From 9f264b815ba7b3f6deb35abb75a55bd404a86fd3 Mon Sep 17 00:00:00 2001 From: DLS Jenkins Date: Sat, 2 Dec 2023 08:20:29 +0000 Subject: [PATCH] update generated tutorial data (master) --- .../master/betalactamase/dials.integrate.log | 32 +++++++++---------- .../master/betalactamase/dials.scale.log | 10 +++--- .../master/betalactamase/dials.scale_cut.log | 6 ++-- tutorial_data/master/last_update | 2 +- .../master/mpro_x0692/dials.integrate.log | 32 +++++++++---------- .../master/mpro_x0692/dials.scale.log | 10 +++--- .../master/mpro_x0692/dials.scale_cut.log | 8 ++--- .../master/multi_crystal/dials.merge.log | 2 +- .../master/multi_crystal/dials.scale.log | 10 +++--- .../master/multi_crystal/dials.scale_cut.log | 10 +++--- .../multi_crystal/dials.scale_exclude.log | 8 ++--- .../master/thaumatin/dials.export.log | 2 +- .../master/thaumatin/dials.integrate.log | 30 ++++++++--------- 13 files changed, 81 insertions(+), 81 deletions(-) diff --git a/tutorial_data/master/betalactamase/dials.integrate.log b/tutorial_data/master/betalactamase/dials.integrate.log index 76aabd97..6af7795a 100644 --- a/tutorial_data/master/betalactamase/dials.integrate.log +++ b/tutorial_data/master/betalactamase/dials.integrate.log @@ -134,9 +134,9 @@ Modelling reflection profiles Memory situation report: Available system memory (excluding swap) :128.6 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.7 GB - Maximum memory for processing (including swap) :123.0 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.5 GB + Maximum memory for processing (including swap) :122.9 GB Maximum memory for processing (excluding swap) :115.7 GB no memory ulimit set Memory required per process : 0.0 GB @@ -850,12 +850,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 62.93 seconds | -| Extract time | 0.54 seconds | +| Read time | 63.08 seconds | +| Extract time | 0.47 seconds | | Pre-process time | 0.12 seconds | -| Process time | 29.27 seconds | +| Process time | 29.52 seconds | | Post-process time | 0.00 seconds | -| Total time | 93.10 seconds | +| Total time | 93.42 seconds | +-------------------+---------------+ ================================================================================ @@ -865,10 +865,10 @@ Integrating reflections Split 109 reflections overlapping job boundaries Memory situation report: - Available system memory (excluding swap) :128.5 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.6 GB - Maximum memory for processing (including swap) :123.0 GB + Available system memory (excluding swap) :128.6 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.5 GB + Maximum memory for processing (including swap) :122.9 GB Maximum memory for processing (excluding swap) :115.7 GB no memory ulimit set Memory required per process : 0.0 GB @@ -1710,12 +1710,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 64.51 seconds | -| Extract time | 2.52 seconds | -| Pre-process time | 0.47 seconds | -| Process time | 149.53 seconds | +| Read time | 64.85 seconds | +| Extract time | 2.89 seconds | +| Pre-process time | 0.49 seconds | +| Process time | 149.00 seconds | | Post-process time | 0.00 seconds | -| Total time | 218.28 seconds | +| Total time | 218.17 seconds | +-------------------+----------------+ Removing 41622 unintegrated reflections of 368699 total diff --git a/tutorial_data/master/betalactamase/dials.scale.log b/tutorial_data/master/betalactamase/dials.scale.log index bcf774f0..e75da7cc 100644 --- a/tutorial_data/master/betalactamase/dials.scale.log +++ b/tutorial_data/master/betalactamase/dials.scale.log @@ -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 3.65 +Time taken for refinement 3.61 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 1.08 +Time taken for refinement 1.03 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 3.77 +Time taken for refinement 3.62 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 1.19 +Time taken for refinement 1.14 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: 19.6713s +Total time taken: 18.9527s ================================================================================ diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.log b/tutorial_data/master/betalactamase/dials.scale_cut.log index 5126c52c..6292c736 100644 --- a/tutorial_data/master/betalactamase/dials.scale_cut.log +++ b/tutorial_data/master/betalactamase/dials.scale_cut.log @@ -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 2.39 +Time taken for refinement 2.38 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 1.13 +Time taken for refinement 1.12 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: 14.0014s +Total time taken: 13.4815s ================================================================================ diff --git a/tutorial_data/master/last_update b/tutorial_data/master/last_update