diff --git a/tutorial_data/master/betalactamase/dials.scale.cmd b/tutorial_data/master/betalactamase/dials.scale.cmd new file mode 100644 index 000000000..311e172a2 --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.scale.cmd @@ -0,0 +1 @@ +dials.scale symmetrized.expt symmetrized.refl \ No newline at end of file diff --git a/tutorial_data/master/betalactamase/dials.scale.log b/tutorial_data/master/betalactamase/dials.scale.log new file mode 100644 index 000000000..a89917ecc --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.scale.log @@ -0,0 +1,391 @@ +DIALS 2.dev.1044-g7a76e757f +The following parameters have been modified: + +input { + experiments = symmetrized.expt + reflections = symmetrized.refl +} + +Checking for the existence of a reflection table +containing multiple datasets + +Found 1 reflection tables & 1 experiments in total. + +Dataset unique identifiers are ['0'] + +Space group being used during scaling is C 1 2 1 + +Scaling models have been initialised for all experiments. + +================================================================================ + +The experiment identifier for this dataset is 0 +Preprocessing data for scaling. The id assigned to this +dataset is 0, and the scaling model type being applied is physical. + +71584/380914 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 66382 +criterion: not integrated by any method, reflections: 59803 +criterion: user excluded, reflections: 14176 + +Determined quasi-random reflection selection parameters: +min_per_area : 41, n_resolution_bins: 20 +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 26 | +| decay | 20 | +| absorption | 24 | +----------------------------- +A round of outlier rejection has been performed, +9291 outliers have been identified. + +306287 reflections were preselected for scale factor determination +out of 309330 suitable reflections: +Reflections passing individual criteria: +criterion: above min partiality ( > 0.95), reflections: 306287 +criterion: in I/sigma range (I/sig > -5.0), reflections: 309330 + +21221 reflections were selected for scale factor determination +out of 309330 suitable reflections. +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 3.2523651123 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 19991 | 1.3444 | +| 1 | 19991 | 1.3264 | +| 2 | 19991 | 1.2545 | +| 3 | 19991 | 1.1456 | +| 4 | 19991 | 1.1036 | +| 5 | 19991 | 1.0464 | +| 6 | 19991 | 1.0222 | +| 7 | 19991 | 1.0025 | +| 8 | 19991 | 0.96281 | +| 9 | 19991 | 0.94713 | +| 10 | 19991 | 0.92242 | +| 11 | 19991 | 0.90991 | +| 12 | 19991 | 0.9018 | +| 13 | 19991 | 0.89149 | +| 14 | 19991 | 0.89046 | +| 15 | 19991 | 0.88132 | +| 16 | 19991 | 0.88032 | +| 17 | 19991 | 0.87716 | +| 18 | 19991 | 0.87405 | +| 19 | 19991 | 0.87112 | +| 20 | 19991 | 0.87003 | +| 21 | 19991 | 0.86906 | +| 22 | 19991 | 0.86783 | +| 23 | 19991 | 0.86703 | +| 24 | 19991 | 0.86576 | +| 25 | 19991 | 0.86481 | +| 26 | 19991 | 0.86443 | +| 27 | 19991 | 0.86404 | +| 28 | 19991 | 0.86376 | +| 29 | 19991 | 0.86329 | +| 30 | 19991 | 0.86288 | +| 31 | 19991 | 0.86252 | +| 32 | 19991 | 0.86235 | +| 33 | 19991 | 0.86201 | +| 34 | 19991 | 0.86193 | +-------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +1204 outliers have been identified. + +Performing profile/summation intensity optimisation. +--------------------------------------- +| Combination | CC1/2 | Rmeas | +--------------------------------------- +| prf only | 0.99909 | 0.07337 | +| sum only | 0.99881 | 0.09195 | +| Imid = 285.12 | 0.99892 | 0.07302 | +| Imid = 48696.01 | 0.99888 | 0.07344 | +| Imid = 4869.6 | 0.9989 | 0.07331 | +| Imid = 486.96 | 0.99892 | 0.07294 | +| Imid = 48.7 | 0.9989 | 0.07503 | +--------------------------------------- +Combined intensities with Imid = 486.96013945 determined to be best for scaling. + +A round of outlier rejection has been performed, +1022 outliers have been identified. + +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 1.24233388901 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 21155 | 0.99742 | +| 1 | 21155 | 0.99431 | +| 2 | 21155 | 0.98852 | +| 3 | 21155 | 0.98173 | +| 4 | 21155 | 0.97882 | +| 5 | 21155 | 0.97687 | +| 6 | 21155 | 0.97651 | +| 7 | 21155 | 0.97628 | +| 8 | 21155 | 0.97577 | +| 9 | 21155 | 0.97557 | +| 10 | 21155 | 0.97527 | +| 11 | 21155 | 0.97522 | +-------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +913 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +------------------------------- +| 0 | 86874 | 0.20996 | +| 1 | 86874 | 0.16538 | +| 2 | 86874 | 0.11176 | +| 3 | 86874 | 0.10233 | +| 4 | 86874 | 0.098341 | +| 5 | 86874 | 0.097741 | +| 6 | 86874 | 0.096059 | +| 7 | 86874 | 0.096025 | +| 8 | 86874 | 0.096025 | +------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00067, b = 0.03655 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 27.338 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 9947.39 - 1921.30 | 868 | 14.127 | 0.791 | +| 1921.30 - 1454.26 | 868 | 11.292 | 0.989 | +| 1454.26 - 1231.64 | 868 | 9.226 | 1.013 | +| 1231.64 - 907.45 | 2024 | 6.823 | 0.905 | +| 907.45 - 498.71 | 5827 | 5.009 | 1.069 | +| 498.71 - 274.08 | 9608 | 3.144 | 1.141 | +| 274.08 - 150.63 | 14478 | 2.172 | 1.165 | +| 150.63 - 82.78 | 19226 | 1.567 | 1.101 | +| 82.78 - 45.50 | 20136 | 1.183 | 0.977 | +| 45.50 - 24.99 | 12971 | 0.97 | 0.872 | +------------------------------------------------------------------------------- + +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 2.14674496651 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 21166 | 0.74379 | +| 1 | 21166 | 0.73739 | +| 2 | 21166 | 0.73525 | +| 3 | 21166 | 0.73208 | +| 4 | 21166 | 0.72942 | +| 5 | 21166 | 0.72859 | +| 6 | 21166 | 0.72848 | +| 7 | 21166 | 0.72845 | +-------------------------- +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 0.494167089462 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 21166 | 0.72845 | +| 1 | 21166 | 0.72845 | +-------------------------- +RMSD no longer decreasing + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +110 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +------------------------------- +| 0 | 86714 | 0.20889 | +| 1 | 86714 | 0.16395 | +| 2 | 86714 | 0.11115 | +| 3 | 86714 | 0.10164 | +| 4 | 86714 | 0.097593 | +| 5 | 86714 | 0.096953 | +| 6 | 86714 | 0.095093 | +| 7 | 86714 | 0.095066 | +| 8 | 86714 | 0.095066 | +------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00044, b = 0.03618 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 27.627 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 9948.69 - 1920.44 | 867 | 13.837 | 0.804 | +| 1920.44 - 1454.16 | 867 | 11.086 | 0.994 | +| 1454.16 - 1231.24 | 867 | 9.182 | 1.025 | +| 1231.24 - 907.50 | 2023 | 6.928 | 0.931 | +| 907.50 - 498.73 | 5836 | 5.019 | 1.078 | +| 498.73 - 274.09 | 9615 | 3.106 | 1.141 | +| 274.09 - 150.63 | 14456 | 2.158 | 1.155 | +| 150.63 - 82.78 | 19172 | 1.522 | 1.068 | +| 82.78 - 45.49 | 20024 | 1.16 | 0.957 | +| 45.49 - 24.99 | 12987 | 0.938 | 0.844 | +------------------------------------------------------------------------------- + + +The reflection table variances have been adjusted to account for the +uncertainty in the scaling model +0 reflections set as outliers: scale factor < 0.001 + +Total