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 
.
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/science/groups/scisoft/DIALS/dials_data/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.1293-g7efd2982c
The following parameters have been modified:
input {
experiments = <image files>
}
--------------------------------------------------------------------------------
format: <class 'dxtbx.format.FormatCBFMiniPilatus.FormatCBFMiniPilatus'>
template: /dls/science/groups/scisoft/DIALS/dials_data/mpro_x0692/Mpro-x0692_1_####.cbf:1:400
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:
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 DIALS will use multiple processors by default to speed this up. Here we have limited it to 4, but feel free to omit this to let DIALS make the choice:
dials.find_spots imported.expt nproc=4
Show/Hide Log
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3
4spotfinder {
5 mp {
6 nproc = 4
7 }
8}
9input {
10 experiments = imported.expt
11}
12
13Setting spotfinder.filter.min_spot_size=3
14Configuring spot finder from input parameters
15--------------------------------------------------------------------------------
16Finding strong spots in imageset 0
17--------------------------------------------------------------------------------
18
19Finding spots in image 1 to 400...
20Setting chunksize=20
21Extracting strong pixels from images
22 Using multiprocessing with 4 parallel job(s)
23
24Found 1591 strong pixels on image 1
25Found 1722 strong pixels on image 2
26Found 1720 strong pixels on image 3
27Found 1811 strong pixels on image 4
28Found 1684 strong pixels on image 5
29Found 1766 strong pixels on image 6
30Found 1684 strong pixels on image 7
31Found 1960 strong pixels on image 8
32Found 2123 strong pixels on image 9
33Found 2048 strong pixels on image 10
34Found 1926 strong pixels on image 11
35Found 2081 strong pixels on image 12
36Found 2282 strong pixels on image 13
37Found 2376 strong pixels on image 14
38Found 2007 strong pixels on image 15
39Found 2167 strong pixels on image 16
40Found 2367 strong pixels on image 17
41Found 2202 strong pixels on image 18
42Found 2280 strong pixels on image 19
43Found 2535 strong pixels on image 20
44Found 2784 strong pixels on image 21
45Found 2473 strong pixels on image 22
46Found 2386 strong pixels on image 23
47Found 2785 strong pixels on image 24
48Found 2816 strong pixels on image 25
49Found 2810 strong pixels on image 26
50Found 2647 strong pixels on image 27
51Found 2712 strong pixels on image 28
52Found 2892 strong pixels on image 29
53Found 2844 strong pixels on image 30
54Found 2724 strong pixels on image 31
55Found 2743 strong pixels on image 32
56Found 2817 strong pixels on image 33
57Found 2936 strong pixels on image 34
58Found 2864 strong pixels on image 35
59Found 2712 strong pixels on image 36
60Found 2757 strong pixels on image 37
61Found 2627 strong pixels on image 38
62Found 2358 strong pixels on image 39
63Found 2586 strong pixels on image 40
64Found 2689 strong pixels on image 41
65Found 2509 strong pixels on image 42
66Found 2694 strong pixels on image 43
67Found 2604 strong pixels on image 44
68Found 2497 strong pixels on image 45
69Found 2627 strong pixels on image 46
70Found 2424 strong pixels on image 47
71Found 2702 strong pixels on image 48
72Found 2504 strong pixels on image 49
73Found 2492 strong pixels on image 50
74Found 2546 strong pixels on image 51
75Found 2352 strong pixels on image 52
76Found 2412 strong pixels on image 53
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78Found 2530 strong pixels on image 55
79Found 2739 strong pixels on image 56
80Found 2729 strong pixels on image 57
81Found 2764 strong pixels on image 58
82Found 2587 strong pixels on image 59
83Found 2434 strong pixels on image 60
84Found 2451 strong pixels on image 61
85Found 2478 strong pixels on image 62
86Found 2250 strong pixels on image 63
87Found 2264 strong pixels on image 64
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90Found 2362 strong pixels on image 67
91Found 2479 strong pixels on image 68
92Found 2439 strong pixels on image 69
93Found 2439 strong pixels on image 70
94Found 2429 strong pixels on image 71
95Found 2432 strong pixels on image 72
96Found 2129 strong pixels on image 73
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98Found 2544 strong pixels on image 75
99Found 2517 strong pixels on image 76
100Found 2311 strong pixels on image 77
101Found 2548 strong pixels on image 78
102Found 2729 strong pixels on image 79
103Found 2458 strong pixels on image 80
104Found 2359 strong pixels on image 81
105Found 2183 strong pixels on image 82
106Found 2117 strong pixels on image 83
107Found 2561 strong pixels on image 84
108Found 2499 strong pixels on image 85
109Found 2443 strong pixels on image 86
110Found 2251 strong pixels on image 87
111Found 2383 strong pixels on image 88
112Found 2256 strong pixels on image 89
113Found 2282 strong pixels on image 90
114Found 2468 strong pixels on image 91
115Found 2393 strong pixels on image 92
116Found 2303 strong pixels on image 93
117Found 2059 strong pixels on image 94
118Found 1929 strong pixels on image 95
119Found 2022 strong pixels on image 96
120Found 2023 strong pixels on image 97
121Found 1926 strong pixels on image 98
122Found 1901 strong pixels on image 99
123Found 1589 strong pixels on image 100
124Found 1885 strong pixels on image 101
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128Found 1889 strong pixels on image 105
129Found 1719 strong pixels on image 106
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131Found 1670 strong pixels on image 108
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133Found 1630 strong pixels on image 110
134Found 1799 strong pixels on image 111
135Found 1805 strong pixels on image 112
136Found 1589 strong pixels on image 113
137Found 1549 strong pixels on image 114
138Found 1797 strong pixels on image 115
139Found 1872 strong pixels on image 116
140Found 1549 strong pixels on image 117
141Found 1456 strong pixels on image 118
142Found 1344 strong pixels on image 119
143Found 1454 strong pixels on image 120
144Found 1589 strong pixels on image 121
145Found 1628 strong pixels on image 122
146Found 1657 strong pixels on image 123
147Found 1643 strong pixels on image 124
148Found 1613 strong pixels on image 125
149Found 1642 strong pixels on image 126
150Found 1624 strong pixels on image 127
151Found 1529 strong pixels on image 128
152Found 1486 strong pixels on image 129
153Found 1531 strong pixels on image 130
154Found 1646 strong pixels on image 131
155Found 1514 strong pixels on image 132
156Found 1583 strong pixels on image 133
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159Found 1305 strong pixels on image 136
160Found 1326 strong pixels on image 137
161Found 1356 strong pixels on image 138
162Found 1406 strong pixels on image 139
163Found 1366 strong pixels on image 140
164Found 1358 strong pixels on image 141
165Found 1164 strong pixels on image 142
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167Found 1232 strong pixels on image 144
168Found 1344 strong pixels on image 145
169Found 1487 strong pixels on image 146
170Found 1359 strong pixels on image 147
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172Found 1323 strong pixels on image 149
173Found 1293 strong pixels on image 150
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178Found 1245 strong pixels on image 155
179Found 1308 strong pixels on image 156
180Found 1395 strong pixels on image 157
181Found 1431 strong pixels on image 158
182Found 1261 strong pixels on image 159
183Found 1125 strong pixels on image 160
184Found 1111 strong pixels on image 161
185Found 1123 strong pixels on image 162
186Found 1011 strong pixels on image 163
187Found 1022 strong pixels on image 164
188Found 1182 strong pixels on image 165
189Found 1132 strong pixels on image 166
190Found 1192 strong pixels on image 167
191Found 1273 strong pixels on image 168
192Found 1366 strong pixels on image 169
193Found 1185 strong pixels on image 170
194Found 1146 strong pixels on image 171
195Found 1154 strong pixels on image 172
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198Found 1094 strong pixels on image 175
199Found 1119 strong pixels on image 176
200Found 1179 strong pixels on image 177
201Found 1096 strong pixels on image 178
202Found 941 strong pixels on image 179
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204Found 956 strong pixels on image 181
205Found 1067 strong pixels on image 182
206Found 1082 strong pixels on image 183
207Found 1090 strong pixels on image 184
208Found 1067 strong pixels on image 185
209Found 1193 strong pixels on image 186
210Found 1075 strong pixels on image 187
211Found 1040 strong pixels on image 188
212Found 1221 strong pixels on image 189
213Found 1139 strong pixels on image 190
214Found 1067 strong pixels on image 191
215Found 1150 strong pixels on image 192
216Found 1085 strong pixels on image 193
217Found 1021 strong pixels on image 194
218Found 1172 strong pixels on image 195
219Found 1130 strong pixels on image 196
220Found 1226 strong pixels on image 197
221Found 995 strong pixels on image 198
222Found 1039 strong pixels on image 199
223Found 1018 strong pixels on image 200
224Found 944 strong pixels on image 201
225Found 1235 strong pixels on image 202
226Found 1273 strong pixels on image 203
227Found 1081 strong pixels on image 204
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229Found 974 strong pixels on image 206
230Found 989 strong pixels on image 207
231Found 874 strong pixels on image 208
232Found 1042 strong pixels on image 209
233Found 1157 strong pixels on image 210
234Found 1094 strong pixels on image 211
235Found 932 strong pixels on image 212
236Found 1100 strong pixels on image 213
237Found 1162 strong pixels on image 214
238Found 1152 strong pixels on image 215
239Found 1078 strong pixels on image 216
240Found 1011 strong pixels on image 217
241Found 908 strong pixels on image 218
242Found 1045 strong pixels on image 219
243Found 1093 strong pixels on image 220
244Found 1195 strong pixels on image 221
245Found 1064 strong pixels on image 222
246Found 957 strong pixels on image 223
247Found 1024 strong pixels on image 224
248Found 1196 strong pixels on image 225
249Found 1041 strong pixels on image 226
250Found 1022 strong pixels on image 227
251Found 1037 strong pixels on image 228
252Found 1018 strong pixels on image 229
253Found 1101 strong pixels on image 230
254Found 942 strong pixels on image 231
255Found 1047 strong pixels on image 232
256Found 1156 strong pixels on image 233
257Found 1040 strong pixels on image 234
258Found 1024 strong pixels on image 235
259Found 962 strong pixels on image 236
260Found 983 strong pixels on image 237
261Found 954 strong pixels on image 238
262Found 994 strong pixels on image 239
263Found 1044 strong pixels on image 240
264Found 1119 strong pixels on image 241
265Found 1079 strong pixels on image 242
266Found 1123 strong pixels on image 243
267Found 990 strong pixels on image 244
268Found 1040 strong pixels on image 245
269Found 1060 strong pixels on image 246
270Found 1082 strong pixels on image 247
271Found 1054 strong pixels on image 248
272Found 1027 strong pixels on image 249
273Found 1090 strong pixels on image 250
274Found 1068 strong pixels on image 251
275Found 1070 strong pixels on image 252
276Found 1051 strong pixels on image 253
277Found 1126 strong pixels on image 254
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279Found 1005 strong pixels on image 256
280Found 1010 strong pixels on image 257
281Found 1173 strong pixels on image 258
282Found 1041 strong pixels on image 259
283Found 1171 strong pixels on image 260
284Found 939 strong pixels on image 261
285Found 1186 strong pixels on image 262
286Found 1195 strong pixels on image 263
287Found 1025 strong pixels on image 264
288Found 1105 strong pixels on image 265
289Found 1202 strong pixels on image 266
290Found 1067 strong pixels on image 267
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292Found 1025 strong pixels on image 269
293Found 1072 strong pixels on image 270
294Found 1135 strong pixels on image 271
295Found 1061 strong pixels on image 272
296Found 1150 strong pixels on image 273
297Found 976 strong pixels on image 274
298Found 1036 strong pixels on image 275
299Found 985 strong pixels on image 276
300Found 1061 strong pixels on image 277
301Found 1107 strong pixels on image 278
302Found 1223 strong pixels on image 279
303Found 1218 strong pixels on image 280
304Found 1187 strong pixels on image 281
305Found 1211 strong pixels on image 282
306Found 1211 strong pixels on image 283
307Found 1333 strong pixels on image 284
308Found 1101 strong pixels on image 285
309Found 1155 strong pixels on image 286
310Found 1188 strong pixels on image 287
311Found 1121 strong pixels on image 288
312Found 1067 strong pixels on image 289
313Found 1091 strong pixels on image 290
314Found 1161 strong pixels on image 291
315Found 1169 strong pixels on image 292
316Found 1058 strong pixels on image 293
317Found 1168 strong pixels on image 294
318Found 1085 strong pixels on image 295
319Found 1013 strong pixels on image 296
320Found 1075 strong pixels on image 297
321Found 1080 strong pixels on image 298
322Found 1230 strong pixels on image 299
323Found 1266 strong pixels on image 300
324Found 1120 strong pixels on image 301
325Found 1073 strong pixels on image 302
326Found 1076 strong pixels on image 303
327Found 1230 strong pixels on image 304
328Found 1184 strong pixels on image 305
329Found 1299 strong pixels on image 306
330Found 1268 strong pixels on image 307
331Found 1235 strong pixels on image 308
332Found 1168 strong pixels on image 309
333Found 1171 strong pixels on image 310
334Found 1131 strong pixels on image 311
335Found 1274 strong pixels on image 312
336Found 1082 strong pixels on image 313
337Found 1119 strong pixels on image 314
338Found 1314 strong pixels on image 315
339Found 1485 strong pixels on image 316
340Found 1395 strong pixels on image 317
341Found 1370 strong pixels on image 318
342Found 1355 strong pixels on image 319
343Found 1376 strong pixels on image 320
344Found 1396 strong pixels on image 321
345Found 1187 strong pixels on image 322
346Found 1226 strong pixels on image 323
347Found 1393 strong pixels on image 324
348Found 1289 strong pixels on image 325
349Found 1554 strong pixels on image 326
350Found 1417 strong pixels on image 327
351Found 1353 strong pixels on image 328
352Found 1396 strong pixels on image 329
353Found 1520 strong pixels on image 330
354Found 1372 strong pixels on image 331
355Found 1434 strong pixels on image 332
356Found 1539 strong pixels on image 333
357Found 1546 strong pixels on image 334
358Found 1819 strong pixels on image 335
359Found 1622 strong pixels on image 336
360Found 1615 strong pixels on image 337
361Found 1472 strong pixels on image 338
362Found 1359 strong pixels on image 339
363Found 1580 strong pixels on image 340
364Found 1499 strong pixels on image 341
365Found 1409 strong pixels on image 342
366Found 1631 strong pixels on image 343
367Found 1606 strong pixels on image 344
368Found 1768 strong pixels on image 345
369Found 1769 strong pixels on image 346
370Found 1584 strong pixels on image 347
371Found 1561 strong pixels on image 348
372Found 1661 strong pixels on image 349
373Found 1639 strong pixels on image 350
374Found 1703 strong pixels on image 351
375Found 1702 strong pixels on image 352
376Found 1807 strong pixels on image 353
377Found 1824 strong pixels on image 354
378Found 1681 strong pixels on image 355
379Found 1618 strong pixels on image 356
380Found 1526 strong pixels on image 357
381Found 1660 strong pixels on image 358
382Found 1599 strong pixels on image 359
383Found 1790 strong pixels on image 360
384Found 1818 strong pixels on image 361
385Found 1868 strong pixels on image 362
386Found 2004 strong pixels on image 363
387Found 1997 strong pixels on image 364
388Found 1920 strong pixels on image 365
389Found 1832 strong pixels on image 366
390Found 2053 strong pixels on image 367
391Found 2223 strong pixels on image 368
392Found 2036 strong pixels on image 369
393Found 2044 strong pixels on image 370
394Found 1893 strong pixels on image 371
395Found 2030 strong pixels on image 372
396Found 1870 strong pixels on image 373
397Found 1770 strong pixels on image 374
398Found 1919 strong pixels on image 375
399Found 1701 strong pixels on image 376
400Found 1867 strong pixels on image 377
401Found 1735 strong pixels on image 378
402Found 2016 strong pixels on image 379
403Found 2119 strong pixels on image 380
404Found 1848 strong pixels on image 381
405Found 1881 strong pixels on image 382
406Found 1810 strong pixels on image 383
407Found 1901 strong pixels on image 384
408Found 1898 strong pixels on image 385
409Found 1843 strong pixels on image 386
410Found 1842 strong pixels on image 387
411Found 1827 strong pixels on image 388
412Found 1807 strong pixels on image 389
413Found 1652 strong pixels on image 390
414Found 1764 strong pixels on image 391
415Found 1852 strong pixels on image 392
416Found 1731 strong pixels on image 393
417Found 1669 strong pixels on image 394
418Found 1551 strong pixels on image 395
419Found 1688 strong pixels on image 396
420Found 1591 strong pixels on image 397
421Found 1459 strong pixels on image 398
422Found 1396 strong pixels on image 399
423Found 1452 strong pixels on image 400
424
425Extracted 31365 spots
426Removed 8034 spots with size < 3 pixels
427Removed 3 spots with size > 1000 pixels
428Calculated 23328 spot centroids
429Calculated 23328 spot intensities
430Filtered 22492 of 23328 spots by peak-centroid distance
431
432Histogram of per-image spot count for imageset 0:
43322492 spots found on 400 images (max 510 / bin)
434**
435******* * **** *
436********* * ******************** *
437********* * ******************************
438************************************************* ** *
439************************************************************
440************************************************************
441************************************************************
442************************************************************
443************************************************************
4441 image 400
445
446--------------------------------------------------------------------------------
447Saved 22492 reflections to strong.refl
Once this has completed, a new reflection file
‘strong.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’.
