From 2511f05d863fe04caec47619dadc679c26c6857d Mon Sep 17 00:00:00 2001 From: DLS Jenkins Date: Sat, 13 Apr 2024 08:18:56 +0100 Subject: [PATCH] update generated tutorial data (master) --- .../master/betalactamase/dials.find_spots.log | 2 +- .../master/betalactamase/dials.import.log | 2 +- .../master/betalactamase/dials.index.log | 2 +- .../master/betalactamase/dials.integrate.log | 30 ++++++------- .../master/betalactamase/dials.refine.log | 4 +- .../dials.refine_bravais_settings.log | 2 +- .../master/betalactamase/dials.reindex.log | 2 +- .../master/betalactamase/dials.report.log | 2 +- .../master/betalactamase/dials.scale.log | 12 ++--- .../master/betalactamase/dials.scale_cut.log | 12 ++--- .../master/betalactamase/dials.symmetry.log | 2 +- tutorial_data/master/last_update | 2 +- .../mpro_x0692/dials.estimate_resolution.log | 2 +- .../master/mpro_x0692/dials.find_spots.log | 2 +- .../master/mpro_x0692/dials.import.log | 2 +- .../master/mpro_x0692/dials.index.log | 2 +- .../master/mpro_x0692/dials.integrate.log | 30 ++++++------- .../master/mpro_x0692/dials.refine.log | 4 +- .../dials.refine_bravais_settings.log | 2 +- .../master/mpro_x0692/dials.reindex.log | 2 +- .../master/mpro_x0692/dials.report.log | 4 +- .../master/mpro_x0692/dials.scale.log | 12 ++--- .../master/mpro_x0692/dials.scale_cut.log | 12 ++--- .../master/mpro_x0692/dials.sv_refine.log | 4 +- .../master/mpro_x0692/dials.symmetry.log | 2 +- .../master/multi_crystal/dials.cosym.log | 2 +- .../dials.estimate_resolution.log | 2 +- .../master/multi_crystal/dials.merge.log | 4 +- .../master/multi_crystal/dials.scale.log | 12 ++--- .../master/multi_crystal/dials.scale_cut.log | 12 ++--- .../multi_crystal/dials.scale_exclude.log | 12 ++--- .../master/multi_crystal/dials.symmetry.log | 2 +- .../master/multi_crystal/xia2.multiplex.html | 44 +++++++++---------- .../master/multi_crystal/xia2.multiplex.log | 4 +- .../master/thaumatin/dials.export.log | 4 +- .../master/thaumatin/dials.find_spots.log | 2 +- .../master/thaumatin/dials.import.log | 2 +- .../master/thaumatin/dials.index.log | 2 +- .../master/thaumatin/dials.integrate.log | 30 ++++++------- .../master/thaumatin/dials.refine.log | 4 +- .../dials.refine_bravais_settings.log | 2 +- .../master/thaumatin/dials.reindex.log | 2 +- .../master/thaumatin/dials.report.log | 8 ++-- .../master/thaumatin/dials.sv_refine.log | 4 +- 44 files changed, 154 insertions(+), 154 deletions(-) diff --git a/tutorial_data/master/betalactamase/dials.find_spots.log b/tutorial_data/master/betalactamase/dials.find_spots.log index 8b0baebf..31fe6c1d 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index ec905ada..9e2b6f11 100644 --- a/tutorial_data/master/betalactamase/dials.import.log +++ b/tutorial_data/master/betalactamase/dials.import.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index c0844d73..2c0b65ea 100644 --- a/tutorial_data/master/betalactamase/dials.index.log +++ b/tutorial_data/master/betalactamase/dials.index.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 18a74914..7245cea9 100644 --- a/tutorial_data/master/betalactamase/dials.integrate.log +++ b/tutorial_data/master/betalactamase/dials.integrate.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: integration { mp { @@ -133,8 +133,8 @@ Modelling reflection profiles Split 13 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.0 GB Processing reflections in the following blocks of images: @@ -846,12 +846,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 61.07 seconds | -| Extract time | 0.64 seconds | -| Pre-process time | 0.12 seconds | -| Process time | 28.91 seconds | +| Read time | 60.62 seconds | +| Extract time | 0.62 seconds | +| Pre-process time | 0.11 seconds | +| Process time | 26.72 seconds | | Post-process time | 0.00 seconds | -| Total time | 91.02 seconds | +| Total time | 88.38 seconds | +-------------------+---------------+ ================================================================================ @@ -861,8 +861,8 @@ Integrating reflections Split 109 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.0 GB Processing reflections in the following blocks of images: @@ -1702,12 +1702,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 63.77 seconds | -| Extract time | 2.83 seconds | -| Pre-process time | 0.48 seconds | -| Process time | 148.34 seconds | +| Read time | 59.47 seconds | +| Extract time | 2.54 seconds | +| Pre-process time | 0.44 seconds | +| Process time | 136.61 seconds | | Post-process time | 0.00 seconds | -| Total time | 216.25 seconds | +| Total time | 200.06 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 index 751c88a6..a6eb7951 100644 --- a/tutorial_data/master/betalactamase/dials.refine.log +++ b/tutorial_data/master/betalactamase/dials.refine.