 |       0 |     470 |     440 |  0.17 |     1.41 |     1.58 |     0.5  |      0.44 |
|    0 |      80 |      479 |       59 |        0 |       0 |     460 |     430 |  0.16 |     1.27 |     1.56 |     0.5  |      0.48 |
|    0 |      81 |      521 |       37 |        0 |       0 |     475 |     457 |  0.16 |     1.18 |     1.15 |     0.5  |      0.45 |
|    0 |      82 |      548 |       21 |        0 |       0 |     473 |     459 |  0.18 |     1.45 |     1.53 |     0.5  |      0.43 |
|    0 |      83 |      463 |       13 |        0 |       0 |     421 |     412 |  0.16 |     1.26 |     1.32 |     0.49 |      0.45 |
|    0 |      84 |      494 |       26 |        0 |       0 |     434 |     423 |  0.17 |     1.34 |     1.47 |     0.49 |      0.44 |
|    0 |      85 |      454 |       46 |        0 |       0 |     428 |     400 |  0.18 |     1.81 |     2.11 |     0.5  |      0.48 |
|    0 |      86 |      467 |       24 |        0 |       0 |     437 |     421 |  0.17 |     1.59 |     1.82 |     0.5  |      0.43 |
|    0 |      87 |      443 |       28 |        0 |       0 |     394 |     377 |  0.17 |     1.78 |     1.96 |     0.5  |      0.44 |
|    0 |      88 |      502 |       45 |        0 |       0 |     462 |     442 |  0.16 |     1.43 |     1.63 |     0.5  |      0.43 |
|    0 |      89 |      544 |       71 |        0 |       0 |     513 |     491 |  0.17 |     1.61 |     1.86 |     0.5  |      0.44 |
|    0 |      90 |      502 |       50 |        0 |       0 |     478 |     453 |  0.16 |     1.17 |     1.17 |     0.49 |      0.45 |
|    0 |      91 |      490 |       50 |        0 |       0 |     459 |     434 |  0.16 |     1.25 |     1.38 |     0.5  |      0.44 |
|    0 |      92 |      461 |       37 |        0 |       0 |     415 |     401 |  0.17 |     1.84 |     2.09 |     0.5  |      0.44 |
|    0 |      93 |      450 |       38 |        0 |       0 |     420 |     405 |  0.16 |     1.37 |     1.48 |     0.5  |      0.46 |
|    0 |      94 |      493 |       22 |        0 |       0 |     446 |     434 |  0.16 |     1.69 |     1.9  |     0.5  |      0.44 |
|    0 |      95 |      447 |       26 |        0 |       0 |     411 |     398 |  0.16 |     1.2  |     1.4  |     0.49 |      0.42 |
|    0 |      96 |      520 |       28 |        0 |       0 |     440 |     431 |  0.16 |     1.47 |     1.49 |     0.49 |      0.42 |
|    0 |      97 |      521 |       34 |        0 |       0 |     482 |     460 |  0.16 |     1.34 |     1.47 |     0.5  |      0.42 |
|    0 |      98 |      489 |       24 |        0 |       0 |     433 |     418 |  0.16 |     1.52 |     1.48 |     0.49 |      0.43 |
|    0 |      99 |      475 |       32 |        0 |       0 |     417 |     405 |  0.16 |     1.7  |     2.05 |     0.49 |      0.45 |
|    0 |     100 |      500 |       35 |        0 |       0 |     435 |     417 |  0.17 |     1.14 |     1.62 |     0.49 |      0.44 |
|    0 |     101 |      456 |       51 |        0 |       0 |     431 |     415 |  0.17 |     1.29 |     1.52 |     0.5  |      0.43 |
|    0 |     102 |      416 |       55 |        0 |       0 |     398 |     367 |  0.17 |     1.72 |     1.61 |     0.5  |      0.51 |
|    0 |     103 |      537 |       52 |        0 |       0 |     503 |     475 |  0.16 |     1.8  |     1.95 |     0.49 |      0.44 |
|    0 |     104 |      501 |       66 |        0 |       0 |     474 |     457 |  0.15 |     1.41 |     1.65 |     0.5  |      0.45 |
|    0 |     105 |      469 |       27 |        0 |       0 |     424 |     411 |  0.16 |     1.43 |     1.5  |     0.49 |      0.43 |
|    0 |     106 |      507 |       21 |        0 |       0 |     448 |     439 |  0.15 |     1.29 |     1.29 |     0.49 |      0.47 |
|    0 |     107 |      446 |       43 |        0 |       0 |     412 |     389 |  0.16 |     1.2  |     1.13 |     0.5  |      0.44 |
|    0 |     108 |      470 |       23 |        0 |       0 |     420 |     405 |  0.17 |     1.23 |     1.19 |     0.5  |      0.44 |
|    0 |     109 |      511 |       16 |        0 |       0 |     449 |     431 |  0.15 |     1.1  |     1.47 |     0.48 |      0.46 |
|    0 |     110 |      481 |       52 |        0 |       0 |     456 |     435 |  0.16 |     1.83 |     1.91 |     0.5  |      0.45 |
|    0 |     111 |      551 |       75 |        0 |       0 |     485 |     463 |  0.15 |     1.2  |     1.49 |     0.49 |      0.45 |
|    0 |     112 |      438 |       22 |        0 |       0 |     394 |     376 |  0.16 |     1.4  |     1.4  |     0.5  |      0.43 |
|    0 |     113 |      454 |       37 |        0 |       0 |     402 |     388 |  0.16 |     1.54 |     1.87 |     0.5  |      0.42 |
|    0 |     114 |      452 |       67 |        0 |       0 |     438 |     408 |  0.16 |     1.16 |     1.19 |     0.5  |      0.46 |
|    0 |     115 |      519 |       55 |        0 |       0 |     496 |     477 |  0.15 |     1.47 |     1.64 |     0.49 |      0.45 |
|    0 |     116 |      537 |       33 |        0 |       0 |     481 |     467 |  0.15 |     1.45 |     1.49 |     0.49 |      0.47 |
|    0 |     117 |      436 |       31 |        0 |       0 |     407 |     396 |  0.16 |     1.29 |     1.51 |     0.49 |      0.46 |
|    0 |     118 |      450 |       25 |        0 |       0 |     415 |     403 |  0.16 |     1.24 |     1.47 |     0.5  |      0.42 |
|    0 |     119 |      507 |       16 |        0 |       0 |     440 |     433 |  0.15 |     1.18 |     1.13 |     0.49 |      0.43 |
|    0 |     120 |      487 |       37 |        0 |       0 |     419 |     398 |  0.14 |     0.92 |     1.24 |     0.47 |      0.48 |
|    0 |     121 |      506 |       13 |        0 |       0 |     439 |     426 |  0.15 |     1.35 |     1.31 |     0.49 |      0.44 |
|    0 |     122 |      464 |       11 |        0 |       0 |     409 |     401 |  0.17 |     1.52 |     1.61 |     0.5  |      0.42 |
|    0 |     123 |      502 |       28 |        0 |       0 |     434 |     421 |  0.15 |     1.39 |     1.31 |     0.49 |      0.44 |
|    0 |     124 |      448 |       38 |        0 |       0 |     408 |     384 |  0.15 |     1.15 |     1.77 |     0.49 |      0.45 |
|    0 |     125 |      498 |       73 |        0 |       0 |     488 |     462 |  0.15 |     1.29 |     1.4  |     0.5  |      0.46 |
|    0 |     126 |      462 |       42 |        0 |       0 |     422 |     404 |  0.16 |     1.39 |     1.42 |     0.5  |      0.44 |
|    0 |     127 |      500 |       72 |        0 |       0 |     480 |     447 |  0.15 |     1.41 |     1.89 |     0.48 |      0.49 |
|    0 |     128 |      477 |       49 |        0 |       0 |     425 |     417 |  0.16 |     1.42 |     2.02 |     0.49 |      0.44 |
|    0 |     129 |      461 |       43 |        0 |       0 |     425 |     414 |  0.15 |     1.3  |     1.49 |     0.49 |      0.43 |
|    0 |     130 |      469 |       62 |        0 |       0 |     434 |     403 |  0.15 |     1.56 |     1.54 |     0.49 |      0.44 |
|    0 |     131 |      516 |       24 |        0 |       0 |     445 |     434 |  0.15 |     1.1  |     1.1  |     0.48 |      0.45 |
|    0 |     132 |      479 |       43 |        0 |       0 |     435 |     418 |  0.15 |     1.14 |     1.41 |     0.49 |      0.46 |
|    0 |     133 |      470 |       36 |        0 |       0 |     412 |     398 |  0.16 |     1.19 |     1.39 |     0.49 |      0.43 |
|    0 |     134 |      494 |       34 |        0 |       0 |     427 |     418 |  0.15 |     1.25 |     1.1  |     0.49 |      0.43 |
|    0 |     135 |      462 |       32 |        0 |       0 |     413 |     401 |  0.15 |     0.99 |     1.19 |     0.48 |      0.43 |
|    0 |     136 |      486 |       69 |        0 |       0 |     434 |     419 |  0.16 |     1.09 |     1.23 |     0.48 |      0.46 |
|    0 |     137 |      474 |       54 |        0 |       0 |     452 |     435 |  0.16 |     1.2  |     1.55 |     0.5  |      0.44 |
|    0 |     138 |      479 |       61 |        0 |       0 |     445 |     417 |  0.15 |     1.25 |     1.4  |     0.49 |      0.47 |
|    0 |     139 |      479 |       86 |        0 |       0 |     456 |     436 |  0.14 |     1.07 |     1    |     0.49 |      0.46 |
|    0 |     140 |      450 |       33 |        0 |       0 |     425 |     413 |  0.15 |     1.46 |     1.65 |     0.49 |      0.44 |
|    0 |     141 |      488 |       42 |        0 |       0 |     456 |     443 |  0.15 |     1.1  |     1.3  |     0.49 |      0.48 |
|    0 |     142 |      489 |       30 |        0 |       0 |     443 |     420 |  0.15 |     0.92 |     1.02 |     0.48 |      0.46 |
|    0 |     143 |      487 |       15 |        0 |       0 |     425 |     412 |  0.14 |     0.69 |     0.64 |     0.47 |      0.47 |
|    0 |     144 |      482 |        4 |        0 |       0 |     405 |     398 |  0.15 |     1.05 |     1.03 |     0.49 |      0.43 |
|    0 |     145 |      477 |       44 |        0 |       0 |     447 |     427 |  0.15 |     0.93 |     1.04 |     0.48 |      0.44 |
|    0 |     146 |      463 |       13 |        0 |       0 |     412 |     400 |  0.15 |     1.63 |     1.61 |     0.49 |      0.44 |
|    0 |     147 |      522 |       29 |        0 |       0 |     455 |     440 |  0.15 |     1.11 |     1.13 |     0.49 |      0.43 |
|    0 |     148 |      461 |       25 |        0 |       0 |     411 |     404 |  0.14 |     1.31 |     1.23 |     0.48 |      0.45 |
|    0 |     149 |      476 |       50 |        0 |       0 |     460 |     434 |  0.14 |     0.92 |     0.9  |     0.48 |      0.46 |
|    0 |     150 |      481 |       59 |        0 |       0 |     462 |     447 |  0.14 |     0.84 |     0.54 |     0.47 |      0.47 |
|    0 |     151 |      461 |       54 |        0 |       0 |     428 |     400 |  0.16 |     1.04 |     1.29 |     0.49 |      0.46 |
|    0 |     152 |      465 |       26 |        0 |       0 |     416 |     404 |  0.15 |     0.87 |     0.7  |     0.47 |      0.46 |
|    0 |     153 |      495 |       73 |        0 |       0 |     467 |     443 |  0.15 |     1.22 |     1.29 |     0.49 |      0.43 |
|    0 |     154 |      481 |       54 |        0 |       0 |     440 |     427 |  0.15 |     1.19 |     1.01 |     0.49 |      0.48 |
|    0 |     155 |      467 |       27 |        0 |       0 |     421 |     409 |  0.15 |     0.99 |     1.05 |     0.49 |      0.43 |
|    0 |     156 |      489 |       38 |        0 |       0 |     439 |     417 |  0.15 |     1.33 |     1.33 |     0.48 |      0.48 |
|    0 |     157 |      478 |       36 |        0 |       0 |     438 |     416 |  0.15 |     1.24 |     1.13 |     0.49 |      0.45 |
|    0 |     158 |      490 |       13 |        0 |       0 |     421 |     407 |  0.15 |     1.29 |     1.15 |     0.48 |      0.45 |
|    0 |     159 |      481 |       39 |        0 |       0 |     423 |     404 |  0.15 |     1.09 |     1.05 |     0.48 |      0.47 |
|    0 |     160 |      494 |       55 |        0 |       0 |     459 |     442 |  0.14 |     0.87 |     0.7  |     0.48 |      0.47 |
|    0 |     161 |      463 |       60 |        0 |       0 |     432 |     413 |  0.14 |     0.87 |     0.78 |     0.47 |      0.48 |
|    0 |     162 |      475 |       66 |        0 |       0 |     470 |     435 |  0.14 |     0.99 |     1.16 |     0.48 |      0.47 |
|    0 |     163 |      465 |       62 |        0 |       0 |     448 |     424 |  0.15 |     0.74 |     0.91 |     0.48 |      0.47 |
|    0 |     164 |      473 |       54 |        0 |       0 |     437 |     420 |  0.14 |     1.16 |     0.96 |     0.49 |      0.46 |
|    0 |     165 |      478 |       37 |        0 |       0 |     431 |     420 |  0.14 |     0.93 |     0.87 |     0.47 |      0.47 |
|    0 |     166 |      472 |       19 |        0 |       0 |     416 |     402 |  0.14 |     0.93 |     0.88 |     0.48 |      0.46 |
|    0 |     167 |      478 |       38 |        0 |       0 |     443 |     426 |  0.14 |     1.36 |     1.32 |     0.49 |      0.45 |
|    0 |     168 |      486 |        7 |        0 |       0 |     413 |     405 |  0.14 |     0.97 |     0.81 |     0.48 |      0.44 |
|    0 |     169 |      490 |       27 |        0 |       0 |     444 |     437 |  0.15 |     1.65 |     1.59 |     0.49 |      0.46 |
|    0 |     170 |      498 |       13 |        0 |       0 |     431 |     421 |  0.15 |     1.06 |     0.97 |     0.48 |      0.45 |
|    0 |     171 |      458 |       45 |        0 |       0 |     427 |     406 |  0.15 |     1.28 |     1.2  |     0.49 |      0.46 |
|    0 |     172 |      495 |       49 |        0 |       0 |     467 |     443 |  0.14 |     0.93 |     0.71 |     0.48 |      0.45 |
|    0 |     173 |      462 |       38 |        0 |       0 |     423 |     408 |  0.14 |     1.06 |     1.08 |     0.47 |      0.46 |
|    0 |     174 |      466 |       54 |        0 |       0 |     458 |     430 |  0.14 |     1.09 |     0.95 |     0.48 |      0.47 |
|    0 |     175 |      483 |       55 |        0 |       0 |     465 |     435 |  0.13 |     0.93 |     0.76 |     0.47 |      0.48 |
|    0 |     176 |      467 |       36 |        0 |       0 |     432 |     419 |  0.15 |     1.12 |     1.15 |     0.48 |      0.46 |
|    0 |     177 |      478 |       34 |        0 |       0 |     427 |     415 |  0.15 |     1.44 |     1.27 |     0.49 |      0.46 |
|    0 |     178 |      500 |       37 |        0 |       0 |     452 |     434 |  0.14 |     1.11 |     0.89 |     0.48 |      0.47 |
|    0 |     179 |      481 |       42 |        0 |       0 |     440 |     419 |  0.13 |     0.63 |     0.67 |     0.46 |      0.48 |
|    0 |     180 |      461 |       24 |        0 |       0 |     412 |     393 |  0.13 |     0.88 |     0.82 |     0.46 |      0.46 |
|    0 |     181 |      509 |       18 |        0 |       0 |     449 |     439 |  0.14 |     0.86 |     0.66 |     0.46 |      0.47 |
|    0 |     182 |      479 |       23 |        0 |       0 |     420 |     407 |  0.14 |     1.13 |     0.9  |     0.47 |      0.48 |
|    0 |     183 |      467 |       31 |        0 |       0 |     428 |     413 |  0.15 |     1.22 |     1.23 |     0.47 |      0.47 |
|    0 |     184 |      467 |       20 |        0 |       0 |     422 |     413 |  0.15 |     1.18 |     1.12 |     0.48 |      0.46 |
|    0 |     185 |      486 |       48 |        0 |       0 |     453 |     439 |  0.13 |     0.94 |     0.7  |     0.47 |      0.46 |
|    0 |     186 |      468 |       48 |        0 |       0 |     437 |     410 |  0.14 |     1.21 |     1.15 |     0.48 |      0.51 |