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
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
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3
4input {
5 experiments = imported.expt
6 reflections = strong.refl
7}
8
9Found max_cell: 73.7 Angstrom
10Setting d_min: 1.56
11FFT gridding: (256,256,256)
12Number of centroids used: 21568
13Candidate solutions:
14+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
15| unit_cell | volume | volume score | #indexed | % indexed | % indexed score | rmsd_xy | rmsd_xy score | overall score |
16|------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------|
17| 44.60 53.36 62.55 115.2 101.8 90.1 | 131183 | 0.01 | 21695 | 96 | 0.01 | 0.13 | 0 | 0.01 |
18| 44.74 53.39 62.63 115.1 102.0 90.2 | 131784 | 0.01 | 21755 | 97 | 0 | 0.14 | 0.03 | 0.04 |
19| 44.60 53.25 62.49 115.0 101.8 90.2 | 130947 | 0 | 21641 | 96 | 0.01 | 0.14 | 0.04 | 0.05 |
20| 44.60 53.25 62.49 115.1 101.8 90.2 | 130920 | 0 | 21612 | 96 | 0.01 | 0.14 | 0.05 | 0.07 |
21| 44.54 53.34 62.54 115.1 101.8 90.2 | 130988 | 0 | 21553 | 96 | 0.01 | 0.14 | 0.05 | 0.07 |
22| 44.60 53.17 62.49 115.0 101.8 90.2 | 130748 | 0 | 21623 | 96 | 0.01 | 0.14 | 0.07 | 0.08 |
23| 44.71 53.41 62.57 64.8 78.1 89.8 | 131687 | 0.01 | 21729 | 97 | 0 | 0.14 | 0.08 | 0.09 |
24| 44.60 53.29 62.49 114.9 101.8 90.2 | 131181 | 0.01 | 21691 | 96 | 0.01 | 0.14 | 0.09 | 0.1 |
25| 44.60 53.25 62.71 115.1 101.8 90.2 | 131302 | 0.01 | 21639 | 96 | 0.01 | 0.14 | 0.08 | 0.1 |
26| 44.65 53.41 62.55 64.8 78.1 89.9 | 131526 | 0.01 | 21723 | 97 | 0 | 0.14 | 0.09 | 0.1 |
27| 44.71 53.41 62.71 64.9 78.1 89.8 | 132067 | 0.01 | 21699 | 96 | 0.01 | 0.14 | 0.08 | 0.1 |
28| 44.60 53.25 62.58 115.0 101.7 90.2 | 131244 | 0.01 | 21549 | 96 | 0.02 | 0.14 | 0.09 | 0.11 |
29| 44.60 53.41 62.49 115.1 101.8 90.0 | 131356 | 0.01 | 21688 | 96 | 0.01 | 0.14 | 0.11 | 0.12 |
30| 44.74 53.40 62.62 115.1 102.0 90.1 | 131757 | 0.01 | 21740 | 97 | 0 | 0.14 | 0.11 | 0.12 |
31| 44.60 53.25 62.47 115.1 101.8 90.2 | 130878 | 0 | 21683 | 96 | 0.01 | 0.14 | 0.12 | 0.13 |
32| 44.65 53.40 62.53 115.2 101.6 90.2 | 131503 | 0.01 | 21685 | 96 | 0.01 | 0.14 | 0.11 | 0.13 |
33| 44.61 53.34 62.45 115.1 101.7 90.1 | 131143 | 0 | 21719 | 97 | 0 | 0.14 | 0.12 | 0.13 |
34| 44.68 53.40 62.62 115.1 102.0 90.1 | 131574 | 0.01 | 21733 | 97 | 0 | 0.15 | 0.13 | 0.14 |
35| 44.59 53.29 62.39 115.0 101.6 90.1 | 130961 | 0 | 21733 | 97 | 0 | 0.15 | 0.14 | 0.15 |
36| 44.60 53.43 62.71 114.9 101.8 90.2 | 131909 | 0.01 | 21694 | 96 | 0.01 | 0.15 | 0.13 | 0.15 |
37| 44.46 53.41 62.34 115.1 101.5 90.0 | 130722 | 0 | 21697 | 96 | 0.01 | 0.15 | 0.15 | 0.15 |
38| 44.66 53.34 62.71 64.9 78.1 90.0 | 131699 | 0.01 | 21667 | 96 | 0.01 | 0.15 | 0.14 | 0.15 |
39| 44.60 53.43 62.53 115.0 101.7 90.2 | 131505 | 0.01 | 21716 | 97 | 0 | 0.15 | 0.15 | 0.16 |
40| 44.60 53.41 62.67 115.1 101.8 90.0 | 131632 | 0.01 | 21691 | 96 | 0.01 | 0.15 | 0.15 | 0.17 |
41| 44.60 53.40 62.62 64.9 78.1 89.9 | 131446 | 0.01 | 21757 | 97 | 0 | 0.15 | 0.16 | 0.17 |
42| 44.74 53.41 62.71 64.9 77.9 89.9 | 132024 | 0.01 | 21667 | 96 | 0.01 | 0.15 | 0.15 | 0.17 |
43| 44.60 53.41 62.55 115.2 101.8 90.0 | 131356 | 0.01 | 21719 | 97 | 0 | 0.15 | 0.16 | 0.17 |
44| 44.58 53.29 62.53 65.0 78.2 90.0 | 131102 | 0 | 21715 | 97 | 0 | 0.15 | 0.17 | 0.18 |
45| 44.60 53.43 62.49 114.9 101.8 90.2 | 131553 | 0.01 | 21703 | 96 | 0 | 0.15 | 0.18 | 0.19 |
46| 44.65 53.29 62.37 115.0 101.7 90.1 | 131075 | 0 | 21743 | 97 | 0 | 0.15 | 0.19 | 0.2 |
47| 44.60 53.43 62.41 115.1 101.8 90.2 | 131138 | 0 | 21742 | 97 | 0 | 0.15 | 0.19 | 0.2 |
48| 44.59 53.41 62.64 64.8 78.2 90.0 | 131525 | 0.01 | 21718 | 97 | 0 | 0.15 | 0.19 | 0.2 |
49| 44.46 53.41 62.53 115.2 101.6 90.0 | 130998 | 0 | 21710 | 97 | 0 | 0.15 | 0.2 | 0.2 |
50| 44.71 53.41 62.56 64.8 78.0 89.8 | 131618 | 0.01 | 21727 | 97 | 0 | 0.15 | 0.2 | 0.21 |
51| 44.71 53.41 62.70 115.2 101.9 90.2 | 131964 | 0.01 | 21776 | 97 | 0 | 0.15 | 0.2 | 0.21 |
52| 44.60 53.41 62.60 64.8 78.1 90.0 | 131338 | 0.01 | 21774 | 97 | 0 | 0.15 | 0.21 | 0.22 |
53| 44.74 53.29 62.71 114.8 102.1 90.1 | 132052 | 0.01 | 21698 | 96 | 0.01 | 0.15 | 0.2 | 0.22 |
54| 44.54 53.41 62.56 64.8 78.0 89.9 | 131086 | 0 | 21726 | 97 | 0 | 0.15 | 0.22 | 0.23 |
55| 44.74 53.29 62.71 65.0 77.9 90.0 | 131849 | 0.01 | 21684 | 96 | 0.01 | 0.15 | 0.22 | 0.24 |
56| 44.77 53.41 62.56 64.8 78.1 89.8 | 131801 | 0.01 | 21726 | 97 | 0 | 0.15 | 0.23 | 0.24 |
57| 44.46 53.41 62.71 115.1 101.7 90.0 | 131402 | 0.01 | 21683 | 96 | 0.01 | 0.16 | 0.24 | 0.26 |
58| 44.60 53.41 62.56 115.2 101.9 90.0 | 131265 | 0.01 | 21728 | 97 | 0 | 0.16 | 0.26 | 0.27 |
59| 44.61 53.41 62.71 115.1 101.9 90.0 | 131747 | 0.01 | 21675 | 96 | 0.01 | 0.16 | 0.25 | 0.27 |
60| 44.60 53.41 62.71 115.1 101.8 90.0 | 131712 | 0.01 | 21680 | 96 | 0.01 | 0.16 | 0.25 | 0.27 |
61| 44.65 53.28 62.36 115.0 101.7 90.1 | 131032 | 0 | 21741 | 97 | 0 | 0.16 | 0.28 | 0.28 |
62| 44.60 53.43 62.71 115.2 101.8 90.0 | 131708 | 0.01 | 21669 | 96 | 0.01 | 0.16 | 0.26 | 0.28 |
63| 44.65 53.41 62.56 64.8 78.3 90.0 | 131525 | 0.01 | 21730 | 97 | 0 | 0.16 | 0.29 | 0.3 |
64| 44.46 53.41 62.56 115.2 101.8 90.0 | 130957 | 0 | 21728 | 97 | 0 | 0.16 | 0.29 | 0.3 |
65| 44.49 53.40 62.62 64.9 78.5 90.0 | 131363 | 0.01 | 21755 | 97 | 0 | 0.16 | 0.3 | 0.31 |
66| 44.65 53.40 62.62 64.9 78.3 90.0 | 131706 | 0.01 | 21764 | 97 | 0 | 0.16 | 0.3 | 0.31 |
67+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
68Using d_min_step 0.0
69
70Indexed crystal models:
71model 1 (21695 reflections):
72Crystal:
73 Unit cell: 44.595, 53.361, 62.547, 115.167, 101.816, 90.135
74 Space group: P 1
75 U matrix: {{-0.8982, -0.4146, 0.1460},
76 {-0.2969, 0.8172, 0.4941},
77 {-0.3241, 0.4005, -0.8571}}
78 B matrix: {{ 0.0224, 0.0000, 0.0000},
79 { 0.0001, 0.0187, 0.0000},
80 { 0.0052, 0.0091, 0.0181}}
81 A = UB: {{-0.0194, -0.0064, 0.0026},
82 {-0.0040, 0.0198, 0.0090},
83 {-0.0117, -0.0003, -0.0155}}
84+------------+-------------+---------------+-------------+
85| Imageset | # indexed | # unindexed | % indexed |
86|------------+-------------+---------------+-------------|
87| 0 | 21695 | 796 | 96.5 |
88+------------+-------------+---------------+-------------+
89
90################################################################################
91Starting refinement (macro-cycle 1)
92################################################################################
93
94
95Summary statistics for 21640 observations matched to predictions:
96+-------------------+--------+---------+---------+---------+--------+
97| | Min | Q1 | Med | Q3 | Max |
98|-------------------+--------+---------+---------+---------+--------|
99| Xc - Xo (mm) | -1.192 | -0.436 | -0.38 | -0.3253 | 0.5261 |
100| Yc - Yo (mm) | -1.764 | -0.3128 | -0.2271 | -0.1394 | 1.674 |
101| Phic - Phio (deg) | -8.356 | -0.1271 | 0.01407 | 0.1253 | 8.607 |
102| X weights | 212.3 | 360.2 | 383.5 | 397.1 | 405.6 |
103| Y weights | 199.2 | 349.1 | 376.4 | 394.2 | 405.6 |
104| Phi weights | 31.78 | 47.24 | 47.78 | 48 | 48 |
105+-------------------+--------+---------+---------+---------+--------+
106
107Detecting centroid outliers using the Tukey algorithm
1082388 reflections have been flagged as outliers
10919252 reflections remain in the manager
110
111Summary statistics for 19252 observations matched to predictions:
112+-------------------+---------+---------+---------+---------+--------+
113| | Min | Q1 | Med | Q3 | Max |
114|-------------------+---------+---------+---------+---------+--------|
115| Xc - Xo (mm) | -1.192 | -0.4321 | -0.38 | -0.3287 | 0.381 |
116| Yc - Yo (mm) | -0.8454 | -0.3037 | -0.2259 | -0.1442 | 0.4329 |
117| Phic - Phio (deg) | -0.7886 | -0.1151 | 0.01473 | 0.1167 | 0.8122 |
118| X weights | 224.2 | 364.4 | 385.4 | 397.6 | 405.6 |
119| Y weights | 199.2 | 354.8 | 379.5 | 395.2 | 405.6 |
120| Phi weights | 37.24 | 47.24 | 47.74 | 48 | 48 |
121+-------------------+---------+---------+---------+---------+--------+
122
123There are 16 parameters to refine against 19252 reflections in 3 dimensions
124
125Refinement steps:
126+--------+--------+----------+----------+------------+
127| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
128| | | (mm) | (mm) | (deg) |
129|--------+--------+----------+----------+------------|
130| 0 | 19252 | 0.41293 | 0.26269 | 0.21238 |
131| 1 | 19252 | 0.11689 | 0.10407 | 0.21695 |
132| 2 | 19252 | 0.093959 | 0.096655 | 0.2231 |
133| 3 | 19252 | 0.087994 | 0.095296 | 0.22861 |
134| 4 | 19252 | 0.087102 | 0.095106 | 0.22963 |
135| 5 | 19252 | 0.087055 | 0.095109 | 0.22965 |
136| 6 | 19252 | 0.087057 | 0.095111 | 0.22964 |
137+--------+--------+----------+----------+------------+
138RMSD no longer decreasing
139
140RMSDs by experiment:
141+-------+--------+----------+----------+------------+
142| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
143| id | | (px) | (px) | (images) |
144|-------+--------+----------+----------+------------|
145| 0 | 19252 | 0.50615 | 0.55297 | 0.45929 |
146+-------+--------+----------+----------+------------+
147
148Refined crystal models:
149model 1 (21695 reflections):
150Crystal:
151 Unit cell: 44.479(5), 53.249(6), 62.503(7), 115.1901(12), 101.7852(11), 90.0042(11)
152 Space group: P 1
153 U matrix: {{-0.8995, -0.4115, 0.1466},
154 {-0.2939, 0.8183, 0.4939},
155 {-0.3233, 0.4012, -0.8570}}
156 B matrix: {{ 0.0225, 0.0000, 0.0000},
157 { 0.0000, 0.0188, 0.0000},
158 { 0.0052, 0.0091, 0.0181}}
159 A = UB: {{-0.0195, -0.0064, 0.0027},
160 {-0.0040, 0.0198, 0.0090},
161 {-0.0117, -0.0002, -0.0156}}
162+------------+-------------+---------------+-------------+
163| Imageset | # indexed | # unindexed | % indexed |
164|------------+-------------+---------------+-------------|
165| 0 | 21695 | 796 | 96.5 |
166+------------+-------------+---------------+-------------+
167
168Indexed crystal models:
169model 1 (21767 reflections):
170Crystal:
171 Unit cell: 44.479(5), 53.249(6), 62.503(7), 115.1901(12), 101.7852(11), 90.0042(11)
172 Space group: P 1
173 U matrix: {{-0.8995, -0.4115, 0.1466},
174 {-0.2939, 0.8183, 0.4939},
175 {-0.3233, 0.4012, -0.8570}}
176 B matrix: {{ 0.0225, 0.0000, 0.0000},
177 { 0.0000, 0.0188, 0.0000},
178 { 0.0052, 0.0091, 0.0181}}
179 A = UB: {{-0.0195, -0.0064, 0.0027},
180 {-0.0040, 0.0198, 0.0090},
181 {-0.0117, -0.0002, -0.0156}}
182+------------+-------------+---------------+-------------+
183| Imageset | # indexed | # unindexed | % indexed |
184|------------+-------------+---------------+-------------|
185| 0 | 21902 | 589 | 97.4 |
186+------------+-------------+---------------+-------------+
187
188################################################################################
189Starting refinement (macro-cycle 2)
190################################################################################
191
192
193Summary statistics for 21712 observations matched to predictions:
194+-------------------+--------+----------+------------+---------+--------+
195| | Min | Q1 | Med | Q3 | Max |
196|-------------------+--------+----------+------------+---------+--------|
197| Xc - Xo (mm) | -0.788 | -0.04762 | 0.001191 | 0.04832 | 0.5832 |
198| Yc - Yo (mm) | -1.701 | -0.04956 | -0.0002726 | 0.04513 | 3.318 |
199| Phic - Phio (deg) | -7.993 | -0.09028 | 0.05623 | 0.1478 | 7.67 |
200| X weights | 224.2 | 360.1 | 383.5 | 397.1 | 405.6 |
201| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
202| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
203+-------------------+--------+----------+------------+---------+--------+
204
205Detecting centroid outliers using the Tukey algorithm
2062747 reflections have been flagged as outliers
20718965 reflections remain in the manager
208
209Summary statistics for 18965 observations matched to predictions:
210+-------------------+---------+----------+----------+---------+--------+
211| | Min | Q1 | Med | Q3 | Max |
212|-------------------+---------+----------+----------+---------+--------|
213| Xc - Xo (mm) | -0.3448 | -0.04196 | 0.003587 | 0.04835 | 0.3273 |
214| Yc - Yo (mm) | -0.3992 | -0.03924 | 0.001483 | 0.04152 | 0.4155 |
215| Phic - Phio (deg) | -0.9095 | -0.06754 | 0.05941 | 0.1417 | 0.6436 |
216| X weights | 224.2 | 364 | 385.4 | 397.6 | 405.6 |
217| Y weights | 199.2 | 355.2 | 379.7 | 395.3 | 405.6 |
218| Phi weights | 38.65 | 47.26 | 47.75 | 48 | 48 |
219+-------------------+---------+----------+----------+---------+--------+
220
221There are 16 parameters to refine against 18965 reflections in 3 dimensions
222
223Refinement steps:
224+--------+--------+----------+----------+------------+
225| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
226| | | (mm) | (mm) | (deg) |
227|--------+--------+----------+----------+------------|
228| 0 | 18965 | 0.080671 | 0.083782 | 0.21438 |
229| 1 | 18965 | 0.079679 | 0.082388 | 0.21724 |
230| 2 | 18965 | 0.078936 | 0.08237 | 0.21803 |
231| 3 | 18965 | 0.078591 | 0.082399 | 0.21846 |
232| 4 | 18965 | 0.078517 | 0.082426 | 0.21853 |
233| 5 | 18965 | 0.078511 | 0.082435 | 0.21852 |
234| 6 | 18965 | 0.078511 | 0.082435 | 0.21852 |
235+--------+--------+----------+----------+------------+
236RMSD no longer decreasing
237
238RMSDs by experiment:
239+-------+--------+----------+----------+------------+
240| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
241| id | | (px) | (px) | (images) |
242|-------+--------+----------+----------+------------|
243| 0 | 18965 | 0.45646 | 0.47927 | 0.43705 |
244+-------+--------+----------+----------+------------+
245
246Refined crystal models:
247model 1 (21767 reflections):
248Crystal:
249 Unit cell: 44.444(5), 53.202(6), 62.452(7), 115.1861(11), 101.7810(10), 90.0081(10)
250 Space group: P 1
251 U matrix: {{-0.8997, -0.4113, 0.1465},
252 {-0.2937, 0.8183, 0.4940},
253 {-0.3230, 0.4014, -0.8570}}
254 B matrix: {{ 0.0225, 0.0000, 0.0000},
255 { 0.0000, 0.0188, 0.0000},
256 { 0.0052, 0.0091, 0.0182}}
257 A = UB: {{-0.0195, -0.0064, 0.0027},
258 {-0.0040, 0.0199, 0.0090},
259 {-0.0117, -0.0002, -0.0156}}
260+------------+-------------+---------------+-------------+
261| Imageset | # indexed | # unindexed | % indexed |
262|------------+-------------+---------------+-------------|
263| 0 | 21767 | 724 | 96.8 |
264+------------+-------------+---------------+-------------+
265
266Indexed crystal models:
267model 1 (21765 reflections):
268Crystal:
269 Unit cell: 44.444(5), 53.202(6), 62.452(7), 115.1861(11), 101.7810(10), 90.0081(10)
270 Space group: P 1
271 U matrix: {{-0.8997, -0.4113, 0.1465},
272 {-0.2937, 0.8183, 0.4940},
273 {-0.3230, 0.4014, -0.8570}}
274 B matrix: {{ 0.0225, 0.0000, 0.0000},
275 { 0.0000, 0.0188, 0.0000},
276 { 0.0052, 0.0091, 0.0182}}
277 A = UB: {{-0.0195, -0.0064, 0.0027},
278 {-0.0040, 0.0199, 0.0090},
279 {-0.0117, -0.0002, -0.0156}}
280+------------+-------------+---------------+-------------+
281| Imageset | # indexed | # unindexed | % indexed |
282|------------+-------------+---------------+-------------|
283| 0 | 21793 | 698 | 96.9 |
284+------------+-------------+---------------+-------------+
285
286################################################################################
287Starting refinement (macro-cycle 3)
288################################################################################
289
290
291Summary statistics for 21710 observations matched to predictions:
292+-------------------+---------+----------+-----------+---------+--------+
293| | Min | Q1 | Med | Q3 | Max |
294|-------------------+---------+----------+-----------+---------+--------|
295| Xc - Xo (mm) | -0.7938 | -0.04601 | 0.001013 | 0.04621 | 0.6398 |
296| Yc - Yo (mm) | -1.704 | -0.05073 | -0.001444 | 0.04437 | 3.268 |
297| Phic - Phio (deg) | -8.001 | -0.1013 | 0.0515 | 0.1469 | 7.494 |
298| X weights | 224.2 | 360.1 | 383.4 | 397.1 | 405.6 |
299| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
300| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
301+-------------------+---------+----------+-----------+---------+--------+
302
303Detecting centroid outliers using the Tukey algorithm
3042823 reflections have been flagged as outliers
30518887 reflections remain in the manager
306
307Summary statistics for 18887 observations matched to predictions:
308+-------------------+---------+----------+-----------+---------+--------+
309| | Min | Q1 | Med | Q3 | Max |
310|-------------------+---------+----------+-----------+---------+--------|
311| Xc - Xo (mm) | -0.3346 | -0.04068 | 0.002551 | 0.04559 | 0.3102 |
312| Yc - Yo (mm) | -0.3945 | -0.04045 | 0.0001806 | 0.04093 | 0.4199 |
313| Phic - Phio (deg) | -0.9259 | -0.07615 | 0.05538 | 0.1399 | 0.5948 |
314| X weights | 224.2 | 364.1 | 385.4 | 397.6 | 405.6 |
315| Y weights | 199.2 | 355.4 | 379.8 | 395.3 | 405.6 |
316| Phi weights | 38.65 | 47.26 | 47.75 | 48 | 48 |
317+-------------------+---------+----------+-----------+---------+--------+
318
319There are 16 parameters to refine against 18887 reflections in 3 dimensions
320
321Refinement steps:
322+--------+--------+----------+----------+------------+
323| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
324| | | (mm) | (mm) | (deg) |
325|--------+--------+----------+----------+------------|
326| 0 | 18887 | 0.077605 | 0.081945 | 0.21645 |
327| 1 | 18887 | 0.077382 | 0.081447 | 0.21791 |
328| 2 | 18887 | 0.077184 | 0.081468 | 0.21817 |
329| 3 | 18887 | 0.077075 | 0.081498 | 0.21829 |
330| 4 | 18887 | 0.077046 | 0.08152 | 0.2183 |
331| 5 | 18887 | 0.077041 | 0.081526 | 0.21829 |
332+--------+--------+----------+----------+------------+
333RMSD no longer decreasing
334
335RMSDs by experiment:
336+-------+--------+----------+----------+------------+
337| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
338| id | | (px) | (px) | (images) |
339|-------+--------+----------+----------+------------|
340| 0 | 18887 | 0.44792 | 0.47399 | 0.43659 |
341+-------+--------+----------+----------+------------+
342
343Refined crystal models:
344model 1 (21765 reflections):
345Crystal:
346 Unit cell: 44.422(5), 53.173(6), 62.420(7), 115.1858(11), 101.7790(10), 90.0096(10)
347 Space group: P 1
348 U matrix: {{-0.8997, -0.4112, 0.1464},
349 {-0.2937, 0.8184, 0.4940},
350 {-0.3230, 0.4015, -0.8570}}
351 B matrix: {{ 0.0225, 0.0000, 0.0000},
352 { 0.0000, 0.0188, 0.0000},
353 { 0.0052, 0.0091, 0.0182}}
354 A = UB: {{-0.0195, -0.0064, 0.0027},
355 {-0.0040, 0.0199, 0.0090},
356 {-0.0117, -0.0002, -0.0156}}
357+------------+-------------+---------------+-------------+
358| Imageset | # indexed | # unindexed | % indexed |
359|------------+-------------+---------------+-------------|
360| 0 | 21765 | 726 | 96.8 |
361+------------+-------------+---------------+-------------+
362
363Indexed crystal models:
364model 1 (21765 reflections):
365Crystal:
366 Unit cell: 44.422(5), 53.173(6), 62.420(7), 115.1858(11), 101.7790(10), 90.0096(10)
367 Space group: P 1
368 U matrix: {{-0.8997, -0.4112, 0.1464},
369 {-0.2937, 0.8184, 0.4940},
370 {-0.3230, 0.4015, -0.8570}}
371 B matrix: {{ 0.0225, 0.0000, 0.0000},
372 { 0.0000, 0.0188, 0.0000},
373 { 0.0052, 0.0091, 0.0182}}
374 A = UB: {{-0.0195, -0.0064, 0.0027},
375 {-0.0040, 0.0199, 0.0090},
376 {-0.0117, -0.0002, -0.0156}}
377+------------+-------------+---------------+-------------+
378| Imageset | # indexed | # unindexed | % indexed |
379|------------+-------------+---------------+-------------|
380| 0 | 21772 | 719 | 96.8 |
381+------------+-------------+---------------+-------------+
382
383################################################################################
384Starting refinement (macro-cycle 4)
385################################################################################
386
387
388Summary statistics for 21710 observations matched to predictions:
389+-------------------+--------+----------+-----------+---------+--------+
390| | Min | Q1 | Med | Q3 | Max |
391|-------------------+--------+----------+-----------+---------+--------|
392| Xc - Xo (mm) | -0.796 | -0.04533 | 0.001171 | 0.04591 | 0.6648 |
393| Yc - Yo (mm) | -1.708 | -0.05117 | -0.001873 | 0.04449 | 3.221 |
394| Phic - Phio (deg) | -8.05 | -0.1044 | 0.05058 | 0.1472 | 7.407 |
395| X weights | 224.2 | 360.1 | 383.4 | 397.1 | 405.6 |
396| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
397| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
398+-------------------+--------+----------+-----------+---------+--------+
399
400Detecting centroid outliers using the Tukey algorithm
4012844 reflections have been flagged as outliers
40218866 reflections remain in the manager
403
404Summary statistics for 18866 observations matched to predictions:
405+-------------------+---------+----------+------------+---------+--------+
406| | Min | Q1 | Med | Q3 | Max |
407|-------------------+---------+----------+------------+---------+--------|
408| Xc - Xo (mm) | -0.3283 | -0.04011 | 0.002532 | 0.04509 | 0.3081 |
409| Yc - Yo (mm) | -0.4047 | -0.04152 | -0.0004137 | 0.04038 | 0.4145 |
410| Phic - Phio (deg) | -0.931 | -0.07883 | 0.05394 | 0.1403 | 0.6102 |
411| X weights | 224.2 | 364.2 | 385.5 | 397.7 | 405.6 |
412| Y weights | 199.2 | 355.4 | 379.9 | 395.3 | 405.6 |
413| Phi weights | 38.65 | 47.26 | 47.75 | 48 | 48 |
414+-------------------+---------+----------+------------+---------+--------+
415
416There are 16 parameters to refine against 18866 reflections in 3 dimensions
417
418Refinement steps:
419+--------+--------+----------+----------+------------+
420| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
421| | | (mm) | (mm) | (deg) |
422|--------+--------+----------+----------+------------|
423| 0 | 18866 | 0.076822 | 0.081447 | 0.21765 |
424| 1 | 18866 | 0.076758 | 0.081219 | 0.21832 |
425| 2 | 18866 | 0.076694 | 0.081231 | 0.21839 |
426| 3 | 18866 | 0.076656 | 0.081247 | 0.21843 |
427| 4 | 18866 | 0.076644 | 0.081258 | 0.21842 |
428| 5 | 18866 | 0.076643 | 0.081261 | 0.21842 |
429+--------+--------+----------+----------+------------+
430RMSD no longer decreasing
431
432RMSDs by experiment:
433+-------+--------+----------+----------+------------+
434| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
435| id | | (px) | (px) | (images) |
436|-------+--------+----------+----------+------------|
437| 0 | 18866 | 0.4456 | 0.47244 | 0.43684 |
438+-------+--------+----------+----------+------------+
439
440Refined crystal models:
441model 1 (21765 reflections):
442Crystal:
443 Unit cell: 44.412(5), 53.160(6), 62.404(7), 115.1854(11), 101.7782(10), 90.0103(10)
444 Space group: P 1
445 U matrix: {{-0.8997, -0.4112, 0.1464},
446 {-0.2936, 0.8184, 0.4940},
447 {-0.3229, 0.4015, -0.8570}}
448 B matrix: {{ 0.0225, 0.0000, 0.0000},
449 { 0.0000, 0.0188, 0.0000},
450 { 0.0052, 0.0091, 0.0182}}
451 A = UB: {{-0.0195, -0.0064, 0.0027},
452 {-0.0040, 0.0199, 0.0090},
453 {-0.0117, -0.0002, -0.0156}}
454+------------+-------------+---------------+-------------+
455| Imageset | # indexed | # unindexed | % indexed |
456|------------+-------------+---------------+-------------|
457| 0 | 21765 | 726 | 96.8 |
458+------------+-------------+---------------+-------------+
459
460Indexed crystal models:
461model 1 (21766 reflections):
462Crystal:
463 Unit cell: 44.412(5), 53.160(6), 62.404(7), 115.1854(11), 101.7782(10), 90.0103(10)
464 Space group: P 1
465 U matrix: {{-0.8997, -0.4112, 0.1464},
466 {-0.2936, 0.8184, 0.4940},
467 {-0.3229, 0.4015, -0.8570}}
468 B matrix: {{ 0.0225, 0.0000, 0.0000},
469 { 0.0000, 0.0188, 0.0000},
470 { 0.0052, 0.0091, 0.0182}}
471 A = UB: {{-0.0195, -0.0064, 0.0027},
472 {-0.0040, 0.0199, 0.0090},
473 {-0.0117, -0.0002, -0.0156}}
474+------------+-------------+---------------+-------------+
475| Imageset | # indexed | # unindexed | % indexed |
476|------------+-------------+---------------+-------------|
477| 0 | 21772 | 719 | 96.8 |
478+------------+-------------+---------------+-------------+
479
480################################################################################
481Starting refinement (macro-cycle 5)
482################################################################################
483
484
485Summary statistics for 21711 observations matched to predictions:
486+-------------------+---------+----------+-----------+---------+--------+
487| | Min | Q1 | Med | Q3 | Max |
488|-------------------+---------+----------+-----------+---------+--------|
489| Xc - Xo (mm) | -0.7964 | -0.04492 | 0.001183 | 0.04616 | 0.6751 |
490| Yc - Yo (mm) | -1.714 | -0.05117 | -0.001689 | 0.04504 | 3.184 |
491| Phic - Phio (deg) | -8.093 | -0.1051 | 0.05072 | 0.1487 | 7.829 |
492| X weights | 224.2 | 360.1 | 383.4 | 397.1 | 405.6 |
493| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
494| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
495+-------------------+---------+----------+-----------+---------+--------+
496
497Detecting centroid outliers using the Tukey algorithm
4982845 reflections have been flagged as outliers
49918866 reflections remain in the manager
500
501Summary statistics for 18866 observations matched to predictions:
502+-------------------+---------+----------+-----------+---------+--------+
503| | Min | Q1 | Med | Q3 | Max |
504|-------------------+---------+----------+-----------+---------+--------|
505| Xc - Xo (mm) | -0.3277 | -0.04005 | 0.002476 | 0.04492 | 0.3065 |
506| Yc - Yo (mm) | -0.3999 | -0.04165 | -0.000127 | 0.04087 | 0.4131 |
507| Phic - Phio (deg) | -0.9145 | -0.08 | 0.05406 | 0.1408 | 0.6018 |
508| X weights | 224.2 | 364.2 | 385.4 | 397.7 | 405.6 |
509| Y weights | 199.2 | 355.4 | 379.9 | 395.3 | 405.6 |
510| Phi weights | 38.65 | 47.26 | 47.75 | 48 | 48 |
511+-------------------+---------+----------+-----------+---------+--------+
512
513There are 16 parameters to refine against 18866 reflections in 3 dimensions
514
515Refinement steps:
516+--------+--------+----------+----------+------------+
517| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
518| | | (mm) | (mm) | (deg) |
519|--------+--------+----------+----------+------------|
520| 0 | 18866 | 0.076637 | 0.08142 | 0.21756 |
521| 1 | 18866 | 0.076617 | 0.081298 | 0.21792 |
522| 2 | 18866 | 0.076597 | 0.081302 | 0.21795 |
523| 3 | 18866 | 0.076585 | 0.081308 | 0.21797 |
524| 4 | 18866 | 0.076581 | 0.081312 | 0.21797 |
525+--------+--------+----------+----------+------------+
526RMSD no longer decreasing
527
528RMSDs by experiment:
529+-------+--------+----------+----------+------------+
530| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
531| id | | (px) | (px) | (images) |
532|-------+--------+----------+----------+------------|
533| 0 | 18866 | 0.44524 | 0.47274 | 0.43594 |
534+-------+--------+----------+----------+------------+
535
536Refined crystal models:
537model 1 (21766 reflections):
538Crystal:
539 Unit cell: 44.409(4), 53.155(5), 62.398(6), 115.1852(11), 101.7774(10), 90.0106(10)
540 Space group: P 1
541 U matrix: {{-0.8997, -0.4112, 0.1464},
542 {-0.2936, 0.8184, 0.4940},
543 {-0.3229, 0.4015, -0.8570}}
544 B matrix: {{ 0.0225, 0.0000, 0.0000},
545 { 0.0000, 0.0188, 0.0000},
546 { 0.0052, 0.0091, 0.0182}}
547 A = UB: {{-0.0195, -0.0064, 0.0027},
548 {-0.0040, 0.0199, 0.0090},
549 {-0.0117, -0.0002, -0.0156}}
550+------------+-------------+---------------+-------------+
551| Imageset | # indexed | # unindexed | % indexed |
552|------------+-------------+---------------+-------------|
553| 0 | 21766 | 725 | 96.8 |
554+------------+-------------+---------------+-------------+
555Saving refined experiments to indexed.expt
556Saving 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:
9Found max_cell: 73.7 Angstrom
10Setting d_min: 1.56
11FFT 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:
126+--------+--------+----------+----------+------------+
127| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
128| | | (mm) | (mm) | (deg) |
129|--------+--------+----------+----------+------------|
130| 0 | 19252 | 0.41293 | 0.26269 | 0.21238 |
131| 1 | 19252 | 0.11689 | 0.10407 | 0.21695 |
132| 2 | 19252 | 0.093959 | 0.096655 | 0.2231 |
133| 3 | 19252 | 0.087994 | 0.095296 | 0.22861 |
134| 4 | 19252 | 0.087102 | 0.095106 | 0.22963 |
135| 5 | 19252 | 0.087055 | 0.095109 | 0.22965 |
136| 6 | 19252 | 0.087057 | 0.095111 | 0.22964 |
137+--------+--------+----------+----------+------------+
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:
550+------------+-------------+---------------+-------------+
551| Imageset | # indexed | # unindexed | % indexed |
552|------------+-------------+---------------+-------------|
553| 0 | 21766 | 725 | 96.8 |
554+------------+-------------+---------------+-------------+
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:
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.