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { @@ -7,7 +7,7 @@ input { } Configuring refiner -Setting outlier.nproc=72 +Setting outlier.nproc=32 Summary statistics for 106891 observations matched to predictions: +-------------------+--------+----------+------------+---------+--------+ diff --git a/tutorial_data/master/betalactamase/dials.refine_bravais_settings.log b/tutorial_data/master/betalactamase/dials.refine_bravais_settings.log index 111cdecf..07b6dc85 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 728cbe61..33f81516 100644 --- a/tutorial_data/master/betalactamase/dials.reindex.log +++ b/tutorial_data/master/betalactamase/dials.reindex.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 32019fa9..cc789b02 100644 --- 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..........................0.07s + Selected 311827 summation-integrated reflections..........................0.06s 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 diff --git a/tutorial_data/master/betalactamase/dials.scale.log b/tutorial_data/master/betalactamase/dials.scale.log index 241ec73d..dd9357f3 100644 --- a/tutorial_data/master/betalactamase/dials.scale.log +++ b/tutorial_data/master/betalactamase/dials.scale.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 3.61 +Time taken for refinement 3.41 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 1.03 +Time taken for refinement 0.95 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 3.66 +Time taken for refinement 3.46 Refinement steps: +--------+--------+----------+ @@ -198,7 +198,7 @@ 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 1.15 +Time taken for refinement 1.09 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: 19.1684s +Total time taken: 17.9283s ================================================================================ diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.log b/tutorial_data/master/betalactamase/dials.scale_cut.log index 3dde59c3..795eae0c 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 0.96 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 0.67 +Time taken for refinement 0.63 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 2.37 +Time taken for refinement 2.28 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 1.12 +Time taken for refinement 1.09 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: 13.5319s +Total time taken: 12.7259s ================================================================================ diff --git a/tutorial_data/master/betalactamase/dials.symmetry.log b/tutorial_data/master/betalactamase/dials.symmetry.log index 4fe35299..f5026d77 100644 --- a/tutorial_data/master/betalactamase/dials.symmetry.log +++ b/tutorial_data/master/betalactamase/dials.symmetry.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/last_update b/tutorial_data/master/last_update index 72c1be53..f6640632 100644 --- a/tutorial_data/master/last_update +++ b/tutorial_data/master/last_update @@ -1 +1 @@ -2024-W13 +2024-W14 diff --git a/tutorial_data/master/mpro_x0692/dials.estimate_resolution.log b/tutorial_data/master/mpro_x0692/dials.estimate_resolution.log index fe37667a..19efdc49 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index ee432b23..87ddd58c 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 9bcd89e5..2dbeea21 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 77a6cb33..8f5b7429 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 6869f7f3..7c796a36 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: integration { mp { @@ -123,8 +123,8 @@ Modelling reflection profiles Split 27 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.0 GB Processing reflections in the following blocks of images: @@ -548,12 +548,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 18.51 seconds | -| Extract time | 0.60 seconds | -| Pre-process time | 0.02 seconds | -| Process time | 9.45 seconds | +| Read time | 15.29 seconds | +| Extract time | 0.41 seconds | +| Pre-process time | 0.03 seconds | +| Process time | 8.50 seconds | | Post-process time | 0.00 seconds | -| Total time | 28.49 seconds | +| Total time | 24.36 seconds | +-------------------+---------------+ ================================================================================ @@ -563,8 +563,8 @@ Integrating reflections Split 681 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.3 GB Processing reflections in the following blocks of images: @@ -1084,12 +1084,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 22.82 seconds | -| Extract time | 6.61 seconds | -| Pre-process time | 0.27 seconds | -| Process time | 141.42 seconds | +| Read time | 16.39 seconds | +| Extract time | 6.04 seconds | +| Pre-process time | 0.26 seconds | +| Process time | 129.15 seconds | | Post-process