|    0 |     187 |      475 |       64 |        0 |       0 |     467 |     442 |  0.14 |     1.15 |     1.04 |     0.48 |      0.47 |
|    0 |     188 |      481 |       56 |        0 |       0 |     449 |     431 |  0.14 |     1.19 |     0.81 |     0.49 |      0.44 |
|    0 |     189 |      479 |       25 |        0 |       0 |     425 |     411 |  0.14 |     1.04 |     1.05 |     0.48 |      0.49 |
|    0 |     190 |      483 |       24 |        0 |       0 |     420 |     406 |  0.14 |     1.05 |     1.06 |     0.48 |      0.47 |
|    0 |     191 |      496 |       21 |        0 |       0 |     467 |     453 |  0.14 |     1.08 |     0.92 |     0.47 |      0.46 |
|    0 |     192 |      483 |       30 |        0 |       0 |     420 |     409 |  0.14 |     1.29 |     1.15 |     0.47 |      0.49 |
|    0 |     193 |      485 |       10 |        0 |       0 |     414 |     400 |  0.13 |     0.86 |     0.83 |     0.47 |      0.46 |
|    0 |     194 |      460 |       47 |        0 |       0 |     444 |     414 |  0.13 |     1.01 |     0.94 |     0.48 |      0.47 |
|    0 |     195 |      502 |       26 |        0 |       0 |     448 |     432 |  0.14 |     0.95 |     0.89 |     0.47 |      0.48 |
|    0 |     196 |      483 |       45 |        0 |       0 |     435 |     418 |  0.14 |     1.09 |     1.17 |     0.48 |      0.46 |
|    0 |     197 |      495 |       49 |        0 |       0 |     457 |     438 |  0.14 |     1.17 |     0.99 |     0.48 |      0.46 |
|    0 |     198 |      429 |       72 |        0 |       0 |     410 |     385 |  0.13 |     0.78 |     0.96 |     0.47 |      0.49 |
|    0 |     199 |      490 |       74 |        0 |       0 |     457 |     435 |  0.15 |     1.05 |     1.05 |     0.48 |      0.49 |
|    0 |     200 |      470 |       31 |        0 |       0 |     430 |     415 |  0.14 |     1.03 |     0.96 |     0.48 |      0.45 |
|    0 |     201 |      477 |       36 |        0 |       0 |     427 |     405 |  0.13 |     1.03 |     0.84 |     0.46 |      0.5  |
|    0 |     202 |      480 |       42 |        0 |       0 |     453 |     429 |  0.15 |     1.14 |     1.02 |     0.48 |      0.48 |
|    0 |     203 |      506 |       28 |        0 |       0 |     440 |     427 |  0.14 |     1.27 |     1.19 |     0.47 |      0.47 |
|    0 |     204 |      482 |        7 |        0 |       0 |     421 |     413 |  0.14 |     0.94 |     0.87 |     0.46 |      0.46 |
|    0 |     205 |      491 |       26 |        0 |       0 |     431 |     416 |  0.13 |     1.11 |     0.95 |     0.47 |      0.47 |
|    0 |     206 |      483 |       34 |        0 |       0 |     441 |     428 |  0.14 |     0.91 |     0.83 |     0.47 |      0.45 |
|    0 |     207 |      475 |       15 |        0 |       0 |     414 |     407 |  0.14 |     0.98 |     0.89 |     0.46 |      0.46 |
|    0 |     208 |      468 |       28 |        0 |       0 |     415 |     400 |  0.14 |     0.74 |     0.56 |     0.46 |      0.45 |
|    0 |     209 |      484 |       71 |        0 |       0 |     484 |     458 |  0.15 |     1.11 |     1.15 |     0.49 |      0.47 |
|    0 |     210 |      458 |       54 |        0 |       0 |     438 |     414 |  0.14 |     0.77 |     0.67 |     0.47 |      0.46 |
|    0 |     211 |      495 |       71 |        0 |       0 |     461 |     433 |  0.13 |     0.89 |     0.72 |     0.47 |      0.5  |
|    0 |     212 |      471 |       41 |        0 |       0 |     448 |     432 |  0.14 |     1.05 |     1.05 |     0.47 |      0.5  |
|    0 |     213 |      468 |       34 |        0 |       0 |     434 |     416 |  0.13 |     1.08 |     1.01 |     0.48 |      0.46 |
|    0 |     214 |      499 |       16 |        0 |       0 |     436 |     423 |  0.13 |     1.1  |     0.97 |     0.47 |      0.49 |
|    0 |     215 |      478 |       17 |        0 |       0 |     423 |     411 |  0.14 |     1.25 |     1.32 |     0.48 |      0.48 |
|    0 |     216 |      486 |        6 |        0 |       0 |     415 |     407 |  0.14 |     0.99 |     0.77 |     0.47 |      0.48 |
|    0 |     217 |      474 |       20 |        0 |       0 |     430 |     417 |  0.14 |     1.12 |     1.04 |     0.46 |      0.47 |
|    0 |     218 |      500 |       28 |        0 |       0 |     444 |     426 |  0.14 |     0.92 |     0.79 |     0.48 |      0.46 |
|    0 |     219 |      463 |       33 |        0 |       0 |     404 |     391 |  0.13 |     0.75 |     0.72 |     0.46 |      0.51 |
|    0 |     220 |      495 |       40 |        0 |       0 |     455 |     435 |  0.14 |     1.01 |     0.96 |     0.47 |      0.46 |
|    0 |     221 |      477 |       47 |        0 |       0 |     443 |     421 |  0.14 |     1.1  |     1.08 |     0.48 |      0.5  |
|    0 |     222 |      470 |       55 |        0 |       0 |     457 |     426 |  0.13 |     1.12 |     0.98 |     0.47 |      0.47 |
|    0 |     223 |      476 |       65 |        0 |       0 |     447 |     425 |  0.13 |     1.18 |     0.94 |     0.48 |      0.5  |
|    0 |     224 |      499 |       27 |        0 |       0 |     445 |     432 |  0.14 |     1.02 |     0.87 |     0.47 |      0.49 |
|    0 |     225 |      460 |       10 |        0 |       0 |     404 |     397 |  0.13 |     1.09 |     0.88 |     0.45 |      0.49 |
|    0 |     226 |      476 |       53 |        0 |       0 |     451 |     432 |  0.14 |     1.2  |     1.24 |     0.48 |      0.47 |
|    0 |     227 |      508 |       31 |        0 |       0 |     434 |     425 |  0.14 |     1.3  |     1.21 |     0.47 |      0.5  |
|    0 |     228 |      471 |       22 |        0 |       0 |     427 |     409 |  0.13 |     1.08 |     0.93 |     0.46 |      0.46 |
|    0 |     229 |      474 |       22 |        0 |       0 |     428 |     413 |  0.14 |     1.14 |     0.99 |     0.47 |      0.5  |
|    0 |     230 |      503 |       16 |        0 |       0 |     435 |     422 |  0.14 |     1.07 |     1.02 |     0.47 |      0.47 |
|    0 |     231 |      475 |       26 |        0 |       0 |     433 |     420 |  0.14 |     1.26 |     1.1  |     0.48 |      0.46 |
|    0 |     232 |      483 |       29 |        0 |       0 |     439 |     416 |  0.14 |     1.09 |     0.99 |     0.47 |      0.48 |
|    0 |     233 |      475 |       41 |        0 |       0 |     430 |     414 |  0.14 |     1.23 |     1.15 |     0.47 |      0.48 |
|    0 |     234 |      471 |       71 |        0 |       0 |     461 |     429 |  0.14 |     0.77 |     0.85 |     0.47 |      0.5  |
|    0 |     235 |      477 |       59 |        0 |       0 |     438 |     420 |  0.14 |     1.24 |     0.88 |     0.48 |      0.5  |
|    0 |     236 |      489 |       40 |        0 |       0 |     446 |     428 |  0.13 |     0.72 |     0.53 |     0.46 |      0.49 |
|    0 |     237 |      465 |       24 |        0 |       0 |     427 |     413 |  0.14 |     1.14 |     0.92 |     0.47 |      0.46 |
|    0 |     238 |      497 |       34 |        0 |       0 |     449 |     431 |  0.14 |     1    |     0.9  |     0.47 |      0.46 |
|    0 |     239 |      476 |       22 |        0 |       0 |     421 |     411 |  0.14 |     1    |     0.79 |     0.46 |      0.48 |
|    0 |     240 |      484 |       29 |        0 |       0 |     433 |     412 |  0.14 |     1.3  |     1.26 |     0.48 |      0.47 |
|    0 |     241 |      514 |       26 |        0 |       0 |     462 |     451 |  0.14 |     1.09 |     0.95 |     0.48 |      0.46 |
|    0 |     242 |      475 |       40 |        0 |       0 |     432 |     413 |  0.14 |     1.32 |     1.14 |     0.47 |      0.49 |
|    0 |     243 |      469 |       44 |        0 |       0 |     410 |     400 |  0.14 |     1.28 |     1.18 |     0.48 |      0.47 |
|    0 |     244 |      486 |       38 |        0 |       0 |     438 |     424 |  0.13 |     0.79 |     0.62 |     0.47 |      0.49 |
|    0 |     245 |      481 |       27 |        0 |       0 |     435 |     422 |  0.14 |     1.16 |     1.03 |     0.47 |      0.47 |
|    0 |     246 |      476 |       63 |        0 |       0 |     431 |     411 |  0.14 |     1.18 |     1.12 |     0.48 |      0.5  |
|    0 |     247 |      465 |       55 |        0 |       0 |     428 |     408 |  0.13 |     0.94 |     0.6  |     0.46 |      0.48 |
|    0 |     248 |      482 |       61 |        0 |       0 |     463 |     431 |  0.13 |     0.79 |     0.8  |     0.47 |      0.5  |
|    0 |     249 |      499 |       41 |        0 |       0 |     444 |     428 |  0.14 |     1.44 |     1.4  |     0.48 |      0.48 |
|    0 |     250 |      471 |       48 |        0 |       0 |     418 |     401 |  0.13 |     1.02 |     0.86 |     0.46 |      0.47 |
|    0 |     251 |      500 |       29 |        0 |       0 |     449 |     429 |  0.14 |     1.29 |     0.99 |     0.48 |      0.48 |
|    0 |     252 |      471 |       24 |        0 |       0 |     423 |     411 |  0.14 |     1.22 |     1.2  |     0.47 |      0.46 |
|    0 |     253 |      493 |       33 |        0 |       0 |     443 |     422 |  0.14 |     0.83 |     0.63 |     0.47 |      0.47 |
|    0 |     254 |      481 |       32 |        0 |       0 |     440 |     424 |  0.13 |     0.9  |     0.71 |     0.47 |      0.47 |
|    0 |     255 |      483 |       16 |        0 |       0 |     414 |     407 |  0.14 |     0.87 |     0.59 |     0.46 |      0.44 |
|    0 |     256 |      481 |       38 |        0 |       0 |     440 |     429 |  0.14 |     1.06 |     0.99 |     0.47 |      0.49 |
|    0 |     257 |      464 |       56 |        0 |       0 |     439 |     422 |  0.15 |     1.03 |     1.03 |     0.49 |      0.45 |
|    0 |     258 |      497 |       46 |        0 |       0 |     452 |     426 |  0.14 |     1.03 |     0.99 |     0.47 |      0.46 |
|    0 |     259 |      469 |       55 |        0 |       0 |     456 |     418 |  0.14 |     0.96 |     0.85 |     0.47 |      0.51 |
|    0 |     260 |      467 |       37 |        0 |       0 |     420 |     401 |  0.14 |     1.26 |     1.11 |     0.48 |      0.5  |
|    0 |     261 |      473 |       41 |        0 |       0 |     442 |     424 |  0.13 |     0.85 |     0.9  |     0.46 |      0.47 |
|    0 |     262 |      489 |       23 |        0 |       0 |     423 |     410 |  0.14 |     1.08 |     0.98 |     0.47 |      0.49 |
|    0 |     263 |      489 |       35 |        0 |       0 |     443 |     427 |  0.14 |     1    |     0.79 |     0.47 |      0.45 |
|    0 |     264 |      489 |       19 |        0 |       0 |     420 |     411 |  0.13 |     0.82 |     0.63 |     0.46 |      0.47 |
|    0 |     265 |      452 |       13 |        0 |       0 |     406 |     397 |  0.14 |     1.13 |     0.98 |     0.47 |      0.47 |
|    0 |     266 |      505 |       52 |        0 |       0 |     438 |     428 |  0.14 |     1.29 |     1.23 |     0.48 |      0.46 |
|    0 |     267 |      503 |       67 |        0 |       0 |     469 |     450 |  0.14 |     1.15 |     0.96 |     0.47 |      0.48 |
|    0 |     268 |      473 |       53 |        0 |       0 |     438 |     420 |  0.14 |     1.02 |     0.78 |     0.48 |      0.47 |
|    0 |     269 |      482 |       42 |        0 |       0 |     451 |     439 |  0.14 |     1.19 |     1.29 |     0.48 |      0.47 |
|    0 |     270 |      459 |       43 |        0 |       0 |     429 |     400 |  0.14 |     0.89 |     0.72 |     0.46 |      0.5  |
|    0 |     271 |      494 |       69 |        0 |       0 |     483 |     451 |  0.14 |     0.93 |     0.73 |     0.48 |      0.48 |
|    0 |     272 |      444 |       16 |        0 |       0 |     382 |     368 |  0.13 |     1.1  |     0.99 |     0.46 |      0.5  |
|    0 |     273 |      513 |       43 |        0 |       0 |     465 |     446 |  0.14 |     0.95 |     0.94 |     0.48 |      0.43 |
|    0 |     274 |      472 |       38 |        0 |       0 |     433 |     408 |  0.14 |     1    |     0.84 |     0.48 |      0.46 |
|    0 |     275 |      485 |       41 |        0 |       0 |     433 |     414 |  0.13 |     0.94 |     0.7  |     0.47 |      0.45 |
|    0 |     276 |      473 |       46 |        0 |       0 |     426 |     414 |  0.14 |     1.18 |     1.13 |     0.47 |      0.49 |
|    0 |     277 |      506 |       18 |        0 |       0 |     444 |     430 |  0.14 |     0.98 |     0.75 |     0.46 |      0.51 |
|    0 |     278 |      492 |       13 |        0 |       0 |     430 |     415 |  0.14 |     1.13 |     1.18 |     0.48 |      0.46 |
|    0 |     279 |      491 |       28 |        0 |       0 |     441 |     425 |  0.14 |     1.12 |     0.83 |     0.48 |      0.44 |
|    0 |     280 |      455 |       25 |        0 |       0 |     407 |     391 |  0.14 |     1.1  |     1.16 |     0.48 |      0.46 |
|    0 |     281 |      491 |       46 |        0 |       0 |     454 |     428 |  0.14 |     1.09 |     0.98 |     0.47 |      0.47 |
|    0 |     282 |      471 |       82 |        0 |       0 |     476 |     443 |  0.15 |     1.14 |     0.68 |     0.49 |      0.47 |
|    0 |     283 |      484 |       60 |        0 |       0 |     459 |     427 |  0.14 |     0.92 |     0.98 |     0.47 |      0.48 |
|    0 |     284 |      466 |       58 |        0 |       0 |     448 |     428 |  0.14 |     1.45 |     1.6  |     0.49 |      0.49 |
|    0 |     285 |      474 |       37 |        0 |       0 |     424 |     406 |  0.14 |     1.13 |     1.09 |     0.47 |      0.44 |
|    0 |     286 |      508 |       21 |        0 |       0 |     441 |     430 |  0.14 |     1.08 |     0.98 |     0.47 |      0.47 |
|    0 |     287 |      440 |       24 |        0 |       0 |     403 |     386 |  0.15 |     0.8  |     0.69 |     0.48 |      0.49 |
|    0 |     288 |      530 |        8 |        0 |       0 |     462 |     448 |  0.14 |     1.12 |     1.08 |     0.48 |      0.44 |
|    0 |     289 |      498 |       38 |        0 |       0 |     443 |     420 |  0.15 |     1.11 |     0.98 |     0.48 |      0.44 |
|    0 |     290 |      455 |       33 |        0 |       0 |     405 |     387 |  0.15 |     0.93 |     0.78 |     0.48 |      0.44 |
|    0 |     291 |      495 |       53 |        0 |       0 |     455 |     436 |  0.14 |     0.87 |     0.63 |     0.48 |      0.46 |
|    0 |     292 |      494 |       39 |        0 |       0 |     428 |     416 |  0.16 |     1.25 |     1.32 |     0.49 |      0.46 |
|    0 |     293 |      455 |       46 |        0 |       0 |     424 |     410 |  0.14 |     0.91 |     0.97 |     0.47 |      0.44 |