Note that here we set the additional parameter best_monoclinic_beta=False.
For centred monoclinic systems, there are two alternative settings, C2/m or I2/m, and
the “conventional” setting would be the setting that gives a beta angle closest to 90°.
However, previously-published structures for this protein are in the C2 setting, hence
we set best_monoclinic_beta=False to force the choice of C2 irrespective of the beta
angle.
dials.refine_bravais_settings indexed.expt indexed.refl best_monoclinic_beta=False
This generates 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 | 0.0251 | 0.107 | 0.775/0.775 | 17996 | mC | 112.89 53.13 44.39 90.00 103.04 90.00 | 259404 | -b-2*c,-b,-a |
| * 1 | 0 | 0.106 | -/- | 18004 | aP | 44.41 53.15 62.39 115.18 101.78 90.01 | 129823 | 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, this is not the case here, so it is necessary to reindex the
indexed.refl file output by using
dials.reindex:
dials.reindex indexed.refl change_of_basis_op=-b-2*c,-b,-a
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
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3
4refinement {
5 parameterisation {
6 scan_varying = False
7 }
8}
9input {
10 experiments = bravais_setting_2.expt
11 reflections = reindexed.refl
12}
13
14Configuring refiner
15Setting outlier.nproc=32
16
17Summary statistics for 21711 observations matched to predictions:
18+-------------------+---------+----------+-----------+---------+--------+
19| | Min | Q1 | Med | Q3 | Max |
20|-------------------+---------+----------+-----------+---------+--------|
21| Xc - Xo (mm) | -0.7978 | -0.04545 | 0.0008118 | 0.04563 | 0.6948 |
22| Yc - Yo (mm) | -1.725 | -0.05087 | -0.00146 | 0.04319 | 3.175 |
23| Phic - Phio (deg) | -8.134 | -0.1067 | 0.05136 | 0.1461 | 7.92 |
24| X weights | 224.2 | 360.1 | 383.4 | 397.1 | 405.6 |
25| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
26| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
27+-------------------+---------+----------+-----------+---------+--------+
28
29Detecting centroid outliers using the MCD algorithm
304237 reflections have been flagged as outliers
3117474 reflections remain in the manager
32
33Summary statistics for 17474 observations matched to predictions:
34+-------------------+---------+----------+-----------+---------+--------+
35| | Min | Q1 | Med | Q3 | Max |
36|-------------------+---------+----------+-----------+---------+--------|
37| Xc - Xo (mm) | -0.3406 | -0.03739 | 0.002755 | 0.04311 | 0.3151 |
38| Yc - Yo (mm) | -0.4419 | -0.03682 | 0.0002971 | 0.03706 | 0.4944 |
39| Phic - Phio (deg) | -0.8712 | -0.06641 | 0.05805 | 0.1371 | 0.5711 |
40| X weights | 224.2 | 366.4 | 386.7 | 398 | 405.6 |
41| Y weights | 199.2 | 358.2 | 381.8 | 396 | 405.6 |
42| Phi weights | 38.65 | 47.26 | 47.73 | 48 | 48 |
43+-------------------+---------+----------+-----------+---------+--------+
44
45There are 14 parameters to refine against 17474 reflections in 3 dimensions
46Performing refinement of a single Experiment...
47
48Refinement steps:
49+--------+--------+----------+----------+------------+
50| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
51| | | (mm) | (mm) | (deg) |
52|--------+--------+----------+----------+------------|
53| 0 | 17474 | 0.069678 | 0.075234 | 0.21231 |
54| 1 | 17474 | 0.069696 | 0.075156 | 0.21242 |
55| 2 | 17474 | 0.069682 | 0.075086 | 0.21259 |
56| 3 | 17474 | 0.069636 | 0.075036 | 0.21278 |
57| 4 | 17474 | 0.069595 | 0.075013 | 0.21292 |
58| 5 | 17474 | 0.069579 | 0.07501 | 0.21295 |
59| 6 | 17474 | 0.069576 | 0.075012 | 0.21296 |
60+--------+--------+----------+----------+------------+
61RMSD no longer decreasing
62
63RMSDs by experiment:
64+-------+--------+----------+----------+------------+
65| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
66| id | | (px) | (px) | (images) |
67|-------+--------+----------+----------+------------|
68| 0 | 17474 | 0.40451 | 0.43612 | 0.42591 |
69+-------+--------+----------+----------+------------+
70Updating predictions for indexed reflections
71
72Final refined crystal model:
73Crystal:
74 Unit cell: 112.869(12), 53.124(6), 44.385(5), 90.0, 103.0360(11), 90.0
75 Space group: C 1 2 1
76 U matrix: {{-0.3454, 0.4111, 0.8436},
77 {-0.5477, -0.8183, 0.1745},
78 { 0.7620, -0.4018, 0.5078}}
79 B matrix: {{ 0.0089, 0.0000, 0.0000},
80 { 0.0000, 0.0188, 0.0000},
81 { 0.0021, -0.0000, 0.0231}}
82 A = UB: {{-0.0013, 0.0077, 0.0195},
83 {-0.0045, -0.0154, 0.0040},
84 { 0.0078, -0.0076, 0.0117}}
85Saving refined experiments to refined.expt
86Saving 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
Show/Hide Log
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3
4refinement {
5 parameterisation {
6 scan_varying = True
7 }
8}
9input {
10 experiments = refined.expt
11 reflections = refined.refl
12}
13
14Configuring refiner
15Setting outlier.nproc=32
16
17Summary statistics for 21710 observations matched to predictions:
18+-------------------+---------+----------+-----------+---------+--------+
19| | Min | Q1 | Med | Q3 | Max |
20|-------------------+---------+----------+-----------+---------+--------|
21| Xc - Xo (mm) | -0.8072 | -0.04592 | 0.0002511 | 0.04443 | 0.6971 |
22| Yc - Yo (mm) | -1.711 | -0.05072 | -0.001627 | 0.0432 | 2.495 |
23| Phic - Phio (deg) | -8.057 | -0.1057 | 0.05082 | 0.1454 | 9.373 |
24| X weights | 224.2 | 360.1 | 383.4 | 397.1 | 405.6 |
25| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
26| Phi weights | 33.79 | 47.24 | 47.78 | 48 | 48 |
27+-------------------+---------+----------+-----------+---------+--------+
28
29Detecting centroid outliers using the MCD algorithm
304266 reflections have been flagged as outliers
3117444 reflections remain in the manager
32
33Summary statistics for 17444 observations matched to predictions:
34+-------------------+---------+----------+-----------+--------+--------+
35| | Min | Q1 | Med | Q3 | Max |
36|-------------------+---------+----------+-----------+--------+--------|
37| Xc - Xo (mm) | -0.3431 | -0.03742 | 0.002293 | 0.0421 | 0.3151 |
38| Yc - Yo (mm) | -0.4391 | -0.03642 | 0.0004453 | 0.0368 | 0.489 |
39| Phic - Phio (deg) | -0.8962 | -0.06631 | 0.05769 | 0.1361 | 0.5586 |
40| X weights | 224.2 | 366.4 | 386.7 | 398 | 405.6 |
41| Y weights | 199.2 | 358.2 | 381.8 | 396 | 405.6 |
42| Phi weights | 38.65 | 47.26 | 47.73 | 48 | 48 |
43+-------------------+---------+----------+-----------+--------+--------+
44
45There are 56 parameters to refine against 17444 reflections in 3 dimensions
46Performing refinement of a single Experiment...
47
48Refinement steps:
49+--------+--------+----------+----------+------------+
50| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
51| | | (mm) | (mm) | (deg) |
52|--------+--------+----------+----------+------------|
53| 0 | 17444 | 0.069259 | 0.074798 | 0.21294 |
54| 1 | 17444 | 0.058151 | 0.069343 | 0.18789 |
55| 2 | 17444 | 0.056934 | 0.066009 | 0.17206 |
56| 3 | 17444 | 0.055252 | 0.06238 | 0.15316 |
57| 4 | 17444 | 0.053309 | 0.060305 | 0.13088 |
58| 5 | 17444 | 0.051378 | 0.058834 | 0.1151 |
59| 6 | 17444 | 0.050068 | 0.058045 | 0.1096 |
60| 7 | 17444 | 0.049523 | 0.057797 | 0.108 |
61| 8 | 17444 | 0.04935 | 0.057755 | 0.10732 |
62| 9 | 17444 | 0.049221 | 0.057742 | 0.10721 |
63| 10 | 17444 | 0.049094 | 0.057731 | 0.10728 |
64| 11 | 17444 | 0.049014 | 0.057727 | 0.10743 |
65| 12 | 17444 | 0.048997 | 0.057725 | 0.1075 |
66| 13 | 17444 | 0.048998 | 0.057723 | 0.1075 |
67+--------+--------+----------+----------+------------+
68RMSD no longer decreasing
69
70RMSDs by experiment:
71+-------+--------+----------+----------+------------+
72| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
73| id | | (px) | (px) | (images) |
74|-------+--------+----------+----------+------------|
75| 0 | 17444 | 0.28487 | 0.3356 | 0.215 |
76+-------+--------+----------+----------+------------+
77Updating predictions for indexed reflections
78
79Final refined crystal model:
80Crystal:
81 Unit cell: 112.869(12), 53.124(6), 44.385(5), 90.0, 103.0360(11), 90.0
82 Space group: C 1 2 1
83 U matrix: {{-0.3454, 0.4111, 0.8436},
84 {-0.5477, -0.8183, 0.1745},
85 { 0.7620, -0.4018, 0.5078}}
86 B matrix: {{ 0.0089, 0.0000, 0.0000},
87 { 0.0000, 0.0188, 0.0000},
88 { 0.0021, -0.0000, 0.0231}}
89 A = UB: {{-0.0013, 0.0077, 0.0195},
90 {-0.0045, -0.0154, 0.0040},
91 { 0.0078, -0.0076, 0.0117}}
92 A sampled at 401 scan points
93Saving refined experiments to refined.expt
94Saving 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:
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
Show/Hide Log
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3integration {
4 mp {
5 nproc = 4
6 }
7}
8input {
9 experiments = refined.expt
10 reflections = refined.refl
11}
12
13
14================================================================================
15
16Experiments
17
18Models for experiment 0
19
20Beam:
21 probe: x-ray
22 wavelength: 0.9126
23 sample to source direction : {0.00177175,-0,0.999998}
24 divergence: 0
25 sigma divergence: 0
26 polarization normal: {0,1,0}
27 polarization fraction: 0.999
28 flux: 1.14122e+11
29 transmission: 1
30 sample to source distance: 0
31
32Detector:
33Panel:
34 name: Panel
35 type: SENSOR_PAD
36 identifier:
37 pixel_size:{0.172,0.172}
38 image_size: {2463,2527}
39 trusted_range: {0,94172}
40 thickness: 0.32
41 material: Si
42 mu: 3.21948
43 gain: 1
44 pedestal: 0
45 fast_axis: {0.999988,0.00492368,-2.93919e-05}
46 slow_axis: {0.00492371,-0.999987,0.00103454}
47 origin: {-214.522,250.557,-324.749}
48 distance: 324.495
49 pixel to millimeter strategy: ParallaxCorrectedPxMmStrategy
50 mu: 3.21948
51 t0: 0.32
52
53Goniometer:
54 Rotation axis: {1,0,0}
55 Fixed rotation: {1,0,0,0,1,0,0,0,1}
56 Setting rotation:{1,0,0,0,1,0,0,0,1}
57
58Scan:
59 number of images: 400
60 image range: {1,400}
61 epoch: 1.58327e+09
62 exposure time: 0.04
63 oscillation: {216,0.5}
64
65Crystal:
66 Unit cell: 112.869(12), 53.124(6), 44.385(5), 90.0, 103.0360(11), 90.0
67 Space group: C 1 2 1
68 U matrix: {{-0.3454, 0.4111, 0.8436},
69 {-0.5477, -0.8183, 0.1745},
70 { 0.7620, -0.4018, 0.5078}}
71 B matrix: {{ 0.0089, 0.0000, 0.0000},
72 { 0.0000, 0.0188, 0.0000},
73 { 0.0021, -0.0000, 0.0231}}
74 A = UB: {{-0.0013, 0.0077, 0.0195},
75 {-0.0045, -0.0154, 0.0040},
76 { 0.0078, -0.0076, 0.0117}}
77 A sampled at 401 scan points
78
79================================================================================
80
81Initialising
82Processing reference reflections
83 read 22492 strong spots
84 removing 726 unindexed reflections
85 removing 4322 reflections marked as bad for refinement
86 using 17444 indexed reflections
87 found 5048 junk reflections
88 masked neighbouring pixels in 2092 shoeboxes
89
90================================================================================
91
92Predicting reflections
93Prediction type: scan varying crystal prediction
94Predicted 198676 reflections
95Matching reference spots with predicted reflections
96 17444 observed reflections input
97 198676 reflections predicted
98 17444 reflections matched
99 17444 reflections accepted
100Using 17443 / 17444 reflections for sigma calculation
101Calculating E.S.D Beam Divergence.
102Calculating E.S.D Reflecting Range (mosaicity).
