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.1243-gd06ef435d
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.1243-gd06ef435d
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 1424 strong pixels on image 1
25Found 1578 strong pixels on image 2
26Found 1555 strong pixels on image 3
27Found 1634 strong pixels on image 4
28Found 1507 strong pixels on image 5
29Found 1590 strong pixels on image 6
30Found 1533 strong pixels on image 7
31Found 1773 strong pixels on image 8
32Found 1920 strong pixels on image 9
33Found 1873 strong pixels on image 10
34Found 1743 strong pixels on image 11
35Found 1923 strong pixels on image 12
36Found 2118 strong pixels on image 13
37Found 2179 strong pixels on image 14
38Found 1838 strong pixels on image 15
39Found 2000 strong pixels on image 16
40Found 2168 strong pixels on image 17
41Found 2002 strong pixels on image 18
42Found 2128 strong pixels on image 19
43Found 2363 strong pixels on image 20
44Found 2597 strong pixels on image 21
45Found 2275 strong pixels on image 22
46Found 2157 strong pixels on image 23
47Found 2565 strong pixels on image 24
48Found 2623 strong pixels on image 25
49Found 2604 strong pixels on image 26
50Found 2438 strong pixels on image 27
51Found 2474 strong pixels on image 28
52Found 2613 strong pixels on image 29
53Found 2594 strong pixels on image 30
54Found 2503 strong pixels on image 31
55Found 2499 strong pixels on image 32
56Found 2585 strong pixels on image 33
57Found 2706 strong pixels on image 34
58Found 2691 strong pixels on image 35
59Found 2532 strong pixels on image 36
60Found 2576 strong pixels on image 37
61Found 2424 strong pixels on image 38
62Found 2177 strong pixels on image 39
63Found 2352 strong pixels on image 40
64Found 2439 strong pixels on image 41
65Found 2259 strong pixels on image 42
66Found 2456 strong pixels on image 43
67Found 2377 strong pixels on image 44
68Found 2284 strong pixels on image 45
69Found 2381 strong pixels on image 46
70Found 2183 strong pixels on image 47
71Found 2512 strong pixels on image 48
72Found 2313 strong pixels on image 49
73Found 2272 strong pixels on image 50
74Found 2327 strong pixels on image 51
75Found 2168 strong pixels on image 52
76Found 2234 strong pixels on image 53
77Found 2298 strong pixels on image 54
78Found 2342 strong pixels on image 55
79Found 2513 strong pixels on image 56
80Found 2494 strong pixels on image 57
81Found 2557 strong pixels on image 58
82Found 2388 strong pixels on image 59
83Found 2290 strong pixels on image 60
84Found 2298 strong pixels on image 61
85Found 2316 strong pixels on image 62
86Found 2071 strong pixels on image 63
87Found 2069 strong pixels on image 64
88Found 2268 strong pixels on image 65
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90Found 2187 strong pixels on image 67
91Found 2266 strong pixels on image 68
92Found 2243 strong pixels on image 69
93Found 2260 strong pixels on image 70
94Found 2237 strong pixels on image 71
95Found 2253 strong pixels on image 72
96Found 1969 strong pixels on image 73
97Found 2299 strong pixels on image 74
98Found 2351 strong pixels on image 75
99Found 2319 strong pixels on image 76
100Found 2145 strong pixels on image 77
101Found 2371 strong pixels on image 78
102Found 2565 strong pixels on image 79
103Found 2332 strong pixels on image 80
104Found 2194 strong pixels on image 81
105Found 1995 strong pixels on image 82
106Found 1934 strong pixels on image 83
107Found 2361 strong pixels on image 84
108Found 2333 strong pixels on image 85
109Found 2238 strong pixels on image 86
110Found 2063 strong pixels on image 87
111Found 2187 strong pixels on image 88
112Found 2099 strong pixels on image 89
113Found 2129 strong pixels on image 90
114Found 2312 strong pixels on image 91
115Found 2236 strong pixels on image 92
116Found 2176 strong pixels on image 93
117Found 1930 strong pixels on image 94
118Found 1752 strong pixels on image 95
119Found 1792 strong pixels on image 96
120Found 1798 strong pixels on image 97
121Found 1762 strong pixels on image 98
122Found 1739 strong pixels on image 99
123Found 1452 strong pixels on image 100
124Found 1729 strong pixels on image 101
125Found 1782 strong pixels on image 102
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128Found 1703 strong pixels on image 105
129Found 1536 strong pixels on image 106
130Found 1621 strong pixels on image 107
131Found 1512 strong pixels on image 108
132Found 1522 strong pixels on image 109
133Found 1473 strong pixels on image 110
134Found 1651 strong pixels on image 111
135Found 1651 strong pixels on image 112
136Found 1454 strong pixels on image 113
137Found 1401 strong pixels on image 114
138Found 1623 strong pixels on image 115
139Found 1704 strong pixels on image 116
140Found 1372 strong pixels on image 117
141Found 1276 strong pixels on image 118
142Found 1175 strong pixels on image 119
143Found 1281 strong pixels on image 120
144Found 1399 strong pixels on image 121
145Found 1419 strong pixels on image 122
146Found 1476 strong pixels on image 123
147Found 1487 strong pixels on image 124
148Found 1477 strong pixels on image 125
149Found 1505 strong pixels on image 126
150Found 1495 strong pixels on image 127
151Found 1351 strong pixels on image 128
152Found 1325 strong pixels on image 129
153Found 1365 strong pixels on image 130
154Found 1500 strong pixels on image 131
155Found 1345 strong pixels on image 132
156Found 1414 strong pixels on image 133
157Found 1325 strong pixels on image 134
158Found 1264 strong pixels on image 135
159Found 1165 strong pixels on image 136
160Found 1185 strong pixels on image 137
161Found 1189 strong pixels on image 138
162Found 1219 strong pixels on image 139
163Found 1226 strong pixels on image 140
164Found 1202 strong pixels on image 141
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166Found 999 strong pixels on image 143
167Found 1086 strong pixels on image 144
168Found 1203 strong pixels on image 145
169Found 1347 strong pixels on image 146
170Found 1222 strong pixels on image 147
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172Found 1186 strong pixels on image 149
173Found 1166 strong pixels on image 150
174Found 951 strong pixels on image 151
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176Found 1165 strong pixels on image 153
177Found 1126 strong pixels on image 154
178Found 1109 strong pixels on image 155
179Found 1191 strong pixels on image 156
180Found 1266 strong pixels on image 157
181Found 1286 strong pixels on image 158
182Found 1104 strong pixels on image 159
183Found 971 strong pixels on image 160
184Found 943 strong pixels on image 161
185Found 980 strong pixels on image 162
186Found 868 strong pixels on image 163
187Found 877 strong pixels on image 164
188Found 1058 strong pixels on image 165
189Found 1005 strong pixels on image 166
190Found 1060 strong pixels on image 167
191Found 1132 strong pixels on image 168
192Found 1223 strong pixels on image 169
193Found 1017 strong pixels on image 170
194Found 1011 strong pixels on image 171
195Found 1013 strong pixels on image 172
196Found 1020 strong pixels on image 173
197Found 1017 strong pixels on image 174
198Found 952 strong pixels on image 175
199Found 973 strong pixels on image 176
200Found 1022 strong pixels on image 177
201Found 937 strong pixels on image 178
202Found 812 strong pixels on image 179
203Found 816 strong pixels on image 180
204Found 808 strong pixels on image 181
205Found 933 strong pixels on image 182
206Found 922 strong pixels on image 183
207Found 941 strong pixels on image 184
208Found 927 strong pixels on image 185
209Found 1036 strong pixels on image 186
210Found 943 strong pixels on image 187
211Found 933 strong pixels on image 188
212Found 1090 strong pixels on image 189
213Found 1020 strong pixels on image 190
214Found 942 strong pixels on image 191
215Found 1006 strong pixels on image 192
216Found 959 strong pixels on image 193
217Found 881 strong pixels on image 194
218Found 1026 strong pixels on image 195
219Found 1014 strong pixels on image 196
220Found 1086 strong pixels on image 197
221Found 857 strong pixels on image 198
222Found 904 strong pixels on image 199
223Found 904 strong pixels on image 200
224Found 831 strong pixels on image 201
225Found 1097 strong pixels on image 202
226Found 1130 strong pixels on image 203
227Found 946 strong pixels on image 204
228Found 826 strong pixels on image 205
229Found 800 strong pixels on image 206
230Found 849 strong pixels on image 207
231Found 737 strong pixels on image 208
232Found 901 strong pixels on image 209
233Found 1043 strong pixels on image 210
234Found 951 strong pixels on image 211
235Found 812 strong pixels on image 212
236Found 973 strong pixels on image 213
237Found 1032 strong pixels on image 214
238Found 995 strong pixels on image 215
239Found 921 strong pixels on image 216
240Found 867 strong pixels on image 217
241Found 785 strong pixels on image 218
242Found 909 strong pixels on image 219
243Found 959 strong pixels on image 220
244Found 1058 strong pixels on image 221
245Found 920 strong pixels on image 222
246Found 817 strong pixels on image 223
247Found 879 strong pixels on image 224
248Found 1069 strong pixels on image 225
249Found 923 strong pixels on image 226
250Found 896 strong pixels on image 227
251Found 906 strong pixels on image 228
252Found 896 strong pixels on image 229
253Found 969 strong pixels on image 230
254Found 804 strong pixels on image 231
255Found 919 strong pixels on image 232
256Found 996 strong pixels on image 233
257Found 908 strong pixels on image 234
258Found 887 strong pixels on image 235
259Found 829 strong pixels on image 236
260Found 860 strong pixels on image 237
261Found 831 strong pixels on image 238
262Found 893 strong pixels on image 239
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264Found 995 strong pixels on image 241
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266Found 1003 strong pixels on image 243
267Found 859 strong pixels on image 244
268Found 907 strong pixels on image 245
269Found 916 strong pixels on image 246
270Found 945 strong pixels on image 247
271Found 917 strong pixels on image 248
272Found 898 strong pixels on image 249
273Found 947 strong pixels on image 250
274Found 940 strong pixels on image 251
275Found 918 strong pixels on image 252
276Found 914 strong pixels on image 253
277Found 959 strong pixels on image 254
278Found 972 strong pixels on image 255
279Found 856 strong pixels on image 256
280Found 860 strong pixels on image 257
281Found 1025 strong pixels on image 258
282Found 918 strong pixels on image 259
283Found 1041 strong pixels on image 260
284Found 813 strong pixels on image 261
285Found 1045 strong pixels on image 262
286Found 1042 strong pixels on image 263
287Found 878 strong pixels on image 264
288Found 959 strong pixels on image 265
289Found 1047 strong pixels on image 266
290Found 922 strong pixels on image 267
291Found 889 strong pixels on image 268
292Found 900 strong pixels on image 269
293Found 934 strong pixels on image 270
294Found 1010 strong pixels on image 271
295Found 928 strong pixels on image 272
296Found 991 strong pixels on image 273
297Found 833 strong pixels on image 274
298Found 888 strong pixels on image 275
299Found 846 strong pixels on image 276
300Found 916 strong pixels on image 277
301Found 963 strong pixels on image 278
302Found 1089 strong pixels on image 279
303Found 1079 strong pixels on image 280
304Found 1067 strong pixels on image 281
305Found 1061 strong pixels on image 282
306Found 1076 strong pixels on image 283
307Found 1193 strong pixels on image 284
308Found 979 strong pixels on image 285
309Found 1001 strong pixels on image 286
310Found 1034 strong pixels on image 287
311Found 973 strong pixels on image 288
312Found 944 strong pixels on image 289
313Found 959 strong pixels on image 290
314Found 1010 strong pixels on image 291
315Found 1010 strong pixels on image 292
316Found 897 strong pixels on image 293
317Found 1037 strong pixels on image 294
318Found 963 strong pixels on image 295
319Found 894 strong pixels on image 296
320Found 948 strong pixels on image 297
321Found 944 strong pixels on image 298
322Found 1076 strong pixels on image 299
323Found 1104 strong pixels on image 300
324Found 976 strong pixels on image 301
325Found 936 strong pixels on image 302
326Found 945 strong pixels on image 303
327Found 1094 strong pixels on image 304
328Found 1056 strong pixels on image 305
329Found 1145 strong pixels on image 306
330Found 1121 strong pixels on image 307
331Found 1065 strong pixels on image 308
332Found 1030 strong pixels on image 309
333Found 1009 strong pixels on image 310
334Found 999 strong pixels on image 311
335Found 1140 strong pixels on image 312
336Found 943 strong pixels on image 313
337Found 981 strong pixels on image 314
338Found 1141 strong pixels on image 315
339Found 1309 strong pixels on image 316
340Found 1257 strong pixels on image 317
341Found 1233 strong pixels on image 318
342Found 1225 strong pixels on image 319
343Found 1238 strong pixels on image 320
344Found 1253 strong pixels on image 321
345Found 1045 strong pixels on image 322
346Found 1068 strong pixels on image 323
347Found 1240 strong pixels on image 324
348Found 1178 strong pixels on image 325
349Found 1429 strong pixels on image 326
350Found 1286 strong pixels on image 327
351Found 1204 strong pixels on image 328
352Found 1258 strong pixels on image 329
353Found 1384 strong pixels on image 330
354Found 1241 strong pixels on image 331
355Found 1296 strong pixels on image 332
356Found 1401 strong pixels on image 333
357Found 1401 strong pixels on image 334
358Found 1666 strong pixels on image 335
359Found 1477 strong pixels on image 336
360Found 1477 strong pixels on image 337
361Found 1308 strong pixels on image 338
362Found 1207 strong pixels on image 339
363Found 1447 strong pixels on image 340
364Found 1360 strong pixels on image 341
365Found 1252 strong pixels on image 342
366Found 1440 strong pixels on image 343
367Found 1392 strong pixels on image 344
368Found 1576 strong pixels on image 345
369Found 1616 strong pixels on image 346
370Found 1419 strong pixels on image 347
371Found 1412 strong pixels on image 348
372Found 1503 strong pixels on image 349
373Found 1479 strong pixels on image 350
374Found 1493 strong pixels on image 351
375Found 1514 strong pixels on image 352
376Found 1625 strong pixels on image 353
377Found 1655 strong pixels on image 354
378Found 1544 strong pixels on image 355
379Found 1430 strong pixels on image 356
380Found 1379 strong pixels on image 357
381Found 1512 strong pixels on image 358
382Found 1458 strong pixels on image 359
383Found 1598 strong pixels on image 360
384Found 1668 strong pixels on image 361
385Found 1662 strong pixels on image 362
386Found 1848 strong pixels on image 363
387Found 1833 strong pixels on image 364
388Found 1731 strong pixels on image 365
389Found 1648 strong pixels on image 366
390Found 1837 strong pixels on image 367
391Found 2029 strong pixels on image 368
392Found 1853 strong pixels on image 369
393Found 1871 strong pixels on image 370
394Found 1741 strong pixels on image 371
395Found 1842 strong pixels on image 372
396Found 1697 strong pixels on image 373
397Found 1611 strong pixels on image 374
398Found 1773 strong pixels on image 375
399Found 1563 strong pixels on image 376
400Found 1705 strong pixels on image 377
401Found 1586 strong pixels on image 378
402Found 1883 strong pixels on image 379
403Found 1955 strong pixels on image 380
404Found 1720 strong pixels on image 381
405Found 1742 strong pixels on image 382
406Found 1667 strong pixels on image 383
407Found 1731 strong pixels on image 384
408Found 1724 strong pixels on image 385
409Found 1661 strong pixels on image 386
410Found 1672 strong pixels on image 387
