update generated tutorial data (master)

dials · Nov 9, 2024 · 452ca6b · 452ca6b
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diff --git a/tutorial_data/master/betalactamase/dials.find_spots.log b/tutorial_data/master/betalactamase/dials.find_spots.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 spotfinder {

diff --git a/tutorial_data/master/betalactamase/dials.import.log b/tutorial_data/master/betalactamase/dials.import.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/betalactamase/dials.index.log b/tutorial_data/master/betalactamase/dials.index.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/betalactamase/dials.integrate.log b/tutorial_data/master/betalactamase/dials.integrate.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 integration {
   mp {
@@ -846,12 +846,12 @@ Processing reflections in the following blocks of images:
 
 Timing information for reference profile formation
 +-------------------+---------------+
-| Read time         | 59.37 seconds |
-| Extract time      | 0.40 seconds  |
+| Read time         | 64.98 seconds |
+| Extract time      | 0.54 seconds  |
 | Pre-process time  | 0.11 seconds  |
-| Process time      | 30.90 seconds |
+| Process time      | 31.26 seconds |
 | Post-process time | 0.00 seconds  |
-| Total time        | 90.96 seconds |
+| Total time        | 97.13 seconds |
 +-------------------+---------------+
 
 ================================================================================
@@ -1702,12 +1702,12 @@ Processing reflections in the following blocks of images:
 
 Timing information for integration
 +-------------------+----------------+
-| Read time         | 57.00 seconds  |
-| Extract time      | 2.66 seconds   |
-| Pre-process time  | 0.46 seconds   |
-| Process time      | 156.56 seconds |
+| Read time         | 63.27 seconds  |
+| Extract time      | 2.87 seconds   |
+| Pre-process time  | 0.47 seconds   |
+| Process time      | 156.80 seconds |
 | Post-process time | 0.00 seconds   |
-| Total time        | 217.60 seconds |
+| Total time        | 224.26 seconds |
 +-------------------+----------------+
 
 Removing 41622 unintegrated reflections of 368699 total

diff --git a/tutorial_data/master/betalactamase/dials.refine.log b/tutorial_data/master/betalactamase/dials.refine.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/betalactamase/dials.refine_bravais_settings.log b/tutorial_data/master/betalactamase/dials.refine_bravais_settings.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/betalactamase/dials.reindex.log b/tutorial_data/master/betalactamase/dials.reindex.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 change_of_basis_op = "a+b,-a+b,c"

diff --git a/tutorial_data/master/betalactamase/dials.report.log b/tutorial_data/master/betalactamase/dials.report.log
@@ -9,7 +9,7 @@ Analysing strong spots
  Selected 95428 strong reflections.........................................0.03s
 Analysing reflection centroids
  Removing 2059 partial reflections
- Selected 311827 summation-integrated reflections..........................0.06s
+ Selected 311827 summation-integrated reflections..........................0.07s
  Analysing centroid differences with I/Sigma > 10
  Analysing centroid differences in x/y with I/Sigma > 10
  Analysing centroid differences in z with I/Sigma > 10
@@ -24,7 +24,7 @@ Analysing reflection intensities
  Analysing distribution of partialities
  Analysing QE map
 Analysing reference profiles
- Selected 312176 integrated reflections....................................0.03s
+ Selected 312176 integrated reflections....................................0.04s
  Analysing reference profile distribution vs x/y
  Analysing reference profile distribution vs z
  Analysing reflection correlations vs resolution

diff --git a/tutorial_data/master/betalactamase/dials.scale.log b/tutorial_data/master/betalactamase/dials.scale.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 input {
   experiments = symmetrized.expt
@@ -67,7 +67,7 @@ Completed preprocessing and initialisation for this dataset.
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 3.54
+Time taken for refinement 3.58
 
 Refinement steps:
 +--------+--------+----------+
@@ -125,7 +125,7 @@ A round of outlier rejection has been performed,
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 1.00
+Time taken for refinement 1.02
 