index ae8220e9..b1c91960 100644 --- a/tutorial_data/master/last_update +++ b/tutorial_data/master/last_update @@ -1 +1 @@ -2023-W47 +2023-W48 diff --git a/tutorial_data/master/mpro_x0692/dials.integrate.log b/tutorial_data/master/mpro_x0692/dials.integrate.log index acd0615e..2031e554 100644 --- a/tutorial_data/master/mpro_x0692/dials.integrate.log +++ b/tutorial_data/master/mpro_x0692/dials.integrate.log @@ -124,10 +124,10 @@ Modelling reflection profiles Memory situation report: Available system memory (excluding swap) :128.8 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.9 GB - Maximum memory for processing (including swap) :123.2 GB - Maximum memory for processing (excluding swap) :115.9 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.8 GB + Maximum memory for processing (including swap) :123.1 GB + Maximum memory for processing (excluding swap) :116.0 GB no memory ulimit set Memory required per process : 0.0 GB @@ -552,12 +552,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 19.46 seconds | -| Extract time | 0.48 seconds | +| Read time | 18.80 seconds | +| Extract time | 0.43 seconds | | Pre-process time | 0.02 seconds | -| Process time | 9.48 seconds | +| Process time | 9.39 seconds | | Post-process time | 0.00 seconds | -| Total time | 29.55 seconds | +| Total time | 28.71 seconds | +-------------------+---------------+ ================================================================================ @@ -568,9 +568,9 @@ Integrating reflections Memory situation report: Available system memory (excluding swap) :128.8 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.9 GB - Maximum memory for processing (including swap) :123.2 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.8 GB + Maximum memory for processing (including swap) :123.1 GB Maximum memory for processing (excluding swap) :115.9 GB no memory ulimit set Memory required per process : 0.3 GB @@ -1092,12 +1092,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 25.92 seconds | -| Extract time | 7.43 seconds | -| Pre-process time | 0.29 seconds | -| Process time | 142.54 seconds | +| Read time | 23.54 seconds | +| Extract time | 6.50 seconds | +| Pre-process time | 0.28 seconds | +| Process time | 141.78 seconds | | Post-process time | 0.00 seconds | -| Total time | 177.18 seconds | +| Total time | 173.22 seconds | +-------------------+----------------+ Removing 22837 unintegrated reflections of 199395 total diff --git a/tutorial_data/master/mpro_x0692/dials.scale.log b/tutorial_data/master/mpro_x0692/dials.scale.log index a9f56e0d..32ece30e 100644 --- a/tutorial_data/master/mpro_x0692/dials.scale.log +++ b/tutorial_data/master/mpro_x0692/dials.scale.log @@ -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 7.23 +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 3.17 +Time taken for refinement 3.14 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 4.44 +Time taken for refinement 4.42 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 0.92 +Time taken for refinement 0.91 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: 21.4173s +Total time taken: 21.2997s ================================================================================ diff --git a/tutorial_data/master/mpro_x0692/dials.scale_cut.log b/tutorial_data/master/mpro_x0692/dials.scale_cut.log index abebb325..e67dd2f0 100644 --- a/tutorial_data/master/mpro_x0692/dials.scale_cut.log +++ b/tutorial_data/master/mpro_x0692/dials.scale_cut.log @@ -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 1.20 +Time taken for refinement 1.19 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 2.52 +Time taken for refinement 2.50 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 0.96 +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: 9.2594s +Total time taken: 9.0998s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.merge.log b/tutorial_data/master/multi_crystal/dials.merge.log index a2727e46..e8e2de77 100644 --- a/tutorial_data/master/multi_crystal/dials.merge.log +++ b/tutorial_data/master/multi_crystal/dials.merge.log @@ -295,7 +295,7 @@ Number of crystals: 2 Number of Miller indices: 20799 Resolution range: 68.3603 1.78117 History: - From DIALS 3.dev.1068-g8f16d0a9a, run on 2023-11-25 at 08:20:54 GMT + From DIALS 3.dev.1068-g8f16d0a9a, run on 2023-12-02 at 08:20:26 GMT 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 034d46d6..2c2cfacb 100644 --- a/tutorial_data/master/multi_crystal/dials.scale.log +++ b/tutorial_data/master/multi_crystal/dials.scale.log @@ -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 27.86 +Time taken for refinement 27.80 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 2.97 +Time taken for refinement 2.95 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 14.52 +Time taken for refinement 14.49 