411Found 1630 strong pixels on image 388
412Found 1630 strong pixels on image 389
413Found 1464 strong pixels on image 390
414Found 1562 strong pixels on image 391
415Found 1651 strong pixels on image 392
416Found 1592 strong pixels on image 393
417Found 1514 strong pixels on image 394
418Found 1399 strong pixels on image 395
419Found 1507 strong pixels on image 396
420Found 1421 strong pixels on image 397
421Found 1309 strong pixels on image 398
422Found 1252 strong pixels on image 399
423Found 1287 strong pixels on image 400
424
425Extracted 30376 spots
426Removed 7811 spots with size < 3 pixels
427Removed 3 spots with size > 1000 pixels
428Calculated 22562 spot centroids
429Calculated 22562 spot intensities
430Filtered 21740 of 22562 spots by peak-centroid distance
431
432Histogram of per-image spot count for imageset 0:
43321740 spots found on 400 images (max 491 / bin)
434**
435******* * * * **** *
436********* ** ******************* *
437********* * * ***************************** *
438**************************************************** *
439************************************************************
440************************************************************
441************************************************************
442************************************************************
443************************************************************
4441 image 400
445
446--------------------------------------------------------------------------------
447Saved 21740 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.1243-gd06ef435d
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: 20836
13Candidate solutions:
14+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
15| unit_cell | volume | volume score | #indexed | % indexed | % indexed score | rmsd_xy | rmsd_xy score | overall score |
16|------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------|
17| 44.74 53.39 62.63 115.1 102.0 90.2 | 131784 | 0.01 | 21005 | 97 | 0 | 0.13 | 0 | 0.01 |
18| 44.60 53.25 62.49 115.1 101.8 90.2 | 130920 | 0 | 20874 | 96 | 0.01 | 0.13 | 0.01 | 0.02 |
19| 44.60 53.25 62.58 115.0 101.7 90.2 | 131244 | 0.01 | 20815 | 96 | 0.01 | 0.13 | 0.01 | 0.03 |
20| 44.60 53.25 62.49 115.0 101.8 90.2 | 130947 | 0 | 20903 | 96 | 0.01 | 0.14 | 0.03 | 0.04 |
21| 44.54 53.34 62.54 115.1 101.8 90.2 | 130988 | 0 | 20817 | 96 | 0.01 | 0.14 | 0.04 | 0.06 |
22| 44.60 53.25 62.71 115.1 101.8 90.2 | 131302 | 0.01 | 20905 | 96 | 0.01 | 0.14 | 0.05 | 0.06 |
23| 44.60 53.41 62.49 115.1 101.8 90.1 | 131333 | 0.01 | 20942 | 96 | 0.01 | 0.14 | 0.05 | 0.06 |
24| 44.69 53.41 62.58 64.8 78.1 89.9 | 131615 | 0.01 | 20979 | 97 | 0 | 0.14 | 0.07 | 0.08 |
25| 44.74 53.40 62.62 115.1 102.0 90.1 | 131757 | 0.01 | 20988 | 97 | 0 | 0.14 | 0.07 | 0.08 |
26| 44.64 53.41 62.55 64.8 78.1 89.9 | 131478 | 0.01 | 20971 | 96 | 0 | 0.14 | 0.07 | 0.08 |
27| 44.66 53.34 62.71 64.9 78.1 90.0 | 131699 | 0.01 | 20934 | 96 | 0.01 | 0.14 | 0.07 | 0.09 |
28| 44.60 53.17 62.49 115.0 101.8 90.2 | 130748 | 0 | 20887 | 96 | 0.01 | 0.14 | 0.09 | 0.1 |
29| 44.60 53.43 62.53 115.0 101.7 90.2 | 131505 | 0.01 | 20977 | 96 | 0 | 0.14 | 0.09 | 0.1 |
30| 44.60 53.29 62.49 114.9 101.8 90.2 | 131181 | 0 | 20949 | 96 | 0.01 | 0.14 | 0.1 | 0.11 |
31| 44.60 53.41 62.68 115.1 101.8 90.1 | 131653 | 0.01 | 20929 | 96 | 0.01 | 0.14 | 0.1 | 0.12 |
32| 44.61 53.34 62.45 115.1 101.7 90.1 | 131143 | 0 | 20978 | 96 | 0 | 0.14 | 0.11 | 0.12 |
33| 44.60 53.25 62.47 115.1 101.8 90.2 | 130878 | 0 | 20942 | 96 | 0.01 | 0.14 | 0.12 | 0.13 |
34| 44.60 53.40 62.62 64.9 78.1 89.9 | 131446 | 0.01 | 21005 | 97 | 0 | 0.14 | 0.12 | 0.13 |
35| 44.69 53.41 62.71 64.9 78.1 89.9 | 131949 | 0.01 | 20942 | 96 | 0.01 | 0.14 | 0.11 | 0.13 |
36| 44.74 53.41 62.71 64.9 77.9 89.9 | 132001 | 0.01 | 20924 | 96 | 0.01 | 0.14 | 0.12 | 0.14 |
37| 44.60 53.41 62.57 115.2 101.9 90.1 | 131286 | 0.01 | 20982 | 97 | 0 | 0.15 | 0.13 | 0.14 |
38| 44.58 53.29 62.53 65.0 78.2 90.0 | 131102 | 0 | 20975 | 96 | 0 | 0.15 | 0.14 | 0.14 |
39| 44.60 53.43 62.49 114.9 101.8 90.2 | 131553 | 0.01 | 20964 | 96 | 0 | 0.15 | 0.13 | 0.15 |
40| 44.74 53.41 62.57 64.8 78.1 89.9 | 131729 | 0.01 | 20986 | 97 | 0 | 0.15 | 0.13 | 0.15 |
41| 44.49 53.41 62.33 115.2 101.5 90.0 | 130749 | 0 | 20972 | 96 | 0 | 0.15 | 0.15 | 0.15 |
42| 44.60 53.41 62.71 115.1 101.8 90.1 | 131689 | 0.01 | 20935 | 96 | 0.01 | 0.15 | 0.14 | 0.16 |
43| 44.59 53.29 62.39 115.0 101.6 90.1 | 130961 | 0 | 20990 | 97 | 0 | 0.15 | 0.15 | 0.16 |
44| 44.74 53.29 62.71 65.0 77.9 90.0 | 131849 | 0.01 | 20950 | 96 | 0.01 | 0.15 | 0.14 | 0.16 |
45| 44.59 53.41 62.65 64.8 78.2 90.0 | 131547 | 0.01 | 20966 | 96 | 0 | 0.15 | 0.15 | 0.16 |
46| 44.60 53.43 62.71 114.9 101.8 90.2 | 131909 | 0.01 | 20958 | 96 | 0 | 0.15 | 0.15 | 0.16 |
47| 44.68 53.40 62.62 115.1 102.0 90.1 | 131574 | 0.01 | 20984 | 97 | 0 | 0.15 | 0.15 | 0.17 |
48| 44.60 53.41 62.60 64.8 78.1 89.9 | 131360 | 0.01 | 21022 | 97 | 0 | 0.15 | 0.16 | 0.17 |
49| 44.65 53.29 62.37 115.0 101.7 90.1 | 131075 | 0 | 21001 | 97 | 0 | 0.15 | 0.17 | 0.17 |
50| 44.69 53.41 62.71 115.1 101.9 90.1 | 131936 | 0.01 | 21025 | 97 | 0 | 0.15 | 0.16 | 0.17 |
51| 44.65 53.40 62.53 115.2 101.6 90.2 | 131503 | 0.01 | 20944 | 96 | 0.01 | 0.15 | 0.17 | 0.19 |
52| 44.54 53.41 62.57 64.8 78.0 90.0 | 131107 | 0 | 20976 | 96 | 0 | 0.15 | 0.18 | 0.19 |
53| 44.60 53.41 62.63 115.0 101.8 90.1 | 131689 | 0.01 | 20899 | 96 | 0.01 | 0.15 | 0.17 | 0.19 |
54| 44.61 53.41 62.57 64.8 78.2 89.9 | 131398 | 0.01 | 20985 | 97 | 0 | 0.15 | 0.2 | 0.21 |
55| 44.64 53.41 62.71 115.1 101.9 90.0 | 131818 | 0.01 | 20938 | 96 | 0.01 | 0.15 | 0.19 | 0.21 |
56| 44.65 53.28 62.36 115.0 101.7 90.1 | 131032 | 0 | 21000 | 97 | 0 | 0.15 | 0.21 | 0.21 |
57| 44.60 53.43 62.71 115.2 101.8 90.0 | 131708 | 0.01 | 20936 | 96 | 0.01 | 0.15 | 0.2 | 0.22 |
58| 44.49 53.41 62.53 115.2 101.6 90.0 | 131069 | 0 | 20967 | 96 | 0 | 0.15 | 0.21 | 0.22 |
59| 44.60 53.43 62.41 115.1 101.8 90.2 | 131138 | 0 | 20999 | 97 | 0 | 0.15 | 0.22 | 0.22 |
60| 44.69 53.41 62.57 64.8 78.0 89.9 | 131546 | 0.01 | 20986 | 97 | 0 | 0.15 | 0.21 | 0.22 |
61| 44.74 53.29 62.71 114.8 102.1 90.1 | 132052 | 0.01 | 20961 | 96 | 0 | 0.15 | 0.22 | 0.24 |
62| 44.65 53.41 62.57 115.2 101.7 90.0 | 131547 | 0.01 | 20990 | 97 | 0 | 0.16 | 0.23 | 0.24 |
63| 44.49 53.41 62.71 115.1 101.7 90.0 | 131474 | 0.01 | 20941 | 96 | 0.01 | 0.16 | 0.24 | 0.25 |
64| 44.49 53.41 62.57 115.2 101.7 90.0 | 131072 | 0 | 20983 | 97 | 0 | 0.16 | 0.25 | 0.26 |
65| 44.49 53.40 62.62 64.9 78.5 90.0 | 131363 | 0.01 | 21005 | 97 | 0 | 0.16 | 0.26 | 0.27 |
66| 44.65 53.40 62.62 64.9 78.3 90.0 | 131706 | 0.01 | 21012 | 97 | 0 | 0.16 | 0.27 | 0.29 |
67+------------------------------------+----------+----------------+------------+-------------+-------------------+-----------+-----------------+-----------------+
68Using d_min_step 0.0
69
70Indexed crystal models:
71model 1 (21005 reflections):
72Crystal:
73 Unit cell: 44.736, 53.392, 62.630, 115.139, 101.959, 90.175
74 Space group: P 1
75 U matrix: {{ 0.9000, -0.4121, -0.1421},
76 { 0.2959, 0.8170, -0.4949},
77 { 0.3200, 0.4034, 0.8572}}
78 B matrix: {{ 0.0224, 0.0000, 0.0000},
79 { 0.0001, 0.0187, 0.0000},
80 { 0.0053, 0.0090, 0.0181}}
81 A = UB: {{ 0.0193, -0.0090, -0.0026},
82 { 0.0041, 0.0108, -0.0090},
83 { 0.0117, 0.0153, 0.0155}}
84+------------+-------------+---------------+-------------+
85| Imageset | # indexed | # unindexed | % indexed |
86|------------+-------------+---------------+-------------|
87| 0 | 21005 | 734 | 96.6 |
88+------------+-------------+---------------+-------------+
89
90################################################################################
91Starting refinement (macro-cycle 1)
92################################################################################
93
94
95Summary statistics for 20952 observations matched to predictions:
96+-------------------+--------+---------+---------+---------+-------+
97| | Min | Q1 | Med | Q3 | Max |
98|-------------------+--------+---------+---------+---------+-------|
99| Xc - Xo (mm) | -1.703 | -0.6229 | -0.3916 | -0.1449 | 2.562 |
100| Yc - Yo (mm) | -2.013 | -0.2842 | -0.2246 | -0.1743 | 2.016 |
101| Phic - Phio (deg) | -7.52 | -0.1586 | 0.00306 | 0.119 | 4.551 |
102| X weights | 224.2 | 360.3 | 383.5 | 397.1 | 405.6 |
103| Y weights | 199.2 | 349 | 376.3 | 394.1 | 405.6 |
104| Phi weights | 33.85 | 47.23 | 47.77 | 48 | 48 |
105+-------------------+--------+---------+---------+---------+-------+
106
107Detecting centroid outliers using the Tukey algorithm
1082347 reflections have been flagged as outliers
10918605 reflections remain in the manager
110
111Summary statistics for 18605 observations matched to predictions:
112+-------------------+---------+---------+----------+---------+--------+
113| | Min | Q1 | Med | Q3 | Max |
114|-------------------+---------+---------+----------+---------+--------|
115| Xc - Xo (mm) | -1.684 | -0.607 | -0.3968 | -0.1734 | 0.9907 |
116| Yc - Yo (mm) | -1.068 | -0.2767 | -0.2246 | -0.1807 | 0.5715 |
117| Phic - Phio (deg) | -0.9351 | -0.1436 | 0.001552 | 0.1063 | 0.7571 |
118| X weights | 224.2 | 362.5 | 384.5 | 397.3 | 405.6 |
119| Y weights | 199.2 | 353.2 | 378.6 | 394.9 | 405.6 |
120| Phi weights | 35.84 | 47.27 | 47.76 | 48 | 48 |
121+-------------------+---------+---------+----------+---------+--------+
122
123There are 16 parameters to refine against 18605 reflections in 3 dimensions
124
125Refinement steps:
126+--------+--------+----------+----------+------------+
127| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
128| | | (mm) | (mm) | (deg) |
129|--------+--------+----------+----------+------------|
130| 0 | 18605 | 0.51841 | 0.26874 | 0.22605 |
131| 1 | 18605 | 0.1268 | 0.10007 | 0.23108 |
132| 2 | 18605 | 0.097838 | 0.098106 | 0.23331 |
133| 3 | 18605 | 0.096656 | 0.096297 | 0.23343 |
134| 4 | 18605 | 0.096506 | 0.095677 | 0.23386 |
135| 5 | 18605 | 0.096504 | 0.095601 | 0.23402 |
136| 6 | 18605 | 0.096504 | 0.095596 | 0.23403 |
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 | 18605 | 0.56107 | 0.55579 | 0.46806 |
146+-------+--------+----------+----------+------------+
147
148Refined crystal models:
149model 1 (21005 reflections):
150Crystal:
151 Unit cell: 44.630(5), 53.435(7), 62.738(8), 115.2234(14), 101.7872(13), 90.0002(12)
152 Space group: P 1
153 U matrix: {{ 0.8996, -0.4114, -0.1464},
154 { 0.2938, 0.8183, -0.4940},
155 { 0.3230, 0.4014, 0.8570}}
156 B matrix: {{ 0.0224, 0.0000, 0.0000},
157 { 0.0000, 0.0187, 0.0000},
158 { 0.0052, 0.0090, 0.0181}}
159 A = UB: {{ 0.0194, -0.0090, -0.0026},
160 { 0.0040, 0.0108, -0.0089},
161 { 0.0117, 0.0153, 0.0155}}
162+------------+-------------+---------------+-------------+
163| Imageset | # indexed | # unindexed | % indexed |
164|------------+-------------+---------------+-------------|
165| 0 | 21005 | 734 | 96.6 |
166+------------+-------------+---------------+-------------+
167
168Indexed crystal models:
169model 1 (21029 reflections):
170Crystal:
171 Unit cell: 44.630(5), 53.435(7), 62.738(8), 115.2234(14), 101.7872(13), 90.0002(12)
172 Space group: P 1
173 U matrix: {{ 0.8996, -0.4114, -0.1464},
174 { 0.2938, 0.8183, -0.4940},
175 { 0.3230, 0.4014, 0.8570}}
176 B matrix: {{ 0.0224, 0.0000, 0.0000},
177 { 0.0000, 0.0187, 0.0000},
178 { 0.0052, 0.0090, 0.0181}}
179 A = UB: {{ 0.0194, -0.0090, -0.0026},
180 { 0.0040, 0.0108, -0.0089},
181 { 0.0117, 0.0153, 0.0155}}
182+------------+-------------+---------------+-------------+
183| Imageset | # indexed | # unindexed | % indexed |
184|------------+-------------+---------------+-------------|
185| 0 | 21163 | 577 | 97.3 |
186+------------+-------------+---------------+-------------+
187
188################################################################################
189Starting refinement (macro-cycle 2)
190################################################################################
191
192
193Summary statistics for 20975 observations matched to predictions:
194+-------------------+---------+----------+----------+---------+--------+
195| | Min | Q1 | Med | Q3 | Max |
196|-------------------+---------+----------+----------+---------+--------|
197| Xc - Xo (mm) | -0.9265 | -0.04435 | 0.002579 | 0.05266 | 0.6455 |
198| Yc - Yo (mm) | -1.8 | -0.04679 | 0.003802 | 0.04913 | 2.53 |
199| Phic - Phio (deg) | -8.051 | -0.1087 | 0.05362 | 0.1561 | 5.29 |
200| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
201| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
202| Phi weights | 33.85 | 47.23 | 47.77 | 48 | 48 |
203+-------------------+---------+----------+----------+---------+--------+
204
205Detecting centroid outliers using the Tukey algorithm
2062632 reflections have been flagged as outliers
20718343 reflections remain in the manager
208
209Summary statistics for 18343 observations matched to predictions:
210+-------------------+---------+----------+----------+---------+--------+
211| | Min | Q1 | Med | Q3 | Max |
212|-------------------+---------+----------+----------+---------+--------|
213| Xc - Xo (mm) | -0.3699 | -0.03984 | 0.003241 | 0.05068 | 0.344 |
214| Yc - Yo (mm) | -0.3939 | -0.03613 | 0.005551 | 0.04528 | 0.4172 |
215| Phic - Phio (deg) | -0.8813 | -0.08308 | 0.05629 | 0.1488 | 0.6562 |
216| X weights | 224.2 | 364.4 | 385.5 | 397.6 | 405.6 |
217| Y weights | 199.2 | 355.6 | 380 | 395.3 | 405.6 |
218| Phi weights | 38.65 | 47.25 | 47.74 | 48 | 48 |
219+-------------------+---------+----------+----------+---------+--------+
220
221There are 16 parameters to refine against 18343 reflections in 3 dimensions
222
223Refinement steps:
224+--------+--------+----------+----------+------------+
225| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
226| | | (mm) | (mm) | (deg) |
227|--------+--------+----------+----------+------------|
228| 0 | 18343 | 0.080738 | 0.083417 | 0.21845 |
229| 1 | 18343 | 0.079354 | 0.082036 | 0.22074 |
230| 2 | 18343 | 0.07875 | 0.082035 | 0.2202 |
231| 3 | 18343 | 0.078446 | 0.082152 | 0.21934 |
232| 4 | 18343 | 0.078361 | 0.08228 | 0.21896 |
233| 5 | 18343 | 0.078348 | 0.082315 | 0.21889 |
234| 6 | 18343 | 0.078347 | 0.082318 | 0.21889 |
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 | 18343 | 0.45551 | 0.47859 | 0.43778 |
244+-------+--------+----------+----------+------------+
245
246Refined crystal models:
247model 1 (21029 reflections):
248Crystal:
249 Unit cell: 44.499(5), 53.267(6), 62.550(7), 115.2255(12), 101.7863(11), 89.9931(10)
250 Space group: P 1
251 U matrix: {{ 0.8997, -0.4112, -0.1464},
252 { 0.2937, 0.8184, -0.4940},
253 { 0.3230, 0.4015, 0.8570}}
254 B matrix: {{ 0.0225, 0.0000, 0.0000},
255 {-0.0000, 0.0188, 0.0000},
256 { 0.0052, 0.0091, 0.0181}}
257 A = UB: {{ 0.0195, -0.0090, -0.0027},
258 { 0.0040, 0.0109, -0.0090},
259 { 0.0117, 0.0153, 0.0155}}
260+------------+-------------+---------------+-------------+
261| Imageset | # indexed | # unindexed | % indexed |
262|------------+-------------+---------------+-------------|
263| 0 | 21029 | 711 | 96.7 |
264+------------+-------------+---------------+-------------+
265
266Indexed crystal models:
267model 1 (21028 reflections):
268Crystal:
269 Unit cell: 44.499(5), 53.267(6), 62.550(7), 115.2255(12), 101.7863(11), 89.9931(10)
270 Space group: P 1
271 U matrix: {{ 0.8997, -0.4112, -0.1464},
272 { 0.2937, 0.8184, -0.4940},
273 { 0.3230, 0.4015, 0.8570}}
274 B matrix: {{ 0.0225, 0.0000, 0.0000},
275 {-0.0000, 0.0188, 0.0000},
276 { 0.0052, 0.0091, 0.0181}}
277 A = UB: {{ 0.0195, -0.0090, -0.0027},
278 { 0.0040, 0.0109, -0.0090},
279 { 0.0117, 0.0153, 0.0155}}
280+------------+-------------+---------------+-------------+
281| Imageset | # indexed | # unindexed | % indexed |
282|------------+-------------+---------------+-------------|
283| 0 | 21054 | 685 | 96.8 |
284+------------+-------------+---------------+-------------+
285