103 sigma b: 0.039495 degrees
104 sigma m: 0.328314 degrees
105================================================================================
106
107Processing reflections
108
109 Processing the following experiments:
110
111 Experiments: 1
112 Beams: 1
113 Detectors: 1
114 Goniometers: 1
115 Scans: 1
116 Crystals: 1
117 Imagesets: 1
118
119================================================================================
120
121Modelling reflection profiles
122
123 Split 26 reflections overlapping job boundaries
124
125Memory situation report:
126 Available system memory : 201.2 GB
127 Maximum memory for processing : 181.1 GB
128 Memory required per process : 0.0 GB
129
130Processing reflections in the following blocks of images:
131
132 block_size: Auto
133
134+-----+---------+--------------+------------+--------------+------------+-----------------+
135| # | Group | Frame From | Frame To | Angle From | Angle To | # Reflections |
136|-----+---------+--------------+------------+--------------+------------+-----------------|
137| 0 | 0 | 1 | 108 | 216 | 270 | 4776 |
138| 1 | 0 | 99 | 206 | 265 | 319 | 5004 |
139| 2 | 0 | 197 | 304 | 314 | 368 | 4692 |
140| 3 | 0 | 295 | 400 | 363 | 416 | 2996 |
141+-----+---------+--------------+------------+--------------+------------+-----------------+
142
143 Using multiprocessing with 4 parallel job(s)
144
145
146 Frames: 1 -> 108
147
148 Number of reflections
149 Partial: 163
150 Full: 4613
151 In ice ring: 0
152 Total: 4776
153
154
155 Frames: 99 -> 206
156
157 Number of reflections
158 Partial: 24
159 Full: 4980
160 In ice ring: 0
161 Total: 5004
162
163
164 Frames: 197 -> 304
165
166 Number of reflections
167 Partial: 17
168 Full: 4675
169 In ice ring: 0
170 Total: 4692
171
172
173 Frames: 295 -> 400
174
175 Number of reflections
176 Partial: 45
177 Full: 2951
178 In ice ring: 0
179 Total: 2996
180
181
182 Summary of profile model
183+------+-----------+-----------+----------+----------+----------+-----------------+
184| ID | Profile | Created | X (px) | Y (px) | Z (im) | # reflections |
185|------+-----------+-----------+----------+----------+----------+-----------------|
186| 0 | 0 | True | 410.5 | 421.17 | 5 | 498 |
187| 0 | 1 | True | 1231.5 | 421.17 | 5 | 566 |
188| 0 | 2 | True | 2052.5 | 421.17 | 5 | 531 |
189| 0 | 3 | True | 410.5 | 1263.5 | 5 | 904 |
190| 0 | 4 | True | 1231.5 | 1263.5 | 5 | 993 |
191| 0 | 5 | True | 2052.5 | 1263.5 | 5 | 902 |
192| 0 | 6 | True | 410.5 | 2105.83 | 5 | 866 |
193| 0 | 7 | True | 1231.5 | 2105.83 | 5 | 953 |
194| 0 | 8 | True | 2052.5 | 2105.83 | 5 | 862 |
195| 0 | 9 | True | 410.5 | 421.17 | 15 | 764 |
196| 0 | 10 | True | 1231.5 | 421.17 | 15 | 864 |
197| 0 | 11 | True | 2052.5 | 421.17 | 15 | 811 |
198| 0 | 12 | True | 410.5 | 1263.5 | 15 | 1356 |
199| 0 | 13 | True | 1231.5 | 1263.5 | 15 | 1492 |
200| 0 | 14 | True | 2052.5 | 1263.5 | 15 | 1370 |
201| 0 | 15 | True | 410.5 | 2105.83 | 15 | 1302 |
202| 0 | 16 | True | 1231.5 | 2105.83 | 15 | 1434 |
203| 0 | 17 | True | 2052.5 | 2105.83 | 15 | 1312 |
204| 0 | 18 | True | 410.5 | 421.17 | 25 | 799 |
205| 0 | 19 | True | 1231.5 | 421.17 | 25 | 907 |
206| 0 | 20 | True | 2052.5 | 421.17 | 25 | 851 |
207| 0 | 21 | True | 410.5 | 1263.5 | 25 | 1329 |
208| 0 | 22 | True | 1231.5 | 1263.5 | 25 | 1477 |
209| 0 | 23 | True | 2052.5 | 1263.5 | 25 | 1364 |
210| 0 | 24 | True | 410.5 | 2105.83 | 25 | 1269 |
211| 0 | 25 | True | 1231.5 | 2105.83 | 25 | 1415 |
212| 0 | 26 | True | 2052.5 | 2105.83 | 25 | 1303 |
213| 0 | 27 | True | 410.5 | 421.17 | 35 | 765 |
214| 0 | 28 | True | 1231.5 | 421.17 | 35 | 862 |
215| 0 | 29 | True | 2052.5 | 421.17 | 35 | 806 |
216| 0 | 30 | True | 410.5 | 1263.5 | 35 | 1197 |
217| 0 | 31 | True | 1231.5 | 1263.5 | 35 | 1327 |
218| 0 | 32 | True | 2052.5 | 1263.5 | 35 | 1235 |
219| 0 | 33 | True | 410.5 | 2105.83 | 35 | 1144 |
220| 0 | 34 | True | 1231.5 | 2105.83 | 35 | 1270 |
221| 0 | 35 | True | 2052.5 | 2105.83 | 35 | 1180 |
222| 0 | 36 | True | 410.5 | 421.17 | 45 | 733 |
223| 0 | 37 | True | 1231.5 | 421.17 | 45 | 837 |
224| 0 | 38 | True | 2052.5 | 421.17 | 45 | 778 |
225| 0 | 39 | True | 410.5 | 1263.5 | 45 | 1128 |
226| 0 | 40 | True | 1231.5 | 1263.5 | 45 | 1258 |
227| 0 | 41 | True | 2052.5 | 1263.5 | 45 | 1162 |
228| 0 | 42 | True | 410.5 | 2105.83 | 45 | 1080 |
229| 0 | 43 | True | 1231.5 | 2105.83 | 45 | 1208 |
230| 0 | 44 | True | 2052.5 | 2105.83 | 45 | 1114 |
231| 0 | 45 | True | 410.5 | 421.17 | 55 | 673 |
232| 0 | 46 | True | 1231.5 | 421.17 | 55 | 767 |
233| 0 | 47 | True | 2052.5 | 421.17 | 55 | 709 |
234| 0 | 48 | True | 410.5 | 1263.5 | 55 | 1094 |
235| 0 | 49 | True | 1231.5 | 1263.5 | 55 | 1211 |
236| 0 | 50 | True | 2052.5 | 1263.5 | 55 | 1111 |
237| 0 | 51 | True | 410.5 | 2105.83 | 55 | 1059 |
238| 0 | 52 | True | 1231.5 | 2105.83 | 55 | 1173 |
239| 0 | 53 | True | 2052.5 | 2105.83 | 55 | 1074 |
240| 0 | 54 | True | 410.5 | 421.17 | 65 | 584 |
241| 0 | 55 | True | 1231.5 | 421.17 | 65 | 658 |
242| 0 | 56 | True | 2052.5 | 421.17 | 65 | 615 |
243| 0 | 57 | True | 410.5 | 1263.5 | 65 | 1032 |
244| 0 | 58 | True | 1231.5 | 1263.5 | 65 | 1122 |
245| 0 | 59 | True | 2052.5 | 1263.5 | 65 | 1029 |
246| 0 | 60 | True | 410.5 | 2105.83 | 65 | 1011 |
247| 0 | 61 | True | 1231.5 | 2105.83 | 65 | 1100 |
248| 0 | 62 | True | 2052.5 | 2105.83 | 65 | 1007 |
249| 0 | 63 | True | 410.5 | 421.17 | 75 | 514 |
250| 0 | 64 | True | 1231.5 | 421.17 | 75 | 563 |
251| 0 | 65 | True | 2052.5 | 421.17 | 75 | 535 |
252| 0 | 66 | True | 410.5 | 1263.5 | 75 | 985 |
253| 0 | 67 | True | 1231.5 | 1263.5 | 75 | 1047 |
254| 0 | 68 | True | 2052.5 | 1263.5 | 75 | 962 |
255| 0 | 69 | True | 410.5 | 2105.83 | 75 | 973 |
256| 0 | 70 | True | 1231.5 | 2105.83 | 75 | 1034 |
257| 0 | 71 | True | 2052.5 | 2105.83 | 75 | 949 |
258| 0 | 72 | True | 410.5 | 421.17 | 85 | 491 |
259| 0 | 73 | True | 1231.5 | 421.17 | 85 | 527 |
260| 0 | 74 | True | 2052.5 | 421.17 | 85 | 507 |
261| 0 | 75 | True | 410.5 | 1263.5 | 85 | 1018 |
262| 0 | 76 | True | 1231.5 | 1263.5 | 85 | 1069 |
263| 0 | 77 | True | 2052.5 | 1263.5 | 85 | 994 |
264| 0 | 78 | True | 410.5 | 2105.83 | 85 | 1010 |
265| 0 | 79 | True | 1231.5 | 2105.83 | 85 | 1061 |
266| 0 | 80 | True | 2052.5 | 2105.83 | 85 | 986 |
267| 0 | 81 | True | 410.5 | 421.17 | 95 | 536 |
268| 0 | 82 | True | 1231.5 | 421.17 | 95 | 577 |
269| 0 | 83 | True | 2052.5 | 421.17 | 95 | 557 |
270| 0 | 84 | True | 410.5 | 1263.5 | 95 | 1129 |
271| 0 | 85 | True | 1231.5 | 1263.5 | 95 | 1194 |
272| 0 | 86 | True | 2052.5 | 1263.5 | 95 | 1099 |
273| 0 | 87 | True | 410.5 | 2105.83 | 95 | 1120 |
274| 0 | 88 | True | 1231.5 | 2105.83 | 95 | 1185 |
275| 0 | 89 | True | 2052.5 | 2105.83 | 95 | 1090 |
276| 0 | 90 | True | 410.5 | 421.17 | 105 | 560 |
277| 0 | 91 | True | 1231.5 | 421.17 | 105 | 599 |
278| 0 | 92 | True | 2052.5 | 421.17 | 105 | 577 |
279| 0 | 93 | True | 410.5 | 1263.5 | 105 | 1200 |
280| 0 | 94 | True | 1231.5 | 1263.5 | 105 | 1268 |
281| 0 | 95 | True | 2052.5 | 1263.5 | 105 | 1170 |
282| 0 | 96 | True | 410.5 | 2105.83 | 105 | 1187 |
283| 0 | 97 | True | 1231.5 | 2105.83 | 105 | 1255 |
284| 0 | 98 | True | 2052.5 | 2105.83 | 105 | 1157 |
285| 0 | 99 | True | 410.5 | 421.17 | 115 | 590 |
286| 0 | 100 | True | 1231.5 | 421.17 | 115 | 637 |
287| 0 | 101 | True | 2052.5 | 421.17 | 115 | 615 |
288| 0 | 102 | True | 410.5 | 1263.5 | 115 | 1257 |
289| 0 | 103 | True | 1231.5 | 1263.5 | 115 | 1333 |
290| 0 | 104 | True | 2052.5 | 1263.5 | 115 | 1227 |
291| 0 | 105 | True | 410.5 | 2105.83 | 115 | 1244 |
292| 0 | 106 | True | 1231.5 | 2105.83 | 115 | 1320 |
293| 0 | 107 | True | 2052.5 | 2105.83 | 115 | 1214 |
294| 0 | 108 | True | 410.5 | 421.17 | 125 | 588 |
295| 0 | 109 | True | 1231.5 | 421.17 | 125 | 634 |
296| 0 | 110 | True | 2052.5 | 421.17 | 125 | 612 |
297| 0 | 111 | True | 410.5 | 1263.5 | 125 | 1296 |
298| 0 | 112 | True | 1231.5 | 1263.5 | 125 | 1368 |
299| 0 | 113 | True | 2052.5 | 1263.5 | 125 | 1262 |
300| 0 | 114 | True | 410.5 | 2105.83 | 125 | 1274 |
301| 0 | 115 | True | 1231.5 | 2105.83 | 125 | 1346 |
302| 0 | 116 | True | 2052.5 | 2105.83 | 125 | 1240 |
303| 0 | 117 | True | 410.5 | 421.17 | 135 | 627 |
304| 0 | 118 | True | 1231.5 | 421.17 | 135 | 671 |
305| 0 | 119 | True | 2052.5 | 421.17 | 135 | 646 |
306| 0 | 120 | True | 410.5 | 1263.5 | 135 | 1356 |
307| 0 | 121 | True | 1231.5 | 1263.5 | 135 | 1425 |
308| 0 | 122 | True | 2052.5 | 1263.5 | 135 | 1306 |
309| 0 | 123 | True | 410.5 | 2105.83 | 135 | 1327 |
310| 0 | 124 | True | 1231.5 | 2105.83 | 135 | 1396 |
311| 0 | 125 | True | 2052.5 | 2105.83 | 135 | 1277 |
312| 0 | 126 | True | 410.5 | 421.17 | 145 | 665 |
313| 0 | 127 | True | 1231.5 | 421.17 | 145 | 708 |
314| 0 | 128 | True | 2052.5 | 421.17 | 145 | 676 |
315| 0 | 129 | True | 410.5 | 1263.5 | 145 | 1395 |
316| 0 | 130 | True | 1231.5 | 1263.5 | 145 | 1468 |
317| 0 | 131 | True | 2052.5 | 1263.5 | 145 | 1340 |
318| 0 | 132 | True | 410.5 | 2105.83 | 145 | 1358 |
319| 0 | 133 | True | 1231.5 | 2105.83 | 145 | 1431 |
320| 0 | 134 | True | 2052.5 | 2105.83 | 145 | 1303 |
321| 0 | 135 | True | 410.5 | 421.17 | 155 | 698 |
322| 0 | 136 | True | 1231.5 | 421.17 | 155 | 735 |
323| 0 | 137 | True | 2052.5 | 421.17 | 155 | 694 |
324| 0 | 138 | True | 410.5 | 1263.5 | 155 | 1407 |
325| 0 | 139 | True | 1231.5 | 1263.5 | 155 | 1473 |
326| 0 | 140 | True | 2052.5 | 1263.5 | 155 | 1334 |
327| 0 | 141 | True | 410.5 | 2105.83 | 155 | 1359 |
328| 0 | 142 | True | 1231.5 | 2105.83 | 155 | 1425 |
329| 0 | 143 | True | 2052.5 | 2105.83 | 155 | 1286 |
330| 0 | 144 | True | 410.5 | 421.17 | 165 | 708 |
331| 0 | 145 | True | 1231.5 | 421.17 | 165 | 749 |
332| 0 | 146 | True | 2052.5 | 421.17 | 165 | 709 |
333| 0 | 147 | True | 410.5 | 1263.5 | 165 | 1404 |
334| 0 | 148 | True | 1231.5 | 1263.5 | 165 | 1477 |
335| 0 | 149 | True | 2052.5 | 1263.5 | 165 | 1341 |
336| 0 | 150 | True | 410.5 | 2105.83 | 165 | 1349 |
337| 0 | 151 | True | 1231.5 | 2105.83 | 165 | 1422 |
338| 0 | 152 | True | 2052.5 | 2105.83 | 165 | 1286 |
339| 0 | 153 | True | 410.5 | 421.17 | 175 | 717 |
340| 0 | 154 | True | 1231.5 | 421.17 | 175 | 752 |
341| 0 | 155 | True | 2052.5 | 421.17 | 175 | 708 |
342| 0 | 156 | True | 410.5 | 1263.5 | 175 | 1389 |
343| 0 | 157 | True | 1231.5 | 1263.5 | 175 | 1453 |
344| 0 | 158 | True | 2052.5 | 1263.5 | 175 | 1318 |
345| 0 | 159 | True | 410.5 | 2105.83 | 175 | 1328 |
346| 0 | 160 | True | 1231.5 | 2105.83 | 175 | 1392 |
347| 0 | 161 | True | 2052.5 | 2105.83 | 175 | 1257 |
348| 0 | 162 | True | 410.5 | 421.17 | 185 | 758 |
349| 0 | 163 | True | 1231.5 | 421.17 | 185 | 808 |
350| 0 | 164 | True | 2052.5 | 421.17 | 185 | 762 |
351| 0 | 165 | True | 410.5 | 1263.5 | 185 | 1406 |
352| 0 | 166 | True | 1231.5 | 1263.5 | 185 | 1489 |
353| 0 | 167 | True | 2052.5 | 1263.5 | 185 | 1361 |
354| 0 | 168 | True | 410.5 | 2105.83 | 185 | 1333 |
355| 0 | 169 | True | 1231.5 | 2105.83 | 185 | 1415 |
356| 0 | 170 | True | 2052.5 | 2105.83 | 185 | 1287 |
357| 0 | 171 | True | 410.5 | 421.17 | 195 | 801 |
358| 0 | 172 | True | 1231.5 | 421.17 | 195 | 869 |
359| 0 | 173 | True | 2052.5 | 421.17 | 195 | 818 |
360| 0 | 174 | True | 410.5 | 1263.5 | 195 | 1429 |
361| 0 | 175 | True | 1231.5 | 1263.5 | 195 | 1526 |
362| 0 | 176 | True | 2052.5 | 1263.5 | 195 | 1399 |
363| 0 | 177 | True | 410.5 | 2105.83 | 195 | 1333 |
364| 0 | 178 | True | 1231.5 | 2105.83 | 195 | 1424 |
365| 0 | 179 | True | 2052.5 | 2105.83 | 195 | 1297 |
366| 0 | 180 | True | 410.5 | 421.17 | 205 | 805 |
367| 0 | 181 | True | 1231.5 | 421.17 | 205 | 904 |
368| 0 | 182 | True | 2052.5 | 421.17 | 205 | 859 |
369| 0 | 183 | True | 410.5 | 1263.5 | 205 | 1401 |
370| 0 | 184 | True | 1231.5 | 1263.5 | 205 | 1533 |
371| 0 | 185 | True | 2052.5 | 1263.5 | 205 | 1422 |
372| 0 | 186 | True | 410.5 | 2105.83 | 205 | 1290 |
373| 0 | 187 | True | 1231.5 | 2105.83 | 205 | 1409 |
374| 0 | 188 | True | 2052.5 | 2105.83 | 205 | 1298 |
375| 0 | 189 | True | 410.5 | 421.17 | 215 | 815 |
376| 0 | 190 | True | 1231.5 | 421.17 | 215 | 925 |
377| 0 | 191 | True | 2052.5 | 421.17 | 215 | 889 |
378| 0 | 192 | True | 410.5 | 1263.5 | 215 | 1393 |
379| 0 | 193 | True | 1231.5 | 1263.5 | 215 | 1539 |
380| 0 | 194 | True | 2052.5 | 1263.5 | 215 | 1448 |
381| 0 | 195 | True | 410.5 | 2105.83 | 215 | 1263 |
382| 0 | 196 | True | 1231.5 | 2105.83 | 215 | 1390 |
383| 0 | 197 | True | 2052.5 | 2105.83 | 215 | 1299 |
384| 0 | 198 | True | 410.5 | 421.17 | 225 | 814 |
385| 0 | 199 | True | 1231.5 | 421.17 | 225 | 922 |
386| 0 | 200 | True | 2052.5 | 421.17 | 225 | 898 |
387| 0 | 201 | True | 410.5 | 1263.5 | 225 | 1350 |
388| 0 | 202 | True | 1231.5 | 1263.5 | 225 | 1497 |
389| 0 | 203 | True | 2052.5 | 1263.5 | 225 | 1428 |
390| 0 | 204 | True | 410.5 | 2105.83 | 225 | 1213 |
391| 0 | 205 | True | 1231.5 | 2105.83 | 225 | 1342 |
392| 0 | 206 | True | 2052.5 | 2105.83 | 225 | 1273 |
393| 0 | 207 | True | 410.5 | 421.17 | 235 | 819 |
394| 0 | 208 | True | 1231.5 | 421.17 | 235 | 909 |
395| 0 | 209 | True | 2052.5 | 421.17 | 235 | 890 |
396| 0 | 210 | True | 410.5 | 1263.5 | 235 | 1341 |
397| 0 | 211 | True | 1231.5 | 1263.5 | 235 | 1468 |
398| 0 | 212 | True | 2052.5 | 1263.5 | 235 | 1404 |
399| 0 | 213 | True | 410.5 | 2105.83 | 235 | 1203 |
400| 0 | 214 | True | 1231.5 | 2105.83 | 235 | 1315 |
401| 0 | 215 | True | 2052.5 | 2105.83 | 235 | 1251 |
402| 0 | 216 | True | 410.5 | 421.17 | 245 | 793 |
403| 0 | 217 | True | 1231.5 | 421.17 | 245 | 873 |
404| 0 | 218 | True | 2052.5 | 421.17 | 245 | 853 |
405| 0 | 219 | True | 410.5 | 1263.5 | 245 | 1286 |
406| 0 | 220 | True | 1231.5 | 1263.5 | 245 | 1395 |
407| 0 | 221 | True | 2052.5 | 1263.5 | 245 | 1343 |
408| 0 | 222 | True | 410.5 | 2105.83 | 245 | 1183 |
409| 0 | 223 | True | 1231.5 | 2105.83 | 245 | 1283 |
410| 0 | 224 | True | 2052.5 | 2105.83 | 245 | 1231 |
411| 0 | 225 | True | 410.5 | 421.17 | 255 | 754 |
412| 0 | 226 | True | 1231.5 | 421.17 | 255 | 832 |
413| 0 | 227 | True | 2052.5 | 421.17 | 255 | 808 |
414| 0 | 228 | True | 410.5 | 1263.5 | 255 | 1216 |
415| 0 | 229 | True | 1231.5 | 1263.5 | 255 | 1320 |
416| 0 | 230 | True | 2052.5 | 1263.5 | 255 | 1272 |
417| 0 | 231 | True | 410.5 | 2105.83 | 255 | 1146 |
418| 0 | 232 | True | 1231.5 | 2105.83 | 255 | 1241 |
419| 0 | 233 | True | 2052.5 | 2105.83 | 255 | 1193 |
420| 0 | 234 | True | 410.5 | 421.17 | 265 | 717 |
421| 0 | 235 | True | 1231.5 | 421.17 | 265 | 800 |
422| 0 | 236 | True | 2052.5 | 421.17 | 265 | 775 |
423| 0 | 237 | True | 410.5 | 1263.5 | 265 | 1150 |
424| 0 | 238 | True | 1231.5 | 1263.5 | 265 | 1255 |
425| 0 | 239 | True | 2052.5 | 1263.5 | 265 | 1214 |
426| 0 | 240 | True | 410.5 | 2105.83 | 265 | 1096 |
427| 0 | 241 | True | 1231.5 | 2105.83 | 265 | 1195 |
428| 0 | 242 | True | 2052.5 | 2105.83 | 265 | 1155 |
429| 0 | 243 | True | 410.5 | 421.17 | 275 | 698 |
430| 0 | 244 | True | 1231.5 | 421.17 | 275 | 781 |
431| 0 | 245 | True | 2052.5 | 421.17 | 275 | 759 |
432| 0 | 246 | True | 410.5 | 1263.5 | 275 | 1101 |