|    0 |     294 |      491 |       41 |        0 |       0 |     452 |     426 |  0.15 |     1.06 |     1.06 |     0.48 |      0.46 |
|    0 |     295 |      457 |      124 |        0 |       0 |     443 |     417 |  0.15 |     1.14 |     1.46 |     0.49 |      0.46 |
|    0 |     296 |      501 |       40 |        0 |       0 |     454 |     438 |  0.15 |     1.02 |     0.86 |     0.48 |      0.45 |
|    0 |     297 |      475 |       33 |        0 |       0 |     429 |     417 |  0.15 |     0.96 |     1    |     0.48 |      0.44 |
|    0 |     298 |      493 |       45 |        0 |       0 |     442 |     428 |  0.15 |     1.07 |     1.11 |     0.48 |      0.45 |
|    0 |     299 |      485 |       16 |        0 |       0 |     431 |     419 |  0.15 |     1.18 |     1.2  |     0.48 |      0.44 |
|    0 |     300 |      479 |       22 |        0 |       0 |     421 |     410 |  0.15 |     1.2  |     1.48 |     0.48 |      0.46 |
|    0 |     301 |      492 |       46 |        0 |       0 |     461 |     441 |  0.15 |     1.07 |     0.87 |     0.49 |      0.45 |
|    0 |     302 |      473 |       37 |        0 |       0 |     421 |     410 |  0.15 |     0.89 |     0.85 |     0.48 |      0.45 |
|    0 |     303 |      495 |       21 |        0 |       0 |     439 |     421 |  0.15 |     0.8  |     0.69 |     0.48 |      0.45 |
|    0 |     304 |      452 |       30 |        0 |       0 |     406 |     387 |  0.16 |     0.86 |     0.8  |     0.49 |      0.45 |
|    0 |     305 |      493 |       58 |        0 |       0 |     452 |     435 |  0.15 |     1.3  |     1.32 |     0.49 |      0.44 |
|    0 |     306 |      460 |       54 |        0 |       0 |     433 |     400 |  0.16 |     0.94 |     1.04 |     0.49 |      0.43 |
|    0 |     307 |      465 |       56 |        0 |       0 |     452 |     426 |  0.16 |     0.97 |     1.05 |     0.49 |      0.44 |
|    0 |     308 |      503 |       55 |        0 |       0 |     464 |     446 |  0.14 |     1.07 |     1.13 |     0.48 |      0.47 |
|    0 |     309 |      469 |       31 |        0 |       0 |     423 |     410 |  0.16 |     1.07 |     1.22 |     0.5  |      0.44 |
|    0 |     310 |      496 |       30 |        0 |       0 |     438 |     421 |  0.14 |     0.82 |     0.78 |     0.47 |      0.46 |
|    0 |     311 |      471 |       18 |        0 |       0 |     423 |     410 |  0.16 |     1.19 |     1.61 |     0.49 |      0.45 |
|    0 |     312 |      505 |       28 |        0 |       0 |     445 |     427 |  0.16 |     1.36 |     1.36 |     0.5  |      0.44 |
|    0 |     313 |      484 |       64 |        0 |       0 |     436 |     413 |  0.15 |     0.92 |     0.96 |     0.49 |      0.45 |
|    0 |     314 |      484 |       17 |        0 |       0 |     438 |     431 |  0.15 |     0.86 |     0.87 |     0.48 |      0.45 |
|    0 |     315 |      451 |       44 |        0 |       0 |     416 |     402 |  0.15 |     0.8  |     0.68 |     0.48 |      0.47 |
|    0 |     316 |      519 |       46 |        0 |       0 |     469 |     449 |  0.16 |     1.51 |     1.68 |     0.49 |      0.44 |
|    0 |     317 |      467 |       49 |        0 |       0 |     441 |     418 |  0.16 |     1.09 |     1.12 |     0.49 |      0.44 |
|    0 |     318 |      500 |       53 |        0 |       0 |     470 |     450 |  0.16 |     0.98 |     1.1  |     0.5  |      0.45 |
|    0 |     319 |      448 |       24 |        0 |       0 |     391 |     370 |  0.16 |     1.43 |     1.58 |     0.48 |      0.44 |
|    0 |     320 |      473 |       57 |        0 |       0 |     439 |     424 |  0.17 |     1.5  |     1.62 |     0.5  |      0.44 |
|    0 |     321 |      489 |       43 |        0 |       0 |     450 |     431 |  0.16 |     1.05 |     1.09 |     0.49 |      0.45 |
|    0 |     322 |      473 |       22 |        0 |       0 |     420 |     405 |  0.16 |     0.85 |     0.94 |     0.49 |      0.42 |
|    0 |     323 |      485 |       21 |        0 |       0 |     443 |     427 |  0.16 |     0.84 |     0.78 |     0.48 |      0.45 |
|    0 |     324 |      502 |       18 |        0 |       0 |     433 |     424 |  0.17 |     1.32 |     1.29 |     0.5  |      0.42 |
|    0 |     325 |      479 |       22 |        0 |       0 |     436 |     419 |  0.16 |     1    |     0.92 |     0.49 |      0.44 |
|    0 |     326 |      477 |       53 |        0 |       0 |     450 |     433 |  0.17 |     1.71 |     1.65 |     0.5  |      0.47 |
|    0 |     327 |      485 |       37 |        0 |       0 |     449 |     434 |  0.16 |     0.9  |     0.91 |     0.49 |      0.43 |
|    0 |     328 |      475 |       29 |        0 |       0 |     408 |     394 |  0.17 |     1.16 |     1.46 |     0.5  |      0.43 |
|    0 |     329 |      491 |       44 |        0 |       0 |     445 |     426 |  0.17 |     1.25 |     1.4  |     0.49 |      0.44 |
|    0 |     330 |      466 |       90 |        0 |       0 |     473 |     438 |  0.18 |     1.3  |     2.05 |     0.51 |      0.45 |
|    0 |     331 |      482 |       69 |        0 |       0 |     473 |     443 |  0.17 |     0.89 |     1    |     0.5  |      0.45 |
|    0 |     332 |      484 |       49 |        0 |       0 |     457 |     443 |  0.18 |     1.3  |     1.19 |     0.5  |      0.41 |
|    0 |     333 |      459 |       57 |        0 |       0 |     415 |     400 |  0.17 |     1.06 |     1.04 |     0.5  |      0.43 |
|    0 |     334 |      486 |       32 |        0 |       0 |     442 |     420 |  0.17 |     1.35 |     1.29 |     0.5  |      0.43 |
|    0 |     335 |      503 |       40 |        0 |       0 |     434 |     424 |  0.18 |     1.5  |     1.37 |     0.51 |      0.41 |
|    0 |     336 |      474 |       25 |        0 |       0 |     411 |     404 |  0.17 |     1.35 |     1.34 |     0.5  |      0.42 |
|    0 |     337 |      501 |       10 |        0 |       0 |     441 |     427 |  0.17 |     1.22 |     1.22 |     0.5  |      0.41 |
|    0 |     338 |      503 |       31 |        0 |       0 |     460 |     438 |  0.18 |     1.39 |     1.33 |     0.51 |      0.42 |
|    0 |     339 |      467 |       28 |        0 |       0 |     399 |     389 |  0.18 |     1.16 |     1    |     0.51 |      0.41 |
|    0 |     340 |      464 |       51 |        0 |       0 |     442 |     420 |  0.18 |     0.93 |     0.84 |     0.51 |      0.43 |
|    0 |     341 |      482 |       53 |        0 |       0 |     431 |     418 |  0.18 |     0.94 |     1.15 |     0.51 |      0.41 |
|    0 |     342 |      472 |       76 |        0 |       0 |     463 |     426 |  0.19 |     0.91 |     1.24 |     0.51 |      0.42 |
|    0 |     343 |      481 |       93 |        0 |       0 |     498 |     460 |  0.19 |     1.34 |     1.37 |     0.53 |      0.43 |
|    0 |     344 |      505 |       29 |        0 |       0 |     444 |     431 |  0.18 |     1.04 |     1.16 |     0.5  |      0.43 |
|    0 |     345 |      454 |       20 |        0 |       0 |     408 |     402 |  0.19 |     1.45 |     1.58 |     0.51 |      0.41 |
|    0 |     346 |      491 |       42 |        0 |       0 |     461 |     441 |  0.19 |     1.3  |     1.34 |     0.52 |      0.4  |
|    0 |     347 |      458 |       26 |        0 |       0 |     400 |     389 |  0.18 |     0.94 |     0.87 |     0.5  |      0.4  |
|    0 |     348 |      480 |       15 |        0 |       0 |     419 |     409 |  0.19 |     1.32 |     1.2  |     0.52 |      0.39 |
|    0 |     349 |      475 |       22 |        0 |       0 |     415 |     396 |  0.19 |     1.34 |     1.29 |     0.52 |      0.4  |
|    0 |     350 |      510 |       25 |        0 |       0 |     455 |     435 |  0.19 |     1.05 |     1.04 |     0.51 |      0.41 |
|    0 |     351 |      501 |       46 |        0 |       0 |     462 |     445 |  0.2  |     1.2  |     1.3  |     0.52 |      0.41 |
|    0 |     352 |      497 |       40 |        0 |       0 |     450 |     437 |  0.19 |     0.93 |     0.96 |     0.51 |      0.4  |
|    0 |     353 |      457 |       55 |        0 |       0 |     416 |     390 |  0.2  |     1.79 |     2.08 |     0.53 |      0.41 |
|    0 |     354 |      437 |       69 |        0 |       0 |     442 |     419 |  0.2  |     1.57 |     1.76 |     0.53 |      0.39 |
|    0 |     355 |      440 |       66 |        0 |       0 |     441 |     417 |  0.21 |     1.53 |     2.23 |     0.53 |      0.43 |
|    0 |     356 |      522 |       50 |        0 |       0 |     487 |     469 |  0.2  |     1.36 |     1.37 |     0.53 |      0.42 |
|    0 |     357 |      464 |       24 |        0 |       0 |     409 |     390 |  0.21 |     0.97 |     1    |     0.52 |      0.38 |
|    0 |     358 |      496 |       31 |        0 |       0 |     451 |     436 |  0.2  |     1.13 |     1.06 |     0.53 |      0.38 |
|    0 |     359 |      548 |       25 |        0 |       0 |     490 |     474 |  0.21 |     1.29 |     1.28 |     0.52 |      0.41 |
|    0 |     360 |      457 |       42 |        0 |       0 |     402 |     389 |  0.21 |     1.37 |     1.36 |     0.53 |      0.41 |
|    0 |     361 |      474 |       32 |        0 |       0 |     433 |     417 |  0.2  |     1.31 |     1.5  |     0.53 |      0.42 |
|    0 |     362 |      447 |       47 |        0 |       0 |     420 |     404 |  0.23 |     1.57 |     1.77 |     0.55 |      0.38 |
|    0 |     363 |      447 |        6 |        0 |       0 |     391 |     384 |  0.21 |     1.21 |     1.27 |     0.53 |      0.37 |
|    0 |     364 |      463 |       25 |        0 |       0 |     400 |     390 |  0.21 |     1.38 |     1.25 |     0.53 |      0.39 |
|    0 |     365 |      540 |       70 |        0 |       0 |     514 |     489 |  0.22 |     1.35 |     1.41 |     0.54 |      0.39 |
|    0 |     366 |      484 |       69 |        0 |       0 |     465 |     434 |  0.21 |     1.21 |     1.21 |     0.53 |      0.4  |
|    0 |     367 |      491 |       57 |        0 |       0 |     441 |     413 |  0.24 |     1.53 |     1.6  |     0.55 |      0.39 |
|    0 |     368 |      483 |       54 |        0 |       0 |     452 |     436 |  0.23 |     1.33 |     1.39 |     0.55 |      0.38 |
|    0 |     369 |      460 |       42 |        0 |       0 |     427 |     410 |  0.24 |     1.21 |     1.34 |     0.55 |      0.39 |
|    0 |     370 |      463 |       33 |        0 |       0 |     427 |     410 |  0.22 |     0.98 |     0.94 |     0.54 |      0.37 |
|    0 |     371 |      493 |       26 |        0 |       0 |     453 |     438 |  0.22 |     1.2  |     1.68 |     0.54 |      0.39 |
|    0 |     372 |      469 |       28 |        0 |       0 |     432 |     414 |  0.23 |     1.55 |     1.72 |     0.55 |      0.39 |
|    0 |     373 |      459 |       13 |        0 |       0 |     420 |     407 |  0.24 |     1.33 |     1.33 |     0.56 |      0.37 |
|    0 |     374 |      469 |       21 |        0 |       0 |     411 |     391 |  0.24 |     1.32 |     1.42 |     0.55 |      0.37 |
|    0 |     375 |      494 |       17 |        0 |       0 |     442 |     430 |  0.24 |     1.17 |     1.11 |     0.55 |      0.35 |
|    0 |     376 |      510 |       36 |        0 |       0 |     456 |     439 |  0.25 |     1.08 |     1.28 |     0.56 |      0.37 |
|    0 |     377 |      486 |       59 |        0 |       0 |     457 |     439 |  0.24 |     1    |     1.19 |     0.57 |      0.36 |
|    0 |     378 |      475 |       79 |        0 |       0 |     442 |     418 |  0.25 |     0.95 |     0.99 |     0.56 |      0.37 |
|    0 |     379 |      485 |       37 |        0 |       0 |     456 |     425 |  0.26 |     1.53 |     1.54 |     0.56 |      0.37 |
|    0 |     380 |      498 |       39 |        0 |       0 |     454 |     439 |  0.25 |     1.11 |     1.01 |     0.56 |      0.38 |
|    0 |     381 |      517 |       30 |        0 |       0 |     456 |     443 |  0.27 |     1.82 |     2.01 |     0.58 |      0.35 |
|    0 |     382 |      446 |       32 |        0 |       0 |     415 |     398 |  0.26 |     1.58 |     1.73 |     0.57 |      0.38 |
|    0 |     383 |      471 |       39 |        0 |       0 |     412 |     397 |  0.24 |     1.2  |     1.29 |     0.56 |      0.37 |
|    0 |     384 |      475 |       28 |        0 |       0 |     422 |     407 |  0.26 |     1.29 |     1.38 |     0.57 |      0.37 |
|    0 |     385 |      502 |       31 |        0 |       0 |     468 |     449 |  0.26 |     0.98 |     1.09 |     0.57 |      0.37 |
|    0 |     386 |      464 |       21 |        0 |       0 |     418 |     402 |  0.27 |     1.13 |     1.21 |     0.57 |      0.36 |
|    0 |     387 |      459 |       27 |        0 |       0 |     405 |     389 |  0.27 |     1.34 |     1.42 |     0.57 |      0.35 |
|    0 |     388 |      455 |       44 |        0 |       0 |     424 |     405 |  0.26 |     1.22 |     1.26 |     0.57 |      0.36 |
|    0 |     389 |      478 |       43 |        0 |       0 |     453 |     430 |  0.27 |     1.13 |     1.01 |     0.57 |      0.35 |
|    0 |     390 |      457 |       70 |        0 |       0 |     455 |     422 |  0.27 |     0.73 |     0.85 |     0.57 |      0.36 |
|    0 |     391 |      466 |       58 |        0 |       0 |     455 |     427 |  0.26 |     0.9  |     1    |     0.57 |      0.36 |
|    0 |     392 |      497 |       80 |        0 |       0 |     480 |     443 |  0.29 |     1.57 |     1.8  |     0.6  |      0.37 |
|    0 |     393 |      487 |       32 |        0 |       0 |     435 |     423 |  0.29 |     1.29 |     1.37 |     0.58 |      0.35 |
|    0 |     394 |      487 |       28 |        0 |       0 |     438 |     423 |  0.28 |     0.98 |     1.07 |     0.58 |      0.35 |
|    0 |     395 |      449 |       35 |        0 |       0 |     410 |     400 |  0.28 |     1.53 |     1.55 |     0.58 |      0.35 |
|    0 |     396 |      456 |       36 |        0 |       0 |     411 |     392 |  0.27 |     0.93 |     1.04 |     0.57 |      0.34 |
|    0 |     397 |      422 |       61 |        0 |       0 |     406 |     400 |  0.28 |     1.13 |     1.2  |     0.57 |      0.36 |
|    0 |     398 |      301 |      218 |        0 |       0 |     431 |     419 |  0.28 |     1.15 |     1.23 |     0.58 |      0.38 |
|    0 |     399 |        7 |      471 |        0 |       0 |     399 |     389 |  0.28 |     0.9  |     1.04 |     0.57 |      0.41 |
|    0 |     400 |        0 |      499 |        0 |       0 |     429 |     416 |  0.28 |     0.78 |     1.11 |     0.57 |      0.47 |
+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+