286################################################################################
287Starting refinement (macro-cycle 3)
288################################################################################
289
290
291Summary statistics for 20974 observations matched to predictions:
292+-------------------+---------+----------+-----------+---------+--------+
293| | Min | Q1 | Med | Q3 | Max |
294|-------------------+---------+----------+-----------+---------+--------|
295| Xc - Xo (mm) | -0.8873 | -0.04424 | 0.00171 | 0.04794 | 0.6379 |
296| Yc - Yo (mm) | -1.717 | -0.05087 | -0.001016 | 0.04519 | 2.886 |
297| Phic - Phio (deg) | -8.105 | -0.1071 | 0.05102 | 0.1496 | 7.001 |
298| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
299| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
300| Phi weights | 33.85 | 47.23 | 47.77 | 48 | 48 |
301+-------------------+---------+----------+-----------+---------+--------+
302
303Detecting centroid outliers using the Tukey algorithm
3042728 reflections have been flagged as outliers
30518246 reflections remain in the manager
306
307Summary statistics for 18246 observations matched to predictions:
308+-------------------+---------+----------+----------+---------+--------+
309| | Min | Q1 | Med | Q3 | Max |
310|-------------------+---------+----------+----------+---------+--------|
311| Xc - Xo (mm) | -0.3408 | -0.03953 | 0.002804 | 0.04673 | 0.307 |
312| Yc - Yo (mm) | -0.3899 | -0.04049 | 0.001011 | 0.04132 | 0.412 |
313| Phic - Phio (deg) | -0.8957 | -0.08015 | 0.05445 | 0.1428 | 0.6317 |
314| X weights | 224.2 | 364.5 | 385.5 | 397.6 | 405.6 |
315| Y weights | 199.2 | 355.7 | 380 | 395.4 | 405.6 |
316| Phi weights | 38.65 | 47.25 | 47.74 | 48 | 48 |
317+-------------------+---------+----------+----------+---------+--------+
318
319There are 16 parameters to refine against 18246 reflections in 3 dimensions
320
321Refinement steps:
322+--------+--------+----------+----------+------------+
323| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
324| | | (mm) | (mm) | (deg) |
325|--------+--------+----------+----------+------------|
326| 0 | 18246 | 0.0772 | 0.081515 | 0.21713 |
327| 1 | 18246 | 0.076915 | 0.081075 | 0.21844 |
328| 2 | 18246 | 0.076743 | 0.081138 | 0.2184 |
329| 3 | 18246 | 0.076641 | 0.081227 | 0.21821 |
330| 4 | 18246 | 0.076606 | 0.081288 | 0.21809 |
331| 5 | 18246 | 0.0766 | 0.081303 | 0.21806 |
332| 6 | 18246 | 0.0766 | 0.081305 | 0.21806 |
333+--------+--------+----------+----------+------------+
334RMSD no longer decreasing
335
336RMSDs by experiment:
337+-------+--------+----------+----------+------------+
338| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
339| id | | (px) | (px) | (images) |
340|-------+--------+----------+----------+------------|
341| 0 | 18246 | 0.44535 | 0.4727 | 0.43612 |
342+-------+--------+----------+----------+------------+
343
344Refined crystal models:
345model 1 (21028 reflections):
346Crystal:
347 Unit cell: 44.444(5), 53.198(6), 62.470(7), 115.2252(12), 101.7854(11), 89.9907(10)
348 Space group: P 1
349 U matrix: {{ 0.8997, -0.4112, -0.1464},
350 { 0.2936, 0.8184, -0.4940},
351 { 0.3229, 0.4015, 0.8570}}
352 B matrix: {{ 0.0225, 0.0000, 0.0000},
353 {-0.0000, 0.0188, 0.0000},
354 { 0.0052, 0.0091, 0.0182}}
355 A = UB: {{ 0.0195, -0.0091, -0.0027},
356 { 0.0040, 0.0109, -0.0090},
357 { 0.0117, 0.0153, 0.0156}}
358+------------+-------------+---------------+-------------+
359| Imageset | # indexed | # unindexed | % indexed |
360|------------+-------------+---------------+-------------|
361| 0 | 21028 | 711 | 96.7 |
362+------------+-------------+---------------+-------------+
363
364Indexed crystal models:
365model 1 (21028 reflections):
366Crystal:
367 Unit cell: 44.444(5), 53.198(6), 62.470(7), 115.2252(12), 101.7854(11), 89.9907(10)
368 Space group: P 1
369 U matrix: {{ 0.8997, -0.4112, -0.1464},
370 { 0.2936, 0.8184, -0.4940},
371 { 0.3229, 0.4015, 0.8570}}
372 B matrix: {{ 0.0225, 0.0000, 0.0000},
373 {-0.0000, 0.0188, 0.0000},
374 { 0.0052, 0.0091, 0.0182}}
375 A = UB: {{ 0.0195, -0.0091, -0.0027},
376 { 0.0040, 0.0109, -0.0090},
377 { 0.0117, 0.0153, 0.0156}}
378+------------+-------------+---------------+-------------+
379| Imageset | # indexed | # unindexed | % indexed |
380|------------+-------------+---------------+-------------|
381| 0 | 21039 | 700 | 96.8 |
382+------------+-------------+---------------+-------------+
383
384################################################################################
385Starting refinement (macro-cycle 4)
386################################################################################
387
388
389Summary statistics for 20974 observations matched to predictions:
390+-------------------+---------+----------+-----------+---------+--------+
391| | Min | Q1 | Med | Q3 | Max |
392|-------------------+---------+----------+-----------+---------+--------|
393| Xc - Xo (mm) | -0.8997 | -0.04434 | 0.001314 | 0.04642 | 0.6643 |
394| Yc - Yo (mm) | -1.72 | -0.0511 | -0.001655 | 0.04466 | 3.05 |
395| Phic - Phio (deg) | -8.12 | -0.1074 | 0.04974 | 0.1479 | 7.662 |
396| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
397| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
398| Phi weights | 31.78 | 47.23 | 47.77 | 48 | 48 |
399+-------------------+---------+----------+-----------+---------+--------+
400
401Detecting centroid outliers using the Tukey algorithm
4022689 reflections have been flagged as outliers
40318285 reflections remain in the manager
404
405Summary statistics for 18285 observations matched to predictions:
406+-------------------+---------+----------+------------+---------+--------+
407| | Min | Q1 | Med | Q3 | Max |
408|-------------------+---------+----------+------------+---------+--------|
409| Xc - Xo (mm) | -0.3321 | -0.03982 | 0.002306 | 0.04524 | 0.3082 |
410| Yc - Yo (mm) | -0.3898 | -0.04183 | -9.738e-05 | 0.04119 | 0.4075 |
411| Phic - Phio (deg) | -0.9054 | -0.08134 | 0.05293 | 0.1411 | 0.6249 |
412| X weights | 224.2 | 364.5 | 385.5 | 397.6 | 405.6 |
413| Y weights | 199.2 | 355.6 | 380 | 395.4 | 405.6 |
414| Phi weights | 38.65 | 47.25 | 47.74 | 48 | 48 |
415+-------------------+---------+----------+------------+---------+--------+
416
417There are 16 parameters to refine against 18285 reflections in 3 dimensions
418
419Refinement steps:
420+--------+--------+----------+----------+------------+
421| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
422| | | (mm) | (mm) | (deg) |
423|--------+--------+----------+----------+------------|
424| 0 | 18285 | 0.076424 | 0.081591 | 0.21765 |
425| 1 | 18285 | 0.076361 | 0.081373 | 0.21833 |
426| 2 | 18285 | 0.076313 | 0.081403 | 0.21832 |
427| 3 | 18285 | 0.076281 | 0.081442 | 0.21826 |
428| 4 | 18285 | 0.076268 | 0.081466 | 0.21822 |
429| 5 | 18285 | 0.076266 | 0.081471 | 0.21821 |
430+--------+--------+----------+----------+------------+
431RMSD no longer decreasing
432
433RMSDs by experiment:
434+-------+--------+----------+----------+------------+
435| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
436| id | | (px) | (px) | (images) |
437|-------+--------+----------+----------+------------|
438| 0 | 18285 | 0.44341 | 0.47367 | 0.43642 |
439+-------+--------+----------+----------+------------+
440
441Refined crystal models:
442model 1 (21028 reflections):
443Crystal:
444 Unit cell: 44.421(5), 53.170(6), 62.437(7), 115.2250(12), 101.7844(11), 89.9899(10)
445 Space group: P 1
446 U matrix: {{ 0.8997, -0.4112, -0.1464},
447 { 0.2936, 0.8184, -0.4940},
448 { 0.3229, 0.4015, 0.8570}}
449 B matrix: {{ 0.0225, 0.0000, 0.0000},
450 {-0.0000, 0.0188, 0.0000},
451 { 0.0052, 0.0091, 0.0182}}
452 A = UB: {{ 0.0195, -0.0091, -0.0027},
453 { 0.0040, 0.0109, -0.0090},
454 { 0.0117, 0.0153, 0.0156}}
455+------------+-------------+---------------+-------------+
456| Imageset | # indexed | # unindexed | % indexed |
457|------------+-------------+---------------+-------------|
458| 0 | 21028 | 711 | 96.7 |
459+------------+-------------+---------------+-------------+
460
461Indexed crystal models:
462model 1 (21027 reflections):
463Crystal:
464 Unit cell: 44.421(5), 53.170(6), 62.437(7), 115.2250(12), 101.7844(11), 89.9899(10)
465 Space group: P 1
466 U matrix: {{ 0.8997, -0.4112, -0.1464},
467 { 0.2936, 0.8184, -0.4940},
468 { 0.3229, 0.4015, 0.8570}}
469 B matrix: {{ 0.0225, 0.0000, 0.0000},
470 {-0.0000, 0.0188, 0.0000},
471 { 0.0052, 0.0091, 0.0182}}
472 A = UB: {{ 0.0195, -0.0091, -0.0027},
473 { 0.0040, 0.0109, -0.0090},
474 { 0.0117, 0.0153, 0.0156}}
475+------------+-------------+---------------+-------------+
476| Imageset | # indexed | # unindexed | % indexed |
477|------------+-------------+---------------+-------------|
478| 0 | 21033 | 706 | 96.8 |
479+------------+-------------+---------------+-------------+
480
481################################################################################
482Starting refinement (macro-cycle 5)
483################################################################################
484
485
486Summary statistics for 20973 observations matched to predictions:
487+-------------------+---------+----------+-----------+---------+--------+
488| | Min | Q1 | Med | Q3 | Max |
489|-------------------+---------+----------+-----------+---------+--------|
490| Xc - Xo (mm) | -0.9039 | -0.04434 | 0.001238 | 0.04604 | 0.6737 |
491| Yc - Yo (mm) | -1.721 | -0.05114 | -0.001455 | 0.04477 | 3.104 |
492| Phic - Phio (deg) | -8.136 | -0.1071 | 0.05018 | 0.1486 | 7.955 |
493| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
494| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
495| Phi weights | 31.78 | 47.23 | 47.77 | 48 | 48 |
496+-------------------+---------+----------+-----------+---------+--------+
497
498Detecting centroid outliers using the Tukey algorithm
4992679 reflections have been flagged as outliers
50018294 reflections remain in the manager
501
502Summary statistics for 18294 observations matched to predictions:
503+-------------------+---------+----------+------------+---------+--------+
504| | Min | Q1 | Med | Q3 | Max |
505|-------------------+---------+----------+------------+---------+--------|
506| Xc - Xo (mm) | -0.3319 | -0.03988 | 0.002168 | 0.04478 | 0.3091 |
507| Yc - Yo (mm) | -0.3894 | -0.04171 | -1.155e-05 | 0.04124 | 0.4076 |
508| Phic - Phio (deg) | -0.9195 | -0.08125 | 0.05369 | 0.1407 | 0.6192 |
509| X weights | 224.2 | 364.4 | 385.4 | 397.6 | 405.6 |
510| Y weights | 199.2 | 355.6 | 380 | 395.3 | 405.6 |
511| Phi weights | 38.65 | 47.25 | 47.75 | 48 | 48 |
512+-------------------+---------+----------+------------+---------+--------+
513
514There are 16 parameters to refine against 18294 reflections in 3 dimensions
515
516Refinement steps:
517+--------+--------+----------+----------+------------+
518| Step | Nref | RMSD_X | RMSD_Y | RMSD_Phi |
519| | | (mm) | (mm) | (deg) |
520|--------+--------+----------+----------+------------|
521| 0 | 18294 | 0.076338 | 0.081412 | 0.21795 |
522| 1 | 18294 | 0.076296 | 0.081315 | 0.2183 |
523| 2 | 18294 | 0.076268 | 0.081329 | 0.21833 |
524| 3 | 18294 | 0.076252 | 0.081346 | 0.21832 |
525| 4 | 18294 | 0.076246 | 0.081356 | 0.21831 |
526| 5 | 18294 | 0.076245 | 0.081358 | 0.2183 |
527+--------+--------+----------+----------+------------+
528RMSD no longer decreasing
529
530RMSDs by experiment:
531+-------+--------+----------+----------+------------+
532| Exp | Nref | RMSD_X | RMSD_Y | RMSD_Z |
533| id | | (px) | (px) | (images) |
534|-------+--------+----------+----------+------------|
535| 0 | 18294 | 0.44329 | 0.47301 | 0.43661 |
536+-------+--------+----------+----------+------------+
537
538Refined crystal models:
539model 1 (21027 reflections):
540Crystal:
541 Unit cell: 44.412(5), 53.159(6), 62.424(7), 115.2251(12), 101.7837(11), 89.9895(10)
542 Space group: P 1
543 U matrix: {{ 0.8997, -0.4112, -0.1464},
544 { 0.2936, 0.8184, -0.4940},
545 { 0.3229, 0.4015, 0.8570}}
546 B matrix: {{ 0.0225, 0.0000, 0.0000},
547 {-0.0000, 0.0188, 0.0000},
548 { 0.0052, 0.0091, 0.0182}}
549 A = UB: {{ 0.0195, -0.0091, -0.0027},
550 { 0.0040, 0.0109, -0.0090},
551 { 0.0117, 0.0153, 0.0156}}
552+------------+-------------+---------------+-------------+
553| Imageset | # indexed | # unindexed | % indexed |
554|------------+-------------+---------------+-------------|
555| 0 | 21027 | 712 | 96.7 |
556+------------+-------------+---------------+-------------+
557Saving refined experiments to indexed.expt
558Saving 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 | 18605 | 0.51841 | 0.26874 | 0.22605 |
131| 1 | 18605 | 0.1268 | 0.10007 | 0.23108 |
132| 2 | 18605 | 0.097838 | 0.098106 | 0.23331 |
133| 3 | 18605 | 0.096656 | 0.096297 | 0.23343 |
134| 4 | 18605 | 0.096506 | 0.095677 | 0.23386 |
135| 5 | 18605 | 0.096504 | 0.095601 | 0.23402 |
136| 6 | 18605 | 0.096504 | 0.095596 | 0.23403 |
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:
552+------------+-------------+---------------+-------------+
553| Imageset | # indexed | # unindexed | % indexed |
554|------------+-------------+---------------+-------------|
555| 0 | 21027 | 712 | 96.7 |
556+------------+-------------+---------------+-------------+
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 | 0.0252 | 0.112 | 0.743/0.743 | 18268 | mC | 112.90 53.14 44.39 90.00 103.04 90.00 | 259466 | -b-2*c,-b,-a |
| * 1 | 0 | 0.111 | -/- | 18292 | aP | 44.41 53.16 62.42 115.23 101.78 89.99 | 129876 | a,b,c |
+------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+--------------+
* = recommended solution
Saving summary as bravais_summary.json
Saving solution 2 as bravais_setting_2.expt
Saving solution 1 as bravais_setting_1.expt
The scores include the metric fit (in degrees), RMSDs (in mm), and the best and worse correlation coefficients for data related by symmetry elements implied by the lowest symmetry space group from the Bravais setting. This uses the raw spot intensity measurement from the spot- finding procedure (uncorrected and unscaled) but provides a very useful check to see if the data does appear to adhere to the proposed symmetry operators.
A separate bravais_setting_N.expt experiments file is written for
each plausible lattice type, corresponding to the solution index. In this
example there is only one option other than P1. We choose to continue processing
with
bravais_setting_2.expt, the C2 solution.
In cases where the change of basis operator to the chosen setting is the
identity operator (a,b,c) we can proceed directly to further
refinement. However, 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.1243-gd06ef435d
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 20973 observations matched to predictions:
18+-------------------+---------+----------+-----------+---------+--------+
19| | Min | Q1 | Med | Q3 | Max |
20|-------------------+---------+----------+-----------+---------+--------|
21| Xc - Xo (mm) | -0.9033 | -0.04467 | 0.001113 | 0.04686 | 0.6841 |
22| Yc - Yo (mm) | -1.746 | -0.05039 | -0.000498 | 0.0441 | 3.105 |
23| Phic - Phio (deg) | -8.283 | -0.1057 | 0.05334 | 0.1476 | 8.03 |
24| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
25| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
26| Phi weights | 31.78 | 47.23 | 47.77 | 48 | 48 |
27+-------------------+---------+----------+-----------+---------+--------+
28
29Detecting centroid outliers using the MCD algorithm
304006 reflections have been flagged as outliers
3116967 reflections remain in the manager
32
33Summary statistics for 16967 observations matched to predictions:
34+-------------------+---------+----------+----------+---------+--------+
35| | Min | Q1 | Med | Q3 | Max |
36|-------------------+---------+----------+----------+---------+--------|
37| Xc - Xo (mm) | -0.3565 | -0.03718 | 0.002731 | 0.0445 | 0.3007 |