time taken: 16.7016s + +================================================================================ + +40.00% of model parameters have signficant uncertainty +(sigma/abs(parameter) > 0.5) + +Summary of dataset partialities +---------------------------- +| Partiality (p) | n_refl | +---------------------------- +| all reflections | 380914 | +| p > 0.99 | 362291 | +| 0.5 < p < 0.99 | 3781 | +| 0.01 < p < 0.5 | 9474 | +| p < 0.01 | 5368 | +---------------------------- + +Reflections below a partiality_cutoff of 0.4 are not considered for any +part of the scaling analysis or for the reporting of merging statistics. +Additionally, if applicable, only reflections with a min_partiality > 0.95 +were considered for use when refining the scaling model. + + + ----------Merging statistics---------- + +Resolution: 69.19 - 1.22 +Observations: 309220 +Unique reflections: 48412 +Redundancy: 6.4 +Completeness: 73.13% +Mean intensity: 72.3 +Mean I/sigma(I): 12.0 +R-merge: 0.066 +R-meas: 0.072 +R-pim: 0.028 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 69.30 3.31 22316 3348 6.67 98.73 547.2 50.3 0.039 0.042 0.016 0.998* 0.312* + 3.31 2.63 21752 3272 6.65 97.58 205.4 34.2 0.049 0.054 0.021 0.998* 0.374* + 2.63 2.29 22231 3219 6.91 96.70 103.9 25.2 0.065 0.071 0.027 0.997* 0.320* + 2.29 2.08 21491 3168 6.78 95.97 72.3 19.2 0.078 0.085 0.032 0.996* 0.215* + 2.08 1.93 21124 3155 6.70 95.37 48.4 14.5 0.096 0.104 0.040 0.994* 0.225* + 1.93 1.82 21220 3145 6.75 94.47 27.9 9.9 0.132 0.143 0.054 0.992* 0.151* + 1.82 1.73 20927 3119 6.71 94.00 17.0 6.8 0.177 0.191 0.073 0.985* 0.181* + 1.73 1.65 20291 3077 6.59 93.33 11.4 4.9 0.229 0.248 0.096 0.976* 0.140* + 1.65 1.59 21131 3061 6.90 92.48 9.1 4.0 0.273 0.296 0.112 0.973* 0.064* + 1.59 1.54 20020 3035 6.60 92.17 6.8 3.1 0.331 0.359 0.139 0.958* 0.084* + 1.54 1.49 19570 3017 6.49 91.48 5.4 2.4 0.401 0.436 0.170 0.945* 0.033 + 1.49 1.44 20173 2986 6.76 90.90 3.8 1.8 0.528 0.572 0.219 0.923* 0.082* + 1.44 1.41 18232 2992 6.09 90.67 3.2 1.4 0.609 0.666 0.265 0.891* 0.070* + 1.41 1.37 13658 2472 5.53 73.79 2.6 1.1 0.724 0.798 0.330 0.837* -0.025 + 1.37 1.34 9252 1727 5.36 53.25 2.3 1.0 0.800 0.884 0.369 0.798* -0.023 + 1.34 1.31 6755 1313 5.14 40.05 2.1 0.9 0.877 0.972 0.409 0.779* 0.048 + 1.31 1.29 4733 1009 4.69 30.20 1.6 0.6 1.105 1.235 0.538 0.664* -0.066 + 1.29 1.26 2725 670 4.07 20.62 1.3 0.5 1.319 1.509 0.712 0.436* 0.043 + 1.26 1.24 1317 441 2.99 13.28 1.0 0.3 1.501 1.787 0.948 0.427* 0.075 + 1.24 1.22 302 186 1.62 5.67 1.2 0.3 1.024 1.350 0.870 0.594* -0.238 + 69.19 1.22 309220 48412 6.39 73.13 72.3 12.0 0.066 0.072 0.028 0.999* 0.260* + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.218 + based on CC(1/2) >= 0.33 : 1.218 + based on mean(I/sigma) >= 2.0 : 1.487 + based on R-merge < 0.5 : 1.487 + based on R-meas < 0.5 : 1.487 + based on completeness >= 90% : 1.407 + based on completeness >= 50% : 1.341 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + +Writing html report to: scaling.html + +================================================================================ + +Saving the experiments to scaled.expt +Time taken: 0.0106061 +Saving the scaled reflections to scaled.refl +Time taken: 0.880502 +See dials.github.io/dials_scale_user_guide.html for more info on scaling options diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.cmd b/tutorial_data/master/betalactamase/dials.scale_cut.cmd new file mode 100644 index 000000000..343c90e9b --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.scale_cut.cmd @@ -0,0 +1 @@ +dials.scale scaled.expt scaled.refl d_min=1.4 \ No newline at end of file diff --git