time | 0.00 seconds | -| Total time | 172.12 seconds | +| Total time | 152.77 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 index adc684cd..4b74c142 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: refinement { @@ -12,7 +12,7 @@ input { } Configuring refiner -Setting outlier.nproc=72 +Setting outlier.nproc=32 Summary statistics for 20973 observations matched to predictions: +-------------------+---------+----------+-----------+---------+--------+ diff --git a/tutorial_data/master/mpro_x0692/dials.refine_bravais_settings.log b/tutorial_data/master/mpro_x0692/dials.refine_bravais_settings.log index 34386168..6d856d5d 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index b0b2a11e..0fb2e9b5 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 index 94bceac4..fe5fe872 100644 --- a/tutorial_data/master/mpro_x0692/dials.report.log +++ b/tutorial_data/master/mpro_x0692/dials.report.log @@ -9,7 +9,7 @@ Analysing strong spots Selected 16901 strong reflections.........................................0.01s Analysing reflection centroids Removing 3840 partial reflections - Selected 164996 summation-integrated reflections..........................0.04s + Selected 164996 summation-integrated reflections..........................0.03s 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 166941 integrated reflections....................................0.04s + Selected 166941 integrated reflections....................................0.03s 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 index 8d643845..b10fee8b 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 7.57 +Time taken for refinement 6.88 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 3.32 +Time taken for refinement 3.02 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 4.69 +Time taken for refinement 4.22 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 0.98 +Time taken for refinement 0.87 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: 22.4983s +Total time taken: 20.3514s ================================================================================ diff --git a/tutorial_data/master/mpro_x0692/dials.scale_cut.log b/tutorial_data/master/mpro_x0692/dials.scale_cut.log index a81ea476..e72506a7 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release 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 1.25 +Time taken for refinement 1.14 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 0.72 +Time taken for refinement 0.65 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 2.58 +Time taken for refinement 2.34 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 0.92 +Time taken for refinement 0.89 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: 9.3384s +Total time taken: 8.6065s ================================================================================ diff --git a/tutorial_data/master/mpro_x0692/dials.sv_refine.log b/tutorial_data/master/mpro_x0692/dials.sv_refine.log index 5839c0a5..e8b1b0b8 100644 --- 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.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: refinement { @@ -12,7 +12,7 @@ input { } Configuring refiner -Setting outlier.nproc=72 +Setting outlier.nproc=32 Summary statistics for 20972 observations matched to predictions: +-------------------+---------+----------+-----------+---------+-------+ diff --git a/tutorial_data/master/mpro_x0692/dials.symmetry.log b/tutorial_data/master/mpro_x0692/dials.symmetry.log index 3b960c18..d2e27457 100644 --- a/tutorial_data/master/mpro_x0692/dials.symmetry.log +++ b/tutorial_data/master/mpro_x0692/dials.symmetry.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: best_monoclinic_beta = False diff --git a/tutorial_data/master/multi_crystal/dials.cosym.log b/tutorial_data/master/multi_crystal/dials.cosym.log index c03e8a70..fdaf42d9 100644 --- a/tutorial_data/master/multi_crystal/dials.cosym.log +++ b/tutorial_data/master/multi_crystal/dials.cosym.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/multi_crystal/dials.estimate_resolution.log b/tutorial_data/master/multi_crystal/dials.estimate_resolution.log index 9d5cb520..2b496d27 100644 --- a/tutorial_data/master/multi_crystal/dials.estimate_resolution.log +++ b/tutorial_data/master/multi_crystal/dials.estimate_resolution.log @@ -5,7 +5,7 @@ input { reflections = scaled.refl } -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release Detected existence of a multi-dataset reflection table containing 4 datasets. diff --git a/tutorial_data/master/multi_crystal/dials.merge.log b/tutorial_data/master/multi_crystal/dials.merge.log index f1e3c320..e74d329d 100644 --- a/tutorial_data/master/multi_crystal/dials.merge.log +++ b/tutorial_data/master/multi_crystal/dials.merge.