 Summary vs resolution
+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
|   ID |   d min |   # full |   # part |   # over |   # ice |   # sum |   # prf |   Ibg |   I/sigI |   I/sigI |   CC prf |   RMSD XY |
|      |         |          |          |          |         |         |         |       |    (sum) |    (prf) |          |           |
|------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------|
|    0 |    1.18 |      205 |        4 |        0 |       0 |     130 |      51 |  0.03 |     0.05 |    -0.01 |     0.29 |      0.93 |
|    0 |    1.2  |      565 |       16 |        0 |       0 |     513 |     383 |  0.03 |     0.06 |    -0.01 |     0.3  |      0.8  |
|    0 |    1.23 |     1060 |       21 |        0 |       0 |     956 |     836 |  0.04 |     0.05 |     0.04 |     0.31 |      0.83 |
|    0 |    1.25 |     1574 |       36 |        0 |       0 |    1355 |    1207 |  0.04 |     0.02 |     0.01 |     0.33 |      0.75 |
|    0 |    1.28 |     2201 |       45 |        0 |       0 |    1945 |    1769 |  0.05 |     0.05 |     0.02 |     0.34 |      0.7  |
|    0 |    1.3  |     2993 |       71 |        0 |       0 |    2536 |    2325 |  0.05 |     0.01 |     0    |     0.35 |      0.66 |
|    0 |    1.33 |     4296 |       91 |        0 |       0 |    3699 |    3358 |  0.06 |     0.01 |     0.02 |     0.36 |      0.63 |
|    0 |    1.37 |     6202 |      132 |        0 |       0 |    5296 |    4886 |  0.06 |     0.02 |     0.02 |     0.36 |      0.62 |
|    0 |    1.4  |     8679 |      203 |        0 |       0 |    7702 |    7288 |  0.07 |     0.05 |     0.03 |     0.37 |      0.6  |
|    0 |    1.45 |     9793 |      226 |        0 |       0 |    8665 |    8418 |  0.07 |     0.07 |     0.04 |     0.38 |      0.57 |
|    0 |    1.49 |    10825 |      261 |        0 |       0 |    9289 |    9014 |  0.08 |     0.1  |     0.06 |     0.39 |      0.54 |
|    0 |    1.55 |    12071 |      869 |        0 |       0 |   10424 |    9935 |  0.09 |     0.13 |     0.08 |     0.41 |      0.51 |
|    0 |    1.61 |    12877 |     2153 |        0 |       0 |   12861 |   12153 |  0.09 |     0.15 |     0.09 |     0.43 |      0.48 |
|    0 |    1.68 |    14297 |     2124 |        0 |       0 |   13897 |   13095 |  0.1  |     0.23 |     0.16 |     0.44 |      0.47 |
|    0 |    1.77 |    16548 |     2311 |        0 |       0 |   15657 |   14816 |  0.13 |     0.33 |     0.24 |     0.47 |      0.43 |
|    0 |    1.88 |    17184 |     2205 |        0 |       0 |   16669 |   16044 |  0.16 |     0.56 |     0.46 |     0.51 |      0.38 |
|    0 |    2.03 |    16957 |     2160 |        0 |       0 |   15262 |   14636 |  0.2  |     0.98 |     0.88 |     0.55 |      0.36 |
|    0 |    2.23 |    17111 |     2383 |        0 |       0 |   16756 |   16102 |  0.22 |     1.38 |     1.28 |     0.57 |      0.35 |
|    0 |    2.55 |    17354 |     2093 |        0 |       0 |   16445 |   15796 |  0.3  |     2.55 |     2.75 |     0.65 |      0.32 |
|    0 |    3.21 |    17389 |     2262 |        0 |       0 |   16750 |   16080 |  0.46 |     7.09 |     7.82 |     0.74 |      0.28 |
+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+