38| Yc - Yo (mm) | -0.4479 | -0.03614 | 0.001424 | 0.03842 | 0.4335 |
39| Phic - Phio (deg) | -0.8575 | -0.06504 | 0.05968 | 0.1383 | 0.5736 |
40| X weights | 224.2 | 366.5 | 386.7 | 398 | 405.6 |
41| Y weights | 199.2 | 358.1 | 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 16967 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 | 16967 | 0.069855 | 0.076289 | 0.21058 |
54| 1 | 16967 | 0.069841 | 0.07608 | 0.21094 |
55| 2 | 16967 | 0.069746 | 0.075965 | 0.21131 |
56| 3 | 16967 | 0.069583 | 0.075866 | 0.21178 |
57| 4 | 16967 | 0.069463 | 0.075811 | 0.21212 |
58| 5 | 16967 | 0.069424 | 0.075799 | 0.21221 |
59| 6 | 16967 | 0.069418 | 0.0758 | 0.21221 |
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 | 16967 | 0.40359 | 0.4407 | 0.42443 |
69+-------+--------+----------+----------+------------+
70Updating predictions for indexed reflections
71
72Final refined crystal model:
73Crystal:
74 Unit cell: 112.880(12), 53.128(6), 44.389(5), 90.0, 103.0373(11), 90.0
75 Space group: C 1 2 1
76 U matrix: {{ 0.3455, 0.4111, -0.8436},
77 { 0.5477, -0.8183, -0.1745},
78 {-0.7620, -0.4018, -0.5079}}
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.1243-gd06ef435d
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 20972 observations matched to predictions:
18+-------------------+---------+----------+-----------+---------+-------+
19| | Min | Q1 | Med | Q3 | Max |
20|-------------------+---------+----------+-----------+---------+-------|
21| Xc - Xo (mm) | -0.9124 | -0.04538 | 0.0002905 | 0.04459 | 0.695 |
22| Yc - Yo (mm) | -1.72 | -0.05097 | -0.00175 | 0.04269 | 2.519 |
23| Phic - Phio (deg) | -8.11 | -0.1061 | 0.05077 | 0.1452 | 8.365 |
24| X weights | 224.2 | 360.3 | 383.6 | 397.1 | 405.6 |
25| Y weights | 199.2 | 349.1 | 376.3 | 394.1 | 405.6 |
26| Phi weights | 31.78 | 47.23 | 47.77 | 48 | 48 |
27+-------------------+---------+----------+-----------+---------+-------+
28
29Detecting centroid outliers using the MCD algorithm
304023 reflections have been flagged as outliers
3116949 reflections remain in the manager
32
33Summary statistics for 16949 observations matched to predictions:
34+-------------------+---------+----------+-----------+---------+--------+
35| | Min | Q1 | Med | Q3 | Max |
36|-------------------+---------+----------+-----------+---------+--------|
37| Xc - Xo (mm) | -0.3629 | -0.03772 | 0.002058 | 0.0421 | 0.3225 |
38| Yc - Yo (mm) | -0.4409 | -0.03702 | 0.0001998 | 0.03677 | 0.4927 |
39| Phic - Phio (deg) | -0.8777 | -0.0656 | 0.05753 | 0.1366 | 0.5653 |
40| X weights | 224.2 | 366.5 | 386.7 | 398 | 405.6 |
41| Y weights | 222.4 | 358.3 | 381.8 | 396 | 405.6 |
42| Phi weights | 38.65 | 47.25 | 47.73 | 48 | 48 |
43+-------------------+---------+----------+-----------+---------+--------+
44
45There are 56 parameters to refine against 16949 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 | 16949 | 0.069573 | 0.075491 | 0.21208 |
54| 1 | 16949 | 0.058323 | 0.069797 | 0.18766 |
55| 2 | 16949 | 0.05713 | 0.066282 | 0.17174 |
56| 3 | 16949 | 0.055477 | 0.062547 | 0.1527 |
57| 4 | 16949 | 0.053549 | 0.060443 | 0.13032 |
58| 5 | 16949 | 0.051594 | 0.058974 | 0.11424 |
59| 6 | 16949 | 0.050231 | 0.058126 | 0.10841 |
60| 7 | 16949 | 0.049663 | 0.057788 | 0.10679 |
61| 8 | 16949 | 0.049507 | 0.057702 | 0.10619 |
62| 9 | 16949 | 0.049393 | 0.057682 | 0.1061 |
63| 10 | 16949 | 0.049287 | 0.057678 | 0.10617 |
64| 11 | 16949 | 0.049219 | 0.057685 | 0.1063 |
65| 12 | 16949 | 0.0492 | 0.057688 | 0.10635 |
66| 13 | 16949 | 0.0492 | 0.057687 | 0.10635 |
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 | 16949 | 0.28605 | 0.33539 | 0.21271 |
76+-------+--------+----------+----------+------------+
77Updating predictions for indexed reflections
78
79Final refined crystal model:
80Crystal:
81 Unit cell: 112.880(12), 53.128(6), 44.389(5), 90.0, 103.0373(11), 90.0
82 Space group: C 1 2 1
83 U matrix: {{ 0.3455, 0.4111, -0.8436},
84 { 0.5477, -0.8183, -0.1745},
85 {-0.7620, -0.4018, -0.5079}}
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.1243-gd06ef435d
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 : {0.00196911,-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: {0.999994,0.00340589,-0.000205118}
46 slow_axis: {0.00340611,-0.999994,0.00105738}
47 origin: {-214.205,250.881,-324.765}
48 distance: 324.543
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: 112.880(12), 53.128(6), 44.389(5), 90.0, 103.0373(11), 90.0
67 Space group: C 1 2 1
68 U matrix: {{ 0.3455, 0.4111, -0.8436},
69 { 0.5477, -0.8183, -0.1745},
70 {-0.7620, -0.4018, -0.5079}}
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 21740 strong spots
84 removing 713 unindexed reflections
85 removing 4078 reflections marked as bad for refinement
86 using 16949 indexed reflections
87 found 4791 junk reflections
88 masked neighbouring pixels in 1509 shoeboxes
89
90================================================================================
91
92Predicting reflections
93Prediction type: scan varying crystal prediction
94Predicted 198714 reflections
95Matching reference spots with predicted reflections
96 16949 observed reflections input
97 198714 reflections predicted
98 16949 reflections matched
99 16949 reflections accepted
100Using 16949 / 16949 reflections for sigma calculation
101Calculating E.S.D Beam Divergence.
102Calculating E.S.D Reflecting Range (mosaicity).
103 sigma b: 0.039475 degrees
104 sigma m: 0.329174 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 27 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 | 4641 |
138| 1 | 0 | 99 | 206 | 265 | 319 | 4838 |
139| 2 | 0 | 197 | 304 | 314 | 368 | 4574 |
140| 3 | 0 | 295 | 400 | 363 | 416 | 2923 |
141+-----+---------+--------------+------------+--------------+------------+-----------------+
142
143 Using multiprocessing with 4 parallel job(s)
144
145
146 Frames: 1 -> 108
147
148 Number of reflections
149 Partial: 158
150 Full: 4483
151 In ice ring: 0
152 Total: 4641
153
154
155 Frames: 99 -> 206
156
157 Number of reflections
158 Partial: 26
159 Full: 4812
160 In ice ring: 0
161 Total: 4838
162
163
164 Frames: 197 -> 304
165
166 Number of reflections
167 Partial: 18
168 Full: 4556
169 In ice ring: 0
170 Total: 4574
171
172
173 Frames: 295 -> 400
174
175 Number of reflections
176 Partial: 45
177 Full: 2878
178 In ice ring: 0
179 Total: 2923
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 | 495 |
187| 0 | 1 | True | 1231.5 | 421.17 | 5 | 561 |
188| 0 | 2 | True | 2052.5 | 421.17 | 5 | 526 |
189| 0 | 3 | True | 410.5 | 1263.5 | 5 | 902 |
190| 0 | 4 | True | 1231.5 | 1263.5 | 5 | 989 |
191| 0 | 5 | True | 2052.5 | 1263.5 | 5 | 897 |
192| 0 | 6 | True | 410.5 | 2105.83 | 5 | 865 |
193| 0 | 7 | True | 1231.5 | 2105.83 | 5 | 950 |
194| 0 | 8 | True | 2052.5 | 2105.83 | 5 | 858 |
195| 0 | 9 | True | 410.5 | 421.17 | 15 | 759 |
196| 0 | 10 | True | 1231.5 | 421.17 | 15 | 858 |
197| 0 | 11 | True | 2052.5 | 421.17 | 15 | 805 |
198| 0 | 12 | True | 410.5 | 1263.5 | 15 | 1354 |
199| 0 | 13 | True | 1231.5 | 1263.5 | 15 | 1489 |
200| 0 | 14 | True | 2052.5 | 1263.5 | 15 | 1365 |
201| 0 | 15 | True | 410.5 | 2105.83 | 15 | 1301 |
202| 0 | 16 | True | 1231.5 | 2105.83 | 15 | 1432 |
203| 0 | 17 | True | 2052.5 | 2105.83 | 15 | 1308 |
204| 0 | 18 | True | 410.5 | 421.17 | 25 | 795 |
205| 0 | 19 | True | 1231.5 | 421.17 | 25 | 902 |
206| 0 | 20 | True | 2052.5 | 421.17 | 25 | 846 |
207| 0 | 21 | True | 410.5 | 1263.5 | 25 | 1332 |
208| 0 | 22 | True | 1231.5 | 1263.5 | 25 | 1479 |
209| 0 | 23 | True | 2052.5 | 1263.5 | 25 | 1365 |
210| 0 | 24 | True | 410.5 | 2105.83 | 25 | 1273 |
211| 0 | 25 | True | 1231.5 | 2105.83 | 25 | 1418 |
212| 0 | 26 | True | 2052.5 | 2105.83 | 25 | 1305 |
213| 0 | 27 | True | 410.5 | 421.17 | 35 | 764 |
214| 0 | 28 | True | 1231.5 | 421.17 | 35 | 860 |
215| 0 | 29 | True | 2052.5 | 421.17 | 35 | 804 |
216| 0 | 30 | True | 410.5 | 1263.5 | 35 | 1209 |
217| 0 | 31 | True | 1231.5 | 1263.5 | 35 | 1338 |
218| 0 | 32 | True | 2052.5 | 1263.5 | 35 | 1243 |
219| 0 | 33 | True | 410.5 | 2105.83 | 35 | 1156 |
220| 0 | 34 | True | 1231.5 | 2105.83 | 35 | 1281 |
221| 0 | 35 | True | 2052.5 | 2105.83 | 35 | 1188 |
222| 0 | 36 | True | 410.5 | 421.17 | 45 | 735 |
223| 0 | 37 | True | 1231.5 | 421.17 | 45 | 837 |
224| 0 | 38 | True | 2052.5 | 421.17 | 45 | 777 |
225| 0 | 39 | True | 410.5 | 1263.5 | 45 | 1145 |
226| 0 | 40 | True | 1231.5 | 1263.5 | 45 | 1273 |
227| 0 | 41 | True | 2052.5 | 1263.5 | 45 | 1173 |
228| 0 | 42 | True | 410.5 | 2105.83 | 45 | 1096 |
229| 0 | 43 | True | 1231.5 | 2105.83 | 45 | 1221 |
230| 0 | 44 | True | 2052.5 | 2105.83 | 45 | 1123 |
231| 0 | 45 | True | 410.5 | 421.17 | 55 | 673 |
232| 0 | 46 | True | 1231.5 | 421.17 | 55 | 766 |
233| 0 | 47 | True | 2052.5 | 421.17 | 55 | 708 |
234| 0 | 48 | True | 410.5 | 1263.5 | 55 | 1103 |
235| 0 | 49 | True | 1231.5 | 1263.5 | 55 | 1219 |
236| 0 | 50 | True | 2052.5 | 1263.5 | 55 | 1116 |
237| 0 | 51 | True | 410.5 | 2105.83 | 55 | 1068 |
238| 0 | 52 | True | 1231.5 | 2105.83 | 55 | 1180 |
239| 0 | 53 | True | 2052.5 | 2105.83 | 55 | 1078 |
240| 0 | 54 | True | 410.5 | 421.17 | 65 | 586 |
241| 0 | 55 | True | 1231.5 | 421.17 | 65 | 661 |
242| 0 | 56 | True | 2052.5 | 421.17 | 65 | 618 |
243| 0 | 57 | True | 410.5 | 1263.5 | 65 | 1038 |
244| 0 | 58 | True | 1231.5 | 1263.5 | 65 | 1129 |
245| 0 | 59 | True | 2052.5 | 1263.5 | 65 | 1035 |
246| 0 | 60 | True | 410.5 | 2105.83 | 65 | 1017 |
247| 0 | 61 | True | 1231.5 | 2105.83 | 65 | 1106 |
248| 0 | 62 | True | 2052.5 | 2105.83 | 65 | 1012 |
249| 0 | 63 | True | 410.5 | 421.17 | 75 | 517 |
250| 0 | 64 | True | 1231.5 | 421.17 | 75 | 566 |
251| 0 | 65 | True | 2052.5 | 421.17 | 75 | 539 |
252| 0 | 66 | True | 410.5 | 1263.5 | 75 | 989 |
253| 0 | 67 | True | 1231.5 | 1263.5 | 75 | 1051 |
254| 0 | 68 | True | 2052.5 | 1263.5 | 75 | 966 |
255| 0 | 69 | True | 410.5 | 2105.83 | 75 | 978 |
256| 0 | 70 | True | 1231.5 | 2105.83 | 75 | 1039 |
257| 0 | 71 | True | 2052.5 | 2105.83 | 75 | 954 |
258| 0 | 72 | True | 410.5 | 421.17 | 85 | 495 |
259| 0 | 73 | True | 1231.5 | 421.17 | 85 | 531 |
260| 0 | 74 | True | 2052.5 | 421.17 | 85 | 511 |
261| 0 | 75 | True | 410.5 | 1263.5 | 85 | 1022 |
262| 0 | 76 | True | 1231.5 | 1263.5 | 85 | 1073 |
263| 0 | 77 | True | 2052.5 | 1263.5 | 85 | 998 |
264| 0 | 78 | True | 410.5 | 2105.83 | 85 | 1014 |
265| 0 | 79 | True | 1231.5 | 2105.83 | 85 | 1065 |
266| 0 | 80 | True | 2052.5 | 2105.83 | 85 | 990 |
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 | 558 |
270| 0 | 84 | True | 410.5 | 1263.5 | 95 | 1131 |
271| 0 | 85 | True | 1231.5 | 1263.5 | 95 | 1195 |
272| 0 | 86 | True | 2052.5 | 1263.5 | 95 | 1099 |
273| 0 | 87 | True | 410.5 | 2105.83 | 95 | 1122 |
274| 0 | 88 | True | 1231.5 | 2105.83 | 95 | 1186 |
275| 0 | 89 | True | 2052.5 | 2105.83 | 95 | 1090 |
276| 0 | 90 | True | 410.5 | 421.17 | 105 | 559 |
277| 0 | 91 | True | 1231.5 | 421.17 | 105 | 599 |
278| 0 | 92 | True | 2052.5 | 421.17 | 105 | 578 |
279| 0 | 93 | True | 410.5 | 1263.5 | 105 | 1198 |
280| 0 | 94 | True | 1231.5 | 1263.5 | 105 | 1266 |
281| 0 | 95 | True | 2052.5 | 1263.5 | 105 | 1167 |
282| 0 | 96 | True | 410.5 | 2105.83 | 105 | 1185 |
283| 0 | 97 | True | 1231.5 | 2105.83 | 105 | 1253 |
284| 0 | 98 | True | 2052.5 | 2105.83 | 105 | 1154 |
285| 0 | 99 | True | 410.5 | 421.17 | 115 | 592 |
286| 0 | 100 | True | 1231.5 | 421.17 | 115 | 644 |
287| 0 | 101 | True | 2052.5 | 421.17 | 115 | 623 |
288| 0 | 102 | True | 410.5 | 1263.5 | 115 | 1254 |
289| 0 | 103 | True | 1231.5 | 1263.5 | 115 | 1334 |
290| 0 | 104 | True | 2052.5 | 1263.5 | 115 | 1227 |
291| 0 | 105 | True | 410.5 | 2105.83 | 115 | 1241 |
292| 0 | 106 | True | 1231.5 | 2105.83 | 115 | 1321 |
293| 0 | 107 | True | 2052.5 | 2105.83 | 115 | 1214 |
294| 0 | 108 | True | 410.5 | 421.17 | 125 | 589 |
295| 0 | 109 | True | 1231.5 | 421.17 | 125 | 640 |
296| 0 | 110 | True | 2052.5 | 421.17 | 125 | 618 |
297| 0 | 111 | True | 410.5 | 1263.5 | 125 | 1284 |
298| 0 | 112 | True | 1231.5 | 1263.5 | 125 | 1361 |
299| 0 | 113 | True | 2052.5 | 1263.5 | 125 | 1257 |
300| 0 | 114 | True | 410.5 | 2105.83 | 125 | 1263 |
301| 0 | 115 | True | 1231.5 | 2105.83 | 125 | 1340 |
302| 0 | 116 | True | 2052.5 | 2105.83 | 125 | 1236 |
303| 0 | 117 | True | 410.5 | 421.17 | 135 | 624 |
304| 0 | 118 | True | 1231.5 | 421.17 | 135 | 672 |
305| 0 | 119 | True | 2052.5 | 421.17 | 135 | 649 |
306| 0 | 120 | True | 410.5 | 1263.5 | 135 | 1338 |
307| 0 | 121 | True | 1231.5 | 1263.5 | 135 | 1410 |
308| 0 | 122 | True | 2052.5 | 1263.5 | 135 | 1297 |
309| 0 | 123 | True | 410.5 | 2105.83 | 135 | 1309 |
310| 0 | 124 | True | 1231.5 | 2105.83 | 135 | 1381 |
311| 0 | 125 | True | 2052.5 | 2105.83 | 135 | 1268 |
312| 0 | 126 | True | 410.5 | 421.17 | 145 | 660 |
313| 0 | 127 | True | 1231.5 | 421.17 | 145 | 703 |
314| 0 | 128 | True | 2052.5 | 421.17 | 145 | 673 |
315| 0 | 129 | True | 410.5 | 1263.5 | 145 | 1379 |
316| 0 | 130 | True | 1231.5 | 1263.5 | 145 | 1451 |
317| 0 | 131 | True | 2052.5 | 1263.5 | 145 | 1328 |
318| 0 | 132 | True | 410.5 | 2105.83 | 145 | 1342 |
319| 0 | 133 | True | 1231.5 | 2105.83 | 145 | 1414 |
320| 0 | 134 | True | 2052.5 | 2105.83 | 145 | 1291 |
321| 0 | 135 | True | 410.5 | 421.17 | 155 | 695 |
322| 0 | 136 | True | 1231.5 | 421.17 | 155 | 731 |
323| 0 | 137 | True | 2052.5 | 421.17 | 155 | 692 |
324| 0 | 138 | True | 410.5 | 1263.5 | 155 | 1399 |
325| 0 | 139 | True | 1231.5 | 1263.5 | 155 | 1463 |
326| 0 | 140 | True | 2052.5 | 1263.5 | 155 | 1327 |
327| 0 | 141 | True | 410.5 | 2105.83 | 155 | 1350 |
328| 0 | 142 | True | 1231.5 | 2105.83 | 155 | 1414 |
329| 0 | 143 | True | 2052.5 | 2105.83 | 155 | 1278 |
330| 0 | 144 | True | 410.5 | 421.17 | 165 | 707 |
331| 0 | 145 | True | 1231.5 | 421.17 | 165 | 748 |
332| 0 | 146 | True | 2052.5 | 421.17 | 165 | 708 |
333| 0 | 147 | True | 410.5 | 1263.5 | 165 | 1401 |
334| 0 | 148 | True | 1231.5 | 1263.5 | 165 | 1474 |
335| 0 | 149 | True | 2052.5 | 1263.5 | 165 | 1339 |
336| 0 | 150 | True | 410.5 | 2105.83 | 165 | 1347 |
337| 0 | 151 | True | 1231.5 | 2105.83 | 165 | 1420 |
338| 0 | 152 | True | 2052.5 | 2105.83 | 165 | 1285 |
339| 0 | 153 | True | 410.5 | 421.17 | 175 | 716 |
340| 0 | 154 | True | 1231.5 | 421.17 | 175 | 751 |
341| 0 | 155 | True | 2052.5 | 421.17 | 175 | 706 |
342| 0 | 156 | True | 410.5 | 1263.5 | 175 | 1387 |
343| 0 | 157 | True | 1231.5 | 1263.5 | 175 | 1451 |
344| 0 | 158 | True | 2052.5 | 1263.5 | 175 | 1316 |
345| 0 | 159 | True | 410.5 | 2105.83 | 175 | 1327 |
346| 0 | 160 | True | 1231.5 | 2105.83 | 175 | 1391 |
347| 0 | 161 | True | 2052.5 | 2105.83 | 175 | 1256 |
348| 0 | 162 | True | 410.5 | 421.17 | 185 | 759 |
349| 0 | 163 | True | 1231.5 | 421.17 | 185 | 809 |
350| 0 | 164 | True | 2052.5 | 421.17 | 185 | 762 |
351| 0 | 165 | True | 410.5 | 1263.5 | 185 | 1408 |
352| 0 | 166 | True | 1231.5 | 1263.5 | 185 | 1491 |
353| 0 | 167 | True | 2052.5 | 1263.5 | 185 | 1362 |
354| 0 | 168 | True | 410.5 | 2105.83 | 185 | 1335 |
355| 0 | 169 | True | 1231.5 | 2105.83 | 185 | 1417 |
356| 0 | 170 | True | 2052.5 | 2105.83 | 185 | 1288 |
357| 0 | 171 | True | 410.5 | 421.17 | 195 | 803 |
358| 0 | 172 | True | 1231.5 | 421.17 | 195 | 871 |
359| 0 | 173 | True | 2052.5 | 421.17 | 195 | 819 |
360| 0 | 174 | True | 410.5 | 1263.5 | 195 | 1433 |
361| 0 | 175 | True | 1231.5 | 1263.5 | 195 | 1530 |
362| 0 | 176 | True | 2052.5 | 1263.5 | 195 | 1401 |
363| 0 | 177 | True | 410.5 | 2105.83 | 195 | 1336 |
364| 0 | 178 | True | 1231.5 | 2105.83 | 195 | 1427 |
365| 0 | 179 | True | 2052.5 | 2105.83 | 195 | 1298 |
366| 0 | 180 | True | 410.5 | 421.17 | 205 | 806 |
367| 0 | 181 | True | 1231.5 | 421.17 | 205 | 905 |
368| 0 | 182 | True | 2052.5 | 421.17 | 205 | 861 |
369| 0 | 183 | True | 410.5 | 1263.5 | 205 | 1404 |
370| 0 | 184 | True | 1231.5 | 1263.5 | 205 | 1536 |
371| 0 | 185 | True | 2052.5 | 1263.5 | 205 | 1425 |