 Refinement steps:
 +--------+--------+----------+
@@ -177,7 +177,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 3.55
+Time taken for refinement 3.58
 
 Refinement steps:
 +--------+--------+----------+
@@ -248,7 +248,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 The reflection table variances have been adjusted to account for the
 uncertainty in the scaling model
 
-Total time taken: 18.6986s 
+Total time taken: 19.0623s 
 
 ================================================================================
 

diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.log b/tutorial_data/master/betalactamase/dials.scale_cut.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 cut_data {
   d_min = 1.4
@@ -68,7 +68,7 @@ Completed preprocessing and initialisation for this dataset.
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 1.00
+Time taken for refinement 1.01
 
 Refinement steps:
 +--------+--------+----------+
@@ -111,7 +111,7 @@ A round of outlier rejection has been performed,
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 0.66
+Time taken for refinement 0.68
 
 Refinement steps:
 +--------+--------+----------+
@@ -161,7 +161,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 2.33
+Time taken for refinement 2.39
 
 Refinement steps:
 +--------+--------+----------+
@@ -180,7 +180,7 @@ RMSD no longer decreasing
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 1.11
+Time taken for refinement 1.13
 
 Refinement steps:
 +--------+--------+----------+
@@ -230,7 +230,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 The reflection table variances have been adjusted to account for the
 uncertainty in the scaling model
 
-Total time taken: 13.3445s 
+Total time taken: 13.7248s 
 
 ================================================================================
 

diff --git a/tutorial_data/master/betalactamase/dials.symmetry.log b/tutorial_data/master/betalactamase/dials.symmetry.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/last_update b/tutorial_data/master/last_update
@@ -1 +1 @@
-2024-W43
+2024-W44
diff --git a/tutorial_data/master/mpro_x0692/dials.estimate_resolution.log b/tutorial_data/master/mpro_x0692/dials.estimate_resolution.log
@@ -5,7 +5,7 @@ input {
   reflections = scaled.refl
 }
 
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 Read 176235 predicted reflections
 Selected 174263 scaled reflections
 Removing 47 Wilson outliers with E^2 >= 16.0

diff --git a/tutorial_data/master/mpro_x0692/dials.find_spots.log b/tutorial_data/master/mpro_x0692/dials.find_spots.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 spotfinder {

diff --git a/tutorial_data/master/mpro_x0692/dials.import.log b/tutorial_data/master/mpro_x0692/dials.import.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/mpro_x0692/dials.index.log b/tutorial_data/master/mpro_x0692/dials.index.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 input {

diff --git a/tutorial_data/master/mpro_x0692/dials.integrate.log b/tutorial_data/master/mpro_x0692/dials.integrate.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 integration {
   mp {
@@ -548,12 +548,12 @@ Processing reflections in the following blocks of images:
 
 Timing information for reference profile formation
 +-------------------+---------------+
-| Read time         | 16.97 seconds |
-| Extract time      | 0.41 seconds  |
+| Read time         | 20.17 seconds |
+| Extract time      | 0.36 seconds  |
 | Pre-process time  | 0.02 seconds  |
-| Process time      | 9.82 seconds  |
+| Process time      | 9.69 seconds  |
 | Post-process time | 0.00 seconds  |
-| Total time        | 27.41 seconds |
+| Total time        | 30.50 seconds |
 +-------------------+---------------+
 
 ================================================================================
@@ -1084,12 +1084,12 @@ Processing reflections in the following blocks of images:
 
 Timing information for integration
 +-------------------+----------------+
-| Read time         | 21.44 seconds  |
-| Extract time      | 6.46 seconds   |
+| Read time         | 23.26 seconds  |
+| Extract time      | 6.72 seconds   |
 | Pre-process time  | 0.27 seconds   |
-| Process time      | 147.16 seconds |
+| Process time      | 146.74 seconds |
 | Post-process time | 0.00 seconds   |
-| Total time        | 176.26 seconds |
+| Total time        | 178.05 seconds |
 +-------------------+----------------+
 