 Summary for experiment 0
+---------------------------------------+-----------+----------+--------+
| Item                                  |   Overall |      Low |   High |
|---------------------------------------+-----------+----------+--------|
| dmin                                  |      1.18 |     3.21 |   1.18 |
| dmax                                  |    110.45 |   110.45 |   1.2  |
| number fully recorded                 | 190181    | 17389    | 205    |
| number partially recorded             |  19666    |  2262    |   4    |
| number with invalid background pixels |  54271    |  4358    | 157    |
| number with invalid foreground pixels |  30995    |  2723    |  79    |
| number with overloaded pixels         |      0    |     0    |   0    |
| number in powder rings                |      0    |     0    |   0    |
| number processed with summation       | 176807    | 16750    | 130    |
| number processed with profile fitting | 168192    | 16080    |  51    |
| number failed in background modelling |      3    |     3    |   0    |
| number failed in summation            |  30995    |  2723    |  79    |
| number failed in profile fitting      |  39610    |  3393    | 158    |
| ibg                                   |      0.17 |     0.46 |   0.03 |
| i/sigi (summation)                    |      1.25 |     7.09 |   0.05 |
| i/sigi (profile fitting)              |      1.3  |     7.82 |  -0.01 |
| cc prf                                |      0.5  |     0.74 |   0.29 |
| cc_pearson sum/prf                    |      0.7  |     0.92 |   0.34 |
| cc_spearman sum/prf                   |      0.67 |     0.9  |   0.22 |
+---------------------------------------+-----------+----------+--------+