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { @@ -295,7 +295,7 @@ Number of crystals: 2 Number of Miller indices: 20799 Resolution range: 68.3603 1.78117 History: - From DIALS 3.dev.1109-g5dd0b6cbf, run on 2024-04-06 at 08:20:45 BST (2024-04-06 + From DIALS 3.dev.1091-g5dd0b6cbf-release, run on 2024-04-13 at 08:18:53 BST (20 Crystal 1: Name: HKL_base Project: HKL_base diff --git a/tutorial_data/master/multi_crystal/dials.scale.log b/tutorial_data/master/multi_crystal/dials.scale.log index c3bedfc8..56e2ec4f 100644 --- a/tutorial_data/master/multi_crystal/dials.scale.log +++ b/tutorial_data/master/multi_crystal/dials.scale.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { experiments = symmetrized.expt @@ -227,7 +227,7 @@ Completed configuration of MultiScaler. 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 31.83 +Time taken for refinement 26.56 Refinement steps: +--------+--------+----------+ @@ -402,7 +402,7 @@ Combined outlier rejection has been performed across multiple datasets, 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 3.40 +Time taken for refinement 2.84 Refinement steps: +--------+--------+----------+ @@ -464,7 +464,7 @@ 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 14.99 +Time taken for refinement 14.35 Refinement steps: +--------+--------+----------+ @@ -487,7 +487,7 @@ 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 3.63 +Time taken for refinement 3.52 Refinement steps: +--------+--------+----------+ @@ -541,7 +541,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 60.9367s +Total time taken: 53.6186s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_cut.log b/tutorial_data/master/multi_crystal/dials.scale_cut.log index e7434e12..7877c97c 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_cut.log +++ b/tutorial_data/master/multi_crystal/dials.scale_cut.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: cut_data { d_min = 1.78 @@ -222,7 +222,7 @@ Completed configuration of MultiScaler. 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 1.67 +Time taken for refinement 1.54 Refinement steps: +--------+--------+----------+ @@ -266,7 +266,7 @@ Combined outlier rejection has been performed across multiple datasets, 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 1.44 +Time taken for refinement 1.33 Refinement steps: +--------+--------+----------+ @@ -320,7 +320,7 @@ 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 11.46 +Time taken for refinement 10.86 Refinement steps: +--------+--------+----------+ @@ -341,7 +341,7 @@ 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 3.72 +Time taken for refinement 3.53 Refinement steps: +--------+--------+----------+ @@ -395,7 +395,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 24.7065s +Total time taken: 23.1749s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_exclude.log b/tutorial_data/master/multi_crystal/dials.scale_exclude.log index efce952a..092e4f63 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_exclude.log +++ b/tutorial_data/master/multi_crystal/dials.scale_exclude.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: cut_data { d_min = 1.78 @@ -222,7 +222,7 @@ Completed configuration of MultiScaler. 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 0.94 +Time taken for refinement 0.77 Refinement steps: +--------+--------+----------+ @@ -262,7 +262,7 @@ Combined outlier rejection has been performed across multiple datasets, 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 0.92 +Time taken for refinement 0.76 Refinement steps: +--------+--------+----------+ @@ -313,7 +313,7 @@ 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 10.94 +Time taken for refinement 8.98 Refinement steps: +--------+--------+----------+ @@ -333,7 +333,7 @@ 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 4.27 +Time taken for refinement 3.50 Refinement steps: +--------+--------+----------+ @@ -387,7 +387,7 @@ The reflection table variances have been adjusted to account for the uncertainty in the scaling models for all datasets Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) -Total time taken: 23.8113s +Total time taken: 19.7634s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.symmetry.log b/tutorial_data/master/multi_crystal/dials.symmetry.log index bfa1c02d..30c13edc 100644 --- a/tutorial_data/master/multi_crystal/dials.symmetry.log +++ b/tutorial_data/master/multi_crystal/dials.symmetry.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: laue_group = None diff --git a/tutorial_data/master/multi_crystal/xia2.multiplex.html b/tutorial_data/master/multi_crystal/xia2.multiplex.html index e730d160..3ad58c87 100644 --- a/tutorial_data/master/multi_crystal/xia2.multiplex.html +++ b/tutorial_data/master/multi_crystal/xia2.multiplex.html @@ -983,7 +983,7 @@