 Removing 22837 unintegrated reflections of 199395 total

diff --git a/tutorial_data/master/mpro_x0692/dials.refine.log b/tutorial_data/master/mpro_x0692/dials.refine.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 refinement {

diff --git a/tutorial_data/master/mpro_x0692/dials.refine_bravais_settings.log b/tutorial_data/master/mpro_x0692/dials.refine_bravais_settings.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 best_monoclinic_beta = False

diff --git a/tutorial_data/master/mpro_x0692/dials.reindex.log b/tutorial_data/master/mpro_x0692/dials.reindex.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 change_of_basis_op = "-b-2*c,-b,-a"

diff --git a/tutorial_data/master/mpro_x0692/dials.report.log b/tutorial_data/master/mpro_x0692/dials.report.log
@@ -24,7 +24,7 @@ Analysing reflection intensities
  Analysing distribution of partialities
  Analysing QE map
 Analysing reference profiles
- Selected 166941 integrated reflections....................................0.03s
+ Selected 166941 integrated reflections....................................0.04s
  Analysing reference profile distribution vs x/y
  Analysing reference profile distribution vs z
  Analysing reflection correlations vs resolution

diff --git a/tutorial_data/master/mpro_x0692/dials.scale.log b/tutorial_data/master/mpro_x0692/dials.scale.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 input {
   experiments = symmetrized.expt
@@ -67,7 +67,7 @@ Completed preprocessing and initialisation for this dataset.
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 7.24
+Time taken for refinement 7.16
 
 Refinement steps:
 +--------+--------+----------+
@@ -146,7 +146,7 @@ A round of outlier rejection has been performed,
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 3.16
+Time taken for refinement 3.15
 
 Refinement steps:
 +--------+--------+----------+
@@ -209,7 +209,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 4.49
+Time taken for refinement 4.34
 
 Refinement steps:
 +--------+--------+----------+
@@ -233,7 +233,7 @@ RMSD no longer decreasing
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 0.93
+Time taken for refinement 0.90
 
 Refinement steps:
 +--------+--------+----------+
@@ -283,7 +283,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 The reflection table variances have been adjusted to account for the
 uncertainty in the scaling model
 
-Total time taken: 21.6759s 
+Total time taken: 21.2869s 
 
 ================================================================================
 

diff --git a/tutorial_data/master/mpro_x0692/dials.scale_cut.log b/tutorial_data/master/mpro_x0692/dials.scale_cut.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 cut_data {
   d_min = 1.62
@@ -68,7 +68,7 @@ Completed preprocessing and initialisation for this dataset.
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 1.19
+Time taken for refinement 1.22
 
 Refinement steps:
 +--------+--------+----------+
@@ -111,7 +111,7 @@ A round of outlier rejection has been performed,
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with an LBFGS minimizer. 
 
-Time taken for refinement 0.68
+Time taken for refinement 0.71
 
 Refinement steps:
 +--------+--------+----------+
@@ -161,7 +161,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 2.70
+Time taken for refinement 2.52
 
 Refinement steps:
 +--------+--------+----------+
@@ -181,7 +181,7 @@ RMSD no longer decreasing
 Components to be refined in this cycle for all datasets: scale, decay, absorption
 Performing a round of scaling with a Levenberg-Marquardt minimizer.
 
-Time taken for refinement 1.01
+Time taken for refinement 0.94
 
 Refinement steps:
 +--------+--------+----------+
@@ -231,7 +231,7 @@ are expected to be ~1.0 for reliable errors (sigmas).
 The reflection table variances have been adjusted to account for the
 uncertainty in the scaling model
 
-Total time taken: 9.5982s 
+Total time taken: 9.2855s 
 
 ================================================================================
 

diff --git a/tutorial_data/master/mpro_x0692/dials.sv_refine.log b/tutorial_data/master/mpro_x0692/dials.sv_refine.log
@@ -1,4 +1,4 @@
-DIALS 3.dev.1223-g98884495f
+DIALS 3.dev.1230-g8e2c33c91
 The following parameters have been modified:
 
 refinement {