Timing information for integration
+-------------------+----------------+
| Read time         | 65.08 seconds  |
| Extract time      | 13.56 seconds  |
| Pre-process time  | 0.40 seconds   |
| Process time      | 243.82 seconds |
| Post-process time | 0.00 seconds   |
| Total time        | 326.29 seconds |
+-------------------+----------------+

Saving 209847 reflections to integrated.refl
Saving the experiments to integrated.expt

Checking the log output, we see that after loading in the reference reflections from refined.refl, new predictions are made up to the highest resolution at the corner of the detector. This is fine, but if we wanted to we could have adjusted the resolution limits using parameters prediction.d_min and prediction.d_max. The predictions are made using the scan-varying crystal model recorded in refined.expt. This ensures that prediction is made using the smoothly varying lattice and orientation that we determined in the refinement step. As this scan-varying model was determined in advance of integration, each of the integration jobs is independent and we can take advantage of true parallelism during processing.

The profile model is calculated from the reflections in refined.refl. First reflections with a too small ‘zeta’ factor are filtered out. This essentially removes reflections that are too close to the spindle axis. In general these reflections require significant Lorentz corrections and as a result have less trustworthy intensities anyway. From the remaining reflection shoeboxes, the average beam divergence and reflecting range is calculated, providing the two Gaussian width parameters \(\sigma_D\) and \(\sigma_M\) used in the 3D profile model.

Following this, independent integration jobs are set up. These jobs overlap, so reflections are assigned to one or more jobs. What follows are blocks of information specific to each integration job.

After these jobs are finished, the reflections are ‘post-processed’, which includes the application of the LP correction to the intensities. Then summary tables are printed giving quality statistics first by frame, and then by resolution bin.

Symmetry analysis

After integration, further assessments of the crystal symmetry are possible. Previously, we made an assessment of the lattice symmetry (i.e. the symmetry of the diffraction spot positions), however now we have determined a set of intensity values and can investigate the full symmetry of the diffraction pattern (i.e. spot positions and intensities). The symmetry analysis consists of two stages, determining the laue group symmetry and analysing absent reflections to suggest the space group symmetry.

dials.symmetry integrated.expt integrated.refl

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:

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

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

Performing Laue group analysis

Filtering reflections for dataset 0
Read 209847 predicted reflections
Selected 168192 reflections integrated by profile and summation methods
Combined 4149 partial reflections with other partial reflections
Removed 3062 reflections below partiality threshold
Removed 0 intensity.sum.value reflections with I/Sig(I) < -5
Removed 527 intensity.prf.value reflections with I/Sig(I) < -5
A round of outlier rejection has been performed, 
79 outliers have been identified. 

Patterson group: F m m m (x-y+z,x+y+z,2*z)

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

Normalising intensities for dataset 1

ML estimate of overall B_cart value:
   6.81, -0.77, -0.19
          5.51,  0.87
                 4.23
ML estimate of  -log of scale factor:
  -3.43

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

Estimation of resolution for Laue group analysis

Resolution estimate from <I>/<σ(I)> > 4.0 : 3.00
Resolution estimate from CC½ > 0.60: 1.85
High resolution limit set to: 1.85
Selecting 65017 reflections with d > 1.85

Input crystal symmetry:
Unit cell: (34.616, 34.616, 112.881, 98.3163, 98.3163, 100.242)
Space group: P 1 (No. 1)
Change of basis op to minimum cell: b,a,-a-b-c
Crystal symmetry in minimum cell:
Unit cell: (34.616, 34.616, 111.588, 96.2426, 96.2426, 100.242)
Space group: P 1 (No. 1)
Lattice point group: F m m m (x-y+z,x+y+z,2*z)

Overall CC for 20000 unrelated pairs: 0.127
Estimated expectation value of true correlation coefficient E(CC) = 0.917
Estimated sd(CC) = 0.939 / sqrt(N)
Estimated E(CC) of true correlation coefficient from identity = 0.931

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

Scoring individual symmetry elements

+--------------+--------+------+-------+----+---------------+
|   likelihood |   Z-CC |   CC |     N |    | Operator      |
|--------------+--------+------+-------+----+---------------|
|        0.898 |   9.26 | 0.93 | 52838 | ** | 1 |(0, 0, 0)  |
|        0.067 |   0.82 | 0.08 | 50622 |    | 2 |(1, 1, 0)  |
|        0.867 |   8.89 | 0.89 | 51694 | ** | 2 |(-1, 1, 0) |
|        0.066 |   0.91 | 0.09 | 51940 |    | 2 |(1, 1, 2)  |
+--------------+--------+------+-------+----+---------------+

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

Scoring all possible sub-groups

+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+
| Patterson group   |     |   Likelihood |   NetZcc |   Zcc+ |   Zcc- |   CC |   CC- |   delta | Reindex operator   |
|-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------|
| C 1 2/m 1         | *** |        0.848 |     8.21 |   9.08 |   0.87 | 0.91 |  0.09 |     0   | a+b,a-b,-a-b-c     |
| P -1              |     |        0.13  |     4.08 |   9.26 |   5.18 | 0.93 |  0.34 |     0   | b,a,-a-b-c         |
| C 1 2/m 1         |     |        0.009 |     0.25 |   6.57 |   6.32 | 0.47 |  0.49 |     1.7 | a-b,-a-b,-a-c      |
| I 1 2/m 1         |     |        0.009 |     0.27 |   6.58 |   6.31 | 0.49 |  0.46 |     1.7 | -b,a+b+2*c,-a      |
| F m m m           |     |        0.004 |     6.45 |   6.45 |   0    | 0.48 |  0    |     1.7 | a+b,a-b,-a-b-2*c   |
+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+

Best solution: C 1 2/m 1
Unit cell: (44.3892, 53.1288, 111.588, 90, 99.7643, 90)
Reindex operator: a+b,a-b,-a-b-c
Laue group probability: 0.848
Laue group confidence: 0.780

+-------------------+--------------------------+
| Patterson group   | Corresponding MX group   |
|-------------------+--------------------------|
| C 1 2/m 1         | C 1 2 1                  |
+-------------------+--------------------------+
================================================================================

Analysing systematic absences

Laue group: C 1 2/m 1
No absences to check for this laue group

Saving reindexed experiments to symmetrized.expt in space group C 1 2 1
Saving 209847 reindexed reflections to symmetrized.refl

The laue group symmetry is the 3D rotational symmetry of the diffraction pattern plus inversion symmetry (due to Friedel’s law that I(h,k,l) = I(-h,-k,-l) when absorption is negligible). To determine the laue group symmetry, all possible symmetry operations of the lattice are scored by comparing the correlation of reflection intensities that would be equivalent under a given operation. The scores for individual symmetry operations are then combined to score the potential laue groups.

Scoring all possible sub-groups

+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+
| Patterson group   |     |   Likelihood |   NetZcc |   Zcc+ |   Zcc- |   CC |   CC- |   delta | Reindex operator   |
|-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------|
| C 1 2/m 1         | *** |        0.848 |     8.21 |   9.08 |   0.87 | 0.91 |  0.09 |     0   | a+b,a-b,-a-b-c     |
| P -1              |     |        0.13  |     4.08 |   9.26 |   5.18 | 0.93 |  0.34 |     0   | b,a,-a-b-c         |
| C 1 2/m 1         |     |        0.009 |     0.25 |   6.57 |   6.32 | 0.47 |  0.49 |     1.7 | a-b,-a-b,-a-c      |
| I 1 2/m 1         |     |        0.009 |     0.27 |   6.58 |   6.31 | 0.49 |  0.46 |     1.7 | -b,a+b+2*c,-a      |
| F m m m           |     |        0.004 |     6.45 |   6.45 |   0    | 0.48 |  0    |     1.7 | a+b,a-b,-a-b-2*c   |
+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+

Best solution: C 1 2/m 1
Unit cell: (44.3892, 53.1288, 111.588, 90, 99.7643, 90)
Reindex operator: a+b,a-b,-a-b-c
Laue group probability: 0.848
Laue group confidence: 0.780

+-------------------+--------------------------+
| Patterson group   | Corresponding MX group   |
|-------------------+--------------------------|
| C 1 2/m 1         | C 1 2 1                  |
+-------------------+--------------------------+
================================================================================

Here we see clearly that the best solution is given by C 1 2/m 1, with a high likelihood. For macromolecules, their chirality means that mirror symmetry is not allowed (the ‘m’ in C 1 2/m 1), therefore the determined symmetry relevant for MX at this point is C2. For some Laue groups, there are multiple space groups possible due additional translational symmetries (e.g P 2, P 21 for Laue group P2/m), which requires an additional analysis of systematic absences. However this is not the case for C 1 2/m 1, therefore the final result of the analysis is the space group C2, in agreement with the result from dials.refine_bravais_settings.

Scaling and Merging

Before the data can be reduced for structure solution, the intensity values must be corrected for experimental effects which occur prior to the reflection being measured on the detector. These primarily include sample illumination/absorption effects and radiation damage, which result in symmetry-equivalent reflections having unequal measured intensities (i.e. a systematic effect in addition to any variance due to counting statistics). Thus the purpose of scaling is to determine a scale factor to apply to each reflection, such that the scaled intensities are representative of the ‘true’ scattering intensity from the contents of the unit cell.