433| 0 | 247 | True | 1231.5 | 1263.5 | 275 | 1210 |
434| 0 | 248 | True | 2052.5 | 1263.5 | 275 | 1174 |
435| 0 | 249 | True | 410.5 | 2105.83 | 275 | 1059 |
436| 0 | 250 | True | 1231.5 | 2105.83 | 275 | 1163 |
437| 0 | 251 | True | 2052.5 | 2105.83 | 275 | 1128 |
438| 0 | 252 | True | 410.5 | 421.17 | 285 | 674 |
439| 0 | 253 | True | 1231.5 | 421.17 | 285 | 748 |
440| 0 | 254 | True | 2052.5 | 421.17 | 285 | 728 |
441| 0 | 255 | True | 410.5 | 1263.5 | 285 | 1068 |
442| 0 | 256 | True | 1231.5 | 1263.5 | 285 | 1173 |
443| 0 | 257 | True | 2052.5 | 1263.5 | 285 | 1142 |
444| 0 | 258 | True | 410.5 | 2105.83 | 285 | 1036 |
445| 0 | 259 | True | 1231.5 | 2105.83 | 285 | 1138 |
446| 0 | 260 | True | 2052.5 | 2105.83 | 285 | 1108 |
447| 0 | 261 | True | 410.5 | 421.17 | 295 | 666 |
448| 0 | 262 | True | 1231.5 | 421.17 | 295 | 735 |
449| 0 | 263 | True | 2052.5 | 421.17 | 295 | 715 |
450| 0 | 264 | True | 410.5 | 1263.5 | 295 | 1040 |
451| 0 | 265 | True | 1231.5 | 1263.5 | 295 | 1140 |
452| 0 | 266 | True | 2052.5 | 1263.5 | 295 | 1110 |
453| 0 | 267 | True | 410.5 | 2105.83 | 295 | 1024 |
454| 0 | 268 | True | 1231.5 | 2105.83 | 295 | 1122 |
455| 0 | 269 | True | 2052.5 | 2105.83 | 295 | 1092 |
456| 0 | 270 | True | 410.5 | 421.17 | 305 | 628 |
457| 0 | 271 | True | 1231.5 | 421.17 | 305 | 688 |
458| 0 | 272 | True | 2052.5 | 421.17 | 305 | 661 |
459| 0 | 273 | True | 410.5 | 1263.5 | 305 | 990 |
460| 0 | 274 | True | 1231.5 | 1263.5 | 305 | 1080 |
461| 0 | 275 | True | 2052.5 | 1263.5 | 305 | 1042 |
462| 0 | 276 | True | 410.5 | 2105.83 | 305 | 980 |
463| 0 | 277 | True | 1231.5 | 2105.83 | 305 | 1068 |
464| 0 | 278 | True | 2052.5 | 2105.83 | 305 | 1030 |
465| 0 | 279 | True | 410.5 | 421.17 | 315 | 598 |
466| 0 | 280 | True | 1231.5 | 421.17 | 315 | 661 |
467| 0 | 281 | True | 2052.5 | 421.17 | 315 | 634 |
468| 0 | 282 | True | 410.5 | 1263.5 | 315 | 942 |
469| 0 | 283 | True | 1231.5 | 1263.5 | 315 | 1035 |
470| 0 | 284 | True | 2052.5 | 1263.5 | 315 | 999 |
471| 0 | 285 | True | 410.5 | 2105.83 | 315 | 936 |
472| 0 | 286 | True | 1231.5 | 2105.83 | 315 | 1029 |
473| 0 | 287 | True | 2052.5 | 2105.83 | 315 | 993 |
474| 0 | 288 | True | 410.5 | 421.17 | 325 | 568 |
475| 0 | 289 | True | 1231.5 | 421.17 | 325 | 624 |
476| 0 | 290 | True | 2052.5 | 421.17 | 325 | 599 |
477| 0 | 291 | True | 410.5 | 1263.5 | 325 | 904 |
478| 0 | 292 | True | 1231.5 | 1263.5 | 325 | 987 |
479| 0 | 293 | True | 2052.5 | 1263.5 | 325 | 953 |
480| 0 | 294 | True | 410.5 | 2105.83 | 325 | 899 |
481| 0 | 295 | True | 1231.5 | 2105.83 | 325 | 982 |
482| 0 | 296 | True | 2052.5 | 2105.83 | 325 | 948 |
483| 0 | 297 | True | 410.5 | 421.17 | 335 | 539 |
484| 0 | 298 | True | 1231.5 | 421.17 | 335 | 588 |
485| 0 | 299 | True | 2052.5 | 421.17 | 335 | 566 |
486| 0 | 300 | True | 410.5 | 1263.5 | 335 | 855 |
487| 0 | 301 | True | 1231.5 | 1263.5 | 335 | 933 |
488| 0 | 302 | True | 2052.5 | 1263.5 | 335 | 902 |
489| 0 | 303 | True | 410.5 | 2105.83 | 335 | 852 |
490| 0 | 304 | True | 1231.5 | 2105.83 | 335 | 930 |
491| 0 | 305 | True | 2052.5 | 2105.83 | 335 | 899 |
492| 0 | 306 | True | 410.5 | 421.17 | 345 | 501 |
493| 0 | 307 | True | 1231.5 | 421.17 | 345 | 537 |
494| 0 | 308 | True | 2052.5 | 421.17 | 345 | 518 |
495| 0 | 309 | True | 410.5 | 1263.5 | 345 | 799 |
496| 0 | 310 | True | 1231.5 | 1263.5 | 345 | 857 |
497| 0 | 311 | True | 2052.5 | 1263.5 | 345 | 829 |
498| 0 | 312 | True | 410.5 | 2105.83 | 345 | 799 |
499| 0 | 313 | True | 1231.5 | 2105.83 | 345 | 857 |
500| 0 | 314 | True | 2052.5 | 2105.83 | 345 | 829 |
501| 0 | 315 | True | 410.5 | 421.17 | 355 | 456 |
502| 0 | 316 | True | 1231.5 | 421.17 | 355 | 484 |
503| 0 | 317 | True | 2052.5 | 421.17 | 355 | 466 |
504| 0 | 318 | True | 410.5 | 1263.5 | 355 | 731 |
505| 0 | 319 | True | 1231.5 | 1263.5 | 355 | 784 |
506| 0 | 320 | True | 2052.5 | 1263.5 | 355 | 760 |
507| 0 | 321 | True | 410.5 | 2105.83 | 355 | 731 |
508| 0 | 322 | True | 1231.5 | 2105.83 | 355 | 784 |
509| 0 | 323 | True | 2052.5 | 2105.83 | 355 | 760 |
510| 0 | 324 | True | 410.5 | 421.17 | 365 | 428 |
511| 0 | 325 | True | 1231.5 | 421.17 | 365 | 455 |
512| 0 | 326 | True | 2052.5 | 421.17 | 365 | 440 |
513| 0 | 327 | True | 410.5 | 1263.5 | 365 | 693 |
514| 0 | 328 | True | 1231.5 | 1263.5 | 365 | 744 |
515| 0 | 329 | True | 2052.5 | 1263.5 | 365 | 725 |
516| 0 | 330 | True | 410.5 | 2105.83 | 365 | 693 |
517| 0 | 331 | True | 1231.5 | 2105.83 | 365 | 744 |
518| 0 | 332 | True | 2052.5 | 2105.83 | 365 | 725 |
519| 0 | 333 | True | 410.5 | 421.17 | 375 | 420 |
520| 0 | 334 | True | 1231.5 | 421.17 | 375 | 439 |
521| 0 | 335 | True | 2052.5 | 421.17 | 375 | 424 |
522| 0 | 336 | True | 410.5 | 1263.5 | 375 | 674 |
523| 0 | 337 | True | 1231.5 | 1263.5 | 375 | 721 |
524| 0 | 338 | True | 2052.5 | 1263.5 | 375 | 703 |
525| 0 | 339 | True | 410.5 | 2105.83 | 375 | 674 |
526| 0 | 340 | True | 1231.5 | 2105.83 | 375 | 721 |
527| 0 | 341 | True | 2052.5 | 2105.83 | 375 | 703 |
528| 0 | 342 | True | 410.5 | 421.17 | 385 | 362 |
529| 0 | 343 | True | 1231.5 | 421.17 | 385 | 376 |
530| 0 | 344 | True | 2052.5 | 421.17 | 385 | 366 |
531| 0 | 345 | True | 410.5 | 1263.5 | 385 | 570 |
532| 0 | 346 | True | 1231.5 | 1263.5 | 385 | 606 |
533| 0 | 347 | True | 2052.5 | 1263.5 | 385 | 595 |
534| 0 | 348 | True | 410.5 | 2105.83 | 385 | 570 |
535| 0 | 349 | True | 1231.5 | 2105.83 | 385 | 606 |
536| 0 | 350 | True | 2052.5 | 2105.83 | 385 | 595 |
537| 0 | 351 | True | 410.5 | 421.17 | 395 | 220 |
538| 0 | 352 | True | 1231.5 | 421.17 | 395 | 224 |
539| 0 | 353 | True | 2052.5 | 421.17 | 395 | 222 |
540| 0 | 354 | True | 410.5 | 1263.5 | 395 | 339 |
541| 0 | 355 | True | 1231.5 | 1263.5 | 395 | 355 |
542| 0 | 356 | True | 2052.5 | 1263.5 | 395 | 353 |
543| 0 | 357 | True | 410.5 | 2105.83 | 395 | 339 |
544| 0 | 358 | True | 1231.5 | 2105.83 | 395 | 355 |
545| 0 | 359 | True | 2052.5 | 2105.83 | 395 | 353 |
546+------+-----------+-----------+----------+----------+----------+-----------------+
547
548
549Timing information for reference profile formation
550+-------------------+---------------+
551| Read time | 15.54 seconds |
552| Extract time | 0.31 seconds |
553| Pre-process time | 0.02 seconds |
554| Process time | 9.31 seconds |
555| Post-process time | 0.00 seconds |
556| Total time | 25.40 seconds |
557+-------------------+---------------+
558
559================================================================================
560
561Integrating reflections
562
563 Split 669 reflections overlapping job boundaries
564
565Memory situation report:
566 Available system memory : 201.2 GB
567 Maximum memory for processing : 181.1 GB
568 Memory required per process : 0.3 GB
569
570Processing reflections in the following blocks of images:
571
572 block_size: Auto
573
574+-----+---------+--------------+------------+--------------+------------+-----------------+
575| # | Group | Frame From | Frame To | Angle From | Angle To | # Reflections |
576|-----+---------+--------------+------------+--------------+------------+-----------------|
577| 0 | 0 | 1 | 109 | 216 | 270.5 | 52191 |
578| 1 | 0 | 98 | 206 | 264.5 | 319 | 47634 |
579| 2 | 0 | 195 | 303 | 313 | 367.5 | 47745 |
580| 3 | 0 | 292 | 400 | 361.5 | 416 | 51445 |
581+-----+---------+--------------+------------+--------------+------------+-----------------+
582
583 Using multiprocessing with 4 parallel job(s)
584
585
586 Frames: 0 -> 109
587
588 Number of reflections
589 Partial: 2535
590 Full: 49656
591 In ice ring: 0
592 Integrate: 52191
593 Total: 52191
594
595
596 Frames: 97 -> 206
597
598 Number of reflections
599 Partial: 336
600 Full: 47298
601 In ice ring: 0
602 Integrate: 47634
603 Total: 47634
604
605
606 Frames: 194 -> 303
607
608 Number of reflections
609 Partial: 331
610 Full: 47414
611 In ice ring: 0
612 Integrate: 47745
613 Total: 47745
614
615
616 Frames: 291 -> 400
617
618 Number of reflections
619 Partial: 2471
620 Full: 48974
621 In ice ring: 0
622 Integrate: 51445
623 Total: 51445
624
625
626 Summary vs image number
627+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
628| ID | Image | # full | # part | # over | # ice | # sum | # prf | Ibg | I/sigI | I/sigI | CC prf | RMSD XY |
629| | | | | | | | | | (sum) | (prf) | | |
630|------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------|
631| 0 | 1 | 0 | 1465 | 0 | 0 | 1245 | 423 | 0.2 | 1.1 | 3.18 | 0.56 | 0.64 |
632| 0 | 2 | 6 | 478 | 0 | 0 | 416 | 436 | 0.21 | 3.35 | 3.47 | 0.58 | 0.45 |
633| 0 | 3 | 329 | 210 | 0 | 0 | 457 | 473 | 0.2 | 3.03 | 3.01 | 0.56 | 0.39 |
634| 0 | 4 | 413 | 76 | 0 | 0 | 413 | 428 | 0.21 | 3.18 | 3.17 | 0.58 | 0.36 |
635| 0 | 5 | 437 | 44 | 0 | 0 | 403 | 417 | 0.21 | 3.55 | 3.54 | 0.58 | 0.38 |
636| 0 | 6 | 468 | 15 | 0 | 0 | 407 | 422 | 0.2 | 3.6 | 3.81 | 0.56 | 0.37 |
637| 0 | 7 | 453 | 12 | 0 | 0 | 391 | 407 | 0.2 | 3.05 | 3.03 | 0.56 | 0.38 |
638| 0 | 8 | 520 | 14 | 0 | 0 | 452 | 472 | 0.2 | 2.99 | 2.93 | 0.57 | 0.37 |
639| 0 | 9 | 510 | 10 | 0 | 0 | 458 | 478 | 0.21 | 3.39 | 3.44 | 0.58 | 0.35 |
640| 0 | 10 | 437 | 6 | 0 | 0 | 373 | 388 | 0.22 | 4.06 | 4.07 | 0.59 | 0.36 |
641| 0 | 11 | 486 | 5 | 0 | 0 | 420 | 438 | 0.2 | 2.77 | 2.93 | 0.56 | 0.38 |
642| 0 | 12 | 486 | 6 | 0 | 0 | 423 | 440 | 0.2 | 3.6 | 3.64 | 0.57 | 0.38 |
643| 0 | 13 | 524 | 5 | 0 | 0 | 449 | 469 | 0.22 | 3.87 | 4.06 | 0.58 | 0.36 |
644| 0 | 14 | 518 | 6 | 0 | 0 | 446 | 465 | 0.22 | 4.3 | 4.35 | 0.59 | 0.36 |
645| 0 | 15 | 438 | 4 | 0 | 0 | 377 | 397 | 0.2 | 3.04 | 2.99 | 0.57 | 0.36 |
646| 0 | 16 | 483 | 5 | 0 | 0 | 410 | 433 | 0.21 | 4.22 | 4.21 | 0.57 | 0.37 |
647| 0 | 17 | 511 | 3 | 0 | 0 | 424 | 442 | 0.22 | 3.64 | 3.77 | 0.58 | 0.37 |
648| 0 | 18 | 498 | 2 | 0 | 0 | 410 | 436 | 0.21 | 3.81 | 3.62 | 0.57 | 0.36 |
649| 0 | 19 | 489 | 4 | 0 | 0 | 414 | 433 | 0.2 | 3.64 | 3.59 | 0.56 | 0.36 |
650| 0 | 20 | 494 | 2 | 0 | 0 | 429 | 448 | 0.22 | 4.22 | 4.12 | 0.58 | 0.38 |
651| 0 | 21 | 501 | 4 | 0 | 0 | 436 | 457 | 0.23 | 4.06 | 4.46 | 0.59 | 0.38 |
652| 0 | 22 | 474 | 1 | 0 | 0 | 405 | 419 | 0.21 | 3.87 | 3.9 | 0.57 | 0.37 |
653| 0 | 23 | 476 | 1 | 0 | 0 | 391 | 422 | 0.21 | 4.67 | 4.69 | 0.58 | 0.37 |
654| 0 | 24 | 516 | 0 | 0 | 0 | 438 | 457 | 0.21 | 3.76 | 3.74 | 0.58 | 0.4 |
655| 0 | 25 | 502 | 1 | 0 | 0 | 430 | 447 | 0.22 | 4.68 | 4.67 | 0.57 | 0.4 |
656| 0 | 26 | 503 | 6 | 0 | 0 | 427 | 444 | 0.21 | 3.95 | 3.95 | 0.57 | 0.37 |
657| 0 | 27 | 478 | 0 | 0 | 0 | 413 | 425 | 0.22 | 4.02 | 4.16 | 0.57 | 0.4 |
658| 0 | 28 | 473 | 2 | 0 | 0 | 389 | 409 | 0.22 | 4.17 | 4.33 | 0.57 | 0.41 |
659| 0 | 29 | 514 | 2 | 0 | 0 | 435 | 455 | 0.22 | 4.22 | 4.18 | 0.57 | 0.4 |
660| 0 | 30 | 488 | 0 | 0 | 0 | 425 | 441 | 0.22 | 4.11 | 4.07 | 0.57 | 0.37 |
661| 0 | 31 | 493 | 0 | 0 | 0 | 433 | 450 | 0.22 | 4.04 | 4.11 | 0.57 | 0.4 |
662| 0 | 32 | 492 | 0 | 0 | 0 | 423 | 446 | 0.21 | 3.7 | 3.6 | 0.57 | 0.39 |
663| 0 | 33 | 504 | 1 | 0 | 0 | 424 | 438 | 0.22 | 4.17 | 4.32 | 0.57 | 0.39 |
664| 0 | 34 | 501 | 0 | 0 | 0 | 416 | 435 | 0.21 | 3.74 | 3.73 | 0.57 | 0.4 |
665| 0 | 35 | 495 | 0 | 0 | 0 | 423 | 442 | 0.21 | 4.23 | 4.23 | 0.56 | 0.39 |
666| 0 | 36 | 510 | 4 | 0 | 0 | 437 | 455 | 0.22 | 4.48 | 4.57 | 0.57 | 0.4 |
667| 0 | 37 | 495 | 1 | 0 | 0 | 414 | 437 | 0.21 | 3.46 | 3.68 | 0.56 | 0.41 |
668| 0 | 38 | 455 | 0 | 0 | 0 | 375 | 398 | 0.2 | 3.73 | 3.81 | 0.55 | 0.41 |
669| 0 | 39 | 496 | 0 | 0 | 0 | 421 | 444 | 0.2 | 3.58 | 3.49 | 0.56 | 0.39 |
670| 0 | 40 | 510 | 2 | 0 | 0 | 436 | 450 | 0.21 | 4.13 | 4.06 | 0.56 | 0.4 |
671| 0 | 41 | 483 | 2 | 0 | 0 | 416 | 432 | 0.2 | 3.28 | 3.29 | 0.55 | 0.4 |
672| 0 | 42 | 488 | 0 | 0 | 0 | 402 | 421 | 0.2 | 3.93 | 3.96 | 0.55 | 0.38 |
673| 0 | 43 | 498 | 2 | 0 | 0 | 423 | 440 | 0.19 | 3.87 | 3.81 | 0.55 | 0.4 |
674| 0 | 44 | 486 | 0 | 0 | 0 | 397 | 416 | 0.19 | 3.89 | 3.82 | 0.55 | 0.41 |
675| 0 | 45 | 498 | 1 | 0 | 0 | 396 | 425 | 0.19 | 3.71 | 3.89 | 0.55 | 0.41 |
676| 0 | 46 | 505 | 1 | 0 | 0 | 419 | 437 | 0.19 | 3.56 | 3.49 | 0.55 | 0.42 |
677| 0 | 47 | 485 | 0 | 0 | 0 | 410 | 431 | 0.2 | 4.37 | 4.45 | 0.56 | 0.41 |
678| 0 | 48 | 508 | 0 | 0 | 0 | 437 | 455 | 0.18 | 3.28 | 3.41 | 0.53 | 0.4 |
679| 0 | 49 | 499 | 5 | 0 | 0 | 431 | 445 | 0.19 | 3.95 | 3.89 | 0.56 | 0.39 |
680| 0 | 50 | 489 | 1 | 0 | 0 | 415 | 437 | 0.17 | 3.03 | 3.04 | 0.53 | 0.4 |
681| 0 | 51 | 507 | 0 | 0 | 0 | 429 | 446 | 0.2 | 4.4 | 4.33 | 0.55 | 0.37 |
682| 0 | 52 | 508 | 0 | 0 | 0 | 436 | 455 | 0.18 | 3 | 3.05 | 0.53 | 0.4 |
683| 0 | 53 | 486 | 0 | 0 | 0 | 417 | 434 | 0.18 | 3.23 | 3.34 | 0.54 | 0.4 |
684| 0 | 54 | 496 | 0 | 0 | 0 | 421 | 436 | 0.18 | 3.46 | 3.46 | 0.54 | 0.4 |
685| 0 | 55 | 485 | 2 | 0 | 0 | 410 | 428 | 0.18 | 3.21 | 3.17 | 0.53 | 0.42 |
686| 0 | 56 | 517 | 2 | 0 | 0 | 444 | 462 | 0.18 | 3.51 | 3.55 | 0.54 | 0.4 |
687| 0 | 57 | 495 | 0 | 0 | 0 | 415 | 430 | 0.19 | 3.31 | 3.36 | 0.54 | 0.42 |
688| 0 | 58 | 479 | 2 | 0 | 0 | 408 | 428 | 0.18 | 4.12 | 4.04 | 0.53 | 0.44 |
689| 0 | 59 | 543 | 0 | 0 | 0 | 461 | 480 | 0.18 | 3.5 | 3.46 | 0.53 | 0.43 |
690| 0 | 60 | 472 | 0 | 0 | 0 | 405 | 425 | 0.18 | 3.14 | 3.28 | 0.53 | 0.41 |
691| 0 | 61 | 526 | 0 | 0 | 0 | 437 | 460 | 0.17 | 3.26 | 3.15 | 0.53 | 0.42 |
692| 0 | 62 | 498 | 0 | 0 | 0 | 426 | 445 | 0.18 | 3.18 | 3.2 | 0.53 | 0.44 |
693| 0 | 63 | 459 | 0 | 0 | 0 | 390 | 410 | 0.17 | 3.25 | 3.19 | 0.53 | 0.42 |
694| 0 | 64 | 520 | 0 | 0 | 0 | 442 | 460 | 0.17 | 2.92 | 2.99 | 0.52 | 0.44 |
695| 0 | 65 | 490 | 0 | 0 | 0 | 411 | 425 | 0.17 | 2.86 | 2.82 | 0.52 | 0.42 |
696| 0 | 66 | 482 | 2 | 0 | 0 | 406 | 424 | 0.18 | 3.77 | 3.71 | 0.53 | 0.43 |
697| 0 | 67 | 512 | 2 | 0 | 0 | 433 | 448 | 0.17 | 3.15 | 3.1 | 0.52 | 0.42 |
698| 0 | 68 | 488 | 0 | 0 | 0 | 419 | 435 | 0.17 | 3.14 | 3.2 | 0.52 | 0.43 |
699| 0 | 69 | 514 | 0 | 0 | 0 | 431 | 445 | 0.18 | 3.5 | 3.44 | 0.53 | 0.42 |
700| 0 | 70 | 506 | 0 | 0 | 0 | 428 | 449 | 0.17 | 2.76 | 2.97 | 0.52 | 0.43 |
701| 0 | 71 | 495 | 4 | 0 | 0 | 426 | 454 | 0.17 | 3.71 | 3.78 | 0.52 | 0.44 |
702| 0 | 72 | 464 | 2 | 0 | 0 | 403 | 413 | 0.17 | 2.92 | 2.86 | 0.51 | 0.41 |
703| 0 | 73 | 503 | 2 | 0 | 0 | 415 | 440 | 0.17 | 3.05 | 2.91 | 0.52 | 0.43 |
704| 0 | 74 | 499 | 2 | 0 | 0 | 427 | 447 | 0.17 | 3.23 | 3.31 | 0.52 | 0.41 |
705| 0 | 75 | 483 | 0 | 0 | 0 | 421 | 440 | 0.17 | 3.61 | 3.51 | 0.52 | 0.43 |
706| 0 | 76 | 491 | 0 | 0 | 0 | 430 | 438 | 0.18 | 3.73 | 3.85 | 0.53 | 0.44 |
707| 0 | 77 | 503 | 8 | 0 | 0 | 431 | 452 | 0.17 | 3.06 | 3.13 | 0.52 | 0.46 |
708| 0 | 78 | 481 | 2 | 0 | 0 | 404 | 418 | 0.16 | 3.31 | 3.24 | 0.52 | 0.48 |
709| 0 | 79 | 538 | 0 | 0 | 0 | 457 | 479 | 0.17 | 3.26 | 3.22 | 0.52 | 0.44 |
710| 0 | 80 | 500 | 2 | 0 | 0 | 426 | 443 | 0.17 | 3.63 | 3.72 | 0.52 | 0.46 |
711| 0 | 81 | 499 | 2 | 0 | 0 | 432 | 444 | 0.17 | 3.04 | 2.96 | 0.52 | 0.43 |
712| 0 | 82 | 504 | 2 | 0 | 0 | 420 | 444 | 0.16 | 2.81 | 2.67 | 0.51 | 0.43 |
713| 0 | 83 | 473 | 0 | 0 | 0 | 409 | 424 | 0.16 | 2.87 | 2.8 | 0.51 | 0.44 |
714| 0 | 84 | 486 | 2 | 0 | 0 | 402 | 424 | 0.17 | 3.45 | 3.37 | 0.52 | 0.44 |
715| 0 | 85 | 496 | 4 | 0 | 0 | 427 | 443 | 0.18 | 3.83 | 3.8 | 0.53 | 0.45 |