@@ -1001,7 +1001,7 @@

@@ -1055,7 +1055,7 @@

@@ -1724,7 +1724,7 @@

@@ -1742,7 +1742,7 @@

@@ -1904,7 +1904,7 @@

@@ -2055,7 +2055,7 @@

@@ -2157,7 +2157,7 @@

Cosym coordinates

@@ -3629,7 +3629,7 @@

- 9.501 + 9.502 @@ -4194,7 +4194,7 @@

CC½ vs resolution

@@ -4212,7 +4212,7 @@

CC½ vs resolution

@@ -4230,7 +4230,7 @@

CC½ vs resolution

@@ -4248,7 +4248,7 @@

CC½ vs resolution

@@ -4317,7 +4317,7 @@

@@ -4335,7 +4335,7 @@

@@ -4371,7 +4371,7 @@

@@ -4389,7 +4389,7 @@

@@ -4407,7 +4407,7 @@

@@ -4595,7 +4595,7 @@

@@ -4619,15 +4619,15 @@

- + - + - + diff --git a/tutorial_data/master/multi_crystal/xia2.multiplex.log b/tutorial_data/master/multi_crystal/xia2.multiplex.log index 523ad82b..fc04cb54 100644 --- a/tutorial_data/master/multi_crystal/xia2.multiplex.log +++ b/tutorial_data/master/multi_crystal/xia2.multiplex.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { @@ -74,7 +74,7 @@ Resolution shells: | 1.92 - 1.88 | 1174 | 719 | 1.63 | 60.27 | 29.2 | 5 | 0.142 | 0.188 | 0.122 | 0.252 | 0.947* | 0.947 | | 1.88 - 1.84 | 819 | 566 | 1.45 | 49 | 25.7 | 4.2 | 0.162 | 0.22 | 0.148 | 0.368 | 0.937* | 0 | | 1.84 - 1.81 | 487 | 381 | 1.28 | 31.54 | 23.3 | 3.6 | 0.196 | 0.269 | 0.184 | 0.325 | 0.903* | 0 | -| 1.81 - 1.78 | 137 | 126 | 1.09 | 10.61 | 15.8 | 2.4 | 0.155 | 0.212 | 0.145 | 9.501 | 0.958* | 0 | +| 1.81 - 1.78 | 137 | 126 | 1.09 | 10.61 | 15.8 | 2.4 | 0.155 | 0.212 | 0.145 | 9.502 | 0.958* | 0 | +------------------+----------+-------------+----------------+----------------+----------+---------------+----------+---------+--------+---------+--------+---------+ Intensity correlation clustering summary: diff --git a/tutorial_data/master/thaumatin/dials.export.log b/tutorial_data/master/thaumatin/dials.export.log index 9c7fd1f1..3fa80116 100644 --- a/tutorial_data/master/thaumatin/dials.export.log +++ b/tutorial_data/master/thaumatin/dials.export.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { @@ -57,4 +57,4 @@ ROT R 1 82.0002 162.999 LP R 1 0.00281027 0.759215 QE R 1 0.714949 0.856056 History (1 lines): -From DIALS 3.dev.1109-g5dd0b6cbf, run on 2024-04-06 at 08:15:12 BST (2024-04-06 at 07:15:12 GMT) +From DIALS 3.dev.1091-g5dd0b6cbf-release, run on 2024-04-13 at 08:14:06 BST (2024-04-13 at 07:14:06 GMT) diff --git a/tutorial_data/master/thaumatin/dials.find_spots.log b/tutorial_data/master/thaumatin/dials.find_spots.log index d908df06..a1d86413 100644 --- a/tutorial_data/master/thaumatin/dials.find_spots.log +++ b/tutorial_data/master/thaumatin/dials.find_spots.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: spotfinder { diff --git a/tutorial_data/master/thaumatin/dials.import.log b/tutorial_data/master/thaumatin/dials.import.log index 3edfeffc..78f11cc9 100644 --- a/tutorial_data/master/thaumatin/dials.import.log +++ b/tutorial_data/master/thaumatin/dials.import.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/thaumatin/dials.index.log b/tutorial_data/master/thaumatin/dials.index.log index e7599bd6..0bd56644 100644 --- a/tutorial_data/master/thaumatin/dials.index.log +++ b/tutorial_data/master/thaumatin/dials.index.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/thaumatin/dials.integrate.log b/tutorial_data/master/thaumatin/dials.integrate.log index da181f65..16c061ed 100644 --- a/tutorial_data/master/thaumatin/dials.integrate.log +++ b/tutorial_data/master/thaumatin/dials.integrate.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: integration { mp { @@ -128,8 +128,8 @@ Modelling reflection profiles Split 61 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.0 GB Processing reflections in the following blocks of images: @@ -346,12 +346,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 33.74 seconds | -| Extract time | 1.02 seconds | -| Pre-process time | 0.14 seconds | -| Process time | 32.49 seconds | +| Read time | 19.82 seconds | +| Extract time | 0.90 seconds | +| Pre-process time | 0.13 seconds | +| Process time | 28.99 seconds | | Post-process time | 0.00 seconds | -| Total time | 67.61 seconds | +| Total time | 50.07 seconds | +-------------------+---------------+ ================================================================================ @@ -361,8 +361,8 @@ Integrating reflections Split 374 reflections overlapping job boundaries