Table 1. Processing outcome on simulated PSI data with different protocols.
| Non-optimal spotfinding and indexing | Equation (1) only | Equations (1) and (2) | Best practice† | |||
|---|---|---|---|---|---|---|
| Protocol | 1 | 2 | 3 | 4 | 5 | 6 |
| Refinement target | ||||||
| Initial triclinic cell | Equation (1) | Equation (1) | Equation (1) | Equation (1) | Equation (2) | Equation (2) |
| Constrained hexagonal cell | Equation (1) | Equation (1) | Equation (1) | Equation (1) | Equation (1) | Equation (2) |
| Indexing practices | ||||||
| Spotfinder spot area (pixels) | 2 | 1 | 1 | 1 | 1 | 1 |
| Spotfinder method 2 cutoff (%) | 5 | 20 | 5 | 5 | 5 | 5 |
| Target unit cell | Provided | Provided | Not given | Provided | Provided | Provided |
| Indexing results | ||||||
| Total No. of images | 20000 | 20000 | 20000 | 20000 | 20000 | 20000 |
| No. of integrated and merged images | 19706 | 19490 | 18926 | 19608 | 19998 | 19984 |
| Model accuracy | ||||||
| R.m.s. Rz misorientation () | 0.039 | 0.041 | 0.040 | 0.017 | 0.017 | 0.017 |
| R.m.s. Rx + Ry misorientation () | 0.379 | 0.586 | 1.108 | 0.584 | 0.083 | 0.031 |
| R.m.s. total angular misorientation () | 0.381 | 0.588 | 1.109 | 0.584 | 0.085 | 0.035 |
| Median total angular misorientation () | 0.130 | 0.087 | 0.134 | 0.078 | 0.054 | 0.021 |
| No. of outliers >0.1 misoriented | 13085 | 9264 | 13136 | 7971 | 4566 | 172 |
| False Bragg predictions, 153.5 (%) | 65.0 | 54.3 | 64.7 | 51.6 | 40.0 | 9.1 |
| Unmodeled Bragg spots, 153.5 (%) | 15.4 | 10.9 | 13.3 | 10.4 | 10.0 | 8.0 |
| Half-width mosaicity‡ () (true value 0) | 0.101 | 0.080 | 0.098 | 0.050 | 0.025 | 0.000 |
| Mosaic block size‡ () (true value 4850) | 5160 | 4660 | 4960 | 4660 | 4780 | 5100 |
| Integrated data results | ||||||
| Individual image CC (%) | 51.6 | 54.1 | 50.6 | 56.3 | 61.2 | 70.1 |
| No. of measurements, 153.5 | 38398465 | 35264088 | 38755029 | 36948917 | 32210606 | 22817281 |
| Positive measurements, 153.5 | 26322687 | 25323211 | 26836439 | 26779348 | 24458975 | 19303707 |
| Negative measurements (%) | 31 | 28 | 31 | 28 | 24 | 15 |
| Structure-factor merging | ||||||
| Unique Miller indices, 153.5 | 92204 | 92204 | 92204 | 92204 | 92204 | 92204 |
| Multiplicity of observation | 286 | 275 | 291 | 290 | 265 | 209 |
| Completeness (%) | 100 | 100 | 100 | 100 | 100 | 100 |
| I/(I) | 33.4 | 36.0 | 33.8 | 38.0 | 40.9 | 46.0 |
| CCiso versus 1jb0 (based on intensities) (%) | 96.6 | 96.6 | 95.8 | 96.8 | 97.5 | 99.0 |
| R iso versus 1jb0 (based on intensities) (%) | 36.7 | 33.0 | 35.5 | 32.1 | 27.7 | 18.1 |
| Structure-factor quality tests | ||||||
| |L| (acentric theoretical = 0.5) | 0.270 | 0.299 | 0.282 | 0.301 | 0.320 | 0.358 |
| L 2 (acentric theoretical = 0.333) | 0.109 | 0.131 | 0.118 | 0.132 | 0.148 | 0.182 |
| P(Z) maximum deviation (acentric) | 0.263 | 0.223 | 0.245 | 0.222 | 0.197 | 0.154 |
| P(Z) maximum deviation (centric) | 0.364 | 0.332 | 0.341 | 0.330 | 0.306 | 0.243 |
†
cctbx.xfel now runs protocol 6 by default, while the other protocols may be accessed by changing the program parameters described at http://cci.lbl.gov/xfel.
‡
Half-width mosaicity and mosaic block size were fitted by the maximum-likelihood approach outlined in Appendix B. The values reported here are D eff and 1/, respectively, where is the average over all merged images.