716| 0 | 86 | 491 | 0 | 0 | 0 | 423 | 448 | 0.17 | 3.05 | 3.05 | 0.52 | 0.44 |
717| 0 | 87 | 491 | 2 | 0 | 0 | 404 | 430 | 0.16 | 3.45 | 3.29 | 0.51 | 0.45 |
718| 0 | 88 | 497 | 2 | 0 | 0 | 427 | 449 | 0.16 | 3.2 | 3.19 | 0.52 | 0.44 |
719| 0 | 89 | 522 | 6 | 0 | 0 | 446 | 461 | 0.16 | 3.35 | 3.34 | 0.52 | 0.42 |
720| 0 | 90 | 508 | 9 | 0 | 0 | 444 | 457 | 0.16 | 2.75 | 2.78 | 0.52 | 0.42 |
721| 0 | 91 | 467 | 0 | 0 | 0 | 394 | 414 | 0.16 | 2.96 | 2.91 | 0.51 | 0.43 |
722| 0 | 92 | 479 | 6 | 0 | 0 | 415 | 432 | 0.17 | 3.97 | 3.81 | 0.53 | 0.44 |
723| 0 | 93 | 495 | 6 | 0 | 0 | 429 | 442 | 0.16 | 2.88 | 2.85 | 0.52 | 0.43 |
724| 0 | 94 | 517 | 4 | 0 | 0 | 455 | 471 | 0.17 | 2.82 | 2.89 | 0.52 | 0.43 |
725| 0 | 95 | 467 | 10 | 0 | 0 | 409 | 430 | 0.16 | 2.75 | 2.67 | 0.51 | 0.42 |
726| 0 | 96 | 511 | 4 | 0 | 0 | 428 | 440 | 0.15 | 2.97 | 2.98 | 0.51 | 0.42 |
727| 0 | 97 | 494 | 10 | 0 | 0 | 427 | 443 | 0.16 | 2.7 | 2.9 | 0.52 | 0.42 |
728| 0 | 98 | 479 | 10 | 0 | 0 | 411 | 432 | 0.17 | 3.41 | 3.4 | 0.53 | 0.43 |
729| 0 | 99 | 477 | 6 | 0 | 0 | 410 | 426 | 0.16 | 3.54 | 3.55 | 0.52 | 0.45 |
730| 0 | 100 | 501 | 11 | 0 | 0 | 431 | 446 | 0.15 | 2.25 | 2.28 | 0.51 | 0.45 |
731| 0 | 101 | 467 | 24 | 0 | 0 | 432 | 438 | 0.15 | 2.71 | 2.8 | 0.51 | 0.45 |
732| 0 | 102 | 484 | 16 | 0 | 0 | 413 | 442 | 0.16 | 3.03 | 2.86 | 0.52 | 0.42 |
733| 0 | 103 | 513 | 40 | 0 | 0 | 469 | 479 | 0.16 | 3.42 | 3.5 | 0.52 | 0.44 |
734| 0 | 104 | 453 | 42 | 0 | 0 | 422 | 431 | 0.16 | 3.05 | 2.96 | 0.53 | 0.44 |
735| 0 | 105 | 450 | 22 | 0 | 0 | 406 | 422 | 0.16 | 3.1 | 3.03 | 0.54 | 0.4 |
736| 0 | 106 | 526 | 10 | 0 | 0 | 465 | 478 | 0.15 | 2.59 | 2.59 | 0.51 | 0.45 |
737| 0 | 107 | 484 | 22 | 0 | 0 | 440 | 454 | 0.15 | 2.42 | 2.53 | 0.51 | 0.43 |
738| 0 | 108 | 472 | 16 | 0 | 0 | 407 | 429 | 0.16 | 2.76 | 2.72 | 0.53 | 0.41 |
739| 0 | 109 | 479 | 12 | 0 | 0 | 403 | 419 | 0.15 | 2.76 | 2.7 | 0.52 | 0.43 |
740| 0 | 110 | 485 | 10 | 0 | 0 | 424 | 440 | 0.16 | 3.23 | 3.21 | 0.53 | 0.44 |
741| 0 | 111 | 508 | 9 | 0 | 0 | 424 | 448 | 0.15 | 2.6 | 2.61 | 0.51 | 0.42 |
742| 0 | 112 | 499 | 4 | 0 | 0 | 430 | 448 | 0.16 | 3.03 | 2.88 | 0.51 | 0.44 |
743| 0 | 113 | 487 | 2 | 0 | 0 | 422 | 445 | 0.16 | 2.88 | 2.76 | 0.52 | 0.43 |
744| 0 | 114 | 442 | 2 | 0 | 0 | 379 | 395 | 0.16 | 2.82 | 2.62 | 0.53 | 0.44 |
745| 0 | 115 | 519 | 4 | 0 | 0 | 449 | 467 | 0.15 | 2.88 | 2.76 | 0.51 | 0.44 |
746| 0 | 116 | 520 | 2 | 0 | 0 | 440 | 460 | 0.16 | 3.06 | 2.94 | 0.52 | 0.44 |
747| 0 | 117 | 497 | 4 | 0 | 0 | 420 | 437 | 0.15 | 2.49 | 2.42 | 0.5 | 0.44 |
748| 0 | 118 | 452 | 2 | 0 | 0 | 395 | 406 | 0.17 | 2.89 | 2.87 | 0.54 | 0.41 |
749| 0 | 119 | 491 | 3 | 0 | 0 | 405 | 426 | 0.15 | 2.49 | 2.38 | 0.51 | 0.44 |
750| 0 | 120 | 504 | 8 | 0 | 0 | 425 | 448 | 0.14 | 1.98 | 1.88 | 0.5 | 0.42 |
751| 0 | 121 | 509 | 2 | 0 | 0 | 440 | 464 | 0.16 | 2.81 | 2.75 | 0.53 | 0.42 |
752| 0 | 122 | 441 | 2 | 0 | 0 | 376 | 393 | 0.16 | 2.83 | 2.89 | 0.53 | 0.4 |
753| 0 | 123 | 512 | 2 | 0 | 0 | 438 | 457 | 0.15 | 2.77 | 2.65 | 0.51 | 0.42 |
754| 0 | 124 | 498 | 4 | 0 | 0 | 419 | 440 | 0.15 | 2.5 | 2.35 | 0.51 | 0.45 |
755| 0 | 125 | 509 | 0 | 0 | 0 | 445 | 466 | 0.15 | 2.65 | 2.58 | 0.52 | 0.43 |
756| 0 | 126 | 448 | 0 | 0 | 0 | 381 | 397 | 0.16 | 3.1 | 2.94 | 0.53 | 0.41 |
757| 0 | 127 | 497 | 2 | 0 | 0 | 425 | 441 | 0.15 | 2.72 | 2.76 | 0.5 | 0.46 |
758| 0 | 128 | 518 | 4 | 0 | 0 | 446 | 463 | 0.15 | 2.34 | 2.38 | 0.52 | 0.42 |
759| 0 | 129 | 504 | 2 | 0 | 0 | 429 | 441 | 0.15 | 2.42 | 2.37 | 0.52 | 0.43 |
760| 0 | 130 | 458 | 2 | 0 | 0 | 384 | 402 | 0.15 | 2.81 | 2.8 | 0.52 | 0.41 |
761| 0 | 131 | 512 | 0 | 0 | 0 | 425 | 452 | 0.15 | 2.7 | 2.55 | 0.51 | 0.42 |
762| 0 | 132 | 445 | 0 | 0 | 0 | 372 | 390 | 0.15 | 2.57 | 2.47 | 0.51 | 0.42 |
763| 0 | 133 | 505 | 2 | 0 | 0 | 422 | 438 | 0.16 | 2.79 | 2.75 | 0.52 | 0.42 |
764| 0 | 134 | 519 | 0 | 0 | 0 | 440 | 468 | 0.15 | 2.37 | 2.17 | 0.51 | 0.43 |
765| 0 | 135 | 466 | 2 | 0 | 0 | 404 | 424 | 0.14 | 2.26 | 2.26 | 0.51 | 0.41 |
766| 0 | 136 | 478 | 0 | 0 | 0 | 413 | 427 | 0.15 | 2.45 | 2.44 | 0.51 | 0.44 |
767| 0 | 137 | 471 | 0 | 0 | 0 | 399 | 419 | 0.15 | 2.52 | 2.42 | 0.52 | 0.42 |
768| 0 | 138 | 532 | 3 | 0 | 0 | 432 | 464 | 0.15 | 2.42 | 2.26 | 0.51 | 0.43 |
769| 0 | 139 | 486 | 0 | 0 | 0 | 416 | 430 | 0.15 | 2.41 | 2.33 | 0.52 | 0.43 |
770| 0 | 140 | 480 | 0 | 0 | 0 | 416 | 429 | 0.15 | 2.67 | 2.53 | 0.52 | 0.39 |
771| 0 | 141 | 491 | 0 | 0 | 0 | 416 | 433 | 0.15 | 2.39 | 2.29 | 0.52 | 0.43 |
772| 0 | 142 | 488 | 0 | 0 | 0 | 407 | 432 | 0.14 | 2.17 | 2.06 | 0.49 | 0.45 |
773| 0 | 143 | 469 | 0 | 0 | 0 | 399 | 418 | 0.14 | 1.86 | 1.74 | 0.5 | 0.45 |
774| 0 | 144 | 490 | 3 | 0 | 0 | 411 | 430 | 0.15 | 2.49 | 2.45 | 0.52 | 0.42 |
775| 0 | 145 | 493 | 0 | 0 | 0 | 425 | 435 | 0.15 | 2.28 | 2.22 | 0.51 | 0.43 |
776| 0 | 146 | 497 | 0 | 0 | 0 | 431 | 452 | 0.16 | 2.65 | 2.64 | 0.52 | 0.42 |
777| 0 | 147 | 497 | 0 | 0 | 0 | 417 | 437 | 0.15 | 2.32 | 2.24 | 0.52 | 0.44 |
778| 0 | 148 | 483 | 0 | 0 | 0 | 404 | 421 | 0.15 | 2.42 | 2.31 | 0.51 | 0.43 |
779| 0 | 149 | 471 | 0 | 0 | 0 | 407 | 422 | 0.14 | 2.32 | 2.35 | 0.5 | 0.46 |
780| 0 | 150 | 518 | 0 | 0 | 0 | 445 | 467 | 0.15 | 2.36 | 2.3 | 0.51 | 0.44 |
781| 0 | 151 | 471 | 0 | 0 | 0 | 399 | 421 | 0.14 | 2.12 | 2.16 | 0.5 | 0.44 |
782| 0 | 152 | 483 | 0 | 0 | 0 | 411 | 428 | 0.13 | 1.71 | 1.62 | 0.49 | 0.45 |
783| 0 | 153 | 488 | 0 | 0 | 0 | 412 | 425 | 0.15 | 2.54 | 2.48 | 0.51 | 0.42 |
784| 0 | 154 | 496 | 0 | 0 | 0 | 424 | 449 | 0.16 | 2.22 | 2.17 | 0.52 | 0.43 |
785| 0 | 155 | 482 | 0 | 0 | 0 | 409 | 430 | 0.15 | 2.15 | 2.16 | 0.52 | 0.41 |
786| 0 | 156 | 511 | 3 | 0 | 0 | 424 | 449 | 0.15 | 2.51 | 2.35 | 0.51 | 0.46 |
787| 0 | 157 | 490 | 0 | 0 | 0 | 429 | 445 | 0.15 | 2.72 | 2.55 | 0.53 | 0.43 |
788| 0 | 158 | 505 | 0 | 0 | 0 | 433 | 455 | 0.15 | 2.29 | 2.32 | 0.52 | 0.43 |
789| 0 | 159 | 471 | 0 | 0 | 0 | 391 | 405 | 0.14 | 2.17 | 2.16 | 0.5 | 0.46 |
790| 0 | 160 | 492 | 0 | 0 | 0 | 431 | 444 | 0.14 | 1.75 | 1.85 | 0.5 | 0.44 |
791| 0 | 161 | 483 | 0 | 0 | 0 | 396 | 418 | 0.14 | 2.21 | 2.1 | 0.51 | 0.46 |
792| 0 | 162 | 482 | 3 | 0 | 0 | 423 | 438 | 0.14 | 2.05 | 1.94 | 0.51 | 0.43 |
793| 0 | 163 | 479 | 7 | 0 | 0 | 420 | 429 | 0.14 | 1.67 | 1.61 | 0.5 | 0.43 |
794| 0 | 164 | 500 | 0 | 0 | 0 | 424 | 435 | 0.13 | 1.82 | 1.73 | 0.5 | 0.45 |
795| 0 | 165 | 483 | 0 | 0 | 0 | 413 | 432 | 0.15 | 2.39 | 2.29 | 0.51 | 0.44 |
796| 0 | 166 | 465 | 0 | 0 | 0 | 386 | 410 | 0.15 | 2.05 | 1.95 | 0.51 | 0.43 |
797| 0 | 167 | 495 | 4 | 0 | 0 | 431 | 441 | 0.15 | 2.42 | 2.35 | 0.52 | 0.42 |
798| 0 | 168 | 475 | 0 | 0 | 0 | 399 | 414 | 0.13 | 1.67 | 1.57 | 0.49 | 0.43 |
799| 0 | 169 | 525 | 2 | 0 | 0 | 451 | 472 | 0.15 | 2.64 | 2.56 | 0.51 | 0.43 |
800| 0 | 170 | 491 | 0 | 0 | 0 | 413 | 430 | 0.14 | 1.78 | 1.87 | 0.5 | 0.43 |
801| 0 | 171 | 461 | 0 | 0 | 0 | 392 | 411 | 0.14 | 2.35 | 2.19 | 0.52 | 0.42 |
802| 0 | 172 | 489 | 0 | 0 | 0 | 406 | 428 | 0.14 | 2.23 | 2.06 | 0.51 | 0.42 |
803| 0 | 173 | 478 | 2 | 0 | 0 | 409 | 428 | 0.14 | 2.14 | 2.02 | 0.5 | 0.42 |
804| 0 | 174 | 496 | 0 | 0 | 0 | 425 | 446 | 0.14 | 2.27 | 2.21 | 0.51 | 0.42 |
805| 0 | 175 | 523 | 6 | 0 | 0 | 449 | 472 | 0.14 | 1.9 | 1.8 | 0.5 | 0.44 |
806| 0 | 176 | 448 | 2 | 0 | 0 | 384 | 393 | 0.14 | 1.96 | 1.93 | 0.51 | 0.45 |
807| 0 | 177 | 496 | 2 | 0 | 0 | 428 | 451 | 0.15 | 2.25 | 2.16 | 0.51 | 0.45 |
808| 0 | 178 | 501 | 2 | 0 | 0 | 416 | 440 | 0.14 | 2.2 | 2.1 | 0.51 | 0.46 |
809| 0 | 179 | 475 | 10 | 0 | 0 | 417 | 430 | 0.13 | 1.49 | 1.41 | 0.49 | 0.44 |
810| 0 | 180 | 479 | 6 | 0 | 0 | 410 | 428 | 0.14 | 1.77 | 1.71 | 0.5 | 0.42 |
811| 0 | 181 | 507 | 6 | 0 | 0 | 437 | 451 | 0.13 | 1.66 | 1.58 | 0.49 | 0.45 |
812| 0 | 182 | 467 | 2 | 0 | 0 | 391 | 409 | 0.14 | 1.91 | 1.77 | 0.49 | 0.47 |
813| 0 | 183 | 487 | 6 | 0 | 0 | 419 | 431 | 0.14 | 2.3 | 2.24 | 0.5 | 0.43 |
814| 0 | 184 | 475 | 0 | 0 | 0 | 414 | 429 | 0.14 | 2 | 1.92 | 0.51 | 0.42 |
815| 0 | 185 | 501 | 0 | 0 | 0 | 423 | 443 | 0.14 | 1.76 | 1.72 | 0.5 | 0.44 |
816| 0 | 186 | 499 | 0 | 0 | 0 | 420 | 433 | 0.14 | 2.2 | 2.15 | 0.51 | 0.46 |
817| 0 | 187 | 481 | 4 | 0 | 0 | 423 | 434 | 0.14 | 1.89 | 1.87 | 0.51 | 0.43 |
818| 0 | 188 | 496 | 0 | 0 | 0 | 413 | 437 | 0.14 | 2.08 | 1.96 | 0.5 | 0.43 |
819| 0 | 189 | 511 | 0 | 0 | 0 | 417 | 447 | 0.14 | 2.05 | 1.99 | 0.51 | 0.45 |
820| 0 | 190 | 478 | 2 | 0 | 0 | 409 | 427 | 0.14 | 2.02 | 1.97 | 0.5 | 0.47 |
821| 0 | 191 | 503 | 2 | 0 | 0 | 438 | 458 | 0.13 | 1.81 | 1.78 | 0.49 | 0.44 |
822| 0 | 192 | 480 | 6 | 0 | 0 | 398 | 421 | 0.14 | 2.52 | 2.28 | 0.5 | 0.44 |
823| 0 | 193 | 483 | 6 | 0 | 0 | 413 | 429 | 0.13 | 1.65 | 1.68 | 0.5 | 0.45 |
824| 0 | 194 | 444 | 10 | 0 | 0 | 403 | 410 | 0.13 | 1.79 | 1.68 | 0.5 | 0.46 |
825| 0 | 195 | 512 | 8 | 0 | 0 | 431 | 450 | 0.14 | 2 | 1.98 | 0.51 | 0.46 |
826| 0 | 196 | 487 | 10 | 0 | 0 | 426 | 442 | 0.14 | 2.14 | 2.12 | 0.51 | 0.45 |
827| 0 | 197 | 504 | 10 | 0 | 0 | 446 | 456 | 0.14 | 2.24 | 2.31 | 0.51 | 0.44 |
828| 0 | 198 | 464 | 15 | 0 | 0 | 398 | 418 | 0.13 | 1.46 | 1.5 | 0.49 | 0.46 |
829| 0 | 199 | 478 | 18 | 0 | 0 | 426 | 438 | 0.14 | 1.86 | 1.83 | 0.5 | 0.46 |
830| 0 | 200 | 467 | 26 | 0 | 0 | 420 | 424 | 0.13 | 1.52 | 1.53 | 0.5 | 0.45 |
831| 0 | 201 | 455 | 50 | 0 | 0 | 421 | 435 | 0.13 | 2.1 | 2.22 | 0.5 | 0.45 |
832| 0 | 202 | 470 | 26 | 0 | 0 | 424 | 442 | 0.14 | 2.12 | 2.05 | 0.52 | 0.45 |
833| 0 | 203 | 530 | 24 | 0 | 0 | 456 | 485 | 0.14 | 2.46 | 2.32 | 0.52 | 0.42 |
834| 0 | 204 | 469 | 12 | 0 | 0 | 411 | 426 | 0.13 | 1.69 | 1.67 | 0.5 | 0.45 |
835| 0 | 205 | 486 | 26 | 0 | 0 | 433 | 458 | 0.14 | 2.21 | 2.23 | 0.51 | 0.44 |
836| 0 | 206 | 487 | 12 | 0 | 0 | 415 | 431 | 0.13 | 1.46 | 1.58 | 0.49 | 0.45 |
837| 0 | 207 | 477 | 8 | 0 | 0 | 420 | 438 | 0.13 | 1.81 | 1.69 | 0.5 | 0.45 |
838| 0 | 208 | 469 | 8 | 0 | 0 | 401 | 421 | 0.13 | 1.39 | 1.34 | 0.49 | 0.46 |
839| 0 | 209 | 489 | 8 | 0 | 0 | 430 | 442 | 0.14 | 2.17 | 2.09 | 0.52 | 0.45 |
840| 0 | 210 | 512 | 14 | 0 | 0 | 453 | 472 | 0.13 | 1.84 | 1.74 | 0.5 | 0.44 |
841| 0 | 211 | 497 | 4 | 0 | 0 | 426 | 445 | 0.14 | 2.01 | 2.01 | 0.5 | 0.43 |
842| 0 | 212 | 471 | 8 | 0 | 0 | 411 | 421 | 0.13 | 1.69 | 1.65 | 0.49 | 0.46 |
843| 0 | 213 | 472 | 6 | 0 | 0 | 408 | 425 | 0.14 | 2.35 | 2.3 | 0.51 | 0.43 |
844| 0 | 214 | 500 | 6 | 0 | 0 | 422 | 449 | 0.14 | 2.18 | 2.07 | 0.51 | 0.47 |
845| 0 | 215 | 511 | 0 | 0 | 0 | 430 | 450 | 0.13 | 1.97 | 1.91 | 0.5 | 0.47 |
846| 0 | 216 | 470 | 0 | 0 | 0 | 391 | 412 | 0.13 | 1.72 | 1.72 | 0.49 | 0.46 |
847| 0 | 217 | 467 | 2 | 0 | 0 | 417 | 428 | 0.14 | 1.93 | 1.98 | 0.5 | 0.44 |
848| 0 | 218 | 510 | 0 | 0 | 0 | 425 | 453 | 0.13 | 1.62 | 1.52 | 0.5 | 0.45 |
849| 0 | 219 | 506 | 2 | 0 | 0 | 426 | 441 | 0.13 | 1.81 | 1.78 | 0.5 | 0.47 |
850| 0 | 220 | 490 | 2 | 0 | 0 | 415 | 427 | 0.14 | 1.97 | 1.95 | 0.5 | 0.45 |
851| 0 | 221 | 458 | 2 | 0 | 0 | 387 | 409 | 0.14 | 2.35 | 2.22 | 0.51 | 0.45 |
852| 0 | 222 | 494 | 6 | 0 | 0 | 426 | 446 | 0.14 | 1.84 | 1.74 | 0.5 | 0.44 |
853| 0 | 223 | 501 | 2 | 0 | 0 | 430 | 456 | 0.13 | 1.87 | 1.76 | 0.5 | 0.46 |
854| 0 | 224 | 480 | 0 | 0 | 0 | 399 | 420 | 0.13 | 1.79 | 1.69 | 0.5 | 0.47 |
855| 0 | 225 | 456 | 0 | 0 | 0 | 396 | 407 | 0.14 | 2.11 | 2.05 | 0.51 | 0.45 |
856| 0 | 226 | 526 | 0 | 0 | 0 | 452 | 467 | 0.14 | 1.8 | 1.82 | 0.51 | 0.44 |
857| 0 | 227 | 497 | 0 | 0 | 0 | 414 | 438 | 0.14 | 2.02 | 1.93 | 0.5 | 0.45 |
858| 0 | 228 | 484 | 0 | 0 | 0 | 414 | 429 | 0.13 | 1.99 | 1.84 | 0.5 | 0.45 |
859| 0 | 229 | 486 | 0 | 0 | 0 | 414 | 433 | 0.13 | 1.75 | 1.73 | 0.49 | 0.45 |
860| 0 | 230 | 542 | 0 | 0 | 0 | 444 | 472 | 0.13 | 1.97 | 1.87 | 0.5 | 0.43 |
861| 0 | 231 | 446 | 0 | 0 | 0 | 383 | 398 | 0.14 | 2.04 | 2.01 | 0.5 | 0.43 |
862| 0 | 232 | 467 | 4 | 0 | 0 | 405 | 420 | 0.14 | 2.09 | 2.09 | 0.5 | 0.46 |
863| 0 | 233 | 499 | 2 | 0 | 0 | 430 | 456 | 0.14 | 1.95 | 1.88 | 0.5 | 0.46 |
864| 0 | 234 | 486 | 2 | 0 | 0 | 413 | 430 | 0.13 | 1.62 | 1.68 | 0.49 | 0.47 |
865| 0 | 235 | 479 | 3 | 0 | 0 | 407 | 421 | 0.14 | 1.93 | 1.83 | 0.5 | 0.45 |
866| 0 | 236 | 551 | 0 | 0 | 0 | 449 | 470 | 0.13 | 1.47 | 1.34 | 0.49 | 0.46 |
867| 0 | 237 | 476 | 0 | 0 | 0 | 416 | 434 | 0.13 | 1.87 | 1.84 | 0.5 | 0.45 |
868| 0 | 238 | 468 | 0 | 0 | 0 | 403 | 418 | 0.14 | 1.71 | 1.63 | 0.49 | 0.45 |
869| 0 | 239 | 470 | 0 | 0 | 0 | 396 | 416 | 0.14 | 2.2 | 2.08 | 0.51 | 0.45 |
870| 0 | 240 | 505 | 0 | 0 | 0 | 426 | 445 | 0.14 | 2.11 | 1.97 | 0.5 | 0.43 |
871| 0 | 241 | 479 | 0 | 0 | 0 | 423 | 436 | 0.14 | 1.96 | 1.86 | 0.5 | 0.43 |
872| 0 | 242 | 509 | 2 | 0 | 0 | 425 | 458 | 0.13 | 2.28 | 2.17 | 0.5 | 0.47 |
873| 0 | 243 | 527 | 0 | 0 | 0 | 428 | 451 | 0.14 | 2.02 | 1.88 | 0.51 | 0.42 |
874| 0 | 244 | 471 | 2 | 0 | 0 | 402 | 420 | 0.13 | 1.68 | 1.66 | 0.49 | 0.46 |
875| 0 | 245 | 465 | 0 | 0 | 0 | 397 | 418 | 0.14 | 2.12 | 2.07 | 0.5 | 0.47 |
876| 0 | 246 | 495 | 0 | 0 | 0 | 417 | 426 | 0.14 | 1.87 | 1.83 | 0.5 | 0.46 |
877| 0 | 247 | 508 | 0 | 0 | 0 | 430 | 452 | 0.13 | 1.67 | 1.55 | 0.48 | 0.46 |
878| 0 | 248 | 495 | 0 | 0 | 0 | 412 | 432 | 0.14 | 2.01 | 1.91 | 0.5 | 0.44 |
879| 0 | 249 | 463 | 3 | 0 | 0 | 393 | 411 | 0.14 | 1.99 | 2 | 0.5 | 0.47 |
880| 0 | 250 | 492 | 0 | 0 | 0 | 430 | 447 | 0.13 | 1.72 | 1.62 | 0.49 | 0.44 |
881| 0 | 251 | 488 | 0 | 0 | 0 | 411 | 426 | 0.13 | 1.99 | 1.95 | 0.49 | 0.46 |
882| 0 | 252 | 507 | 0 | 0 | 0 | 432 | 454 | 0.14 | 2.13 | 2.14 | 0.51 | 0.44 |
883| 0 | 253 | 485 | 0 | 0 | 0 | 407 | 432 | 0.13 | 1.77 | 1.68 | 0.49 | 0.46 |
884| 0 | 254 | 492 | 0 | 0 | 0 | 418 | 436 | 0.14 | 1.92 | 1.84 | 0.5 | 0.44 |
885| 0 | 255 | 487 | 0 | 0 | 0 | 409 | 434 | 0.14 | 1.88 | 1.77 | 0.5 | 0.43 |
886| 0 | 256 | 528 | 0 | 0 | 0 | 448 | 470 | 0.13 | 1.74 | 1.67 | 0.49 | 0.46 |
887| 0 | 257 | 470 | 3 | 0 | 0 | 395 | 418 | 0.14 | 1.96 | 1.88 | 0.5 | 0.45 |
888| 0 | 258 | 496 | 4 | 0 | 0 | 408 | 434 | 0.14 | 2.08 | 2 | 0.51 | 0.42 |
889| 0 | 259 | 479 | 0 | 0 | 0 | 411 | 430 | 0.14 | 2.06 | 1.98 | 0.49 | 0.45 |
890| 0 | 260 | 522 | 0 | 0 | 0 | 459 | 477 | 0.14 | 2.03 | 1.92 | 0.5 | 0.43 |
891| 0 | 261 | 465 | 0 | 0 | 0 | 397 | 411 | 0.12 | 1.58 | 1.53 | 0.47 | 0.46 |
892| 0 | 262 | 496 | 0 | 0 | 0 | 417 | 433 | 0.14 | 2.03 | 1.95 | 0.5 | 0.46 |
893| 0 | 263 | 471 | 4 | 0 | 0 | 395 | 411 | 0.14 | 2.23 | 2.09 | 0.51 | 0.44 |
894| 0 | 264 | 499 | 3 | 0 | 0 | 425 | 443 | 0.13 | 1.49 | 1.4 | 0.48 | 0.45 |
895| 0 | 265 | 487 | 0 | 0 | 0 | 423 | 437 | 0.14 | 1.87 | 1.85 | 0.49 | 0.45 |
896| 0 | 266 | 494 | 0 | 0 | 0 | 415 | 434 | 0.14 | 2.16 | 2.06 | 0.51 | 0.43 |
897| 0 | 267 | 505 | 0 | 0 | 0 | 428 | 452 | 0.14 | 1.83 | 1.76 | 0.49 | 0.45 |
898| 0 | 268 | 483 | 0 | 0 | 0 | 399 | 422 | 0.13 | 1.8 | 1.65 | 0.49 | 0.46 |
899| 0 | 269 | 492 | 6 | 0 | 0 | 423 | 438 | 0.14 | 2.03 | 1.89 | 0.5 | 0.44 |
900| 0 | 270 | 458 | 2 | 0 | 0 | 395 | 412 | 0.14 | 1.94 | 1.86 | 0.5 | 0.46 |
901| 0 | 271 | 516 | 3 | 0 | 0 | 445 | 462 | 0.13 | 1.6 | 1.59 | 0.48 | 0.46 |
902| 0 | 272 | 490 | 0 | 0 | 0 | 425 | 444 | 0.14 | 2 | 1.95 | 0.5 | 0.46 |
903| 0 | 273 | 484 | 0 | 0 | 0 | 399 | 428 | 0.15 | 2.05 | 1.96 | 0.51 | 0.41 |