a/tutorial_data/master/betalactamase/dials.scale_cut.log b/tutorial_data/master/betalactamase/dials.scale_cut.log new file mode 100644 index 000000000..3c1335df6 --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.scale_cut.log @@ -0,0 +1,354 @@ +DIALS 2.dev.1044-g7a76e757f +The following parameters have been modified: + +cut_data { + d_min = 1.4 +} +input { + experiments = scaled.expt + reflections = scaled.refl +} + +Checking for the existence of a reflection table +containing multiple datasets + +Found 1 reflection tables & 1 experiments in total. + +Dataset unique identifiers are ['0'] + +Space group being used during scaling is C 1 2 1 + +Scaling models have been initialised for all experiments. + +================================================================================ + +The experiment identifier for this dataset is 0 +Preprocessing data for scaling. The id assigned to this +dataset is 0, and the scaling model type being applied is physical. + +107349/380914 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 66382 +criterion: not integrated by any method, reflections: 59803 +criterion: user excluded, reflections: 60683 + +Determined quasi-random reflection selection parameters: +min_per_area : 41, n_resolution_bins: 20 +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 26 | +| decay | 20 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: 486.9601 + +270547 reflections were preselected for scale factor determination +out of 273565 suitable reflections: +Reflections passing individual criteria: +criterion: above min partiality ( > 0.95), reflections: 270547 +criterion: in I/sigma range (I/sig > -5.0), reflections: 273565 + +21407 reflections were selected for scale factor determination +out of 273565 suitable reflections. +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 0.683251857758 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 21404 | 1.1939 | +| 1 | 21404 | 1.1929 | +| 2 | 21404 | 1.1921 | +| 3 | 21404 | 1.1917 | +| 4 | 21404 | 1.1912 | +| 5 | 21404 | 1.1912 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +903 outliers have been identified. + +Performing profile/summation intensity optimisation. +--------------------------------------- +| Combination | CC1/2 | Rmeas | +--------------------------------------- +| prf only | 0.99915 | 0.06734 | +| sum only | 0.99919 | 0.08332 | +| Imid = 326.87 | 0.99928 | 0.0668 | +| Imid = 48696.01 | 0.99921 | 0.06729 | +| Imid = 4869.6 | 0.99926 | 0.06706 | +| Imid = 486.96 | 0.99928 | 0.06669 | +| Imid = 48.7 | 0.99926 | 0.0693 | +--------------------------------------- +Combined intensities with Imid = 486.96013945 determined to be best for scaling. + +A round of outlier rejection has been performed, +903 outliers have been identified. + +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 0.676669836044 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 21313 | 1.0749 | +| 1 | 21313 | 1.0745 | +| 2 | 21313 | 1.074 | +| 3 | 21313 | 1.0736 | +| 4 | 21313 | 1.0734 | +| 5 | 21313 | 1.0733 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +906 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +------------------------------- +| 0 | 86716 | 0.20732 | +| 1 | 86716 | 0.16254 | +| 2 | 86716 | 0.11021 | +| 3 | 86716 | 0.101 | +| 4 | 86716 | 0.097216 | +| 5 | 86716 | 0.09657 | +| 6 | 86716 | 0.094688 | +| 7 | 86716 | 0.09468 | +------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00043, b = 0.03608 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 27.707 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 9941.90 - 1916.03 | 867 | 13.618 | 0.805 | +| 1916.03 - 1453.75 | 867 | 11.058 | 1.005 | +| 1453.75 - 1230.72 | 867 | 9.12 | 1.029 | +| 1230.72 - 907.11 | 2025 | 6.815 | 0.927 | +| 907.11 - 498.55 | 5838 | 4.993 | 1.08 | +| 498.55 - 274.00 | 9618 | 3.097 | 1.139 | +| 274.00 - 150.59 | 14462 | 2.139 | 1.152 | +| 150.59 - 82.77 | 19163 | 1.516 | 1.066 | +| 82.77 - 45.49 | 20025 | 1.157 | 0.955 | +| 45.49 - 24.99 | 12984 | 0.938 | 0.845 | +------------------------------------------------------------------------------- + +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 1.40140914917 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 21309 | 0.79928 | +| 1 | 21309 | 0.79702 | +| 2 | 21309 | 0.79694 | +| 3 | 21309 | 0.79684 | +| 4 | 21309 | 0.79679 | +-------------------------- +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 0.522313833237 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 21309 | 0.79679 | +| 1 | 21309 | 0.79678 | +-------------------------- +RMSD no longer decreasing + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all reflections for dataset 0. + +A round of outlier rejection has been performed, +112 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +------------------------------- +| 0 | 86723 | 0.20925 | +| 1 | 86723 | 0.16412 | +| 2 | 86723 | 0.11106 | +| 3 | 86723 | 0.10127 | +| 4 | 86723 | 0.096979 | +| 5 | 86723 | 0.096331 | +| 6 | 86723 | 0.094465 | +| 7 | 86723 | 0.094411 | +| 8 | 86723 | 0.09441 | +------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00042, b = 0.03616 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 27.643 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 9938.13 - 1918.43 | 867 | 14.099 | 0.812 | +| 1918.43 - 1453.97 | 867 | 11.015 | 0.995 | +| 1453.97 - 1231.46 | 867 | 9.242 | 1.027 | +| 1231.46 - 906.92 | 2034 | 6.895 | 0.932 | +| 906.92 - 498.47 | 5830 | 5.015 | 1.082 | +| 498.47 - 273.97 | 9620 | 3.104 | 1.138 | +| 273.97 - 150.58 | 14469 | 2.144 | 1.151 | +| 150.58 - 82.76 | 19164 | 1.518 | 1.066 | +| 82.76 - 45.49 | 20041 | 1.151 | 0.95 | +| 45.49 - 24.99 | 12964 | 0.945 | 0.851 | +------------------------------------------------------------------------------- + + +The reflection table variances have been adjusted to account for the +uncertainty in the scaling model +0 reflections set as outliers: scale factor < 0.001 + +Total time taken: 12.1000s + +================================================================================ + +38.57% of model parameters have signficant uncertainty +(sigma/abs(parameter) > 0.5) + +Summary of dataset partialities +---------------------------- +| Partiality (p) | n_refl | +---------------------------- +| all reflections | 380914 | +| p > 0.99 | 362291 | +| 0.5 < p < 0.99 | 3781 | +| 0.01 < p < 0.5 | 9474 | +| p < 0.01 | 5368 | +---------------------------- + +Reflections below a partiality_cutoff of 0.4 are not considered for any +part of the scaling analysis or for the reporting of merging statistics. +Additionally, if applicable, only reflections with a min_partiality > 0.95 +were considered for use when refining the scaling model. + + + ----------Merging statistics---------- + +Resolution: 69.19 - 1.40 +Observations: 273452 +Unique reflections: 41123 +Redundancy: 6.6 +Completeness: 94.09% +Mean intensity: 84.6 +Mean I/sigma(I): 14.0 +R-merge: 0.064 +R-meas: 0.069 +R-pim: 0.026 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 69.28 3.80 14830 2234 6.64 99.02 574.9 51.7 0.038 0.041 0.016 0.998* 0.295* + 3.80 3.02 14561 2172 6.70 97.97 394.3 44.1 0.041 0.045 0.017 0.998* 0.311* + 3.02 2.63 14160 2137 6.63 97.49 164.6 31.3 0.054 0.059 0.023 0.998* 0.337* + 2.63 2.39 14765 2114 6.98 