372| 0 | 186 | True | 410.5 | 2105.83 | 205 | 1292 |
373| 0 | 187 | True | 1231.5 | 2105.83 | 205 | 1411 |
374| 0 | 188 | True | 2052.5 | 2105.83 | 205 | 1300 |
375| 0 | 189 | True | 410.5 | 421.17 | 215 | 812 |
376| 0 | 190 | True | 1231.5 | 421.17 | 215 | 922 |
377| 0 | 191 | True | 2052.5 | 421.17 | 215 | 887 |
378| 0 | 192 | True | 410.5 | 1263.5 | 215 | 1389 |
379| 0 | 193 | True | 1231.5 | 1263.5 | 215 | 1534 |
380| 0 | 194 | True | 2052.5 | 1263.5 | 215 | 1445 |
381| 0 | 195 | True | 410.5 | 2105.83 | 215 | 1259 |
382| 0 | 196 | True | 1231.5 | 2105.83 | 215 | 1385 |
383| 0 | 197 | True | 2052.5 | 2105.83 | 215 | 1296 |
384| 0 | 198 | True | 410.5 | 421.17 | 225 | 811 |
385| 0 | 199 | True | 1231.5 | 421.17 | 225 | 919 |
386| 0 | 200 | True | 2052.5 | 421.17 | 225 | 896 |
387| 0 | 201 | True | 410.5 | 1263.5 | 225 | 1344 |
388| 0 | 202 | True | 1231.5 | 1263.5 | 225 | 1488 |
389| 0 | 203 | True | 2052.5 | 1263.5 | 225 | 1422 |
390| 0 | 204 | True | 410.5 | 2105.83 | 225 | 1208 |
391| 0 | 205 | True | 1231.5 | 2105.83 | 225 | 1334 |
392| 0 | 206 | True | 2052.5 | 2105.83 | 225 | 1268 |
393| 0 | 207 | True | 410.5 | 421.17 | 235 | 819 |
394| 0 | 208 | True | 1231.5 | 421.17 | 235 | 910 |
395| 0 | 209 | True | 2052.5 | 421.17 | 235 | 891 |
396| 0 | 210 | True | 410.5 | 1263.5 | 235 | 1337 |
397| 0 | 211 | True | 1231.5 | 1263.5 | 235 | 1462 |
398| 0 | 212 | True | 2052.5 | 1263.5 | 235 | 1401 |
399| 0 | 213 | True | 410.5 | 2105.83 | 235 | 1199 |
400| 0 | 214 | True | 1231.5 | 2105.83 | 235 | 1309 |
401| 0 | 215 | True | 2052.5 | 2105.83 | 235 | 1248 |
402| 0 | 216 | True | 410.5 | 421.17 | 245 | 794 |
403| 0 | 217 | True | 1231.5 | 421.17 | 245 | 875 |
404| 0 | 218 | True | 2052.5 | 421.17 | 245 | 855 |
405| 0 | 219 | True | 410.5 | 1263.5 | 245 | 1285 |
406| 0 | 220 | True | 1231.5 | 1263.5 | 245 | 1393 |
407| 0 | 221 | True | 2052.5 | 1263.5 | 245 | 1343 |
408| 0 | 222 | True | 410.5 | 2105.83 | 245 | 1182 |
409| 0 | 223 | True | 1231.5 | 2105.83 | 245 | 1281 |
410| 0 | 224 | True | 2052.5 | 2105.83 | 245 | 1231 |
411| 0 | 225 | True | 410.5 | 421.17 | 255 | 755 |
412| 0 | 226 | True | 1231.5 | 421.17 | 255 | 835 |
413| 0 | 227 | True | 2052.5 | 421.17 | 255 | 811 |
414| 0 | 228 | True | 410.5 | 1263.5 | 255 | 1217 |
415| 0 | 229 | True | 1231.5 | 1263.5 | 255 | 1323 |
416| 0 | 230 | True | 2052.5 | 1263.5 | 255 | 1276 |
417| 0 | 231 | True | 410.5 | 2105.83 | 255 | 1145 |
418| 0 | 232 | True | 1231.5 | 2105.83 | 255 | 1242 |
419| 0 | 233 | True | 2052.5 | 2105.83 | 255 | 1195 |
420| 0 | 234 | True | 410.5 | 421.17 | 265 | 715 |
421| 0 | 235 | True | 1231.5 | 421.17 | 265 | 799 |
422| 0 | 236 | True | 2052.5 | 421.17 | 265 | 774 |
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 | 1095 |
427| 0 | 241 | True | 1231.5 | 2105.83 | 265 | 1194 |
428| 0 | 242 | True | 2052.5 | 2105.83 | 265 | 1154 |
429| 0 | 243 | True | 410.5 | 421.17 | 275 | 697 |
430| 0 | 244 | True | 1231.5 | 421.17 | 275 | 780 |
431| 0 | 245 | True | 2052.5 | 421.17 | 275 | 758 |
432| 0 | 246 | True | 410.5 | 1263.5 | 275 | 1101 |
433| 0 | 247 | True | 1231.5 | 1263.5 | 275 | 1209 |
434| 0 | 248 | True | 2052.5 | 1263.5 | 275 | 1173 |
435| 0 | 249 | True | 410.5 | 2105.83 | 275 | 1058 |
436| 0 | 250 | True | 1231.5 | 2105.83 | 275 | 1161 |
437| 0 | 251 | True | 2052.5 | 2105.83 | 275 | 1126 |
438| 0 | 252 | True | 410.5 | 421.17 | 285 | 675 |
439| 0 | 253 | True | 1231.5 | 421.17 | 285 | 748 |
440| 0 | 254 | True | 2052.5 | 421.17 | 285 | 727 |
441| 0 | 255 | True | 410.5 | 1263.5 | 285 | 1069 |
442| 0 | 256 | True | 1231.5 | 1263.5 | 285 | 1172 |
443| 0 | 257 | True | 2052.5 | 1263.5 | 285 | 1140 |
444| 0 | 258 | True | 410.5 | 2105.83 | 285 | 1037 |
445| 0 | 259 | True | 1231.5 | 2105.83 | 285 | 1137 |
446| 0 | 260 | True | 2052.5 | 2105.83 | 285 | 1106 |
447| 0 | 261 | True | 410.5 | 421.17 | 295 | 667 |
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 | 1041 |
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 | 1025 |
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 | 662 |
459| 0 | 273 | True | 410.5 | 1263.5 | 305 | 993 |
460| 0 | 274 | True | 1231.5 | 1263.5 | 305 | 1083 |
461| 0 | 275 | True | 2052.5 | 1263.5 | 305 | 1046 |
462| 0 | 276 | True | 410.5 | 2105.83 | 305 | 983 |
463| 0 | 277 | True | 1231.5 | 2105.83 | 305 | 1071 |
464| 0 | 278 | True | 2052.5 | 2105.83 | 305 | 1034 |
465| 0 | 279 | True | 410.5 | 421.17 | 315 | 596 |
466| 0 | 280 | True | 1231.5 | 421.17 | 315 | 659 |
467| 0 | 281 | True | 2052.5 | 421.17 | 315 | 634 |
468| 0 | 282 | True | 410.5 | 1263.5 | 315 | 943 |
469| 0 | 283 | True | 1231.5 | 1263.5 | 315 | 1036 |
470| 0 | 284 | True | 2052.5 | 1263.5 | 315 | 1001 |
471| 0 | 285 | True | 410.5 | 2105.83 | 315 | 937 |
472| 0 | 286 | True | 1231.5 | 2105.83 | 315 | 1030 |
473| 0 | 287 | True | 2052.5 | 2105.83 | 315 | 995 |
474| 0 | 288 | True | 410.5 | 421.17 | 325 | 566 |
475| 0 | 289 | True | 1231.5 | 421.17 | 325 | 622 |
476| 0 | 290 | True | 2052.5 | 421.17 | 325 | 599 |
477| 0 | 291 | True | 410.5 | 1263.5 | 325 | 905 |
478| 0 | 292 | True | 1231.5 | 1263.5 | 325 | 988 |
479| 0 | 293 | True | 2052.5 | 1263.5 | 325 | 955 |
480| 0 | 294 | True | 410.5 | 2105.83 | 325 | 900 |
481| 0 | 295 | True | 1231.5 | 2105.83 | 325 | 983 |
482| 0 | 296 | True | 2052.5 | 2105.83 | 325 | 950 |
483| 0 | 297 | True | 410.5 | 421.17 | 335 | 538 |
484| 0 | 298 | True | 1231.5 | 421.17 | 335 | 587 |
485| 0 | 299 | True | 2052.5 | 421.17 | 335 | 566 |
486| 0 | 300 | True | 410.5 | 1263.5 | 335 | 854 |
487| 0 | 301 | True | 1231.5 | 1263.5 | 335 | 932 |
488| 0 | 302 | True | 2052.5 | 1263.5 | 335 | 901 |
489| 0 | 303 | True | 410.5 | 2105.83 | 335 | 851 |
490| 0 | 304 | True | 1231.5 | 2105.83 | 335 | 929 |
491| 0 | 305 | True | 2052.5 | 2105.83 | 335 | 898 |
492| 0 | 306 | True | 410.5 | 421.17 | 345 | 499 |
493| 0 | 307 | True | 1231.5 | 421.17 | 345 | 535 |
494| 0 | 308 | True | 2052.5 | 421.17 | 345 | 517 |
495| 0 | 309 | True | 410.5 | 1263.5 | 345 | 797 |
496| 0 | 310 | True | 1231.5 | 1263.5 | 345 | 855 |
497| 0 | 311 | True | 2052.5 | 1263.5 | 345 | 828 |
498| 0 | 312 | True | 410.5 | 2105.83 | 345 | 797 |
499| 0 | 313 | True | 1231.5 | 2105.83 | 345 | 855 |
500| 0 | 314 | True | 2052.5 | 2105.83 | 345 | 828 |
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 | 467 |
504| 0 | 318 | True | 410.5 | 1263.5 | 355 | 730 |
505| 0 | 319 | True | 1231.5 | 1263.5 | 355 | 783 |
506| 0 | 320 | True | 2052.5 | 1263.5 | 355 | 760 |
507| 0 | 321 | True | 410.5 | 2105.83 | 355 | 730 |
508| 0 | 322 | True | 1231.5 | 2105.83 | 355 | 783 |
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 | 441 |
513| 0 | 327 | True | 410.5 | 1263.5 | 365 | 692 |
514| 0 | 328 | True | 1231.5 | 1263.5 | 365 | 743 |
515| 0 | 329 | True | 2052.5 | 1263.5 | 365 | 725 |
516| 0 | 330 | True | 410.5 | 2105.83 | 365 | 692 |
517| 0 | 331 | True | 1231.5 | 2105.83 | 365 | 743 |
518| 0 | 332 | True | 2052.5 | 2105.83 | 365 | 725 |
519| 0 | 333 | True | 410.5 | 421.17 | 375 | 421 |
520| 0 | 334 | True | 1231.5 | 421.17 | 375 | 440 |
521| 0 | 335 | True | 2052.5 | 421.17 | 375 | 426 |
522| 0 | 336 | True | 410.5 | 1263.5 | 375 | 675 |
523| 0 | 337 | True | 1231.5 | 1263.5 | 375 | 722 |
524| 0 | 338 | True | 2052.5 | 1263.5 | 375 | 705 |
525| 0 | 339 | True | 410.5 | 2105.83 | 375 | 675 |
526| 0 | 340 | True | 1231.5 | 2105.83 | 375 | 722 |
527| 0 | 341 | True | 2052.5 | 2105.83 | 375 | 705 |
528| 0 | 342 | True | 410.5 | 421.17 | 385 | 363 |
529| 0 | 343 | True | 1231.5 | 421.17 | 385 | 377 |
530| 0 | 344 | True | 2052.5 | 421.17 | 385 | 367 |
531| 0 | 345 | True | 410.5 | 1263.5 | 385 | 571 |
532| 0 | 346 | True | 1231.5 | 1263.5 | 385 | 607 |
533| 0 | 347 | True | 2052.5 | 1263.5 | 385 | 596 |
534| 0 | 348 | True | 410.5 | 2105.83 | 385 | 571 |
535| 0 | 349 | True | 1231.5 | 2105.83 | 385 | 607 |
536| 0 | 350 | True | 2052.5 | 2105.83 | 385 | 596 |
537| 0 | 351 | True | 410.5 | 421.17 | 395 | 221 |
538| 0 | 352 | True | 1231.5 | 421.17 | 395 | 225 |
539| 0 | 353 | True | 2052.5 | 421.17 | 395 | 223 |
540| 0 | 354 | True | 410.5 | 1263.5 | 395 | 340 |
541| 0 | 355 | True | 1231.5 | 1263.5 | 395 | 356 |
542| 0 | 356 | True | 2052.5 | 1263.5 | 395 | 354 |
543| 0 | 357 | True | 410.5 | 2105.83 | 395 | 340 |
544| 0 | 358 | True | 1231.5 | 2105.83 | 395 | 356 |
545| 0 | 359 | True | 2052.5 | 2105.83 | 395 | 354 |
546+------+-----------+-----------+----------+----------+----------+-----------------+
547
548
549Timing information for reference profile formation
550+-------------------+---------------+
551| Read time | 15.04 seconds |
552| Extract time | 0.48 seconds |
553| Pre-process time | 0.02 seconds |
554| Process time | 9.16 seconds |
555| Post-process time | 0.00 seconds |
556| Total time | 24.64 seconds |
557+-------------------+---------------+
558
559================================================================================
560
561Integrating reflections
562
563 Split 681 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 | 52200 |
578| 1 | 0 | 98 | 206 | 264.5 | 319 | 47641 |
579| 2 | 0 | 195 | 303 | 313 | 367.5 | 47756 |
580| 3 | 0 | 292 | 400 | 361.5 | 416 | 51458 |
581+-----+---------+--------------+------------+--------------+------------+-----------------+
582
583 Using multiprocessing with 4 parallel job(s)
584
585
586 Frames: 0 -> 109
587
588 Number of reflections
589 Partial: 2536
590 Full: 49664
591 In ice ring: 0
592 Integrate: 52200
593 Total: 52200
594
595
596 Frames: 97 -> 206
597
598 Number of reflections
599 Partial: 340
600 Full: 47301
601 In ice ring: 0
602 Integrate: 47641
603 Total: 47641
604
605
606 Frames: 194 -> 303
607
608 Number of reflections
609 Partial: 338
610 Full: 47418
611 In ice ring: 0
612 Integrate: 47756
613 Total: 47756
614
615
616 Frames: 291 -> 400
617
618 Number of reflections
619 Partial: 2483
620 Full: 48975
621 In ice ring: 0
622 Integrate: 51458
623 Total: 51458
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 | 1470 | 0 | 0 | 1242 | 427 | 0.2 | 1.1 | 3.22 | 0.56 | 0.63 |
632| 0 | 2 | 4 | 476 | 0 | 0 | 411 | 431 | 0.21 | 3.24 | 3.27 | 0.58 | 0.44 |
633| 0 | 3 | 333 | 211 | 0 | 0 | 461 | 476 | 0.2 | 3 | 3.02 | 0.56 | 0.4 |
634| 0 | 4 | 410 | 77 | 0 | 0 | 411 | 428 | 0.21 | 3.14 | 3.11 | 0.58 | 0.36 |
635| 0 | 5 | 430 | 41 | 0 | 0 | 396 | 409 | 0.22 | 4.01 | 4.03 | 0.58 | 0.38 |
636| 0 | 6 | 469 | 16 | 0 | 0 | 406 | 424 | 0.2 | 3.24 | 3.41 | 0.57 | 0.39 |
637| 0 | 7 | 466 | 15 | 0 | 0 | 403 | 417 | 0.2 | 3.22 | 3.27 | 0.56 | 0.38 |
638| 0 | 8 | 523 | 14 | 0 | 0 | 456 | 477 | 0.2 | 2.87 | 2.78 | 0.56 | 0.37 |
639| 0 | 9 | 510 | 5 | 0 | 0 | 451 | 473 | 0.21 | 3.27 | 3.26 | 0.58 | 0.36 |
640| 0 | 10 | 435 | 8 | 0 | 0 | 375 | 387 | 0.22 | 4.22 | 4.31 | 0.59 | 0.36 |
641| 0 | 11 | 482 | 7 | 0 | 0 | 417 | 437 | 0.2 | 2.77 | 2.93 | 0.56 | 0.38 |
642| 0 | 12 | 490 | 6 | 0 | 0 | 427 | 443 | 0.2 | 3.55 | 3.59 | 0.57 | 0.39 |
643| 0 | 13 | 525 | 2 | 0 | 0 | 451 | 468 | 0.21 | 3.79 | 4.01 | 0.58 | 0.36 |
644| 0 | 14 | 517 | 4 | 0 | 0 | 441 | 460 | 0.22 | 4.26 | 4.31 | 0.59 | 0.36 |
645| 0 | 15 | 440 | 6 | 0 | 0 | 380 | 399 | 0.21 | 3.15 | 3.1 | 0.57 | 0.36 |
646| 0 | 16 | 476 | 5 | 0 | 0 | 405 | 427 | 0.21 | 4.24 | 4.2 | 0.57 | 0.37 |
647| 0 | 17 | 515 | 4 | 0 | 0 | 429 | 446 | 0.22 | 3.68 | 3.83 | 0.58 | 0.36 |
648| 0 | 18 | 493 | 2 | 0 | 0 | 404 | 430 | 0.21 | 3.77 | 3.6 | 0.57 | 0.34 |
649| 0 | 19 | 500 | 2 | 0 | 0 | 424 | 443 | 0.21 | 3.66 | 3.59 | 0.57 | 0.35 |
650| 0 | 20 | 487 | 3 | 0 | 0 | 424 | 442 | 0.22 | 4.19 | 4.08 | 0.58 | 0.38 |
651| 0 | 21 | 501 | 2 | 0 | 0 | 436 | 458 | 0.23 | 4.08 | 4.5 | 0.59 | 0.38 |
652| 0 | 22 | 475 | 3 | 0 | 0 | 406 | 421 | 0.21 | 3.91 | 3.93 | 0.57 | 0.37 |
653| 0 | 23 | 474 | 1 | 0 | 0 | 389 | 420 | 0.21 | 4.43 | 4.45 | 0.58 | 0.37 |
654| 0 | 24 | 517 | 0 | 0 | 0 | 440 | 459 | 0.21 | 3.98 | 3.97 | 0.58 | 0.4 |
655| 0 | 25 | 504 | 1 | 0 | 0 | 431 | 449 | 0.22 | 4.49 | 4.46 | 0.57 | 0.4 |
656| 0 | 26 | 496 | 3 | 0 | 0 | 420 | 437 | 0.21 | 4.19 | 4.18 | 0.58 | 0.37 |
657| 0 | 27 | 485 | 2 | 0 | 0 | 422 | 433 | 0.22 | 3.93 | 4.08 | 0.57 | 0.4 |
658| 0 | 28 | 474 | 3 | 0 | 0 | 388 | 408 | 0.22 | 4.19 | 4.35 | 0.57 | 0.39 |
659| 0 | 29 | 509 | 1 | 0 | 0 | 432 | 453 | 0.21 | 4.21 | 4.17 | 0.57 | 0.41 |
660| 0 | 30 | 491 | 1 | 0 | 0 | 427 | 441 | 0.22 | 4.14 | 4.11 | 0.57 | 0.37 |
661| 0 | 31 | 490 | 0 | 0 | 0 | 427 | 445 | 0.22 | 4.04 | 4.13 | 0.57 | 0.41 |
662| 0 | 32 | 495 | 0 | 0 | 0 | 427 | 449 | 0.21 | 3.73 | 3.64 | 0.57 | 0.39 |
663| 0 | 33 | 502 | 1 | 0 | 0 | 423 | 437 | 0.22 | 4.13 | 4.26 | 0.57 | 0.39 |
664| 0 | 34 | 505 | 2 | 0 | 0 | 420 | 438 | 0.21 | 3.71 | 3.7 | 0.57 | 0.4 |
665| 0 | 35 | 492 | 0 | 0 | 0 | 418 | 437 | 0.21 | 4.23 | 4.21 | 0.56 | 0.38 |
666| 0 | 36 | 512 | 1 | 0 | 0 | 438 | 456 | 0.22 | 4.53 | 4.61 | 0.57 | 0.4 |
667| 0 | 37 | 496 | 1 | 0 | 0 | 417 | 439 | 0.21 | 3.42 | 3.64 | 0.56 | 0.41 |
668| 0 | 38 | 457 | 0 | 0 | 0 | 377 | 400 | 0.2 | 3.73 | 3.8 | 0.55 | 0.41 |
669| 0 | 39 | 492 | 0 | 0 | 0 | 417 | 440 | 0.2 | 3.61 | 3.51 | 0.56 | 0.39 |
670| 0 | 40 | 509 | 2 | 0 | 0 | 435 | 449 | 0.21 | 4.12 | 4.06 | 0.56 | 0.4 |
671| 0 | 41 | 484 | 2 | 0 | 0 | 417 | 432 | 0.2 | 3.31 | 3.32 | 0.55 | 0.4 |
672| 0 | 42 | 485 | 0 | 0 | 0 | 399 | 418 | 0.2 | 3.76 | 3.8 | 0.55 | 0.39 |
673| 0 | 43 | 496 | 2 | 0 | 0 | 419 | 436 | 0.19 | 3.98 | 3.91 | 0.55 | 0.4 |
674| 0 | 44 | 490 | 0 | 0 | 0 | 403 | 424 | 0.2 | 3.94 | 3.86 | 0.55 | 0.41 |
675| 0 | 45 | 502 | 1 | 0 | 0 | 399 | 427 | 0.19 | 3.66 | 3.87 | 0.55 | 0.4 |
676| 0 | 46 | 504 | 0 | 0 | 0 | 419 | 435 | 0.19 | 3.54 | 3.5 | 0.55 | 0.43 |
677| 0 | 47 | 481 | 0 | 0 | 0 | 406 | 426 | 0.2 | 4.4 | 4.49 | 0.56 | 0.4 |
678| 0 | 48 | 512 | 2 | 0 | 0 | 442 | 460 | 0.18 | 3.28 | 3.4 | 0.53 | 0.4 |
679| 0 | 49 | 495 | 0 | 0 | 0 | 426 | 440 | 0.19 | 3.97 | 3.92 | 0.56 | 0.39 |
680| 0 | 50 | 495 | 3 | 0 | 0 | 420 | 442 | 0.18 | 3.03 | 3.05 | 0.53 | 0.39 |
681| 0 | 51 | 505 | 1 | 0 | 0 | 428 | 445 | 0.2 | 4.37 | 4.32 | 0.55 | 0.37 |
682| 0 | 52 | 508 | 0 | 0 | 0 | 438 | 455 | 0.18 | 2.99 | 3.05 | 0.53 | 0.4 |
683| 0 | 53 | 483 | 0 | 0 | 0 | 413 | 431 | 0.18 | 3.24 | 3.37 | 0.54 | 0.4 |
684| 0 | 54 | 500 | 0 | 0 | 0 | 424 | 438 | 0.18 | 3.42 | 3.42 | 0.54 | 0.4 |
685| 0 | 55 | 481 | 2 | 0 | 0 | 407 | 425 | 0.18 | 3.24 | 3.19 | 0.53 | 0.41 |
686| 0 | 56 | 519 | 0 | 0 | 0 | 446 | 464 | 0.18 | 3.5 | 3.54 | 0.54 | 0.4 |
687| 0 | 57 | 495 | 0 | 0 | 0 | 415 | 431 | 0.19 | 3.33 | 3.35 | 0.54 | 0.41 |
688| 0 | 58 | 480 | 2 | 0 | 0 | 408 | 427 | 0.18 | 4.13 | 4.05 | 0.53 | 0.44 |
689| 0 | 59 | 543 | 0 | 0 | 0 | 462 | 481 | 0.18 | 3.49 | 3.45 | 0.53 | 0.43 |
690| 0 | 60 | 471 | 0 | 0 | 0 | 405 | 424 | 0.18 | 3.18 | 3.32 | 0.53 | 0.41 |
691| 0 | 61 | 527 | 0 | 0 | 0 | 439 | 463 | 0.17 | 3.2 | 3.1 | 0.53 | 0.42 |
692| 0 | 62 | 499 | 0 | 0 | 0 | 426 | 444 | 0.18 | 3.19 | 3.22 | 0.53 | 0.43 |
693| 0 | 63 | 460 | 0 | 0 | 0 | 391 | 411 | 0.17 | 3.25 | 3.18 | 0.52 | 0.42 |
694| 0 | 64 | 519 | 0 | 0 | 0 | 441 | 459 | 0.17 | 2.93 | 2.99 | 0.52 | 0.43 |
695| 0 | 65 | 488 | 0 | 0 | 0 | 410 | 423 | 0.17 | 2.85 | 2.83 | 0.52 | 0.43 |
696| 0 | 66 | 486 | 2 | 0 | 0 | 409 | 427 | 0.18 | 3.76 | 3.71 | 0.53 | 0.43 |
697| 0 | 67 | 507 | 0 | 0 | 0 | 429 | 442 | 0.17 | 3.15 | 3.12 | 0.52 | 0.42 |
698| 0 | 68 | 493 | 2 | 0 | 0 | 423 | 439 | 0.17 | 3.1 | 3.16 | 0.52 | 0.43 |
699| 0 | 69 | 515 | 0 | 0 | 0 | 430 | 446 | 0.18 | 3.49 | 3.42 | 0.53 | 0.43 |
700| 0 | 70 | 499 | 0 | 0 | 0 | 424 | 445 | 0.17 | 2.78 | 3 | 0.52 | 0.43 |
701| 0 | 71 | 499 | 2 | 0 | 0 | 430 | 457 | 0.17 | 3.69 | 3.77 | 0.52 | 0.43 |
702| 0 | 72 | 464 | 3 | 0 | 0 | 402 | 412 | 0.17 | 2.93 | 2.85 | 0.51 | 0.41 |
703| 0 | 73 | 500 | 2 | 0 | 0 | 410 | 436 | 0.17 | 3.15 | 3.01 | 0.52 | 0.42 |
704| 0 | 74 | 504 | 2 | 0 | 0 | 430 | 450 | 0.17 | 3.16 | 3.22 | 0.52 | 0.41 |
705| 0 | 75 | 483 | 0 | 0 | 0 | 421 | 440 | 0.17 | 3.62 | 3.53 | 0.52 | 0.42 |