904| 0 | 274 | 496 | 0 | 0 | 0 | 405 | 419 | 0.13 | 1.6 | 1.53 | 0.48 | 0.48 |
905| 0 | 275 | 487 | 0 | 0 | 0 | 420 | 437 | 0.13 | 1.8 | 1.76 | 0.49 | 0.43 |
906| 0 | 276 | 472 | 2 | 0 | 0 | 413 | 428 | 0.14 | 1.93 | 1.89 | 0.5 | 0.45 |
907| 0 | 277 | 496 | 2 | 0 | 0 | 424 | 441 | 0.14 | 2.01 | 1.84 | 0.49 | 0.46 |
908| 0 | 278 | 478 | 0 | 0 | 0 | 412 | 423 | 0.14 | 1.89 | 1.91 | 0.49 | 0.45 |
909| 0 | 279 | 487 | 4 | 0 | 0 | 413 | 430 | 0.15 | 2.01 | 1.94 | 0.51 | 0.43 |
910| 0 | 280 | 493 | 2 | 0 | 0 | 419 | 442 | 0.14 | 1.91 | 1.83 | 0.49 | 0.45 |
911| 0 | 281 | 515 | 2 | 0 | 0 | 445 | 462 | 0.14 | 2.05 | 1.98 | 0.5 | 0.45 |
912| 0 | 282 | 484 | 2 | 0 | 0 | 412 | 433 | 0.15 | 2.19 | 2.09 | 0.52 | 0.44 |
913| 0 | 283 | 507 | 2 | 0 | 0 | 426 | 450 | 0.14 | 2.02 | 2.09 | 0.49 | 0.44 |
914| 0 | 284 | 510 | 3 | 0 | 0 | 438 | 455 | 0.15 | 2.34 | 2.26 | 0.51 | 0.46 |
915| 0 | 285 | 474 | 4 | 0 | 0 | 409 | 427 | 0.14 | 2.16 | 2.06 | 0.5 | 0.43 |
916| 0 | 286 | 513 | 4 | 0 | 0 | 430 | 459 | 0.14 | 1.94 | 1.84 | 0.5 | 0.46 |
917| 0 | 287 | 463 | 6 | 0 | 0 | 409 | 422 | 0.14 | 1.71 | 1.81 | 0.5 | 0.46 |
918| 0 | 288 | 496 | 7 | 0 | 0 | 430 | 441 | 0.14 | 1.98 | 1.99 | 0.5 | 0.44 |
919| 0 | 289 | 472 | 8 | 0 | 0 | 411 | 421 | 0.15 | 2.2 | 2.09 | 0.5 | 0.43 |
920| 0 | 290 | 492 | 10 | 0 | 0 | 415 | 428 | 0.14 | 1.75 | 1.73 | 0.5 | 0.43 |
921| 0 | 291 | 484 | 9 | 0 | 0 | 413 | 431 | 0.15 | 1.87 | 1.82 | 0.5 | 0.44 |
922| 0 | 292 | 511 | 2 | 0 | 0 | 440 | 465 | 0.15 | 2.03 | 2 | 0.5 | 0.44 |
923| 0 | 293 | 459 | 8 | 0 | 0 | 394 | 410 | 0.14 | 2.04 | 1.99 | 0.5 | 0.43 |
924| 0 | 294 | 513 | 15 | 0 | 0 | 442 | 453 | 0.15 | 2.1 | 1.88 | 0.51 | 0.44 |
925| 0 | 295 | 453 | 29 | 0 | 0 | 407 | 419 | 0.15 | 2.25 | 2.21 | 0.51 | 0.44 |
926| 0 | 296 | 485 | 24 | 0 | 0 | 425 | 444 | 0.14 | 1.78 | 1.71 | 0.49 | 0.44 |
927| 0 | 297 | 481 | 36 | 0 | 0 | 440 | 442 | 0.15 | 2.07 | 2.02 | 0.5 | 0.43 |
928| 0 | 298 | 473 | 30 | 0 | 0 | 421 | 438 | 0.15 | 1.97 | 1.97 | 0.51 | 0.42 |
929| 0 | 299 | 479 | 24 | 0 | 0 | 421 | 438 | 0.16 | 2.19 | 2.09 | 0.52 | 0.42 |
930| 0 | 300 | 467 | 18 | 0 | 0 | 416 | 435 | 0.14 | 1.86 | 1.76 | 0.5 | 0.45 |
931| 0 | 301 | 498 | 30 | 0 | 0 | 447 | 471 | 0.15 | 2.1 | 2.01 | 0.51 | 0.44 |
932| 0 | 302 | 500 | 18 | 0 | 0 | 433 | 457 | 0.15 | 1.83 | 1.78 | 0.51 | 0.43 |
933| 0 | 303 | 459 | 10 | 0 | 0 | 404 | 419 | 0.15 | 1.92 | 1.8 | 0.51 | 0.45 |
934| 0 | 304 | 471 | 4 | 0 | 0 | 412 | 428 | 0.15 | 2.28 | 2.09 | 0.51 | 0.42 |
935| 0 | 305 | 507 | 10 | 0 | 0 | 441 | 456 | 0.15 | 2.33 | 2.22 | 0.51 | 0.4 |
936| 0 | 306 | 473 | 8 | 0 | 0 | 414 | 431 | 0.15 | 1.99 | 1.86 | 0.51 | 0.43 |
937| 0 | 307 | 487 | 2 | 0 | 0 | 413 | 425 | 0.15 | 2.31 | 2.18 | 0.51 | 0.43 |
938| 0 | 308 | 508 | 2 | 0 | 0 | 430 | 451 | 0.15 | 2.19 | 2.04 | 0.51 | 0.43 |
939| 0 | 309 | 498 | 6 | 0 | 0 | 434 | 454 | 0.15 | 2.01 | 1.97 | 0.5 | 0.41 |
940| 0 | 310 | 496 | 8 | 0 | 0 | 428 | 447 | 0.15 | 1.68 | 1.64 | 0.49 | 0.45 |
941| 0 | 311 | 458 | 2 | 0 | 0 | 389 | 409 | 0.15 | 2.15 | 2.04 | 0.5 | 0.43 |
942| 0 | 312 | 513 | 6 | 0 | 0 | 440 | 464 | 0.17 | 2.74 | 2.67 | 0.53 | 0.42 |
943| 0 | 313 | 477 | 5 | 0 | 0 | 398 | 418 | 0.15 | 1.94 | 1.81 | 0.49 | 0.43 |
944| 0 | 314 | 500 | 0 | 0 | 0 | 424 | 442 | 0.14 | 1.91 | 1.77 | 0.49 | 0.43 |
945| 0 | 315 | 475 | 2 | 0 | 0 | 406 | 425 | 0.15 | 1.8 | 1.74 | 0.5 | 0.43 |
946| 0 | 316 | 492 | 0 | 0 | 0 | 424 | 438 | 0.17 | 3.11 | 2.97 | 0.52 | 0.42 |
947| 0 | 317 | 473 | 0 | 0 | 0 | 404 | 418 | 0.16 | 2.51 | 2.38 | 0.51 | 0.41 |
948| 0 | 318 | 521 | 0 | 0 | 0 | 454 | 476 | 0.16 | 1.93 | 1.85 | 0.51 | 0.43 |
949| 0 | 319 | 492 | 4 | 0 | 0 | 404 | 430 | 0.16 | 2.33 | 2.14 | 0.51 | 0.42 |
950| 0 | 320 | 485 | 2 | 0 | 0 | 413 | 429 | 0.16 | 2.63 | 2.51 | 0.51 | 0.42 |
951| 0 | 321 | 486 | 2 | 0 | 0 | 422 | 442 | 0.16 | 2.61 | 2.49 | 0.52 | 0.41 |
952| 0 | 322 | 488 | 0 | 0 | 0 | 402 | 422 | 0.15 | 1.77 | 1.77 | 0.5 | 0.41 |
953| 0 | 323 | 471 | 0 | 0 | 0 | 407 | 424 | 0.15 | 2.19 | 2.11 | 0.5 | 0.44 |
954| 0 | 324 | 514 | 4 | 0 | 0 | 428 | 452 | 0.17 | 2.47 | 2.28 | 0.52 | 0.4 |
955| 0 | 325 | 489 | 0 | 0 | 0 | 422 | 440 | 0.16 | 2.09 | 1.91 | 0.51 | 0.41 |
956| 0 | 326 | 499 | 0 | 0 | 0 | 423 | 436 | 0.17 | 2.76 | 2.7 | 0.52 | 0.42 |
957| 0 | 327 | 494 | 0 | 0 | 0 | 426 | 448 | 0.16 | 2.54 | 2.45 | 0.51 | 0.41 |
958| 0 | 328 | 483 | 0 | 0 | 0 | 401 | 417 | 0.15 | 2 | 1.87 | 0.5 | 0.44 |
959| 0 | 329 | 487 | 0 | 0 | 0 | 413 | 435 | 0.16 | 2.57 | 2.4 | 0.52 | 0.41 |
960| 0 | 330 | 496 | 4 | 0 | 0 | 431 | 455 | 0.18 | 2.66 | 2.48 | 0.52 | 0.39 |
961| 0 | 331 | 500 | 0 | 0 | 0 | 421 | 445 | 0.16 | 2.58 | 2.42 | 0.51 | 0.43 |
962| 0 | 332 | 483 | 0 | 0 | 0 | 407 | 430 | 0.17 | 2.55 | 2.43 | 0.52 | 0.41 |
963| 0 | 333 | 489 | 3 | 0 | 0 | 407 | 428 | 0.17 | 2.49 | 2.39 | 0.53 | 0.4 |
964| 0 | 334 | 488 | 0 | 0 | 0 | 411 | 434 | 0.16 | 2.43 | 2.32 | 0.51 | 0.43 |
965| 0 | 335 | 518 | 0 | 0 | 0 | 438 | 459 | 0.18 | 2.65 | 2.57 | 0.53 | 0.4 |
966| 0 | 336 | 465 | 0 | 0 | 0 | 402 | 420 | 0.18 | 2.73 | 2.63 | 0.53 | 0.42 |
967| 0 | 337 | 476 | 0 | 0 | 0 | 417 | 432 | 0.18 | 2.6 | 2.61 | 0.52 | 0.4 |
968| 0 | 338 | 538 | 0 | 0 | 0 | 461 | 479 | 0.17 | 2.18 | 2.07 | 0.52 | 0.41 |
969| 0 | 339 | 487 | 0 | 0 | 0 | 407 | 424 | 0.18 | 2.15 | 2.1 | 0.52 | 0.4 |
970| 0 | 340 | 470 | 0 | 0 | 0 | 400 | 417 | 0.18 | 2.46 | 2.33 | 0.53 | 0.4 |
971| 0 | 341 | 478 | 2 | 0 | 0 | 414 | 437 | 0.17 | 2.38 | 2.22 | 0.51 | 0.4 |
972| 0 | 342 | 498 | 2 | 0 | 0 | 421 | 440 | 0.18 | 2.16 | 2.12 | 0.53 | 0.38 |
973| 0 | 343 | 500 | 0 | 0 | 0 | 424 | 443 | 0.18 | 2.59 | 2.67 | 0.53 | 0.39 |
974| 0 | 344 | 497 | 0 | 0 | 0 | 404 | 422 | 0.18 | 2.3 | 2.3 | 0.52 | 0.42 |
975| 0 | 345 | 462 | 0 | 0 | 0 | 390 | 411 | 0.19 | 2.8 | 2.73 | 0.53 | 0.4 |
976| 0 | 346 | 498 | 0 | 0 | 0 | 423 | 441 | 0.19 | 2.75 | 2.67 | 0.53 | 0.38 |
977| 0 | 347 | 499 | 2 | 0 | 0 | 424 | 444 | 0.18 | 2.33 | 2.16 | 0.52 | 0.39 |
978| 0 | 348 | 489 | 0 | 0 | 0 | 416 | 436 | 0.18 | 2.54 | 2.42 | 0.53 | 0.39 |
979| 0 | 349 | 476 | 0 | 0 | 0 | 397 | 415 | 0.19 | 3.15 | 2.91 | 0.53 | 0.38 |
980| 0 | 350 | 497 | 0 | 0 | 0 | 427 | 438 | 0.2 | 2.59 | 2.43 | 0.53 | 0.42 |
981| 0 | 351 | 492 | 2 | 0 | 0 | 405 | 426 | 0.19 | 2.73 | 2.63 | 0.54 | 0.39 |
982| 0 | 352 | 493 | 2 | 0 | 0 | 429 | 441 | 0.18 | 1.98 | 2.01 | 0.52 | 0.4 |
983| 0 | 353 | 494 | 2 | 0 | 0 | 405 | 429 | 0.2 | 3.23 | 3.02 | 0.55 | 0.39 |
984| 0 | 354 | 483 | 2 | 0 | 0 | 423 | 436 | 0.2 | 3.2 | 3.18 | 0.54 | 0.36 |
985| 0 | 355 | 505 | 0 | 0 | 0 | 436 | 447 | 0.2 | 2.71 | 2.55 | 0.54 | 0.4 |
986| 0 | 356 | 511 | 0 | 0 | 0 | 427 | 448 | 0.21 | 2.85 | 2.74 | 0.54 | 0.39 |
987| 0 | 357 | 463 | 0 | 0 | 0 | 390 | 408 | 0.19 | 1.95 | 1.9 | 0.53 | 0.38 |
988| 0 | 358 | 463 | 0 | 0 | 0 | 392 | 415 | 0.2 | 2.45 | 2.37 | 0.54 | 0.37 |
989| 0 | 359 | 518 | 0 | 0 | 0 | 447 | 458 | 0.2 | 2.85 | 2.69 | 0.54 | 0.38 |
990| 0 | 360 | 470 | 0 | 0 | 0 | 397 | 417 | 0.2 | 2.47 | 2.23 | 0.54 | 0.39 |
991| 0 | 361 | 522 | 0 | 0 | 0 | 453 | 469 | 0.21 | 2.81 | 2.8 | 0.54 | 0.38 |
992| 0 | 362 | 492 | 1 | 0 | 0 | 413 | 438 | 0.21 | 2.43 | 2.48 | 0.55 | 0.36 |
993| 0 | 363 | 467 | 0 | 0 | 0 | 392 | 410 | 0.22 | 3.09 | 2.95 | 0.55 | 0.36 |
994| 0 | 364 | 477 | 5 | 0 | 0 | 406 | 422 | 0.22 | 2.97 | 2.85 | 0.55 | 0.39 |
995| 0 | 365 | 528 | 1 | 0 | 0 | 434 | 457 | 0.21 | 2.73 | 2.57 | 0.55 | 0.36 |
996| 0 | 366 | 472 | 2 | 0 | 0 | 399 | 417 | 0.21 | 2.55 | 2.46 | 0.54 | 0.38 |
997| 0 | 367 | 493 | 0 | 0 | 0 | 404 | 425 | 0.23 | 3.24 | 3.08 | 0.56 | 0.38 |
998| 0 | 368 | 477 | 1 | 0 | 0 | 416 | 436 | 0.23 | 2.64 | 2.54 | 0.56 | 0.36 |
999| 0 | 369 | 481 | 0 | 0 | 0 | 410 | 431 | 0.23 | 3.32 | 3.24 | 0.56 | 0.39 |
1000| 0 | 370 | 518 | 1 | 0 | 0 | 440 | 461 | 0.21 | 2.38 | 2.25 | 0.55 | 0.37 |
1001| 0 | 371 | 491 | 2 | 0 | 0 | 419 | 435 | 0.22 | 2.92 | 2.86 | 0.55 | 0.36 |
1002| 0 | 372 | 496 | 0 | 0 | 0 | 433 | 450 | 0.25 | 2.95 | 3.03 | 0.57 | 0.36 |
1003| 0 | 373 | 486 | 2 | 0 | 0 | 418 | 435 | 0.25 | 2.92 | 2.76 | 0.58 | 0.35 |
1004| 0 | 374 | 484 | 1 | 0 | 0 | 409 | 428 | 0.23 | 3 | 2.95 | 0.56 | 0.38 |
1005| 0 | 375 | 481 | 2 | 0 | 0 | 413 | 433 | 0.23 | 2.89 | 2.74 | 0.56 | 0.35 |
1006| 0 | 376 | 497 | 3 | 0 | 0 | 423 | 449 | 0.24 | 2.44 | 2.38 | 0.57 | 0.36 |
1007| 0 | 377 | 495 | 1 | 0 | 0 | 417 | 441 | 0.24 | 2.27 | 2.16 | 0.56 | 0.36 |
1008| 0 | 378 | 465 | 3 | 0 | 0 | 391 | 413 | 0.24 | 2.6 | 2.47 | 0.56 | 0.36 |
1009| 0 | 379 | 493 | 0 | 0 | 0 | 425 | 448 | 0.26 | 2.94 | 2.77 | 0.58 | 0.35 |
1010| 0 | 380 | 494 | 1 | 0 | 0 | 422 | 443 | 0.27 | 2.93 | 2.83 | 0.58 | 0.34 |
1011| 0 | 381 | 500 | 0 | 0 | 0 | 421 | 449 | 0.26 | 3.12 | 2.9 | 0.57 | 0.34 |
1012| 0 | 382 | 472 | 1 | 0 | 0 | 394 | 414 | 0.25 | 3.09 | 3.02 | 0.57 | 0.35 |
1013| 0 | 383 | 504 | 4 | 0 | 0 | 433 | 442 | 0.26 | 2.5 | 2.44 | 0.57 | 0.36 |
1014| 0 | 384 | 493 | 2 | 0 | 0 | 419 | 433 | 0.26 | 2.53 | 2.51 | 0.57 | 0.34 |
1015| 0 | 385 | 503 | 6 | 0 | 0 | 440 | 460 | 0.26 | 2.65 | 2.62 | 0.58 | 0.37 |
1016| 0 | 386 | 475 | 0 | 0 | 0 | 399 | 417 | 0.27 | 2.23 | 2.24 | 0.57 | 0.34 |
1017| 0 | 387 | 454 | 5 | 0 | 0 | 390 | 405 | 0.27 | 2.71 | 2.64 | 0.58 | 0.34 |
1018| 0 | 388 | 484 | 4 | 0 | 0 | 412 | 432 | 0.27 | 2.52 | 2.44 | 0.58 | 0.35 |
1019| 0 | 389 | 511 | 0 | 0 | 0 | 445 | 464 | 0.28 | 2.41 | 2.43 | 0.58 | 0.33 |
1020| 0 | 390 | 476 | 6 | 0 | 0 | 419 | 437 | 0.27 | 2.46 | 2.35 | 0.58 | 0.34 |
1021| 0 | 391 | 470 | 8 | 0 | 0 | 410 | 435 | 0.27 | 1.91 | 1.8 | 0.58 | 0.35 |
1022| 0 | 392 | 507 | 10 | 0 | 0 | 427 | 449 | 0.3 | 3.11 | 3.06 | 0.59 | 0.34 |
1023| 0 | 393 | 481 | 14 | 0 | 0 | 413 | 435 | 0.29 | 2.31 | 2.2 | 0.59 | 0.34 |
1024| 0 | 394 | 488 | 23 | 0 | 0 | 433 | 457 | 0.27 | 2.15 | 2.13 | 0.58 | 0.34 |
1025| 0 | 395 | 449 | 18 | 0 | 0 | 408 | 419 | 0.29 | 2.63 | 2.49 | 0.59 | 0.35 |
1026| 0 | 396 | 475 | 29 | 0 | 0 | 431 | 453 | 0.27 | 2.02 | 1.95 | 0.58 | 0.33 |
1027| 0 | 397 | 395 | 56 | 0 | 0 | 371 | 390 | 0.29 | 2.34 | 2.28 | 0.58 | 0.34 |
1028| 0 | 398 | 302 | 184 | 0 | 0 | 413 | 435 | 0.29 | 2.5 | 2.52 | 0.58 | 0.38 |
1029| 0 | 399 | 4 | 485 | 0 | 0 | 413 | 434 | 0.28 | 2.17 | 2.18 | 0.59 | 0.39 |
1030| 0 | 400 | 0 | 491 | 0 | 0 | 419 | 436 | 0.28 | 1.59 | 2.12 | 0.58 | 0.48 |
1031+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
1032
1033 Summary vs resolution
1034+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
1035| ID | d min | # full | # part | # over | # ice | # sum | # prf | Ibg | I/sigI | I/sigI | CC prf | RMSD XY |
1036| | | | | | | | | | (sum) | (prf) | | |
1037|------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------|
1038| 0 | 1.18 | 195 | 4 | 0 | 0 | 113 | 160 | 0.03 | -0.03 | 0 | 0.29 | 0.83 |
1039| 0 | 1.2 | 586 | 17 | 0 | 0 | 521 | 561 | 0.03 | 0.08 | 0.03 | 0.31 | 0.8 |
1040| 0 | 1.23 | 1078 | 20 | 0 | 0 | 980 | 1027 | 0.04 | 0 | 0.02 | 0.31 | 0.82 |
1041| 0 | 1.25 | 1532 | 32 | 0 | 0 | 1307 | 1390 | 0.04 | 0.03 | 0.02 | 0.33 | 0.75 |
1042| 0 | 1.28 | 2212 | 54 | 0 | 0 | 1964 | 2047 | 0.05 | 0.04 | 0.03 | 0.34 | 0.71 |
1043| 0 | 1.3 | 2974 | 57 | 0 | 0 | 2466 | 2642 | 0.05 | 0.03 | 0.03 | 0.35 | 0.67 |
1044| 0 | 1.33 | 4339 | 105 | 0 | 0 | 3730 | 3940 | 0.06 | 0.03 | 0.04 | 0.36 | 0.65 |
1045| 0 | 1.37 | 6169 | 138 | 0 | 0 | 5292 | 5644 | 0.06 | 0.04 | 0.04 | 0.37 | 0.62 |
1046| 0 | 1.4 | 8667 | 193 | 0 | 0 | 7673 | 7974 | 0.07 | 0.09 | 0.06 | 0.37 | 0.6 |
1047| 0 | 1.45 | 9836 | 214 | 0 | 0 | 8689 | 8978 | 0.07 | 0.12 | 0.09 | 0.38 | 0.56 |
1048| 0 | 1.49 | 10954 | 267 | 0 | 0 | 9411 | 9836 | 0.08 | 0.16 | 0.12 | 0.39 | 0.53 |
1049| 0 | 1.55 | 12245 | 344 | 0 | 0 | 10251 | 10725 | 0.09 | 0.23 | 0.18 | 0.41 | 0.5 |
1050| 0 | 1.61 | 13280 | 503 | 0 | 0 | 11940 | 12284 | 0.09 | 0.29 | 0.23 | 0.43 | 0.46 |
1051| 0 | 1.68 | 14615 | 523 | 0 | 0 | 12973 | 13341 | 0.11 | 0.43 | 0.34 | 0.45 | 0.44 |
1052| 0 | 1.77 | 16877 | 571 | 0 | 0 | 14619 | 15148 | 0.13 | 0.65 | 0.54 | 0.48 | 0.41 |
1053| 0 | 1.88 | 17474 | 579 | 0 | 0 | 15714 | 16050 | 0.16 | 1.08 | 0.95 | 0.53 | 0.36 |
1054| 0 | 2.03 | 17485 | 594 | 0 | 0 | 14510 | 15074 | 0.2 | 1.81 | 1.67 | 0.58 | 0.33 |
1055| 0 | 2.23 | 17445 | 585 | 0 | 0 | 15814 | 16141 | 0.22 | 2.73 | 2.63 | 0.62 | 0.31 |
1056| 0 | 2.55 | 17613 | 623 | 0 | 0 | 15395 | 15775 | 0.3 | 5.34 | 5.35 | 0.72 | 0.28 |
1057| 0 | 3.21 | 17776 | 570 | 0 | 0 | 15653 | 15999 | 0.47 | 15.16 | 15.77 | 0.84 | 0.24 |
1058+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
1059
1060 Summary for experiment 0
1061+---------------------------------------+-----------+----------+--------+
1062| Item | Overall | Low | High |
1063|---------------------------------------+-----------+----------+--------|
1064| dmin | 1.18 | 3.21 | 1.18 |
1065| dmax | 55.04 | 55.04 | 1.2 |
1066| number fully recorded | 193352 | 17776 | 195 |
1067| number partially recorded | 5993 | 570 | 4 |
1068| number with invalid background pixels | 52762 | 4242 | 158 |
1069| number with invalid foreground pixels | 30000 | 2656 | 86 |
1070| number with overloaded pixels | 0 | 0 | 0 |
1071| number in powder rings | 0 | 0 | 0 |
1072| number processed with summation | 169015 | 15653 | 113 |
1073| number processed with profile fitting | 174736 | 15999 | 160 |
1074| number failed in background modelling | 4 | 4 | 0 |
1075| number failed in summation | 30000 | 2656 | 86 |
1076| number failed in profile fitting | 24279 | 2310 | 39 |
1077| ibg | 0.17 | 0.47 | 0.03 |
1078| i/sigi (summation) | 2.55 | 15.16 | -0.03 |
1079| i/sigi (profile fitting) | 2.52 | 15.77 | 0 |
1080| cc prf | 0.52 | 0.84 | 0.29 |
1081| cc_pearson sum/prf | 1 | 1 | 0.38 |
1082| cc_spearman sum/prf | 0.83 | 1 | 0.32 |
1083+---------------------------------------+-----------+----------+--------+
1084
1085Timing information for integration
1086+-------------------+----------------+
1087| Read time | 15.44 seconds |
1088| Extract time | 5.99 seconds |
1089| Pre-process time | 0.26 seconds |
1090| Process time | 138.05 seconds |
1091| Post-process time | 0.00 seconds |
1092| Total time | 160.73 seconds |
1093+-------------------+----------------+
1094
1095Removing 22813 unintegrated reflections of 199345 total
1096Saving 176532 reflections to integrated.refl
1097Saving 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 best_monoclinic_beta=False
Show/Hide Log
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3
4best_monoclinic_beta = False
5input {
6 experiments = integrated.expt
7 reflections = integrated.refl
8}
9
10================================================================================
11
12Performing Laue group analysis
13
14Mapping all input cells to a common minimum cell
15Filtering reflections for dataset 0
16Read 176532 predicted reflections
17Selected 167219 reflections integrated by profile and summation methods
18Combined 307 partial reflections with other partial reflections
19Removed 3 intensity.sum.value reflections with I/Sig(I) < -5
20Removed 61 intensity.prf.value reflections with I/Sig(I) < -5
21A round of outlier rejection has been performed,
22124 outliers have been identified.