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 3.54 +Time taken for refinement 3.53 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: 55.5383s +Total time taken: 55.3844s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_cut.log b/tutorial_data/master/multi_crystal/dials.scale_cut.log index 01881fb5..1366adc4 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_cut.log +++ b/tutorial_data/master/multi_crystal/dials.scale_cut.log @@ -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 1.60 +Time taken for refinement 1.65 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 1.39 +Time taken for refinement 1.42 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 10.90 +Time taken for refinement 11.26 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 3.54 +Time taken for refinement 3.67 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: 23.6585s +Total time taken: 24.4361s ================================================================================ diff --git a/tutorial_data/master/multi_crystal/dials.scale_exclude.log b/tutorial_data/master/multi_crystal/dials.scale_exclude.log index 741f869d..eb73435c 100644 --- a/tutorial_data/master/multi_crystal/dials.scale_exclude.log +++ b/tutorial_data/master/multi_crystal/dials.scale_exclude.log @@ -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 0.81 +Time taken for refinement 0.96 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 9.04 +Time taken for refinement 9.57 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 3.52 +Time taken for refinement 4.24 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: 20.2308s +Total time taken: 22.0902s ================================================================================ diff --git a/tutorial_data/master/thaumatin/dials.export.log b/tutorial_data/master/thaumatin/dials.export.log index 2408648f..e17bcb28 100644 --- a/tutorial_data/master/thaumatin/dials.export.log +++ b/tutorial_data/master/thaumatin/dials.export.log @@ -29,7 +29,7 @@ Number of crystals: 1 Number of Miller indices: 324697 Resolution range: 150.003 1.16828 History: - From DIALS 3.dev.1068-g8f16d0a9a, run on 2023-11-25 at 08:15:33 GMT + From DIALS 3.dev.1068-g8f16d0a9a, run on 2023-12-02 at 08:15:09 GMT Crystal 1: Name: XTAL Project: DIALS diff --git a/tutorial_data/master/thaumatin/dials.integrate.log b/tutorial_data/master/thaumatin/dials.integrate.log index 11771544..0e74683f 100644 --- a/tutorial_data/master/thaumatin/dials.integrate.log +++ b/tutorial_data/master/thaumatin/dials.integrate.log @@ -129,10 +129,10 @@ Modelling reflection profiles Memory situation report: Available system memory (excluding swap) :128.5 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.6 GB - Maximum memory for processing (including swap) :123.0 GB - Maximum memory for processing (excluding swap) :115.7 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.5 GB + Maximum memory for processing (including swap) :122.8 GB + Maximum memory for processing (excluding swap) :115.6 GB no memory ulimit set Memory required per process : 0.0 GB @@ -350,12 +350,12 @@ Processing reflections in the following blocks of images: Timing information for reference profile formation +-------------------+---------------+ -| Read time | 33.13 seconds | -| Extract time | 0.72 seconds | +| Read time | 30.58 seconds | +| Extract time | 0.75 seconds | | Pre-process time | 0.14 seconds | -| Process time | 31.80 seconds | +| Process time | 32.07 seconds | | Post-process time | 0.00 seconds | -| Total time | 66.13 seconds | +| Total time | 63.75 seconds | +-------------------+---------------+ ================================================================================ @@ -366,9 +366,9 @@ Integrating reflections Memory situation report: Available system memory (excluding swap) :128.5 GB - Available swap memory : 8.1 GB - Available system memory (including swap) :136.6 GB - Maximum memory for processing (including swap) :122.9 GB + Available swap memory : 8.0 GB + Available system memory (including swap) :136.5 GB + Maximum memory for processing (including swap) :122.8 GB Maximum memory for processing (excluding swap) :115.7 GB no memory ulimit set Memory required per process : 0.0 GB @@ -1030,12 +1030,12 @@ Processing reflections in the following blocks of images: Timing information for integration +-------------------+----------------+ -| Read time | 34.79 seconds | -| Extract time | 3.51 seconds | +| Read time | 29.22 seconds | +| Extract time | 3.13 seconds | | Pre-process time | 0.53 seconds | -| Process time | 122.74 seconds | +| Process time | 121.56 seconds | | Post-process time | 0.00 seconds | -| Total time | 162.72 seconds | +| Total time | 155.48 seconds | +-------------------+----------------+ Removing 40904 unintegrated reflections of 384161 total