The following parameters have been modified:

refinement {
  parameterisation {
    crystal {
      scan_varying = True
    }
  }
}
input {
  experiments = bravais_setting_9.json
  reflections = indexed.pickle
}

Configuring refiner

Summary statistics for 113247 observations matched to predictions:
--------------------------------------------------------------------------
|                   | Min     | Q1       | Med        | Q3      | Max    |
--------------------------------------------------------------------------
| Xc - Xo (mm)      | -0.5257 | -0.03392 | -0.002959  | 0.03191 | 0.6438 |
| Yc - Yo (mm)      | -1.402  | -0.03054 | -0.001345  | 0.02846 | 1.257  |
| Phic - Phio (deg) | -1.409  | -0.01535 | -0.0008392 | 0.01382 | 0.9103 |
| X weights         | 135.2   | 371.6    | 393.4      | 402.6   | 405.6  |
| Y weights         | 153.1   | 361.8    | 389        | 401.2   | 405.6  |
| Phi weights       | 318.9   | 519.5    | 530.4      | 533.3   | 533.3  |
--------------------------------------------------------------------------

11434 reflections have been flagged as outliers

Summary statistics for 101813 observations matched to predictions:
----------------------------------------------------------------------------
|                   | Min      | Q1       | Med        | Q3      | Max     |
----------------------------------------------------------------------------
| Xc - Xo (mm)      | -0.1536  | -0.03252 | -0.002648  | 0.03021 | 0.1385  |
| Yc - Yo (mm)      | -0.1259  | -0.02752 | -0.0008168 | 0.02679 | 0.1165  |
| Phic - Phio (deg) | -0.05984 | -0.01327 | -0.0003616 | 0.01312 | 0.06268 |
| X weights         | 135.2    | 377.6    | 395.1      | 402.9   | 405.6   |
| Y weights         | 153.1    | 369.3    | 391.6      | 401.8   | 405.6   |
| Phi weights       | 318.9    | 519.2    | 529.8      | 533.3   | 533.3   |
----------------------------------------------------------------------------

Performing refinement...

Refinement steps:
------------------------------------------------
| Step | Nref | RMSD_X   | RMSD_Y   | RMSD_Phi |
|      |      | (mm)     | (mm)     | (deg)    |
------------------------------------------------
| 0    | 8099 | 0.045699 | 0.039879 | 0.019944 |
| 1    | 8099 | 0.04521  | 0.038045 | 0.019945 |
| 2    | 8099 | 0.045239 | 0.037898 | 0.019908 |
| 3    | 8099 | 0.045257 | 0.037767 | 0.01988  |
| 4    | 8099 | 0.045264 | 0.037683 | 0.019781 |
| 5    | 8099 | 0.045269 | 0.037656 | 0.019627 |
| 6    | 8099 | 0.045271 | 0.037653 | 0.019546 |
| 7    | 8099 | 0.045271 | 0.037653 | 0.019535 |
| 8    | 8099 | 0.045271 | 0.037652 | 0.019534 |
------------------------------------------------
RMSD no longer decreasing

RMSDs by experiment:
--------------------------------------------
| Exp | Nref | RMSD_X | RMSD_Y  | RMSD_Z   |
|     |      | (px)   | (px)    | (images) |
--------------------------------------------
| 0   | 8099 | 0.2632 | 0.21891 | 0.13022  |
--------------------------------------------
Saving refined experiments to refined_experiments.json
Updating predictions for indexed reflections
Saving reflections with updated predictions to refined.pickle