23
24Patterson group: C 1 2/m 1 (-z,x+y,2*x)
25
26--------------------------------------------------------------------------------
27
28Normalising intensities for dataset 1
29
30ML estimate of overall B_cart value:
31 8.42, -0.16, -1.15
32 9.32, 0.90
33 5.75
34ML estimate of -log of scale factor:
35 -3.21
36
37--------------------------------------------------------------------------------
38
39Estimation of resolution for Laue group analysis
40
41Removing 12 Wilson outliers with E^2 >= 16.0
42Resolution estimate from <I>/<σ(I)> > 4.0 : 2.84
43Resolution estimate from CC½ > 0.60: 1.92
44High resolution limit set to: 1.92
45Selecting 61907 reflections with d > 1.92
46
47Input crystal symmetry:
48Unit cell: (44.3853, 53.1239, 62.3731, 115.205, 101.776, 90)
49Space group: P 1 (No. 1)
50Change of basis op to minimum cell: a,b,c
51Crystal symmetry in minimum cell:
52Unit cell: (44.3853, 53.1239, 62.3731, 115.205, 101.776, 90)
53Space group: P 1 (No. 1)
54Lattice point group: C 1 2/m 1 (-z,x+y,2*x)
55
56Overall CC for 20000 unrelated pairs: 0.247
57Estimated expectation value of true correlation coefficient E(CC) = 0.926
58Estimated sd(CC) = 0.879 / sqrt(N)
59Estimated E(CC) of true correlation coefficient from identity = 0.929
60
61--------------------------------------------------------------------------------
62
63Scoring individual symmetry elements
64
65+--------------+--------+------+-------+----+--------------+
66| likelihood | Z-CC | CC | N | | Operator |
67|--------------+--------+------+-------+----+--------------|
68| 0.898 | 9.27 | 0.93 | 51416 | ** | 1 |(0, 0, 0) |
69| 0.853 | 8.77 | 0.88 | 50724 | ** | 2 |(0, 1, 0) |
70+--------------+--------+------+-------+----+--------------+
71
72--------------------------------------------------------------------------------
73
74Scoring all possible sub-groups
75
76+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+
77| Patterson group | | Likelihood | NetZcc | Zcc+ | Zcc- | CC | CC- | delta | Reindex operator |
78|-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------|
79| C 1 2/m 1 | *** | 0.853 | 9.02 | 9.02 | 0 | 0.9 | 0 | 0 | -b-2*c,-b,-a |
80| P -1 | | 0.147 | 0.5 | 9.27 | 8.77 | 0.93 | 0.88 | 0 | a,b,c |
81+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+
82
83Best solution: C 1 2/m 1
84Unit cell: 112.869, 53.124, 44.385, 90.000, 103.036, 90.000
85Reindex operator: -b-2*c,-b,-a
86Laue group probability: 0.853
87Laue group confidence: 0.775
88
89+-------------------+--------------------------+
90| Patterson group | Corresponding MX group |
91|-------------------+--------------------------|
92| C 1 2/m 1 | C 1 2 1 |
93+-------------------+--------------------------+
94================================================================================
95
96Analysing systematic absences
97
98Laue group: C 1 2/m 1
99No absences to check for this laue group
100
101Saving reindexed experiments to symmetrized.expt in space group C 1 2 1
102Saving 176532 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 | *** | 0.853 | 9.02 | 9.02 | 0 | 0.9 | 0 | 0 | -b-2*c,-b,-a |
| P -1 | | 0.147 | 0.5 | 9.27 | 8.77 | 0.93 | 0.88 | 0 | a,b,c |
+-------------------+-----+--------------+----------+--------+--------+------+-------+---------+--------------------+
Best solution: C 1 2/m 1
Unit cell: 112.869, 53.124, 44.385, 90.000, 103.036, 90.000
Reindex operator: -b-2*c,-b,-a
Laue group probability: 0.853
Laue group confidence: 0.775
+-------------------+--------------------------+
| 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
Show/Hide Log
1DIALS 3.dev.1293-g7efd2982c
2The following parameters have been modified:
3input {
4 experiments = symmetrized.expt
5 reflections = symmetrized.refl
6}
7
8Checking for the existence of a reflection table
9containing multiple datasets
10
11Found 1 reflection tables & 1 experiments in total.
12
13Dataset ids are: 0
14
15Space group being used during scaling is C 1 2 1
16
17Scaling models have been initialised for all experiments.
18
19================================================================================
20
21The experiment id for this dataset is 0.
22The scaling model type being applied is physical.
23
24Applying filter of min_isigi > -5.0, partiality > 0.4
25Read 176532 predicted reflections
26Selected 176532 reflections integrated by profile or summation methods
27Removed 1867 reflections below partiality threshold
28Removed 3 intensity.sum.value reflections with I/Sig(I) < -5.0
29Removed 0 intensity.prf.value reflections with I/Sig(I) < -5.0
30Combined 316 partial reflections with other partial reflections
31Excluding 1652/176216 reflections
32Reflections passing individual criteria:
33criterion: user excluded, reflections: 1649
34criterion: excluded for scaling, reflections: 1652
35
36The following corrections will be applied to this dataset:
37
38+--------------+----------------+
39| correction | n_parameters |
40|--------------+----------------|
41| scale | 16 |
42| decay | 12 |
43| absorption | 24 |
44+--------------+----------------+
45Loaded error model:
46Error model details:
47 Type: basic
48 Parameters: a = 1.00000, b = 0.02000
49 Error model formula: σ'² = a²(σ² + (bI)²)
50 estimated I/sigma asymptotic limit: 50.000
51
52A round of outlier rejection has been performed,
532483 outliers have been identified.
54
55172947 reflections were preselected for scale factor determination
56out of 174564 suitable reflections:
57Reflections passing individual criteria:
58criterion: in I/sigma range (I/sig > -5.0), reflections: 174518
59criterion: above min partiality ( > 0.95), reflections: 172993
60
61Randomly selected 15286/48766 groups (m>1) to use for scaling model
62minimisation (49875 reflections)
63Completed preprocessing and initialisation for this dataset.
64
65================================================================================
66
67Components to be refined in this cycle for all datasets: scale, decay, absorption
68Performing a round of scaling with an LBFGS minimizer.
69
70Time taken for refinement 8.02
71
72Refinement steps:
73+--------+--------+----------+
74| Step | Nref | RMSD_I |
75| | | (a.u) |
76|--------+--------+----------|
77| 0 | 49127 | 0.87368 |
78| 1 | 49127 | 0.85176 |
79| 2 | 49127 | 0.69546 |
80| 3 | 49127 | 0.65844 |
81| 4 | 49127 | 0.62261 |
82| 5 | 49127 | 0.60962 |
83| 6 | 49127 | 0.57026 |
84| 7 | 49127 | 0.55556 |
85| 8 | 49127 | 0.55342 |
86| 9 | 49127 | 0.55186 |
87| 10 | 49127 | 0.55096 |
88| 11 | 49127 | 0.54987 |
89| 12 | 49127 | 0.54948 |
90| 13 | 49127 | 0.54872 |
91| 14 | 49127 | 0.54845 |
92| 15 | 49127 | 0.54815 |
93| 16 | 49127 | 0.54778 |
94| 17 | 49127 | 0.54743 |
95| 18 | 49127 | 0.54727 |
96| 19 | 49127 | 0.54712 |
97| 20 | 49127 | 0.54695 |
98| 21 | 49127 | 0.54667 |
99| 22 | 49127 | 0.54613 |
100| 23 | 49127 | 0.54573 |
101| 24 | 49127 | 0.54544 |
102| 25 | 49127 | 0.54473 |
103| 26 | 49127 | 0.54427 |
104| 27 | 49127 | 0.54381 |
105| 28 | 49127 | 0.54351 |
106| 29 | 49127 | 0.54294 |
107| 30 | 49127 | 0.54239 |
108| 31 | 49127 | 0.54199 |
109| 32 | 49127 | 0.54151 |
110| 33 | 49127 | 0.54087 |
111| 34 | 49127 | 0.5404 |
112| 35 | 49127 | 0.53957 |
113| 36 | 49127 | 0.53911 |
114| 37 | 49127 | 0.53862 |
115| 38 | 49127 | 0.53833 |
116| 39 | 49127 | 0.53827 |
117| 40 | 49127 | 0.5382 |
118| 41 | 49127 | 0.53815 |
119+--------+--------+----------+
120RMSD no longer decreasing
121lbfgs minimizer stop: callback_after_step is True
122
123================================================================================
124
125Scale factors determined during minimisation have now been
126applied to all reflections for dataset 0.
127
128A round of outlier rejection has been performed,
129165 outliers have been identified.
130
131Performing profile/summation intensity optimisation.
132+----------------+---------+---------+
133| Combination | CC1/2 | Rmeas |
134|----------------+---------+---------|
135| prf only | 0.99434 | 0.09881 |
136| sum only | 0.99175 | 0.12653 |
137| Imid = 70.1 | 0.9933 | 0.10499 |
138| Imid = 3237.22 | 0.99439 | 0.09879 |
139| Imid = 323.72 | 0.99422 | 0.09943 |
140| Imid = 32.37 | 0.99314 | 0.11308 |
141+----------------+---------+---------+
142Combined intensities with Imid = 3237.22 determined to be best for scaling.
143
144A round of outlier rejection has been performed,
145166 outliers have been identified.
146
147Components to be refined in this cycle for all datasets: scale, decay, absorption
148Performing a round of scaling with an LBFGS minimizer.
149
150Time taken for refinement 3.27
151
152Refinement steps:
153+--------+--------+----------+
154| Step | Nref | RMSD_I |
155| | | (a.u) |
156|--------+--------+----------|
157| 0 | 49828 | 0.59265 |
158| 1 | 49828 | 0.59097 |
159| 2 | 49828 | 0.57776 |
160| 3 | 49828 | 0.57703 |
161| 4 | 49828 | 0.57633 |
162| 5 | 49828 | 0.57608 |
163| 6 | 49828 | 0.57552 |
164| 7 | 49828 | 0.57514 |
165| 8 | 49828 | 0.57496 |
166| 9 | 49828 | 0.57483 |
167| 10 | 49828 | 0.57474 |
168| 11 | 49828 | 0.57464 |
169| 12 | 49828 | 0.57452 |
170| 13 | 49828 | 0.57445 |
171| 14 | 49828 | 0.57439 |
172| 15 | 49828 | 0.57435 |
173+--------+--------+----------+
174RMSD no longer decreasing
175lbfgs minimizer stop: callback_after_step is True
176
177================================================================================
178
179Scale factors determined during minimisation have now been
180applied to all reflections for dataset 0.
181
182A round of outlier rejection has been performed,
183126 outliers have been identified.
184
185Performing a round of error model refinement.
186
187Error model details:
188 Type: basic
189 Parameters: a = 0.52086, b = 0.05457
190 Error model formula: σ'² = a²(σ² + (bI)²)
191 estimated I/sigma asymptotic limit: 35.185
192
193Results of error model refinement. Uncorrected and corrected variances
194of normalised intensity deviations for given intensity ranges. Variances
195are expected to be ~1.0 for reliable errors (sigmas).
196+--------------------------+----------+------------------------+----------------------+
197| Intensity range (<Ih>) | n_refl | Uncorrected variance | Corrected variance |
198|--------------------------+----------+------------------------+----------------------|
199| 2420.16 - 584.95 | 250 | 2.294 | 0.735 |
200| 584.95 - 446.15 | 250 | 1.965 | 1.076 |
201| 446.15 - 376.07 | 250 | 1.622 | 1.046 |
202| 376.07 - 326.97 | 250 | 1.57 | 1.168 |
203| 326.97 - 246.02 | 699 | 1.279 | 1.197 |
204| 246.02 - 155.74 | 1774 | 1.037 | 1.288 |
205| 155.74 - 98.59 | 2797 | 0.651 | 1.147 |
206| 98.59 - 62.41 | 3563 | 0.555 | 1.269 |
207| 62.41 - 39.51 | 3792 | 0.463 | 1.285 |
208| 39.51 - 25.00 | 3028 | 0.419 | 1.296 |
209+--------------------------+----------+------------------------+----------------------+
210
211Components to be refined in this cycle for all datasets: scale, decay, absorption
212Performing a round of scaling with a Levenberg-Marquardt minimizer.
213
214Time taken for refinement 4.33
215
216Refinement steps:
217+--------+--------+----------+
218| Step | Nref | RMSD_I |
219| | | (a.u) |
220|--------+--------+----------|
221| 0 | 49846 | 0.98917 |
222| 1 | 49846 | 0.98339 |
223| 2 | 49846 | 0.97789 |
224| 3 | 49846 | 0.9731 |
225| 4 | 49846 | 0.97095 |
226| 5 | 49846 | 0.97014 |
227| 6 | 49846 | 0.96962 |
228| 7 | 49846 | 0.96937 |
229| 8 | 49846 | 0.96933 |
230+--------+--------+----------+
231RMSD no longer decreasing
232
233================================================================================
234
235Components to be refined in this cycle for all datasets: scale, decay, absorption
236Performing a round of scaling with a Levenberg-Marquardt minimizer.
237
238Time taken for refinement 0.89
239
240Refinement steps:
241+--------+--------+----------+
242| Step | Nref | RMSD_I |
243| | | (a.u) |
244|--------+--------+----------|
245| 0 | 49846 | 0.96933 |
246| 1 | 49846 | 0.96933 |
247+--------+--------+----------+
248RMSD no longer decreasing
249
250================================================================================
251
252Scale factors determined during minimisation have now been
253applied to all reflections for dataset 0.
254
255A round of outlier rejection has been performed,
256299 outliers have been identified.
257
258Performing a round of error model refinement.
259
260Error model details:
261 Type: basic
262 Parameters: a = 0.49549, b = 0.05545
263 Error model formula: σ'² = a²(σ² + (bI)²)
264 estimated I/sigma asymptotic limit: 36.396
265
266Results of error model refinement. Uncorrected and corrected variances
267of normalised intensity deviations for given intensity ranges. Variances
268are expected to be ~1.0 for reliable errors (sigmas).
269+--------------------------+----------+------------------------+----------------------+
270| Intensity range (<Ih>) | n_refl | Uncorrected variance | Corrected variance |
271|--------------------------+----------+------------------------+----------------------|
272| 2421.44 - 597.76 | 250 | 2.411 | 0.825 |
273| 597.76 - 449.16 | 250 | 1.533 | 0.962 |
274| 449.16 - 375.85 | 250 | 1.56 | 1.116 |
275| 375.85 - 329.42 | 250 | 1.507 | 1.158 |
276| 329.42 - 246.09 | 707 | 1.14 | 1.128 |
277| 246.09 - 155.77 | 1759 | 0.884 | 1.189 |
278| 155.77 - 98.60 | 2793 | 0.563 | 1.104 |
279| 98.60 - 62.42 | 3500 | 0.49 | 1.212 |
280| 62.42 - 39.51 | 3784 | 0.39 | 1.202 |
281| 39.51 - 25.00 | 3009 | 0.345 | 1.195 |
282+--------------------------+----------+------------------------+----------------------+
283
284
285The reflection table variances have been adjusted to account for the
286uncertainty in the scaling model
287
288Total time taken: 21.8878s
289
290================================================================================
291
29236.54% of model parameters have significant uncertainty
293(sigma/abs(parameter) > 0.5)
294
295Summary of dataset partialities
296+------------------+----------+
297| Partiality (p) | n_refl |
298|------------------+----------|
299| all reflections | 176216 |
300| p > 0.99 | 172383 |
301| 0.5 < p < 0.99 | 2035 |
302| 0.01 < p < 0.5 | 1534 |
303| p < 0.01 | 264 |
304+------------------+----------+
305
306Reflections below a partiality_cutoff of 0.4 are not considered for any
307part of the scaling analysis or for the reporting of merging statistics.
308Additionally, if applicable, only reflections with a min_partiality > 0.95
309were considered for use when refining the scaling model.
310
311
312 ----------Merging statistics by resolution bin----------
313
314 d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas r_pim r_anom cc1/2 cc_ano
315 55.04 3.22 15836 4256 3.72 99.95 108.1 36.8 0.051 0.059 0.030 0.063 0.996* -0.031
316 3.22 2.56 15551 4161 3.74 99.98 33.0 17.8 0.104 0.122 0.062 0.136 0.987* -0.018
317 2.56 2.23 16026 4148 3.86 100.00 14.5 9.9 0.177 0.206 0.104 0.225 0.963* 0.006
318 2.23 2.03 14925 4148 3.60 99.93 9.1 6.3 0.254 0.298 0.155 0.339 0.933* 0.068*
319 2.03 1.88 15845 4140 3.83 99.86 5.1 3.8 0.379 0.441 0.223 0.457 0.874* -0.066
320 1.88 1.77 15084 4104 3.68 99.93 2.5 2.1 0.601 0.702 0.358 0.739 0.746* -0.008
321 1.77 1.68 13289 4150 3.20 99.88 1.5 1.3 0.860 1.032 0.562 1.099 0.526* -0.008
322 1.68 1.61 12285 4131 2.97 99.95 1.0 0.8 1.250 1.526 0.862 1.373 0.313* -0.044
323 1.61 1.55 10707 4080 2.62 99.01 0.8 0.6 1.490 1.850 1.076 1.555 0.173* 0.002
324 1.55 1.49 9785 4040 2.42 98.06 0.5 0.4 2.166 2.709 1.598 1.790 0.153* -0.017
325 1.49 1.45 8955 3933 2.28 95.37 0.4 0.3 2.976 3.770 2.277 1.868 0.055* -0.087
326 1.45 1.41 8130 3866 2.10 93.65 0.3 0.2 4.273 5.461 3.350 2.005 0.035 -0.003
327 1.41 1.37 5718 3398 1.68 82.52 0.2 0.1 5.774 7.544 4.783 2.361 0.033 0.095
328 1.37 1.34 4009 2786 1.44 68.02 0.2 0.1 7.428 9.952 6.544 2.828 -0.023 0.010
329 1.34 1.31 2765 2240 1.23 54.61 0.1 0.1 14.938 20.506 13.972 3.393 0.050 -0.364
330 1.31 1.28 2064 1745 1.18 42.29 0.1 0.1 8.312 11.734 8.280 4.415 -0.028 0.000
331 1.28 1.25 1435 1243 1.15 30.41 0.1 0.0 28.326 40.059 28.326 4.556 0.021 0.000
332 1.25 1.23 1040 910 1.14 22.08 0.1 0.1 -9.676 -13.683 -9.676 5.816 0.011 0.000
333 1.23 1.21 603 529 1.14 12.95 0.1 0.1 14.780 20.902 14.780 4.988 0.110 0.000
334 1.21 1.19 213 190 1.12 4.60 -0.0 -0.0 -16.661 -23.562 -16.661 3.917 -0.373 0.000
335 54.98 1.19 174265 62198 2.80 75.26 12.0 5.4 0.129 0.154 0.081 0.182 0.995* -0.013
336
337
338Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.59
339
340 -------------Summary of merging statistics--------------
341
342 Suggested Low High Overall
343High resolution limit 1.59 4.33 1.59 1.19
344Low resolution limit 54.98 55.01 1.62 54.98
345Completeness 99.9 99.9 99.8 75.3
346Multiplicity 3.6 3.8 2.9 2.8
347I/sigma 9.7 40.7 0.7 5.4
348Rmerge(I) 0.112 0.044 1.495 0.129
349Rmerge(I+/-) 0.094 0.037 1.435 0.104
350Rmeas(I) 0.132 0.051 1.846 0.154
351Rmeas(I+/-) 0.127 0.051 1.968 0.141
352Rpim(I) 0.068 0.026 1.064 0.081
353Rpim(I+/-) 0.085 0.034 1.340 0.094
354CC half 0.996 0.997 0.122 0.995
355Anomalous completeness 94.3 98.0 87.0 55.2
356Anomalous multiplicity 1.9 2.0 1.6 1.6
357Anomalous correlation -0.010 -0.100 0.075 -0.013
358Anomalous slope 1.011
359dF/F 0.124
360dI/s(dI) 0.964
361Total observations 121627 6713 4787 174265
362Total unique 34216 1785 1669 62198
363
364Writing html report to dials.scale.html
365Saving the scaled experiments to scaled.expt
366Saving the scaled reflections to scaled.refl
367See 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 r_anom cc1/2 cc_ano
55.04 3.22 15836 4256 3.72 99.95 108.1 36.8 0.051 0.059 0.030 0.063 0.996* -0.031
3.22 2.56 15551 4161 3.74 99.98 33.0 17.8 0.104 0.122 0.062 0.136 0.987* -0.018
2.56 2.23 16026 4148 3.86 100.00 14.5 9.9 0.177 0.206 0.104 0.225 0.963* 0.006
2.23 2.03 14925 4148 3.60 99.93 9.1 6.3 0.254 0.298 0.155 0.339 0.933* 0.068*
2.03 1.88 15845 4140 3.83 99.86 5.1 3.8 0.379 0.441 0.223 0.457 0.874* -0.066
1.88 1.77 15084 4104 3.68 99.93 2.5 2.1 0.601 0.702 0.358 0.739 0.746* -0.008
1.77 1.68 13289 4150 3.20 99.88 1.5 1.3 0.860 1.032 0.562 1.099 0.526* -0.008
1.68 1.61 12285 4131 2.97 99.95 1.0 0.8 1.250 1.526 0.862 1.373 0.313* -0.044
1.61 1.55 10707 4080 2.62 99.01 0.8 0.6 1.490 1.850 1.076 1.555 0.173* 0.002
1.55 1.49 9785 4040 2.42 98.06 0.5 0.4 2.166 2.709 1.598 1.790 0.153* -0.017
1.49 1.45 8955 3933 2.28 95.37 0.4 0.3 2.976 3.770 2.277 1.868 0.055* -0.087
1.45 1.41 8130 3866 2.10 93.65 0.3 0.2 4.273 5.461 3.350 2.005 0.035 -0.003
1.41 1.37 5718 3398 1.68 82.52 0.2 0.1 5.774 7.544 4.783 2.361 0.033 0.095
1.37 1.34 4009 2786 1.44 68.02 0.2 0.1 7.428 9.952 6.544 2.828 -0.023 0.010
1.34 1.31 2765 2240 1.23 54.61 0.1 0.1 14.938 20.506 13.972 3.393 0.050 -0.364
1.31 1.28 2064 1745 1.18 42.29 0.1 0.1 8.312 11.734 8.280 4.415 -0.028 0.000
1.28 1.25 1435 1243 1.15 30.41 0.1 0.0 28.326 40.059 28.326 4.556 0.021 0.000
1.25 1.23 1040 910 1.14 22.08 0.1 0.1 -9.676 -13.683 -9.676 5.816 0.011 0.000
1.23 1.21 603 529 1.14 12.95 0.1 0.1 14.780 20.902 14.780 4.988 0.110 0.000
1.21 1.19 213 190 1.12 4.60 -0.0 -0.0 -16.661 -23.562 -16.661 3.917 -0.373 0.000
54.98 1.19 174265 62198 2.80 75.26 12.0 5.4 0.129 0.154 0.081 0.182 0.995* -0.013
Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.59
-------------Summary of merging statistics--------------
Suggested Low High Overall
High resolution limit 1.59 4.33 1.59 1.19
Low resolution limit 54.98 55.01 1.62 54.98
Completeness 99.9 99.9 99.8 75.3
Multiplicity 3.6 3.8 2.9 2.8
I/sigma 9.7 40.7 0.7 5.4
Rmerge(I) 0.112 0.044 1.495 0.129
Rmerge(I+/-) 0.094 0.037 1.435 0.104
Rmeas(I) 0.132 0.051 1.846 0.154
Rmeas(I+/-) 0.127 0.051 1.968 0.141
Rpim(I) 0.068 0.026 1.064 0.081
Rpim(I+/-) 0.085 0.034 1.340 0.094
CC half 0.996 0.997 0.122 0.995
Anomalous completeness 94.3 98.0 87.0 55.2
Anomalous multiplicity 1.9 2.0 1.6 1.6
Anomalous correlation -0.010 -0.100 0.075 -0.013
Anomalous slope 1.011
dF/F 0.124
dI/s(dI) 0.964
Total observations 121627 6713 4787 174265
Total unique 34216 1785 1669 62198
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=1.62
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 function 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