706| 0 | 76 | 492 | 0 | 0 | 0 | 432 | 440 | 0.18 | 3.68 | 3.81 | 0.53 | 0.44 |
707| 0 | 77 | 502 | 10 | 0 | 0 | 431 | 452 | 0.17 | 3.05 | 3.13 | 0.52 | 0.45 |
708| 0 | 78 | 479 | 0 | 0 | 0 | 402 | 416 | 0.16 | 3.34 | 3.27 | 0.52 | 0.47 |
709| 0 | 79 | 543 | 0 | 0 | 0 | 460 | 484 | 0.17 | 3.26 | 3.21 | 0.52 | 0.44 |
710| 0 | 80 | 499 | 2 | 0 | 0 | 425 | 442 | 0.17 | 3.63 | 3.73 | 0.52 | 0.46 |
711| 0 | 81 | 496 | 2 | 0 | 0 | 429 | 442 | 0.17 | 3.04 | 2.95 | 0.52 | 0.43 |
712| 0 | 82 | 504 | 2 | 0 | 0 | 421 | 443 | 0.16 | 2.8 | 2.67 | 0.51 | 0.43 |
713| 0 | 83 | 473 | 0 | 0 | 0 | 410 | 425 | 0.16 | 2.88 | 2.82 | 0.51 | 0.44 |
714| 0 | 84 | 488 | 2 | 0 | 0 | 404 | 425 | 0.17 | 3.42 | 3.35 | 0.52 | 0.44 |
715| 0 | 85 | 497 | 4 | 0 | 0 | 428 | 445 | 0.17 | 3.81 | 3.77 | 0.53 | 0.44 |
716| 0 | 86 | 490 | 0 | 0 | 0 | 422 | 448 | 0.17 | 3.12 | 3.12 | 0.52 | 0.44 |
717| 0 | 87 | 490 | 2 | 0 | 0 | 403 | 428 | 0.16 | 3.37 | 3.24 | 0.51 | 0.45 |
718| 0 | 88 | 499 | 0 | 0 | 0 | 425 | 447 | 0.16 | 3.23 | 3.2 | 0.52 | 0.44 |
719| 0 | 89 | 521 | 8 | 0 | 0 | 449 | 464 | 0.17 | 3.39 | 3.38 | 0.53 | 0.42 |
720| 0 | 90 | 508 | 10 | 0 | 0 | 445 | 459 | 0.16 | 2.69 | 2.77 | 0.52 | 0.42 |
721| 0 | 91 | 463 | 0 | 0 | 0 | 391 | 410 | 0.16 | 2.95 | 2.91 | 0.51 | 0.42 |
722| 0 | 92 | 481 | 5 | 0 | 0 | 414 | 431 | 0.17 | 3.96 | 3.8 | 0.53 | 0.44 |
723| 0 | 93 | 497 | 7 | 0 | 0 | 432 | 444 | 0.16 | 2.9 | 2.88 | 0.52 | 0.43 |
724| 0 | 94 | 517 | 4 | 0 | 0 | 454 | 471 | 0.16 | 2.83 | 2.88 | 0.52 | 0.43 |
725| 0 | 95 | 466 | 10 | 0 | 0 | 411 | 429 | 0.16 | 2.73 | 2.66 | 0.51 | 0.42 |
726| 0 | 96 | 510 | 4 | 0 | 0 | 427 | 439 | 0.15 | 2.97 | 2.98 | 0.51 | 0.42 |
727| 0 | 97 | 496 | 10 | 0 | 0 | 428 | 445 | 0.16 | 2.7 | 2.9 | 0.52 | 0.42 |
728| 0 | 98 | 478 | 9 | 0 | 0 | 411 | 432 | 0.17 | 3.42 | 3.4 | 0.53 | 0.43 |
729| 0 | 99 | 479 | 6 | 0 | 0 | 410 | 426 | 0.16 | 3.55 | 3.55 | 0.52 | 0.46 |
730| 0 | 100 | 503 | 12 | 0 | 0 | 433 | 448 | 0.15 | 2.23 | 2.27 | 0.5 | 0.45 |
731| 0 | 101 | 463 | 26 | 0 | 0 | 429 | 435 | 0.15 | 2.73 | 2.87 | 0.52 | 0.46 |
732| 0 | 102 | 485 | 14 | 0 | 0 | 413 | 443 | 0.16 | 3.01 | 2.75 | 0.52 | 0.42 |
733| 0 | 103 | 511 | 34 | 0 | 0 | 464 | 475 | 0.17 | 3.45 | 3.48 | 0.52 | 0.44 |
734| 0 | 104 | 457 | 49 | 0 | 0 | 431 | 438 | 0.16 | 3.01 | 2.94 | 0.53 | 0.44 |
735| 0 | 105 | 446 | 24 | 0 | 0 | 404 | 420 | 0.16 | 3.1 | 2.98 | 0.54 | 0.4 |
736| 0 | 106 | 530 | 12 | 0 | 0 | 471 | 484 | 0.15 | 2.57 | 2.57 | 0.51 | 0.46 |
737| 0 | 107 | 478 | 18 | 0 | 0 | 431 | 444 | 0.15 | 2.47 | 2.59 | 0.51 | 0.43 |
738| 0 | 108 | 477 | 16 | 0 | 0 | 410 | 433 | 0.16 | 2.75 | 2.69 | 0.53 | 0.41 |
739| 0 | 109 | 479 | 12 | 0 | 0 | 404 | 421 | 0.15 | 2.76 | 2.7 | 0.52 | 0.43 |
740| 0 | 110 | 484 | 12 | 0 | 0 | 423 | 439 | 0.16 | 3.23 | 3.21 | 0.53 | 0.44 |
741| 0 | 111 | 508 | 9 | 0 | 0 | 423 | 447 | 0.15 | 2.58 | 2.6 | 0.51 | 0.42 |
742| 0 | 112 | 501 | 4 | 0 | 0 | 432 | 450 | 0.16 | 3.06 | 2.89 | 0.52 | 0.44 |
743| 0 | 113 | 484 | 2 | 0 | 0 | 420 | 442 | 0.16 | 2.87 | 2.77 | 0.52 | 0.42 |
744| 0 | 114 | 441 | 2 | 0 | 0 | 378 | 394 | 0.16 | 2.83 | 2.63 | 0.53 | 0.43 |
745| 0 | 115 | 523 | 4 | 0 | 0 | 453 | 470 | 0.15 | 2.86 | 2.75 | 0.51 | 0.44 |
746| 0 | 116 | 519 | 2 | 0 | 0 | 440 | 461 | 0.16 | 3.07 | 2.94 | 0.52 | 0.44 |
747| 0 | 117 | 495 | 4 | 0 | 0 | 418 | 436 | 0.15 | 2.49 | 2.42 | 0.5 | 0.44 |
748| 0 | 118 | 457 | 2 | 0 | 0 | 400 | 411 | 0.17 | 2.86 | 2.85 | 0.54 | 0.41 |
749| 0 | 119 | 486 | 3 | 0 | 0 | 400 | 421 | 0.15 | 2.51 | 2.39 | 0.51 | 0.44 |
750| 0 | 120 | 508 | 8 | 0 | 0 | 427 | 450 | 0.14 | 1.97 | 1.87 | 0.5 | 0.41 |
751| 0 | 121 | 508 | 2 | 0 | 0 | 441 | 466 | 0.16 | 2.82 | 2.74 | 0.53 | 0.42 |
752| 0 | 122 | 437 | 2 | 0 | 0 | 372 | 389 | 0.16 | 2.84 | 2.9 | 0.53 | 0.41 |
753| 0 | 123 | 515 | 2 | 0 | 0 | 441 | 459 | 0.15 | 2.76 | 2.64 | 0.51 | 0.42 |
754| 0 | 124 | 497 | 4 | 0 | 0 | 416 | 437 | 0.15 | 2.5 | 2.41 | 0.51 | 0.45 |
755| 0 | 125 | 508 | 0 | 0 | 0 | 446 | 467 | 0.15 | 2.68 | 2.61 | 0.52 | 0.42 |
756| 0 | 126 | 448 | 0 | 0 | 0 | 380 | 396 | 0.16 | 3.06 | 2.92 | 0.53 | 0.41 |
757| 0 | 127 | 498 | 2 | 0 | 0 | 426 | 442 | 0.15 | 2.72 | 2.74 | 0.5 | 0.46 |
758| 0 | 128 | 518 | 4 | 0 | 0 | 445 | 462 | 0.15 | 2.3 | 2.29 | 0.52 | 0.42 |
759| 0 | 129 | 502 | 2 | 0 | 0 | 427 | 439 | 0.15 | 2.43 | 2.38 | 0.52 | 0.42 |
760| 0 | 130 | 460 | 2 | 0 | 0 | 388 | 406 | 0.15 | 2.92 | 3.04 | 0.52 | 0.41 |
761| 0 | 131 | 512 | 0 | 0 | 0 | 424 | 452 | 0.15 | 2.75 | 2.59 | 0.51 | 0.41 |
762| 0 | 132 | 444 | 0 | 0 | 0 | 371 | 389 | 0.15 | 2.52 | 2.4 | 0.51 | 0.42 |
763| 0 | 133 | 506 | 2 | 0 | 0 | 423 | 439 | 0.16 | 2.8 | 2.75 | 0.52 | 0.42 |
764| 0 | 134 | 521 | 0 | 0 | 0 | 442 | 471 | 0.15 | 2.37 | 2.16 | 0.51 | 0.43 |
765| 0 | 135 | 468 | 2 | 0 | 0 | 405 | 425 | 0.15 | 2.25 | 2.27 | 0.51 | 0.41 |
766| 0 | 136 | 476 | 0 | 0 | 0 | 413 | 425 | 0.15 | 2.44 | 2.45 | 0.51 | 0.43 |
767| 0 | 137 | 473 | 0 | 0 | 0 | 401 | 420 | 0.15 | 2.52 | 2.42 | 0.52 | 0.42 |
768| 0 | 138 | 528 | 2 | 0 | 0 | 430 | 461 | 0.15 | 2.43 | 2.27 | 0.51 | 0.43 |
769| 0 | 139 | 488 | 0 | 0 | 0 | 416 | 430 | 0.15 | 2.32 | 2.24 | 0.52 | 0.42 |
770| 0 | 140 | 481 | 0 | 0 | 0 | 418 | 431 | 0.15 | 2.64 | 2.5 | 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 | 483 | 0 | 0 | 0 | 403 | 427 | 0.14 | 2.16 | 2.07 | 0.49 | 0.45 |
773| 0 | 143 | 473 | 0 | 0 | 0 | 402 | 420 | 0.14 | 1.86 | 1.73 | 0.5 | 0.45 |
774| 0 | 144 | 489 | 3 | 0 | 0 | 411 | 431 | 0.15 | 2.48 | 2.43 | 0.52 | 0.41 |
775| 0 | 145 | 492 | 0 | 0 | 0 | 422 | 431 | 0.15 | 2.3 | 2.24 | 0.51 | 0.43 |
776| 0 | 146 | 498 | 0 | 0 | 0 | 434 | 455 | 0.15 | 2.63 | 2.62 | 0.52 | 0.42 |
777| 0 | 147 | 498 | 0 | 0 | 0 | 417 | 437 | 0.15 | 2.3 | 2.2 | 0.52 | 0.43 |
778| 0 | 148 | 480 | 0 | 0 | 0 | 402 | 418 | 0.15 | 2.44 | 2.35 | 0.51 | 0.43 |
779| 0 | 149 | 478 | 0 | 0 | 0 | 411 | 426 | 0.14 | 2.36 | 2.38 | 0.5 | 0.45 |
780| 0 | 150 | 513 | 0 | 0 | 0 | 441 | 464 | 0.15 | 2.33 | 2.26 | 0.51 | 0.44 |
781| 0 | 151 | 472 | 0 | 0 | 0 | 399 | 421 | 0.14 | 2.1 | 2.16 | 0.5 | 0.43 |
782| 0 | 152 | 485 | 0 | 0 | 0 | 413 | 430 | 0.13 | 1.7 | 1.62 | 0.49 | 0.45 |
783| 0 | 153 | 485 | 0 | 0 | 0 | 410 | 422 | 0.15 | 2.54 | 2.5 | 0.51 | 0.41 |
784| 0 | 154 | 500 | 0 | 0 | 0 | 427 | 452 | 0.16 | 2.22 | 2.16 | 0.52 | 0.44 |
785| 0 | 155 | 480 | 0 | 0 | 0 | 408 | 429 | 0.14 | 2.14 | 2.16 | 0.52 | 0.42 |
786| 0 | 156 | 510 | 3 | 0 | 0 | 423 | 448 | 0.15 | 2.5 | 2.36 | 0.51 | 0.46 |
787| 0 | 157 | 492 | 0 | 0 | 0 | 430 | 446 | 0.15 | 2.71 | 2.55 | 0.53 | 0.42 |
788| 0 | 158 | 503 | 0 | 0 | 0 | 431 | 453 | 0.15 | 2.3 | 2.33 | 0.52 | 0.42 |
789| 0 | 159 | 471 | 0 | 0 | 0 | 392 | 406 | 0.14 | 2.16 | 2.16 | 0.5 | 0.47 |
790| 0 | 160 | 493 | 0 | 0 | 0 | 432 | 445 | 0.14 | 1.77 | 1.87 | 0.5 | 0.45 |
791| 0 | 161 | 486 | 0 | 0 | 0 | 398 | 421 | 0.14 | 2.17 | 2.06 | 0.51 | 0.46 |
792| 0 | 162 | 478 | 7 | 0 | 0 | 418 | 433 | 0.15 | 2.07 | 1.97 | 0.52 | 0.43 |
793| 0 | 163 | 477 | 3 | 0 | 0 | 419 | 428 | 0.14 | 1.67 | 1.61 | 0.5 | 0.43 |
794| 0 | 164 | 503 | 0 | 0 | 0 | 427 | 439 | 0.13 | 1.81 | 1.71 | 0.5 | 0.44 |
795| 0 | 165 | 484 | 0 | 0 | 0 | 415 | 433 | 0.15 | 2.37 | 2.28 | 0.51 | 0.44 |
796| 0 | 166 | 463 | 0 | 0 | 0 | 383 | 407 | 0.15 | 2.06 | 1.96 | 0.51 | 0.43 |
797| 0 | 167 | 492 | 0 | 0 | 0 | 429 | 440 | 0.15 | 2.43 | 2.35 | 0.52 | 0.42 |
798| 0 | 168 | 478 | 4 | 0 | 0 | 402 | 417 | 0.13 | 1.67 | 1.57 | 0.49 | 0.43 |
799| 0 | 169 | 527 | 2 | 0 | 0 | 453 | 474 | 0.15 | 2.63 | 2.55 | 0.51 | 0.43 |
800| 0 | 170 | 489 | 0 | 0 | 0 | 410 | 428 | 0.14 | 1.79 | 1.87 | 0.5 | 0.43 |
801| 0 | 171 | 463 | 0 | 0 | 0 | 391 | 410 | 0.15 | 2.34 | 2.2 | 0.52 | 0.41 |
802| 0 | 172 | 486 | 0 | 0 | 0 | 406 | 428 | 0.14 | 2.23 | 2.06 | 0.51 | 0.43 |
803| 0 | 173 | 478 | 2 | 0 | 0 | 409 | 428 | 0.14 | 2.14 | 2.02 | 0.5 | 0.42 |
804| 0 | 174 | 495 | 4 | 0 | 0 | 423 | 444 | 0.14 | 2.28 | 2.22 | 0.51 | 0.43 |
805| 0 | 175 | 524 | 2 | 0 | 0 | 450 | 473 | 0.14 | 1.89 | 1.79 | 0.5 | 0.44 |
806| 0 | 176 | 451 | 2 | 0 | 0 | 387 | 396 | 0.14 | 1.95 | 1.93 | 0.51 | 0.45 |
807| 0 | 177 | 492 | 2 | 0 | 0 | 426 | 448 | 0.15 | 2.26 | 2.17 | 0.51 | 0.45 |
808| 0 | 178 | 501 | 2 | 0 | 0 | 416 | 440 | 0.14 | 2.15 | 2.06 | 0.51 | 0.47 |
809| 0 | 179 | 480 | 6 | 0 | 0 | 422 | 434 | 0.13 | 1.54 | 1.46 | 0.49 | 0.44 |
810| 0 | 180 | 476 | 8 | 0 | 0 | 409 | 426 | 0.14 | 1.76 | 1.7 | 0.5 | 0.43 |
811| 0 | 181 | 508 | 8 | 0 | 0 | 435 | 450 | 0.13 | 1.66 | 1.58 | 0.49 | 0.44 |
812| 0 | 182 | 462 | 2 | 0 | 0 | 387 | 405 | 0.13 | 1.9 | 1.77 | 0.49 | 0.47 |
813| 0 | 183 | 489 | 2 | 0 | 0 | 418 | 432 | 0.14 | 2.23 | 2.16 | 0.5 | 0.43 |
814| 0 | 184 | 476 | 4 | 0 | 0 | 417 | 432 | 0.14 | 2.08 | 2 | 0.51 | 0.42 |
815| 0 | 185 | 500 | 0 | 0 | 0 | 422 | 442 | 0.14 | 1.76 | 1.72 | 0.5 | 0.44 |
816| 0 | 186 | 505 | 0 | 0 | 0 | 423 | 438 | 0.14 | 2.19 | 2.13 | 0.51 | 0.45 |
817| 0 | 187 | 477 | 4 | 0 | 0 | 419 | 429 | 0.14 | 1.91 | 1.89 | 0.51 | 0.43 |
818| 0 | 188 | 496 | 0 | 0 | 0 | 414 | 439 | 0.14 | 2.08 | 1.95 | 0.5 | 0.44 |
819| 0 | 189 | 510 | 0 | 0 | 0 | 417 | 446 | 0.14 | 2.05 | 2 | 0.51 | 0.45 |
820| 0 | 190 | 480 | 2 | 0 | 0 | 411 | 429 | 0.14 | 2.01 | 2 | 0.5 | 0.46 |
821| 0 | 191 | 503 | 2 | 0 | 0 | 438 | 458 | 0.13 | 1.82 | 1.79 | 0.49 | 0.43 |
822| 0 | 192 | 479 | 6 | 0 | 0 | 397 | 421 | 0.14 | 2.51 | 2.24 | 0.5 | 0.44 |
823| 0 | 193 | 482 | 6 | 0 | 0 | 412 | 427 | 0.13 | 1.64 | 1.66 | 0.5 | 0.44 |
824| 0 | 194 | 444 | 10 | 0 | 0 | 403 | 411 | 0.13 | 1.79 | 1.63 | 0.5 | 0.45 |
825| 0 | 195 | 513 | 6 | 0 | 0 | 432 | 451 | 0.14 | 1.99 | 1.98 | 0.5 | 0.47 |
826| 0 | 196 | 486 | 13 | 0 | 0 | 426 | 441 | 0.14 | 2.14 | 2.13 | 0.52 | 0.45 |
827| 0 | 197 | 507 | 10 | 0 | 0 | 448 | 458 | 0.14 | 2.21 | 2.3 | 0.51 | 0.43 |
828| 0 | 198 | 462 | 15 | 0 | 0 | 398 | 417 | 0.13 | 1.46 | 1.5 | 0.49 | 0.46 |
829| 0 | 199 | 479 | 17 | 0 | 0 | 426 | 438 | 0.14 | 1.86 | 1.83 | 0.5 | 0.47 |
830| 0 | 200 | 467 | 27 | 0 | 0 | 420 | 425 | 0.13 | 1.52 | 1.53 | 0.5 | 0.45 |
831| 0 | 201 | 454 | 48 | 0 | 0 | 420 | 434 | 0.13 | 2.11 | 2.24 | 0.5 | 0.45 |
832| 0 | 202 | 473 | 28 | 0 | 0 | 429 | 447 | 0.14 | 2.09 | 2.02 | 0.52 | 0.46 |
833| 0 | 203 | 527 | 24 | 0 | 0 | 453 | 483 | 0.14 | 2.48 | 2.33 | 0.52 | 0.43 |
834| 0 | 204 | 472 | 12 | 0 | 0 | 414 | 430 | 0.13 | 1.66 | 1.66 | 0.49 | 0.45 |
835| 0 | 205 | 482 | 26 | 0 | 0 | 430 | 454 | 0.14 | 2.23 | 2.22 | 0.51 | 0.44 |
836| 0 | 206 | 488 | 14 | 0 | 0 | 416 | 433 | 0.13 | 1.46 | 1.6 | 0.49 | 0.46 |
837| 0 | 207 | 477 | 6 | 0 | 0 | 420 | 439 | 0.13 | 1.81 | 1.69 | 0.5 | 0.44 |
838| 0 | 208 | 469 | 6 | 0 | 0 | 398 | 418 | 0.13 | 1.4 | 1.35 | 0.49 | 0.46 |
839| 0 | 209 | 490 | 10 | 0 | 0 | 433 | 445 | 0.14 | 2.18 | 2.09 | 0.52 | 0.45 |
840| 0 | 210 | 513 | 14 | 0 | 0 | 453 | 472 | 0.13 | 1.82 | 1.72 | 0.5 | 0.44 |
841| 0 | 211 | 495 | 4 | 0 | 0 | 425 | 444 | 0.14 | 2.01 | 2.02 | 0.5 | 0.43 |
842| 0 | 212 | 471 | 8 | 0 | 0 | 412 | 421 | 0.13 | 1.69 | 1.65 | 0.49 | 0.45 |
843| 0 | 213 | 474 | 6 | 0 | 0 | 410 | 427 | 0.14 | 2.37 | 2.31 | 0.51 | 0.43 |
844| 0 | 214 | 499 | 6 | 0 | 0 | 421 | 448 | 0.14 | 2.17 | 2.06 | 0.51 | 0.47 |
845| 0 | 215 | 511 | 0 | 0 | 0 | 430 | 449 | 0.13 | 1.97 | 1.87 | 0.5 | 0.47 |
846| 0 | 216 | 473 | 0 | 0 | 0 | 391 | 413 | 0.13 | 1.71 | 1.71 | 0.49 | 0.47 |
847| 0 | 217 | 466 | 2 | 0 | 0 | 416 | 428 | 0.14 | 1.95 | 2 | 0.5 | 0.44 |
848| 0 | 218 | 509 | 0 | 0 | 0 | 426 | 452 | 0.13 | 1.59 | 1.51 | 0.5 | 0.45 |
849| 0 | 219 | 507 | 2 | 0 | 0 | 427 | 442 | 0.13 | 1.8 | 1.77 | 0.49 | 0.47 |
850| 0 | 220 | 490 | 2 | 0 | 0 | 415 | 428 | 0.14 | 1.98 | 1.95 | 0.5 | 0.45 |
851| 0 | 221 | 458 | 2 | 0 | 0 | 387 | 409 | 0.14 | 2.34 | 2.22 | 0.51 | 0.45 |
852| 0 | 222 | 495 | 6 | 0 | 0 | 429 | 449 | 0.14 | 1.88 | 1.82 | 0.51 | 0.44 |
853| 0 | 223 | 500 | 2 | 0 | 0 | 429 | 455 | 0.13 | 1.84 | 1.71 | 0.5 | 0.46 |
854| 0 | 224 | 479 | 0 | 0 | 0 | 396 | 418 | 0.13 | 1.8 | 1.69 | 0.49 | 0.46 |
855| 0 | 225 | 456 | 0 | 0 | 0 | 396 | 407 | 0.14 | 2.11 | 2.04 | 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 | 498 | 0 | 0 | 0 | 415 | 439 | 0.14 | 2.01 | 1.92 | 0.5 | 0.45 |
858| 0 | 228 | 483 | 0 | 0 | 0 | 413 | 428 | 0.13 | 2 | 1.85 | 0.5 | 0.45 |
859| 0 | 229 | 487 | 0 | 0 | 0 | 415 | 434 | 0.13 | 1.75 | 1.72 | 0.49 | 0.45 |
860| 0 | 230 | 542 | 0 | 0 | 0 | 442 | 470 | 0.13 | 1.9 | 1.81 | 0.5 | 0.43 |
861| 0 | 231 | 450 | 2 | 0 | 0 | 390 | 405 | 0.14 | 2.14 | 2.2 | 0.51 | 0.43 |
862| 0 | 232 | 464 | 2 | 0 | 0 | 401 | 416 | 0.14 | 2.1 | 2.1 | 0.5 | 0.46 |
863| 0 | 233 | 497 | 2 | 0 | 0 | 429 | 455 | 0.14 | 1.95 | 1.88 | 0.5 | 0.46 |
864| 0 | 234 | 487 | 0 | 0 | 0 | 414 | 431 | 0.13 | 1.62 | 1.68 | 0.49 | 0.47 |
865| 0 | 235 | 480 | 4 | 0 | 0 | 408 | 422 | 0.14 | 1.93 | 1.83 | 0.5 | 0.45 |
866| 0 | 236 | 548 | 0 | 0 | 0 | 447 | 468 | 0.13 | 1.48 | 1.34 | 0.49 | 0.46 |
867| 0 | 237 | 482 | 0 | 0 | 0 | 421 | 440 | 0.13 | 1.85 | 1.81 | 0.5 | 0.46 |
868| 0 | 238 | 464 | 0 | 0 | 0 | 400 | 414 | 0.14 | 1.73 | 1.64 | 0.49 | 0.44 |
869| 0 | 239 | 472 | 0 | 0 | 0 | 397 | 417 | 0.14 | 2.18 | 2.06 | 0.51 | 0.45 |
870| 0 | 240 | 507 | 0 | 0 | 0 | 427 | 446 | 0.14 | 2.11 | 1.98 | 0.5 | 0.43 |
871| 0 | 241 | 474 | 0 | 0 | 0 | 420 | 433 | 0.14 | 1.98 | 1.87 | 0.5 | 0.42 |
872| 0 | 242 | 511 | 2 | 0 | 0 | 426 | 459 | 0.13 | 2.27 | 2.16 | 0.49 | 0.46 |
873| 0 | 243 | 527 | 0 | 0 | 0 | 429 | 452 | 0.14 | 2.07 | 1.94 | 0.51 | 0.43 |
874| 0 | 244 | 472 | 2 | 0 | 0 | 403 | 420 | 0.13 | 1.62 | 1.6 | 0.49 | 0.46 |
875| 0 | 245 | 464 | 0 | 0 | 0 | 396 | 417 | 0.14 | 2.11 | 2.07 | 0.5 | 0.48 |
876| 0 | 246 | 496 | 0 | 0 | 0 | 418 | 427 | 0.14 | 1.87 | 1.83 | 0.5 | 0.45 |
877| 0 | 247 | 509 | 0 | 0 | 0 | 431 | 453 | 0.13 | 1.67 | 1.55 | 0.49 | 0.46 |
878| 0 | 248 | 494 | 0 | 0 | 0 | 410 | 431 | 0.14 | 2.03 | 1.91 | 0.5 | 0.44 |
879| 0 | 249 | 467 | 3 | 0 | 0 | 396 | 414 | 0.14 | 1.99 | 2 | 0.5 | 0.47 |
880| 0 | 250 | 490 | 0 | 0 | 0 | 427 | 445 | 0.13 | 1.74 | 1.65 | 0.49 | 0.43 |
881| 0 | 251 | 485 | 0 | 0 | 0 | 408 | 423 | 0.13 | 1.97 | 1.93 | 0.49 | 0.47 |
882| 0 | 252 | 512 | 0 | 0 | 0 | 435 | 458 | 0.14 | 2.11 | 2.12 | 0.51 | 0.44 |
883| 0 | 253 | 485 | 0 | 0 | 0 | 408 | 432 | 0.13 | 1.77 | 1.69 | 0.49 | 0.46 |
884| 0 | 254 | 491 | 0 | 0 | 0 | 417 | 435 | 0.14 | 1.91 | 1.83 | 0.5 | 0.44 |
885| 0 | 255 | 484 | 0 | 0 | 0 | 407 | 432 | 0.14 | 1.88 | 1.78 | 0.5 | 0.43 |
886| 0 | 256 | 526 | 0 | 0 | 0 | 447 | 468 | 0.13 | 1.74 | 1.67 | 0.49 | 0.46 |
887| 0 | 257 | 472 | 3 | 0 | 0 | 396 | 420 | 0.14 | 1.96 | 1.87 | 0.5 | 0.45 |
888| 0 | 258 | 494 | 4 | 0 | 0 | 407 | 432 | 0.14 | 2.09 | 2.01 | 0.51 | 0.42 |
889| 0 | 259 | 482 | 0 | 0 | 0 | 413 | 432 | 0.14 | 2.09 | 1.99 | 0.49 | 0.45 |
890| 0 | 260 | 521 | 0 | 0 | 0 | 457 | 475 | 0.14 | 2.01 | 1.91 | 0.5 | 0.43 |
891| 0 | 261 | 468 | 0 | 0 | 0 | 401 | 415 | 0.12 | 1.59 | 1.52 | 0.47 | 0.46 |
892| 0 | 262 | 492 | 0 | 0 | 0 | 414 | 429 | 0.14 | 1.97 | 1.91 | 0.5 | 0.46 |
893| 0 | 263 | 473 | 4 | 0 | 0 | 397 | 414 | 0.14 | 2.32 | 2.18 | 0.51 | 0.43 |
894| 0 | 264 | 497 | 4 | 0 | 0 | 423 | 440 | 0.13 | 1.47 | 1.37 | 0.48 | 0.46 |
895| 0 | 265 | 487 | 0 | 0 | 0 | 424 | 437 | 0.14 | 1.88 | 1.85 | 0.49 | 0.45 |
896| 0 | 266 | 496 | 0 | 0 | 0 | 418 | 436 | 0.14 | 2.14 | 2.05 | 0.51 | 0.43 |
897| 0 | 267 | 505 | 0 | 0 | 0 | 428 | 452 | 0.14 | 1.85 | 1.77 | 0.49 | 0.45 |
898| 0 | 268 | 484 | 0 | 0 | 0 | 401 | 423 | 0.13 | 1.79 | 1.65 | 0.49 | 0.46 |
899| 0 | 269 | 492 | 6 | 0 | 0 | 422 | 438 | 0.14 | 2.03 | 1.89 | 0.5 | 0.43 |
900| 0 | 270 | 458 | 2 | 0 | 0 | 396 | 412 | 0.14 | 1.93 | 1.86 | 0.5 | 0.46 |
901| 0 | 271 | 515 | 3 | 0 | 0 | 444 | 461 | 0.13 | 1.6 | 1.59 | 0.48 | 0.47 |
902| 0 | 272 | 488 | 0 | 0 | 0 | 422 | 442 | 0.14 | 2.01 | 1.95 | 0.5 | 0.46 |
903| 0 | 273 | 486 | 0 | 0 | 0 | 401 | 429 | 0.15 | 2.05 | 1.96 | 0.51 | 0.41 |
904| 0 | 274 | 494 | 0 | 0 | 0 | 406 | 417 | 0.13 | 1.58 | 1.53 | 0.48 | 0.48 |
905| 0 | 275 | 489 | 0 | 0 | 0 | 422 | 439 | 0.13 | 1.82 | 1.76 | 0.49 | 0.44 |