During scaling, a scaling model is created, from which scale factors are calculated for each reflection. Three physically motivated corrections are used to create an scaling model, in a similar manner to that used in the program aimless. This model consists of a smoothly varying scale factor as a function of rotation angle, a smoothly varying B-factor to account for radiation damage as a function of rotation angle and an absorption surface correction, dependent on the direction of the incoming and scattered beam vector relative to the crystal.

dials.scale symmetrized.expt symmetrized.refl

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DIALS 3.dev.146-gf69fc319a
The following parameters have been modified:
input {
  experiments = symmetrized.expt
  reflections = symmetrized.refl
}

Checking for the existence of a reflection table 
containing multiple datasets 

Found 1 reflection tables & 1 experiments in total.

Dataset ids are: 0 

Space group being used during scaling is C 1 2 1

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
Combined 4149 partial reflections with other partial reflections
Excluding 40629/205698 reflections
Reflections passing individual criteria:
criterion: user excluded, reflections: 10857
criterion: excluded for scaling, reflections: 40629

The following corrections will be applied to this dataset: 

+--------------+----------------+
| correction   |   n_parameters |
|--------------+----------------|
| scale        |             16 |
| decay        |             12 |
| absorption   |             24 |
+--------------+----------------+
A round of outlier rejection has been performed, 
1337 outliers have been identified. 

163304 reflections were preselected for scale factor determination 
out of 165069 suitable reflections: 
Reflections passing individual criteria:
criterion: in I/sigma range (I/sig > -5.0), reflections: 164924
criterion: above min partiality ( > 0.95), reflections: 163440

Randomly selected 15783/47064 groups (m>1) to use for scaling model
minimisation (50130 reflections)
Completed preprocessing and initialisation for this dataset.

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

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 7.33

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  49692 |  0.77522 |
|      1 |  49692 |  0.75004 |
|      2 |  49692 |  0.69716 |
|      3 |  49692 |  0.64094 |
|      4 |  49692 |  0.63575 |
|      5 |  49692 |  0.62034 |
|      6 |  49692 |  0.59006 |
|      7 |  49692 |  0.57197 |
|      8 |  49692 |  0.56539 |
|      9 |  49692 |  0.55942 |
|     10 |  49692 |  0.55811 |
|     11 |  49692 |  0.55318 |
|     12 |  49692 |  0.55168 |
|     13 |  49692 |  0.55048 |
|     14 |  49692 |  0.55013 |
|     15 |  49692 |  0.54978 |
|     16 |  49692 |  0.54928 |
|     17 |  49692 |  0.54902 |
|     18 |  49692 |  0.54856 |
|     19 |  49692 |  0.54833 |
|     20 |  49692 |  0.5482  |
|     21 |  49692 |  0.54815 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

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

Scale factors determined during minimisation have now been
applied to all reflections for dataset 0.

A round of outlier rejection has been performed, 
291 outliers have been identified. 

Performing profile/summation intensity optimisation.
+----------------+---------+---------+
| Combination    |   CC1/2 |   Rmeas |
|----------------+---------+---------|
| prf only       | 0.99325 | 0.10312 |
| sum only       | 0.98879 | 0.14097 |
| Imid = 32.14   | 0.99149 | 0.11782 |
| Imid = 1805.23 | 0.99355 | 0.10258 |
| Imid = 180.52  | 0.99371 | 0.1026  |
| Imid = 18.05   | 0.99016 | 0.12817 |
+----------------+---------+---------+
Combined intensities with Imid = 1805.23 determined to be best for scaling. 

A round of outlier rejection has been performed, 
284 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 12.71

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  50063 |  0.59267 |
|      1 |  50063 |  0.58763 |
|      2 |  50063 |  0.58169 |
|      3 |  50063 |  0.57874 |
|      4 |  50063 |  0.5785  |
|      5 |  50063 |  0.57819 |
|      6 |  50063 |  0.5775  |
|      7 |  50063 |  0.57697 |
|      8 |  50063 |  0.57691 |
|      9 |  50063 |  0.57656 |
|     10 |  50063 |  0.57648 |
|     11 |  50063 |  0.57635 |
|     12 |  50063 |  0.57628 |
|     13 |  50063 |  0.5762  |
|     14 |  50063 |  0.57595 |
|     15 |  50063 |  0.57563 |
|     16 |  50063 |  0.57528 |
|     17 |  50063 |  0.57506 |
|     18 |  50063 |  0.57491 |
|     19 |  50063 |  0.57475 |
|     20 |  50063 |  0.57439 |
|     21 |  50063 |  0.5739  |
|     22 |  50063 |  0.57367 |
|     23 |  50063 |  0.5733  |
|     24 |  50063 |  0.57294 |
|     25 |  50063 |  0.57259 |
|     26 |  50063 |  0.57231 |
|     27 |  50063 |  0.57182 |
|     28 |  50063 |  0.57117 |
|     29 |  50063 |  0.57068 |
|     30 |  50063 |  0.5703  |
|     31 |  50063 |  0.56995 |
|     32 |  50063 |  0.56961 |
|     33 |  50063 |  0.56938 |
|     34 |  50063 |  0.56904 |
|     35 |  50063 |  0.5687  |
|     36 |  50063 |  0.56831 |
|     37 |  50063 |  0.56803 |
|     38 |  50063 |  0.56783 |
|     39 |  50063 |  0.56777 |
|     40 |  50063 |  0.56768 |
|     41 |  50063 |  0.56764 |
+--------+--------+----------+
RMSD no longer decreasing
lbfgs minimizer stop: callback_after_step is True

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

Scale factors determined during minimisation have now been
applied to all reflections for dataset 0.

A round of outlier rejection has been performed, 
194 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 0.52029, b = 0.05526
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 34.784

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 |
|--------------------------+----------+------------------------+----------------------|
| 1452.88 - 432.00         |      250 |                  1.336 |                0.726 |
| 432.00 - 310.13          |      250 |                  1.245 |                0.95  |
| 310.13 - 252.67          |      250 |                  1.016 |                1.043 |
| 252.67 - 212.66          |      250 |                  0.976 |                1.126 |
| 212.66 - 183.80          |      250 |                  1.307 |                1.676 |
| 183.80 - 126.96          |      872 |                  0.688 |                1.123 |
| 126.96 - 84.58           |     1266 |                  0.575 |                1.206 |
| 84.58 - 56.34            |     1502 |                  0.503 |                1.265 |
| 56.34 - 37.53            |     1561 |                  0.501 |                1.443 |
| 37.53 - 24.99            |     1196 |                  0.413 |                1.286 |
+--------------------------+----------+------------------------+----------------------+

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 6.76

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  50091 |  0.8587  |
|      1 |  50091 |  0.85085 |
|      2 |  50091 |  0.84871 |
|      3 |  50091 |  0.84567 |
|      4 |  50091 |  0.84327 |
|      5 |  50091 |  0.84236 |
|      6 |  50091 |  0.84211 |
|      7 |  50091 |  0.84201 |
|      8 |  50091 |  0.84197 |
+--------+--------+----------+
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 1.29

Refinement steps:
+--------+--------+----------+
|   Step |   Nref |   RMSD_I |
|        |        |    (a.u) |
|--------+--------+----------|
|      0 |  50091 |  0.84197 |
|      1 |  50091 |  0.84197 |
+--------+--------+----------+
RMSD no longer decreasing

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

Scale factors determined during minimisation have now been
applied to all reflections for dataset 0.

A round of outlier rejection has been performed, 
303 outliers have been identified. 

Performing a round of error model refinement.

Error model details:
  Type: basic
  Parameters: a = 0.48274, b = 0.05955
  Error model formula: σ'² = a²(σ² + (bI)²)
  estimated I/sigma asymptotic limit: 34.786

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 |
|--------------------------+----------+------------------------+----------------------|
| 1453.11 - 440.26         |      250 |                  1.775 |                0.889 |
| 440.26 - 316.04          |      250 |                  1.239 |                0.933 |
| 316.04 - 256.09          |      250 |                  1.052 |                1.087 |
| 256.09 - 215.99          |      250 |                  0.897 |                1.004 |
| 215.99 - 185.52          |      250 |                  1.084 |                1.401 |
| 185.52 - 127.00          |      883 |                  0.583 |                0.993 |
| 127.00 - 84.60           |     1266 |                  0.495 |                1.082 |
| 84.60 - 56.36            |     1471 |                  0.441 |                1.233 |
| 56.36 - 37.54            |     1571 |                  0.404 |                1.295 |
| 37.54 - 25.00            |     1194 |                  0.389 |                1.397 |
+--------------------------+----------+------------------------+----------------------+


The reflection table variances have been adjusted to account for the
uncertainty in the scaling model

Total time taken: 37.6982s 

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

48.08% of model parameters have signficant uncertainty
(sigma/abs(parameter) > 0.5)

Summary of dataset partialities
+------------------+----------+
| Partiality (p)   |   n_refl |
|------------------+----------|
| all reflections  |   205698 |
| p > 0.99         |   192601 |
| 0.5 < p < 0.99   |     3716 |
| 0.01 < p < 0.5   |     5838 |
| p < 0.01         |     3543 |
+------------------+----------+

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   cc1/2   cc_ano
110.44   3.23  14966   4215    3.55  99.79      53.0    17.6    0.057    0.067    0.035   0.997*   0.073*
  3.23   2.56  14719   4145    3.55  99.95      16.7     8.7    0.137    0.161    0.085   0.960*   0.023
  2.56   2.24  15257   4111    3.71  99.95       7.4     4.8    0.255    0.298    0.153   0.961*  -0.053
  2.24   2.03  13717   4075    3.37  99.71       5.0     3.2    0.383    0.461    0.253   0.563*  -0.008
  2.03   1.89  14985   4123    3.63  99.59       2.7     1.9    0.611    0.718    0.372   0.832*   0.036
  1.89   1.78  14232   4099    3.47  99.64       1.4     1.1    1.031    1.222    0.643   0.649*  -0.002
  1.78   1.69  12400   4076    3.04  99.51       0.8     0.6    1.568    1.905    1.063   0.448*   0.007
  1.69   1.61  11558   4095    2.82  99.47       0.5     0.4    2.457    3.042    1.762   0.186*  -0.065
  1.61   1.55  10060   3991    2.52  97.60       0.4     0.3    3.298    4.126    2.433   0.095*  -0.049
  1.55   1.50   9205   3953    2.33  97.53       0.3     0.2    3.946    4.965    2.959   0.094*  -0.010
  1.50   1.45   8557   3827    2.24  93.21       0.2     0.1    6.912    8.769    5.308   0.073*  -0.030
  1.45   1.41   7858   3855    2.04  93.50       0.1     0.1   10.410   13.382    8.287   0.029  -0.115
  1.41   1.37   5417   3270    1.66  80.62       0.1     0.0   11.602   15.242    9.746   0.009  -0.006
  1.37   1.34   3923   2729    1.44  67.04       0.0     0.0   57.539   77.077   50.702  -0.035   0.236
  1.34   1.31   2609   2116    1.23  51.50       0.0     0.0    5.854    8.027    5.459  -0.001  -0.004
  1.31   1.28   2019   1720    1.17  42.84      -0.0     0.0   45.934   64.554   45.307  -0.052   0.000
  1.28   1.26   1444   1244    1.16  30.14      -0.0     0.0   41.258   58.348   41.258   0.034   0.000
  1.26   1.23   1024    896    1.14  22.19       0.1     0.1   14.846   20.995   14.846  -0.052   0.000
  1.23   1.21    604    539    1.12  12.99      -0.0     0.0   25.038   35.409   25.038   0.045   0.000
  1.21   1.19    212    188    1.13   4.66       0.6     0.2   -2.797   -3.956   -2.797   0.024   0.000
109.97   1.19 164766  61267    2.69  74.69       6.0     2.7    0.202    0.244    0.134   0.985*  -0.006


Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.63

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

                                            Suggested   Low    High  Overall
High resolution limit                           1.63    4.43    1.63    1.19
Low resolution limit                          109.97  110.22    1.66  109.97
Completeness                                   99.7    99.7    99.6    74.7
Multiplicity                                    3.4     3.6     2.8     2.7
I/sigma                                         5.0    19.4     0.4     2.7
Rmerge(I)                                     0.160   0.047   2.539   0.202
Rmerge(I+/-)                                  0.133   0.039   2.296   0.160
Rmeas(I)                                      0.189   0.054   3.135   0.244
Rmeas(I+/-)                                   0.180   0.053   3.148   0.217
Rpim(I)                                       0.100   0.028   1.807   0.134
Rpim(I+/-)                                    0.121   0.035   2.144   0.146
CC half                                       0.986   0.998   0.250   0.985
Anomalous completeness                         92.1    95.9    87.6    53.2
Anomalous multiplicity                          1.8     2.0     1.5     1.6
Anomalous correlation                        -0.009   0.029  -0.102  -0.006
Anomalous slope                               0.812                        
dF/F                                          0.145                        
dI/s(dI)                                      0.794                        
Total observations                           108752    5924    4534  164766
Total unique                                  31817    1641    1598   61267

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

As can be seen from the output text, 52 parameters are used to parameterise the scaling model for this dataset. Outlier rejection is performed at several stages, as outliers have a disproportionately large effect during scaling and can lead to poor scaling results. During scaling, the distribution of the intensity uncertainties are also analysed and a correction is applied based on a prior expectation of the intensity error distribution. At the end of the output, a table and summary of the merging statistics are presented, which give indications of the quality of the scaled dataset:

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

 d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   cc1/2   cc_ano
110.44   3.23  14966   4215    3.55  99.79      53.0    17.6    0.057    0.067    0.035   0.997*   0.073*
  3.23   2.56  14719   4145    3.55  99.95      16.7     8.7    0.137    0.161    0.085   0.960*   0.023
  2.56   2.24  15257   4111    3.71  99.95       7.4     4.8    0.255    0.298    0.153   0.961*  -0.053
  2.24   2.03  13717   4075    3.37  99.71       5.0     3.2    0.383    0.461    0.253   0.563*  -0.008
  2.03   1.89  14985   4123    3.63  99.59       2.7     1.9    0.611    0.718    0.372   0.832*   0.036
  1.89   1.78  14232   4099    3.47  99.64       1.4     1.1    1.031    1.222    0.643   0.649*  -0.002
  1.78   1.69  12400   4076    3.04  99.51       0.8     0.6    1.568    1.905    1.063   0.448*   0.007
  1.69   1.61  11558   4095    2.82  99.47       0.5     0.4    2.457    3.042    1.762   0.186*  -0.065
  1.61   1.55  10060   3991    2.52  97.60       0.4     0.3    3.298    4.126    2.433   0.095*  -0.049
  1.55   1.50   9205   3953    2.33  97.53       0.3     0.2    3.946    4.965    2.959   0.094*  -0.010
  1.50   1.45   8557   3827    2.24  93.21       0.2     0.1    6.912    8.769    5.308   0.073*  -0.030
  1.45   1.41   7858   3855    2.04  93.50       0.1     0.1   10.410   13.382    8.287   0.029  -0.115
  1.41   1.37   5417   3270    1.66  80.62       0.1     0.0   11.602   15.242    9.746   0.009  -0.006
  1.37   1.34   3923   2729    1.44  67.04       0.0     0.0   57.539   77.077   50.702  -0.035   0.236
  1.34   1.31   2609   2116    1.23  51.50       0.0     0.0    5.854    8.027    5.459  -0.001  -0.004
  1.31   1.28   2019   1720    1.17  42.84      -0.0     0.0   45.934   64.554   45.307  -0.052   0.000
  1.28   1.26   1444   1244    1.16  30.14      -0.0     0.0   41.258   58.348   41.258   0.034   0.000
  1.26   1.23   1024    896    1.14  22.19       0.1     0.1   14.846   20.995   14.846  -0.052   0.000
  1.23   1.21    604    539    1.12  12.99      -0.0     0.0   25.038   35.409   25.038   0.045   0.000
  1.21   1.19    212    188    1.13   4.66       0.6     0.2   -2.797   -3.956   -2.797   0.024   0.000
109.97   1.19 164766  61267    2.69  74.69       6.0     2.7    0.202    0.244    0.134   0.985*  -0.006


Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.63

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

                                            Suggested   Low    High  Overall
High resolution limit                           1.63    4.43    1.63    1.19
Low resolution limit                          109.97  110.22    1.66  109.97
Completeness                                   99.7    99.7    99.6    74.7
Multiplicity                                    3.4     3.6     2.8     2.7
I/sigma                                         5.0    19.4     0.4     2.7
Rmerge(I)                                     0.160   0.047   2.539   0.202
Rmerge(I+/-)                                  0.133   0.039   2.296   0.160
Rmeas(I)                                      0.189   0.054   3.135   0.244
Rmeas(I+/-)                                   0.180   0.053   3.148   0.217
Rpim(I)                                       0.100   0.028   1.807   0.134
Rpim(I+/-)                                    0.121   0.035   2.144   0.146
CC half                                       0.986   0.998   0.250   0.985
Anomalous completeness                         92.1    95.9    87.6    53.2
Anomalous multiplicity                          1.8     2.0     1.5     1.6
Anomalous correlation                        -0.009   0.029  -0.102  -0.006
Anomalous slope                               0.812                        
dF/F                                          0.145                        
dI/s(dI)                                      0.794                        
Total observations                           108752    5924    4534  164766
Total unique                                  31817    1641    1598   61267

Looking at the resolution-dependent merging statistics, we can see that the CC1/2 falls significantly beyond about 1.65 Å resolution. If desired, a resolution cutoff can be applied and the data rescaled (using the output of the previous scaling run as input to the next run to load the existing state of the scaling model):

dials.scale scaled.expt scaled.refl d_min=1.65

The merging statistics, as well as a number of scaling and merging plots, are output into a html report called dials.scale.html. This can be opened in your browser - navigate to the section “scaling model plots” and take a look. The two peaks in the scale term are at angles 180° apart. This indicates that the way the illuminated volume changed during the experiment, with the volumes at positions 180° apart being very similar. significantly during the experiment: a reflection would be measured as almost twice as intense if it was measured at rotation angle of ~120° compared to at ~210°. The absorption surface parameters are fairly flat across the whole experiment and the relative B-factor shows low overall variation, suggesting little overall radiation damage.

Once we are happy with the dataset quality, the final step of dials processing is to merge the data and produce a merged mtz file, suitable for input to downstream structure solution. To do this we can use the command:

dials.merge scaled.expt scaled.refl

The log output reports intensity statistics, the symmetry equivalent reflections are merged and a truncation procedure is performed, to give strictly positive merged structure factors (Fs) in addition to merged intensities.

HTML report

Much more information from the various steps of data processing can be found within an HTML report generated using the program dials.report. This is run simply with:

dials.report scaled.expt scaled.refl

which produces the file dials.report.html.

This report includes plots showing the scan-varying crystal orientation and unit cell parameters. The latter of these is useful to check that changes to the cell during processing appear reasonable. We can at least see from this and the low final refined RMSDs that this is a very well- behaved dataset.

Some of the most useful plots are

  • Difference between observed and calculated centroids vs phi, which shows how the average residuals in each of X, Y, and φ vary as a fuction of φ. If scan-varying refinement has been successful in capturing the real changes during the scan then we would expect these plots to be straight lines.

  • Centroid residuals in X and Y, in which the X, Y residuals are shown directly. The key point here is to look for a globular shape centred at the origin.

  • Difference between observed and calculated centroids in X and Y, which show the difference between predicted and observed reflection positions in either X or Y as functions of detector position. From these plots it is very easy to see whole tiles that are worse than their neighbours, and whether those tiles might be simply shifted or slightly rotated compared to the model detector.

  • Reflection and reference correlations binned in X/Y. These are useful companions to the plots of centroid residual as a function of detector position above. Whereas the above plots show systematic errors in the positions and orientations of tiles of a multi-panel detector, these plots indicate what effect that (and any other position-specific systematic error) has on the integrated data quality. The first of these plots shows the correlation between reflections and their reference profiles for all reflections in the dataset. The second shows only the correlations between the strong reference reflections and their profiles (thus these are expected to be higher and do not extend to such high resolution).

  • Distribution of I/Sigma vs Z. This reproduces the \(\frac{I}{\sigma_I}\) information versus frame number given in the log file in a graphical form. Here we see that \(\frac{I}{\sigma_I}\) is fairly flat over the whole dataset, which we might use as an indication that there were no bad frames, not much radiation damage occurred and that scale factors are likely to be fairly uniform.

Exporting to unmerged MTZ

It is possible that an unmerged mtz file is desired for further processing before merging. To produce a scaled unmerged mtz file, one can use the dials.export command on the scaled datafiles:

dials.export scaled.refl scaled.expt

It is also possible to export the integrated (unscaled) data in mtz format using dials.export. If you have an installation of CCP4, symmetry analysis and scaling can then be continued with the ccp4 programs pointless, aimless and ctruncate to generate a merged mtz file:

dials.export integrated.refl integrated.expt
pointless hklin integrated.mtz hklout sorted.mtz > pointless.log
aimless hklin sorted.mtz hklout scaled.mtz > aimless.log << EOF
resolution 1.4
anomalous off
EOF
ctruncate -hklin scaled.mtz -hklout truncated.mtz \
-colin '/*/*/[IMEAN,SIGIMEAN]' > ctruncate.log