Memory situation report: - Available system memory : 134.6 GB - Maximum memory for processing : 121.1 GB + Available system memory : 201.2 GB + Maximum memory for processing : 181.1 GB Memory required per process : 0.0 GB Processing reflections in the following blocks of images: @@ -1022,12 +1022,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 35.79 seconds | -| Extract time | 4.51 seconds | -| Pre-process time | 0.54 seconds | -| Process time | 124.16 seconds | +| Read time | 20.82 seconds | +| Extract time | 3.41 seconds | +| Pre-process time | 0.47 seconds | +| Process time | 112.41 seconds | | Post-process time | 0.00 seconds | -| Total time | 166.24 seconds | +| Total time | 137.92 seconds | +-------------------+----------------+ Removing 40904 unintegrated reflections of 384161 total diff --git a/tutorial_data/master/thaumatin/dials.refine.log b/tutorial_data/master/thaumatin/dials.refine.log index 66d05ba6..294ae751 100644 --- a/tutorial_data/master/thaumatin/dials.refine.log +++ b/tutorial_data/master/thaumatin/dials.refine.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: refinement { @@ -12,7 +12,7 @@ input { } Configuring refiner -Setting outlier.nproc=72 +Setting outlier.nproc=32 Summary statistics for 125120 observations matched to predictions: +-------------------+--------+----------+------------+---------+-------+ diff --git a/tutorial_data/master/thaumatin/dials.refine_bravais_settings.log b/tutorial_data/master/thaumatin/dials.refine_bravais_settings.log index f730bff8..33a1d7e3 100644 --- a/tutorial_data/master/thaumatin/dials.refine_bravais_settings.log +++ b/tutorial_data/master/thaumatin/dials.refine_bravais_settings.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/thaumatin/dials.reindex.log b/tutorial_data/master/thaumatin/dials.reindex.log index 78e31be5..28cdd91f 100644 --- a/tutorial_data/master/thaumatin/dials.reindex.log +++ b/tutorial_data/master/thaumatin/dials.reindex.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: input { diff --git a/tutorial_data/master/thaumatin/dials.report.log b/tutorial_data/master/thaumatin/dials.report.log index 98a58002..7d3f8ab7 100644 --- a/tutorial_data/master/thaumatin/dials.report.log +++ b/tutorial_data/master/thaumatin/dials.report.log @@ -6,17 +6,17 @@ input { } Analysing strong spots - Selected 110392 strong reflections........................................0.04s + Selected 110392 strong reflections........................................0.03s Analysing reflection centroids Removing 9990 partial reflections - Selected 323344 summation-integrated reflections..........................0.10s + Selected 323344 summation-integrated reflections..........................0.06s 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 Analysing centroid differences vs phi with I/Sigma > 10 Analysing reflection intensities Removing 41644 reflections with intensity <= 0 - Selected 301613 integrated reflections....................................0.09s + Selected 301613 integrated reflections....................................0.05s Analysing distribution of I/Sigma Analysing distribution of I/Sigma vs xy Analysing distribution of I/Sigma vs xy @@ -24,7 +24,7 @@ Analysing reflection intensities Analysing distribution of partialities Analysing QE map Analysing reference profiles - Selected 324852 integrated reflections....................................0.11s + Selected 324852 integrated reflections....................................0.06s Analysing reference profile distribution vs x/y Analysing reference profile distribution vs z Analysing reflection correlations vs resolution diff --git a/tutorial_data/master/thaumatin/dials.sv_refine.log b/tutorial_data/master/thaumatin/dials.sv_refine.log index ccbfee36..b6250bec 100644 --- a/tutorial_data/master/thaumatin/dials.sv_refine.log +++ b/tutorial_data/master/thaumatin/dials.sv_refine.log @@ -1,4 +1,4 @@ -DIALS 3.dev.1109-g5dd0b6cbf +DIALS 3.dev.1091-g5dd0b6cbf-release The following parameters have been modified: refinement { @@ -12,7 +12,7 @@ input { } Configuring refiner -Setting outlier.nproc=72 +Setting outlier.nproc=32 Summary statistics for 125121 observations matched to predictions: +-------------------+--------+----------+------------+---------+-------+