906| 0 | 276 | 469 | 2 | 0 | 0 | 408 | 424 | 0.14 | 1.92 | 1.86 | 0.5 | 0.45 |
907| 0 | 277 | 500 | 2 | 0 | 0 | 427 | 444 | 0.14 | 2.04 | 1.87 | 0.49 | 0.45 |
908| 0 | 278 | 475 | 0 | 0 | 0 | 408 | 421 | 0.14 | 1.89 | 1.91 | 0.49 | 0.45 |
909| 0 | 279 | 488 | 4 | 0 | 0 | 415 | 431 | 0.15 | 2.01 | 1.94 | 0.51 | 0.43 |
910| 0 | 280 | 497 | 2 | 0 | 0 | 423 | 445 | 0.14 | 1.89 | 1.78 | 0.49 | 0.45 |
911| 0 | 281 | 514 | 2 | 0 | 0 | 444 | 463 | 0.14 | 2.04 | 1.97 | 0.5 | 0.45 |
912| 0 | 282 | 484 | 2 | 0 | 0 | 412 | 432 | 0.15 | 2.17 | 2.09 | 0.52 | 0.44 |
913| 0 | 283 | 506 | 2 | 0 | 0 | 427 | 450 | 0.14 | 2.02 | 2.09 | 0.49 | 0.44 |
914| 0 | 284 | 505 | 7 | 0 | 0 | 437 | 452 | 0.15 | 2.34 | 2.27 | 0.51 | 0.46 |
915| 0 | 285 | 477 | 4 | 0 | 0 | 412 | 430 | 0.14 | 2.13 | 2.04 | 0.5 | 0.43 |
916| 0 | 286 | 511 | 4 | 0 | 0 | 429 | 457 | 0.14 | 1.94 | 1.85 | 0.5 | 0.45 |
917| 0 | 287 | 463 | 7 | 0 | 0 | 410 | 423 | 0.14 | 1.68 | 1.78 | 0.5 | 0.47 |
918| 0 | 288 | 499 | 6 | 0 | 0 | 432 | 444 | 0.14 | 2 | 2.01 | 0.5 | 0.44 |
919| 0 | 289 | 468 | 8 | 0 | 0 | 408 | 419 | 0.15 | 2.2 | 2.1 | 0.5 | 0.44 |
920| 0 | 290 | 494 | 10 | 0 | 0 | 417 | 430 | 0.14 | 1.74 | 1.74 | 0.5 | 0.44 |
921| 0 | 291 | 483 | 9 | 0 | 0 | 411 | 429 | 0.15 | 1.89 | 1.81 | 0.5 | 0.43 |
922| 0 | 292 | 510 | 4 | 0 | 0 | 441 | 466 | 0.15 | 2.02 | 1.99 | 0.5 | 0.44 |
923| 0 | 293 | 461 | 6 | 0 | 0 | 395 | 411 | 0.14 | 2.04 | 1.99 | 0.5 | 0.43 |
924| 0 | 294 | 515 | 15 | 0 | 0 | 444 | 455 | 0.15 | 2.11 | 1.83 | 0.51 | 0.44 |
925| 0 | 295 | 451 | 26 | 0 | 0 | 404 | 416 | 0.15 | 2.26 | 2.26 | 0.51 | 0.44 |
926| 0 | 296 | 486 | 26 | 0 | 0 | 426 | 445 | 0.14 | 1.77 | 1.68 | 0.49 | 0.44 |
927| 0 | 297 | 481 | 34 | 0 | 0 | 438 | 441 | 0.15 | 2.08 | 1.98 | 0.5 | 0.42 |
928| 0 | 298 | 472 | 34 | 0 | 0 | 424 | 440 | 0.15 | 1.95 | 2.01 | 0.51 | 0.42 |
929| 0 | 299 | 483 | 20 | 0 | 0 | 421 | 438 | 0.16 | 2.14 | 2.03 | 0.51 | 0.43 |
930| 0 | 300 | 464 | 22 | 0 | 0 | 416 | 435 | 0.15 | 1.94 | 1.83 | 0.5 | 0.44 |
931| 0 | 301 | 496 | 30 | 0 | 0 | 445 | 470 | 0.14 | 2.04 | 1.98 | 0.5 | 0.44 |
932| 0 | 302 | 503 | 20 | 0 | 0 | 438 | 462 | 0.15 | 1.82 | 1.73 | 0.51 | 0.43 |
933| 0 | 303 | 456 | 10 | 0 | 0 | 401 | 416 | 0.15 | 1.92 | 1.8 | 0.51 | 0.45 |
934| 0 | 304 | 469 | 4 | 0 | 0 | 410 | 426 | 0.15 | 2.28 | 2.1 | 0.51 | 0.42 |
935| 0 | 305 | 508 | 10 | 0 | 0 | 442 | 457 | 0.15 | 2.31 | 2.21 | 0.51 | 0.4 |
936| 0 | 306 | 472 | 8 | 0 | 0 | 414 | 430 | 0.16 | 2 | 1.88 | 0.51 | 0.42 |
937| 0 | 307 | 488 | 2 | 0 | 0 | 413 | 426 | 0.15 | 2.31 | 2.17 | 0.51 | 0.43 |
938| 0 | 308 | 510 | 2 | 0 | 0 | 432 | 453 | 0.15 | 2.18 | 2.03 | 0.51 | 0.44 |
939| 0 | 309 | 495 | 6 | 0 | 0 | 430 | 450 | 0.15 | 2.02 | 1.98 | 0.5 | 0.41 |
940| 0 | 310 | 498 | 8 | 0 | 0 | 431 | 450 | 0.15 | 1.68 | 1.64 | 0.49 | 0.44 |
941| 0 | 311 | 461 | 2 | 0 | 0 | 390 | 409 | 0.15 | 2.15 | 2.05 | 0.5 | 0.43 |
942| 0 | 312 | 513 | 4 | 0 | 0 | 440 | 464 | 0.17 | 2.73 | 2.66 | 0.53 | 0.41 |
943| 0 | 313 | 476 | 7 | 0 | 0 | 398 | 417 | 0.15 | 1.93 | 1.82 | 0.49 | 0.44 |
944| 0 | 314 | 502 | 0 | 0 | 0 | 426 | 444 | 0.14 | 1.89 | 1.77 | 0.49 | 0.42 |
945| 0 | 315 | 476 | 2 | 0 | 0 | 407 | 426 | 0.15 | 1.79 | 1.72 | 0.5 | 0.44 |
946| 0 | 316 | 489 | 0 | 0 | 0 | 421 | 435 | 0.17 | 3.19 | 3.06 | 0.53 | 0.41 |
947| 0 | 317 | 477 | 0 | 0 | 0 | 408 | 421 | 0.16 | 2.43 | 2.3 | 0.51 | 0.41 |
948| 0 | 318 | 516 | 0 | 0 | 0 | 450 | 471 | 0.16 | 1.95 | 1.86 | 0.51 | 0.43 |
949| 0 | 319 | 495 | 4 | 0 | 0 | 408 | 434 | 0.16 | 2.32 | 2.11 | 0.51 | 0.42 |
950| 0 | 320 | 482 | 2 | 0 | 0 | 411 | 426 | 0.16 | 2.64 | 2.53 | 0.51 | 0.42 |
951| 0 | 321 | 490 | 2 | 0 | 0 | 423 | 444 | 0.16 | 2.61 | 2.46 | 0.52 | 0.41 |
952| 0 | 322 | 490 | 0 | 0 | 0 | 406 | 426 | 0.15 | 1.76 | 1.77 | 0.5 | 0.41 |
953| 0 | 323 | 467 | 0 | 0 | 0 | 403 | 420 | 0.15 | 2.2 | 2.12 | 0.5 | 0.44 |
954| 0 | 324 | 514 | 4 | 0 | 0 | 427 | 451 | 0.17 | 2.47 | 2.29 | 0.52 | 0.4 |
955| 0 | 325 | 489 | 0 | 0 | 0 | 423 | 440 | 0.16 | 2.07 | 1.9 | 0.5 | 0.42 |
956| 0 | 326 | 499 | 0 | 0 | 0 | 423 | 436 | 0.17 | 2.78 | 2.71 | 0.53 | 0.41 |
957| 0 | 327 | 493 | 0 | 0 | 0 | 426 | 447 | 0.16 | 2.52 | 2.45 | 0.51 | 0.42 |
958| 0 | 328 | 486 | 0 | 0 | 0 | 403 | 420 | 0.15 | 2.01 | 1.86 | 0.5 | 0.44 |
959| 0 | 329 | 486 | 2 | 0 | 0 | 411 | 433 | 0.16 | 2.59 | 2.41 | 0.52 | 0.41 |
960| 0 | 330 | 495 | 2 | 0 | 0 | 431 | 455 | 0.18 | 2.63 | 2.45 | 0.52 | 0.4 |
961| 0 | 331 | 500 | 0 | 0 | 0 | 420 | 446 | 0.16 | 2.61 | 2.49 | 0.51 | 0.43 |
962| 0 | 332 | 485 | 0 | 0 | 0 | 409 | 432 | 0.17 | 2.54 | 2.42 | 0.52 | 0.41 |
963| 0 | 333 | 488 | 3 | 0 | 0 | 403 | 425 | 0.17 | 2.47 | 2.38 | 0.52 | 0.4 |
964| 0 | 334 | 487 | 4 | 0 | 0 | 413 | 436 | 0.16 | 2.43 | 2.32 | 0.51 | 0.42 |
965| 0 | 335 | 519 | 0 | 0 | 0 | 438 | 458 | 0.18 | 2.66 | 2.57 | 0.53 | 0.39 |
966| 0 | 336 | 468 | 3 | 0 | 0 | 406 | 423 | 0.18 | 2.72 | 2.62 | 0.53 | 0.41 |
967| 0 | 337 | 470 | 0 | 0 | 0 | 410 | 425 | 0.18 | 2.61 | 2.62 | 0.53 | 0.4 |
968| 0 | 338 | 543 | 0 | 0 | 0 | 466 | 485 | 0.17 | 2.18 | 2.07 | 0.52 | 0.41 |
969| 0 | 339 | 485 | 0 | 0 | 0 | 407 | 422 | 0.18 | 2.16 | 2.11 | 0.52 | 0.4 |
970| 0 | 340 | 470 | 0 | 0 | 0 | 400 | 418 | 0.18 | 2.44 | 2.33 | 0.53 | 0.41 |
971| 0 | 341 | 478 | 2 | 0 | 0 | 414 | 436 | 0.17 | 2.37 | 2.23 | 0.51 | 0.4 |
972| 0 | 342 | 501 | 2 | 0 | 0 | 423 | 442 | 0.18 | 2.16 | 2.12 | 0.53 | 0.38 |
973| 0 | 343 | 497 | 0 | 0 | 0 | 423 | 442 | 0.18 | 2.59 | 2.67 | 0.53 | 0.39 |
974| 0 | 344 | 496 | 0 | 0 | 0 | 405 | 422 | 0.18 | 2.3 | 2.31 | 0.52 | 0.41 |
975| 0 | 345 | 459 | 0 | 0 | 0 | 388 | 409 | 0.18 | 2.78 | 2.71 | 0.53 | 0.4 |
976| 0 | 346 | 501 | 0 | 0 | 0 | 425 | 444 | 0.19 | 2.79 | 2.7 | 0.53 | 0.38 |
977| 0 | 347 | 500 | 2 | 0 | 0 | 426 | 445 | 0.18 | 2.3 | 2.14 | 0.52 | 0.39 |
978| 0 | 348 | 485 | 0 | 0 | 0 | 412 | 432 | 0.18 | 2.57 | 2.45 | 0.52 | 0.39 |
979| 0 | 349 | 479 | 0 | 0 | 0 | 400 | 418 | 0.19 | 3.13 | 2.89 | 0.53 | 0.38 |
980| 0 | 350 | 496 | 0 | 0 | 0 | 425 | 436 | 0.2 | 2.6 | 2.43 | 0.53 | 0.41 |
981| 0 | 351 | 496 | 2 | 0 | 0 | 410 | 430 | 0.19 | 2.73 | 2.62 | 0.53 | 0.38 |
982| 0 | 352 | 491 | 2 | 0 | 0 | 427 | 438 | 0.18 | 2 | 2.03 | 0.52 | 0.4 |
983| 0 | 353 | 492 | 1 | 0 | 0 | 402 | 427 | 0.2 | 3.25 | 3.04 | 0.55 | 0.39 |
984| 0 | 354 | 484 | 5 | 0 | 0 | 424 | 437 | 0.2 | 3.18 | 3.17 | 0.54 | 0.37 |
985| 0 | 355 | 507 | 0 | 0 | 0 | 438 | 449 | 0.2 | 2.71 | 2.54 | 0.54 | 0.39 |
986| 0 | 356 | 512 | 0 | 0 | 0 | 427 | 448 | 0.21 | 2.86 | 2.75 | 0.54 | 0.38 |
987| 0 | 357 | 461 | 0 | 0 | 0 | 389 | 406 | 0.19 | 1.92 | 1.89 | 0.53 | 0.37 |
988| 0 | 358 | 462 | 0 | 0 | 0 | 392 | 415 | 0.2 | 2.43 | 2.37 | 0.54 | 0.36 |
989| 0 | 359 | 522 | 0 | 0 | 0 | 449 | 461 | 0.2 | 2.84 | 2.67 | 0.54 | 0.38 |
990| 0 | 360 | 469 | 0 | 0 | 0 | 396 | 415 | 0.21 | 2.47 | 2.24 | 0.54 | 0.39 |
991| 0 | 361 | 524 | 0 | 0 | 0 | 456 | 473 | 0.21 | 2.81 | 2.81 | 0.54 | 0.38 |
992| 0 | 362 | 489 | 1 | 0 | 0 | 410 | 435 | 0.21 | 2.42 | 2.46 | 0.55 | 0.37 |
993| 0 | 363 | 468 | 4 | 0 | 0 | 393 | 411 | 0.22 | 3.1 | 2.94 | 0.55 | 0.36 |
994| 0 | 364 | 473 | 1 | 0 | 0 | 402 | 418 | 0.22 | 2.97 | 2.86 | 0.55 | 0.39 |
995| 0 | 365 | 531 | 1 | 0 | 0 | 437 | 459 | 0.21 | 2.72 | 2.58 | 0.55 | 0.37 |
996| 0 | 366 | 472 | 1 | 0 | 0 | 399 | 419 | 0.21 | 2.61 | 2.51 | 0.54 | 0.38 |
997| 0 | 367 | 495 | 1 | 0 | 0 | 405 | 426 | 0.23 | 3.17 | 3.02 | 0.56 | 0.37 |
998| 0 | 368 | 475 | 1 | 0 | 0 | 413 | 434 | 0.23 | 2.65 | 2.54 | 0.56 | 0.36 |
999| 0 | 369 | 486 | 0 | 0 | 0 | 416 | 437 | 0.23 | 3.27 | 3.2 | 0.56 | 0.38 |
1000| 0 | 370 | 512 | 1 | 0 | 0 | 434 | 455 | 0.22 | 2.42 | 2.28 | 0.55 | 0.36 |
1001| 0 | 371 | 494 | 2 | 0 | 0 | 422 | 439 | 0.22 | 2.91 | 2.83 | 0.55 | 0.36 |
1002| 0 | 372 | 492 | 0 | 0 | 0 | 430 | 446 | 0.25 | 2.98 | 3.06 | 0.57 | 0.36 |
1003| 0 | 373 | 492 | 2 | 0 | 0 | 424 | 441 | 0.25 | 2.95 | 2.78 | 0.58 | 0.35 |
1004| 0 | 374 | 485 | 1 | 0 | 0 | 410 | 429 | 0.23 | 2.92 | 2.89 | 0.56 | 0.38 |
1005| 0 | 375 | 480 | 2 | 0 | 0 | 413 | 433 | 0.23 | 2.88 | 2.73 | 0.56 | 0.36 |
1006| 0 | 376 | 495 | 3 | 0 | 0 | 420 | 446 | 0.24 | 2.43 | 2.38 | 0.57 | 0.36 |
1007| 0 | 377 | 495 | 1 | 0 | 0 | 418 | 441 | 0.24 | 2.27 | 2.17 | 0.56 | 0.35 |
1008| 0 | 378 | 468 | 3 | 0 | 0 | 393 | 414 | 0.24 | 2.64 | 2.51 | 0.56 | 0.36 |
1009| 0 | 379 | 485 | 1 | 0 | 0 | 419 | 444 | 0.26 | 2.91 | 2.73 | 0.58 | 0.35 |
1010| 0 | 380 | 499 | 1 | 0 | 0 | 423 | 445 | 0.27 | 2.95 | 2.85 | 0.58 | 0.35 |
1011| 0 | 381 | 502 | 0 | 0 | 0 | 424 | 453 | 0.26 | 3.07 | 2.85 | 0.57 | 0.34 |
1012| 0 | 382 | 469 | 1 | 0 | 0 | 392 | 411 | 0.25 | 3.13 | 3.05 | 0.57 | 0.35 |
1013| 0 | 383 | 503 | 3 | 0 | 0 | 431 | 441 | 0.26 | 2.48 | 2.43 | 0.57 | 0.36 |
1014| 0 | 384 | 499 | 1 | 0 | 0 | 422 | 438 | 0.26 | 2.51 | 2.5 | 0.57 | 0.35 |
1015| 0 | 385 | 500 | 7 | 0 | 0 | 441 | 460 | 0.26 | 2.7 | 2.69 | 0.58 | 0.37 |
1016| 0 | 386 | 475 | 0 | 0 | 0 | 398 | 417 | 0.27 | 2.17 | 2.19 | 0.57 | 0.35 |
1017| 0 | 387 | 457 | 4 | 0 | 0 | 391 | 407 | 0.27 | 2.69 | 2.6 | 0.58 | 0.34 |
1018| 0 | 388 | 479 | 5 | 0 | 0 | 406 | 427 | 0.27 | 2.57 | 2.48 | 0.58 | 0.35 |
1019| 0 | 389 | 520 | 2 | 0 | 0 | 454 | 474 | 0.28 | 2.37 | 2.37 | 0.58 | 0.33 |
1020| 0 | 390 | 470 | 5 | 0 | 0 | 414 | 430 | 0.27 | 2.53 | 2.43 | 0.58 | 0.34 |
1021| 0 | 391 | 472 | 7 | 0 | 0 | 411 | 435 | 0.27 | 1.86 | 1.74 | 0.58 | 0.35 |
1022| 0 | 392 | 510 | 11 | 0 | 0 | 428 | 452 | 0.3 | 3.14 | 3.09 | 0.59 | 0.34 |
1023| 0 | 393 | 475 | 14 | 0 | 0 | 408 | 430 | 0.29 | 2.29 | 2.17 | 0.59 | 0.34 |
1024| 0 | 394 | 490 | 20 | 0 | 0 | 434 | 456 | 0.27 | 2.18 | 2.16 | 0.58 | 0.34 |
1025| 0 | 395 | 446 | 21 | 0 | 0 | 409 | 420 | 0.29 | 2.6 | 2.45 | 0.59 | 0.35 |
1026| 0 | 396 | 471 | 30 | 0 | 0 | 428 | 449 | 0.27 | 2 | 1.95 | 0.58 | 0.33 |
1027| 0 | 397 | 398 | 54 | 0 | 0 | 373 | 391 | 0.29 | 2.35 | 2.28 | 0.58 | 0.34 |
1028| 0 | 398 | 300 | 189 | 0 | 0 | 413 | 435 | 0.29 | 2.52 | 2.54 | 0.58 | 0.39 |
1029| 0 | 399 | 4 | 483 | 0 | 0 | 415 | 436 | 0.28 | 2.23 | 2.28 | 0.58 | 0.4 |
1030| 0 | 400 | 0 | 493 | 0 | 0 | 418 | 437 | 0.28 | 1.51 | 2 | 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 | 196 | 5 | 0 | 0 | 113 | 159 | 0.03 | -0.04 | 0.01 | 0.29 | 0.83 |
1039| 0 | 1.2 | 591 | 17 | 0 | 0 | 522 | 567 | 0.03 | 0.08 | 0.03 | 0.31 | 0.81 |
1040| 0 | 1.23 | 1082 | 21 | 0 | 0 | 984 | 1030 | 0.04 | 0 | 0.02 | 0.31 | 0.82 |
1041| 0 | 1.25 | 1530 | 32 | 0 | 0 | 1307 | 1389 | 0.04 | 0.04 | 0.02 | 0.33 | 0.75 |
1042| 0 | 1.28 | 2213 | 55 | 0 | 0 | 1963 | 2049 | 0.05 | 0.04 | 0.02 | 0.34 | 0.71 |
1043| 0 | 1.3 | 2979 | 58 | 0 | 0 | 2473 | 2649 | 0.05 | 0.03 | 0.02 | 0.35 | 0.66 |
1044| 0 | 1.33 | 4341 | 103 | 0 | 0 | 3734 | 3944 | 0.06 | 0.03 | 0.04 | 0.36 | 0.64 |
1045| 0 | 1.37 | 6172 | 138 | 0 | 0 | 5293 | 5649 | 0.06 | 0.03 | 0.04 | 0.36 | 0.62 |
1046| 0 | 1.4 | 8672 | 194 | 0 | 0 | 7676 | 7975 | 0.07 | 0.09 | 0.06 | 0.37 | 0.59 |
1047| 0 | 1.45 | 9833 | 220 | 0 | 0 | 8693 | 8970 | 0.07 | 0.12 | 0.09 | 0.38 | 0.56 |
1048| 0 | 1.49 | 10956 | 268 | 0 | 0 | 9414 | 9838 | 0.08 | 0.16 | 0.12 | 0.39 | 0.53 |
1049| 0 | 1.55 | 12248 | 340 | 0 | 0 | 10252 | 10730 | 0.09 | 0.23 | 0.18 | 0.41 | 0.49 |
1050| 0 | 1.61 | 13279 | 504 | 0 | 0 | 11943 | 12280 | 0.09 | 0.29 | 0.23 | 0.43 | 0.46 |
1051| 0 | 1.68 | 14619 | 527 | 0 | 0 | 12987 | 13349 | 0.11 | 0.43 | 0.34 | 0.45 | 0.44 |
1052| 0 | 1.77 | 16875 | 576 | 0 | 0 | 14610 | 15145 | 0.13 | 0.65 | 0.54 | 0.48 | 0.41 |
1053| 0 | 1.88 | 17479 | 579 | 0 | 0 | 15719 | 16051 | 0.16 | 1.08 | 0.95 | 0.53 | 0.36 |
1054| 0 | 2.03 | 17482 | 591 | 0 | 0 | 14510 | 15067 | 0.2 | 1.81 | 1.67 | 0.58 | 0.33 |
1055| 0 | 2.23 | 17440 | 595 | 0 | 0 | 15812 | 16140 | 0.22 | 2.73 | 2.64 | 0.62 | 0.31 |
1056| 0 | 2.55 | 17610 | 629 | 0 | 0 | 15398 | 15776 | 0.3 | 5.34 | 5.35 | 0.72 | 0.28 |
1057| 0 | 3.22 | 17776 | 570 | 0 | 0 | 15652 | 16001 | 0.47 | 15.15 | 15.76 | 0.84 | 0.24 |
1058+------+---------+----------+----------+----------+---------+---------+---------+-------+----------+----------+----------+-----------+
1059
1060 Summary for experiment 0
1061+---------------------------------------+-----------+----------+--------+
1062| Item | Overall | Low | High |
1063|---------------------------------------+-----------+----------+--------|
1064| dmin | 1.18 | 3.22 | 1.18 |
1065| dmax | 55.04 | 55.04 | 1.2 |
1066| number fully recorded | 193373 | 17776 | 196 |
1067| number partially recorded | 6022 | 570 | 5 |
1068| number with invalid background pixels | 52769 | 4243 | 158 |
1069| number with invalid foreground pixels | 30000 | 2658 | 88 |
1070| number with overloaded pixels | 0 | 0 | 0 |
1071| number in powder rings | 0 | 0 | 0 |
1072| number processed with summation | 169055 | 15652 | 113 |
1073| number processed with profile fitting | 174758 | 16001 | 159 |
1074| number failed in background modelling | 4 | 4 | 0 |
1075| number failed in summation | 30000 | 2658 | 88 |
1076| number failed in profile fitting | 24297 | 2309 | 42 |
1077| ibg | 0.17 | 0.47 | 0.03 |
1078| i/sigi (summation) | 2.55 | 15.15 | -0.04 |
1079| i/sigi (profile fitting) | 2.52 | 15.76 | 0.01 |
1080| cc prf | 0.52 | 0.84 | 0.29 |
1081| cc_pearson sum/prf | 1 | 1 | 0.43 |
1082| cc_spearman sum/prf | 0.83 | 1 | 0.33 |
1083+---------------------------------------+-----------+----------+--------+
1084
1085Timing information for integration
1086+-------------------+----------------+
1087| Read time | 15.84 seconds |
1088| Extract time | 6.13 seconds |
1089| Pre-process time | 0.25 seconds |
1090| Process time | 136.63 seconds |
1091| Post-process time | 0.00 seconds |
1092| Total time | 159.84 seconds |
1093+-------------------+----------------+
1094
1095Removing 22837 unintegrated reflections of 199395 total
1096Saving 176558 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.1243-gd06ef435d
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 176558 predicted reflections
17Selected 167255 reflections integrated by profile and summation methods
18Combined 314 partial reflections with other partial reflections
19Removed 0 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,
22123 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 8.41, -0.16, -1.14
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 61803 reflections with d > 1.92
46
47Input crystal symmetry:
48Unit cell: (44.3888, 53.1283, 62.3788, 115.205, 101.777, 90)
49Space group: P 1 (No. 1)
50Change of basis op to minimum cell: -a,b,-b-c
51Crystal symmetry in minimum cell:
52Unit cell: (44.3888, 53.1283, 62.3788, 115.205, 101.777, 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: 0.248
57Estimated expectation value of true correlation coefficient E(CC) = 0.927
58Estimated sd(CC) = 0.912 / 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 | 51318 | ** | 1 |(0, 0, 0) |
69| 0.853 | 8.77 | 0.88 | 50628 | ** | 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 | 9.03 | 9.03 | 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: 112.880, 53.128, 44.389, 90.000, 103.037, 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 176558 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 | 9.03 | 9.03 | 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: 112.880, 53.128, 44.389, 90.000, 103.037, 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.1243-gd06ef435d
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 176558 predicted reflections
26Selected 176558 reflections integrated by profile or summation methods
27Removed 1875 reflections below partiality threshold
28Removed 0 intensity.sum.value reflections with I/Sig(I) < -5.0
29Removed 0 intensity.prf.value reflections with I/Sig(I) < -5.0
30Combined 323 partial reflections with other partial reflections
31Excluding 1654/176235 reflections
32Reflections passing individual criteria:
33criterion: user excluded, reflections: 1654
34criterion: excluded for scaling, reflections: 1654
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,
532493 outliers have been identified.
54
55172960 reflections were preselected for scale factor determination
56out of 174581 suitable reflections:
57Reflections passing individual criteria:
58criterion: in I/sigma range (I/sig > -5.0), reflections: 174532
59criterion: above min partiality ( > 0.95), reflections: 173009
60
61Randomly selected 15287/48772 groups (m>1) to use for scaling model
62minimisation (49961 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 7.07
71
72Refinement steps:
73+--------+--------+----------+
74| Step | Nref | RMSD_I |
75| | | (a.u) |
76|--------+--------+----------|
77| 0 | 49195 | 0.86962 |
78| 1 | 49195 | 0.84699 |
79| 2 | 49195 | 0.68902 |
80| 3 | 49195 | 0.64811 |
81| 4 | 49195 | 0.61143 |
82| 5 | 49195 | 0.59561 |
83| 6 | 49195 | 0.55316 |
84| 7 | 49195 | 0.53633 |
85| 8 | 49195 | 0.53407 |
86| 9 | 49195 | 0.53263 |
87| 10 | 49195 | 0.53176 |
88| 11 | 49195 | 0.53061 |
89| 12 | 49195 | 0.52974 |
90| 13 | 49195 | 0.52887 |
91| 14 | 49195 | 0.52842 |
92| 15 | 49195 | 0.52804 |
93| 16 | 49195 | 0.52761 |
94| 17 | 49195 | 0.52734 |
95| 18 | 49195 | 0.52714 |
96| 19 | 49195 | 0.52701 |
97| 20 | 49195 | 0.52687 |
98| 21 | 49195 | 0.52644 |
99| 22 | 49195 | 0.52596 |
100| 23 | 49195 | 0.52554 |
101| 24 | 49195 | 0.5247 |
102| 25 | 49195 | 0.52445 |
103| 26 | 49195 | 0.52397 |
104| 27 | 49195 | 0.52345 |
105| 28 | 49195 | 0.52311 |
106| 29 | 49195 | 0.52264 |
107| 30 | 49195 | 0.52191 |
108| 31 | 49195 | 0.52119 |
109| 32 | 49195 | 0.52074 |
110| 33 | 49195 | 0.52026 |
111| 34 | 49195 | 0.51956 |
112| 35 | 49195 | 0.51878 |
113| 36 | 49195 | 0.51862 |
114| 37 | 49195 | 0.51821 |
115| 38 | 49195 | 0.51811 |
116| 39 | 49195 | 0.51795 |
117| 40 | 49195 | 0.5179 |
118+--------+--------+----------+
119RMSD no longer decreasing
120lbfgs minimizer stop: callback_after_step is True
121
122================================================================================
123
124Scale factors determined during minimisation have now been
125applied to all reflections for dataset 0.
126
127A round of outlier rejection has been performed,
128153 outliers have been identified.
129
130Performing profile/summation intensity optimisation.
131+---------------+---------+---------+
132| Combination | CC1/2 | Rmeas |
133|---------------+---------+---------|
134| prf only | 0.99453 | 0.09768 |
135| sum only | 0.99161 | 0.12619 |
136| Imid = 70.58 | 0.99366 | 0.10408 |
137| Imid = 3237.4 | 0.9945 | 0.09771 |
138| Imid = 323.74 | 0.99429 | 0.09844 |
139| Imid = 32.37 | 0.99298 | 0.11241 |
140+---------------+---------+---------+
141Profile intensities determined to be best for scaling.
142
143A round of outlier rejection has been performed,
144153 outliers have been identified.
145
146Components to be refined in this cycle for all datasets: scale, decay, absorption
147Performing a round of scaling with an LBFGS minimizer.
148
149Time taken for refinement 3.09
150
151Refinement steps:
152+--------+--------+----------+
153| Step | Nref | RMSD_I |
154| | | (a.u) |
155|--------+--------+----------|
156| 0 | 49935 | 0.58133 |
157| 1 | 49935 | 0.57988 |
158| 2 | 49935 | 0.57059 |
159| 3 | 49935 | 0.56975 |
160| 4 | 49935 | 0.56933 |
161| 5 | 49935 | 0.56899 |
162| 6 | 49935 | 0.56849 |
163| 7 | 49935 | 0.56838 |
164| 8 | 49935 | 0.56826 |
165| 9 | 49935 | 0.56809 |
166| 10 | 49935 | 0.56798 |
167| 11 | 49935 | 0.56787 |
168| 12 | 49935 | 0.56777 |
169| 13 | 49935 | 0.5677 |
170| 14 | 49935 | 0.56765 |
171+--------+--------+----------+
172RMSD no longer decreasing
173lbfgs minimizer stop: callback_after_step is True
174
175================================================================================
176
177Scale factors determined during minimisation have now been
178applied to all reflections for dataset 0.
179
180A round of outlier rejection has been performed,
181131 outliers have been identified.
182
183Performing a round of error model refinement.
184
185Error model details:
186 Type: basic
187 Parameters: a = 0.52354, b = 0.05329
188 Error model formula: σ'² = a²(σ² + (bI)²)
189 estimated I/sigma asymptotic limit: 35.842
190
191Results of error model refinement. Uncorrected and corrected variances
192of normalised intensity deviations for given intensity ranges. Variances
193are expected to be ~1.0 for reliable errors (sigmas).
194+--------------------------+----------+------------------------+----------------------+
195| Intensity range (<Ih>) | n_refl | Uncorrected variance | Corrected variance |
196|--------------------------+----------+------------------------+----------------------|
197| 2425.44 - 587.12 | 250 | 2.155 | 0.728 |
198| 587.12 - 446.09 | 250 | 1.859 | 1.087 |
199| 446.09 - 376.01 | 250 | 1.465 | 1.031 |
200| 376.01 - 327.99 | 250 | 1.552 | 1.182 |
201| 327.99 - 246.25 | 699 | 1.23 | 1.202 |
202| 246.25 - 155.84 | 1772 | 1.002 | 1.287 |
203| 155.84 - 98.63 | 2796 | 0.638 | 1.16 |
204| 98.63 - 62.42 | 3564 | 0.555 | 1.279 |
205| 62.42 - 39.50 | 3774 | 0.468 | 1.286 |
206| 39.50 - 24.99 | 3045 | 0.418 | 1.294 |
207+--------------------------+----------+------------------------+----------------------+
208
209Components to be refined in this cycle for all datasets: scale, decay, absorption
210Performing a round of scaling with a Levenberg-Marquardt minimizer.
211
212Time taken for refinement 4.27
213
214Refinement steps:
215+--------+--------+----------+
216| Step | Nref | RMSD_I |
217| | | (a.u) |
218|--------+--------+----------|
219| 0 | 49941 | 0.97255 |
220| 1 | 49941 | 0.96614 |
221| 2 | 49941 | 0.95999 |
222| 3 | 49941 | 0.95478 |
223| 4 | 49941 | 0.95249 |
224| 5 | 49941 | 0.95156 |
225| 6 | 49941 | 0.95093 |
226| 7 | 49941 | 0.95067 |
227| 8 | 49941 | 0.95064 |
228+--------+--------+----------+
229RMSD no longer decreasing
230
231================================================================================
232
233Components to be refined in this cycle for all datasets: scale, decay, absorption
234Performing a round of scaling with a Levenberg-Marquardt minimizer.
235
236Time taken for refinement 0.89
237
238Refinement steps:
239+--------+--------+----------+
240| Step | Nref | RMSD_I |
241| | | (a.u) |
242|--------+--------+----------|
243| 0 | 49941 | 0.95064 |
244| 1 | 49941 | 0.95064 |
245+--------+--------+----------+
246RMSD no longer decreasing
247
248================================================================================
249
250Scale factors determined during minimisation have now been
251applied to all reflections for dataset 0.
252
253A round of outlier rejection has been performed,
254318 outliers have been identified.
255
256Performing a round of error model refinement.
257
258Error model details:
259 Type: basic
260 Parameters: a = 0.49883, b = 0.05341
261 Error model formula: σ'² = a²(σ² + (bI)²)
262 estimated I/sigma asymptotic limit: 37.532
263
264Results of error model refinement. Uncorrected and corrected variances
265of normalised intensity deviations for given intensity ranges. Variances
266are expected to be ~1.0 for reliable errors (sigmas).
267+--------------------------+----------+------------------------+----------------------+
268| Intensity range (<Ih>) | n_refl | Uncorrected variance | Corrected variance |
269|--------------------------+----------+------------------------+----------------------|
270| 2416.68 - 595.01 | 250 | 2.398 | 0.831 |
271| 595.01 - 449.72 | 250 | 1.507 | 0.977 |
272| 449.72 - 376.11 | 250 | 1.382 | 1.039 |
273| 376.11 - 329.33 | 250 | 1.476 | 1.192 |
274| 329.33 - 245.83 | 711 | 1.061 | 1.125 |
275| 245.83 - 155.64 | 1755 | 0.848 | 1.194 |
276| 155.64 - 98.54 | 2799 | 0.549 | 1.113 |
277| 98.54 - 62.38 | 3503 | 0.473 | 1.215 |
278| 62.38 - 39.50 | 3773 | 0.395 | 1.214 |
279| 39.50 - 25.00 | 2993 | 0.346 | 1.192 |
280+--------------------------+----------+------------------------+----------------------+
281
282
283The reflection table variances have been adjusted to account for the
284uncertainty in the scaling model
285
286Total time taken: 20.8151s
287
288================================================================================
289
29038.46% of model parameters have significant uncertainty
291(sigma/abs(parameter) > 0.5)
292
293Summary of dataset partialities
294+------------------+----------+
295| Partiality (p) | n_refl |
296|------------------+----------|
297| all reflections | 176235 |
298| p > 0.99 | 172395 |
299| 0.5 < p < 0.99 | 2040 |
300| 0.01 < p < 0.5 | 1524 |
301| p < 0.01 | 276 |
302+------------------+----------+
303
304Reflections below a partiality_cutoff of 0.4 are not considered for any
305part of the scaling analysis or for the reporting of merging statistics.
306Additionally, if applicable, only reflections with a min_partiality > 0.95
307were considered for use when refining the scaling model.
308
309
310 ----------Merging statistics by resolution bin----------
311
312 d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas r_pim r_anom cc1/2 cc_ano
313 55.04 3.22 15826 4256 3.72 99.95 107.8 37.2 0.050 0.059 0.030 0.063 0.996* -0.023
314 3.22 2.56 15548 4161 3.74 99.98 32.9 17.8 0.104 0.121 0.062 0.136 0.987* 0.005
315 2.56 2.23 16023 4148 3.86 100.00 14.4 9.9 0.177 0.206 0.104 0.225 0.964* -0.027
316 2.23 2.03 14920 4147 3.60 99.93 9.1 6.2 0.254 0.299 0.155 0.341 0.932* -0.004
317 2.03 1.88 15842 4141 3.83 99.86 5.0 3.8 0.378 0.440 0.222 0.458 0.875* -0.083
318 1.88 1.77 15071 4102 3.67 99.93 2.5 2.1 0.601 0.702 0.358 0.738 0.740* -0.022
319 1.77 1.68 13299 4152 3.20 99.88 1.5 1.2 0.858 1.030 0.561 1.103 0.526* -0.019
320 1.68 1.61 12281 4130 2.97 99.95 1.0 0.8 1.250 1.526 0.861 1.378 0.305* -0.028
321 1.61 1.55 10702 4077 2.62 99.00 0.8 0.6 1.493 1.852 1.076 1.558 0.180* -0.033
322 1.55 1.50 9802 4043 2.42 98.04 0.5 0.4 2.156 2.695 1.587 1.786 0.151* 0.022
323 1.50 1.45 8951 3933 2.28 95.32 0.4 0.3 3.017 3.819 2.304 1.873 0.058* 0.000
324 1.45 1.41 8125 3864 2.10 93.65 0.3 0.2 4.344 5.551 3.404 2.009 0.023 -0.071
325 1.41 1.37 5725 3403 1.68 82.62 0.2 0.1 5.822 7.602 4.814 2.392 0.031 0.029
326 1.37 1.34 4011 2783 1.44 67.96 0.2 0.1 7.317 9.802 6.445 2.821 -0.020 -0.019
327 1.34 1.31 2773 2243 1.24 54.64 0.1 0.1 15.627 21.358 14.455 3.454 0.037 0.880
328 1.31 1.28 2065 1746 1.18 42.33 0.1 0.1 9.363 13.204 9.306 4.390 -0.025 0.000
329 1.28 1.25 1435 1243 1.15 30.38 0.1 0.1 62.669 88.627 62.669 4.622 0.032 0.000
330 1.25 1.23 1041 911 1.14 22.11 0.1 0.1 -10.357 -14.648 -10.357 5.920 0.011 0.000
331 1.23 1.21 610 535 1.14 13.08 0.1 0.1 -74.250 -105.006 -74.250 5.613 0.080 0.000
332 1.21 1.19 213 190 1.12 4.59 -0.0 0.0 29.252 41.368 29.252 4.212 -0.311 0.000
333 54.99 1.19 174263 62208 2.80 75.28 12.0 5.5 0.129 0.153 0.081 0.182 0.995* -0.021
334
335
336Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.60
337
338 -------------Summary of merging statistics--------------
339
340 Suggested Low High Overall
341High resolution limit 1.60 4.33 1.60 1.19
342Low resolution limit 54.99 55.02 1.62 54.99
343Completeness 99.9 99.9 99.8 75.3
344Multiplicity 3.6 3.8 2.9 2.8
345I/sigma 9.7 41.3 0.7 5.5
346Rmerge(I) 0.112 0.043 1.483 0.129
347Rmerge(I+/-) 0.093 0.037 1.426 0.104
348Rmeas(I) 0.131 0.050 1.829 0.153
349Rmeas(I+/-) 0.126 0.050 1.953 0.141
350Rpim(I) 0.068 0.025 1.052 0.081
351Rpim(I+/-) 0.084 0.033 1.328 0.094
352CC half 0.996 0.997 0.139 0.995
353Anomalous completeness 94.3 98.0 86.8 55.2
354Anomalous multiplicity 1.9 2.0 1.6 1.6
355Anomalous correlation -0.017 0.017 -0.021 -0.021
356Anomalous slope 1.006
357dF/F 0.124
358dI/s(dI) 0.961
359Total observations 121474 6705 4777 174263
360Total unique 34173 1784 1666 62208
361
362Writing html report to dials.scale.html
363Saving the scaled experiments to scaled.expt
364Saving the scaled reflections to scaled.refl
365See 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 15826 4256 3.72 99.95 107.8 37.2 0.050 0.059 0.030 0.063 0.996* -0.023
3.22 2.56 15548 4161 3.74 99.98 32.9 17.8 0.104 0.121 0.062 0.136 0.987* 0.005
2.56 2.23 16023 4148 3.86 100.00 14.4 9.9 0.177 0.206 0.104 0.225 0.964* -0.027
2.23 2.03 14920 4147 3.60 99.93 9.1 6.2 0.254 0.299 0.155 0.341 0.932* -0.004
2.03 1.88 15842 4141 3.83 99.86 5.0 3.8 0.378 0.440 0.222 0.458 0.875* -0.083
1.88 1.77 15071 4102 3.67 99.93 2.5 2.1 0.601 0.702 0.358 0.738 0.740* -0.022
1.77 1.68 13299 4152 3.20 99.88 1.5 1.2 0.858 1.030 0.561 1.103 0.526* -0.019
1.68 1.61 12281 4130 2.97 99.95 1.0 0.8 1.250 1.526 0.861 1.378 0.305* -0.028
1.61 1.55 10702 4077 2.62 99.00 0.8 0.6 1.493 1.852 1.076 1.558 0.180* -0.033
1.55 1.50 9802 4043 2.42 98.04 0.5 0.4 2.156 2.695 1.587 1.786 0.151* 0.022
1.50 1.45 8951 3933 2.28 95.32 0.4 0.3 3.017 3.819 2.304 1.873 0.058* 0.000
1.45 1.41 8125 3864 2.10 93.65 0.3 0.2 4.344 5.551 3.404 2.009 0.023 -0.071
1.41 1.37 5725 3403 1.68 82.62 0.2 0.1 5.822 7.602 4.814 2.392 0.031 0.029
1.37 1.34 4011 2783 1.44 67.96 0.2 0.1 7.317 9.802 6.445 2.821 -0.020 -0.019
1.34 1.31 2773 2243 1.24 54.64 0.1 0.1 15.627 21.358 14.455 3.454 0.037 0.880
1.31 1.28 2065 1746 1.18 42.33 0.1 0.1 9.363 13.204 9.306 4.390 -0.025 0.000
1.28 1.25 1435 1243 1.15 30.38 0.1 0.1 62.669 88.627 62.669 4.622 0.032 0.000
1.25 1.23 1041 911 1.14 22.11 0.1 0.1 -10.357 -14.648 -10.357 5.920 0.011 0.000
1.23 1.21 610 535 1.14 13.08 0.1 0.1 -74.250 -105.006 -74.250 5.613 0.080 0.000
1.21 1.19 213 190 1.12 4.59 -0.0 0.0 29.252 41.368 29.252 4.212 -0.311 0.000
54.99 1.19 174263 62208 2.80 75.28 12.0 5.5 0.129 0.153 0.081 0.182 0.995* -0.021
Resolution limit suggested from CC½ fit (limit CC½=0.3): 1.60
-------------Summary of merging statistics--------------
Suggested Low High Overall
High resolution limit 1.60 4.33 1.60 1.19
Low resolution limit 54.99 55.02 1.62 54.99
Completeness 99.9 99.9 99.8 75.3
Multiplicity 3.6 3.8 2.9 2.8
I/sigma 9.7 41.3 0.7 5.5
Rmerge(I) 0.112 0.043 1.483 0.129
Rmerge(I+/-) 0.093 0.037 1.426 0.104
Rmeas(I) 0.131 0.050 1.829 0.153
Rmeas(I+/-) 0.126 0.050 1.953 0.141
Rpim(I) 0.068 0.025 1.052 0.081
Rpim(I+/-) 0.084 0.033 1.328 0.094
CC half 0.996 0.997 0.139 0.995
Anomalous completeness 94.3 98.0 86.8 55.2
Anomalous multiplicity 1.9 2.0 1.6 1.6
Anomalous correlation -0.017 0.017 -0.021 -0.021
Anomalous slope 1.006
dF/F 0.124
dI/s(dI) 0.961
Total observations 121474 6705 4777 174263
Total unique 34173 1784 1666 62208
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