96.93 110.4 26.5 0.064 0.069 0.026 0.997* 0.356* + 2.39 2.22 14252 2135 6.68 96.56 86.7 21.7 0.071 0.077 0.030 0.997* 0.285* + 2.22 2.09 14447 2091 6.91 95.52 70.1 19.0 0.079 0.086 0.032 0.996* 0.240* + 2.09 1.99 13557 2073 6.54 95.44 52.4 15.2 0.090 0.098 0.038 0.995* 0.212* + 1.99 1.90 14529 2090 6.95 95.39 38.1 12.4 0.112 0.121 0.046 0.994* 0.162* + 1.90 1.83 13755 2053 6.70 94.17 26.4 9.5 0.136 0.147 0.056 0.991* 0.188* + 1.83 1.76 13625 2044 6.67 94.02 19.1 7.4 0.164 0.178 0.068 0.987* 0.140* + 1.76 1.71 13346 2045 6.53 93.89 13.8 5.8 0.199 0.216 0.084 0.979* 0.139* + 1.71 1.66 13612 2039 6.68 93.19 11.2 4.7 0.231 0.251 0.096 0.979* 0.133* + 1.66 1.62 13863 2000 6.93 92.55 9.5 4.2 0.263 0.284 0.107 0.974* 0.093* + 1.62 1.58 13675 2032 6.73 92.45 8.0 3.6 0.300 0.325 0.125 0.969* 0.069* + 1.58 1.54 13262 2005 6.61 91.76 6.7 3.1 0.331 0.360 0.139 0.952* 0.080* + 1.54 1.51 12857 1993 6.45 92.06 5.6 2.5 0.379 0.413 0.161 0.952* 0.065* + 1.51 1.48 13305 2009 6.62 91.78 4.9 2.2 0.438 0.476 0.184 0.940* 0.071* + 1.48 1.45 13071 1932 6.77 90.24 3.8 1.8 0.534 0.579 0.221 0.917* 0.087* + 1.45 1.42 13053 1998 6.53 90.82 3.2 1.5 0.618 0.671 0.259 0.894* 0.052 + 1.42 1.40 10927 1927 5.67 90.17 3.0 1.3 0.640 0.705 0.291 0.880* 0.027 + 69.19 1.40 273452 41123 6.65 94.09 84.6 14.0 0.064 0.069 0.026 0.999* 0.303* + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.400 + based on CC(1/2) >= 0.33 : 1.400 + based on mean(I/sigma) >= 2.0 : 1.478 + based on R-merge < 0.5 : 1.478 + based on R-meas < 0.5 : 1.478 + based on completeness >= 90% : 1.400 + based on completeness >= 50% : 1.400 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + +Writing html report to: scaling.html + +================================================================================ + +Saving the experiments to scaled.expt +Time taken: 0.00806999 +Saving the scaled reflections to scaled.refl +Time taken: 0.870752 +See dials.github.io/dials_scale_user_guide.html for more info on scaling options diff --git a/tutorial_data/master/betalactamase/dials.symmetry.cmd b/tutorial_data/master/betalactamase/dials.symmetry.cmd new file mode 100644 index 000000000..525195a30 --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.symmetry.cmd @@ -0,0 +1 @@ +dials.symmetry integrated.expt integrated.refl \ No newline at end of file diff --git a/tutorial_data/master/betalactamase/dials.symmetry.log b/tutorial_data/master/betalactamase/dials.symmetry.log new file mode 100644 index 000000000..296716b5d --- /dev/null +++ b/tutorial_data/master/betalactamase/dials.symmetry.log @@ -0,0 +1,100 @@ +DIALS 2.dev.1038-g79d8dbacd +The following parameters have been modified: + +input { + experiments = integrated.expt + reflections = integrated.refl +} + +================================================================================ + +Performing Laue group analysis + +Filtering reflections for dataset 0 +Read 380914 predicted reflections +Selected 314532 reflections integrated by profile and summation methods +Combined 5340 partial reflections with other partial reflections +Removed 1154 reflections below partiality threshold +Removed 0 intensity.sum.value reflections with I/Sig(I) < -5 +Removed 405 intensity.prf.value reflections with I/Sig(I) < -5 +A round of outlier rejection has been performed, +692 outliers have been identified. + +Patterson group: C 1 2/m 1 (x-y,x+y,z) + +-------------------------------------------------------------------------------- + +Normalising intensities for dataset 1 + +ML estimate of overall B_cart value: + 13.49, -1.04, -0.67 + 13.47, -1.30 + 10.73 +ML estimate of -log of scale factor: + -2.16 + +-------------------------------------------------------------------------------- + +Estimation of resolution for Laue group analysis + +Resolution estimate from / > 4.0 : 1.85 +Resolution estimate from CC1/2 > 0.60: 1.38 +High resolution limit set to: 1.38 +Selecting 274272 reflections with d > 1.38 + +Input crystal symmetry: +Unit cell: (53.1698, 61.2427, 69.2884, 90, 93.0456, 90) +Space group: C 1 2 1 (No. 5) +Change of basis op to minimum cell: -x-y,-x+y,-z +Crystal symmetry in minimum cell: +Unit cell: (40.5515, 40.5515, 69.2884, 91.9961, 91.9961, 98.0721) +Space group: P 1 (No. 1) +Lattice point group: C 1 2/m 1 (x-y,x+y,z) + +Overall CC for 20000 unrelated pairs: 0.385 +Estimated expectation value of true correlation coefficient E(CC) = 0.981 +Estimated sd(CC) = 0.657 / sqrt(N) +Estimated E(CC) of true correlation coefficient from identity = 0.982 + +-------------------------------------------------------------------------------- + +Scoring individual symmetry elements + +--------------------------------------------------- +likelihood Z-CC CC N Operator +--------------------------------------------------- +0.936 9.79 0.98 273056 *** 1 |(0, 0, 0) +0.932 9.71 0.97 271743 *** 2 |(-1, 1, 0) +--------------------------------------------------- + +-------------------------------------------------------------------------------- + +Scoring all possible sub-groups + +--------------------------------------------------------------------------------------------- +Patterson group Likelihood NetZcc Zcc+ Zcc- CC CC- delta Reindex operator +--------------------------------------------------------------------------------------------- +C 1 2/m 1 *** 0.932 9.75 9.75 0.00 0.98 0.00 0.0 a,b,c +P -1 0.068 0.09 9.79 9.71 0.98 0.97 0.0 -x-y,-x+y,-z +--------------------------------------------------------------------------------------------- + +Best solution: C 1 2/m 1 +Unit cell: (53.1698, 61.2427, 69.2884, 90, 93.0456, 90) +Reindex operator: a,b,c +Laue group probability: 0.932 +Laue group confidence: 0.897 + +================================================================================ + +Analysing systematic absences + +Performing systematic absence checks on unscaled profile-integrated data +Read 380914 predicted reflections +Selected 314532 profile integrated reflections +Removed 28574 reflections with d < 1.38 +Combined 5340 partial reflections with other partial reflections +Removed 1129 reflections below partiality threshold +Laue group: C 1 2/m 1 +No absences to check for this laue group +Saving reindexed experiments to symmetrized.expt +Saving 380914 reindexed reflections to symmetrized.refl diff --git a/tutorial_data/master/multi_crystal/dials-symmetry.html b/tutorial_data/master/multi_crystal/dials-symmetry.html new file mode 100644 index 000000000..31a833383 --- /dev/null +++ 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DIALS systematic absences report

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+ + + + diff --git a/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.cmd b/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.cmd new file mode 100644 index 000000000..dd6922401 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.cmd @@ -0,0 +1 @@ +dials.compute_delta_cchalf scaled.refl scaled.expt \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.log b/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.log new file mode 100644 index 000000000..80b9d7c6b --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.compute_delta_cchalf.log @@ -0,0 +1,32 @@ +Resolution bins +0: 68.380, 5.675 +1: 5.675, 4.020 +2: 4.020, 3.284 +3: 3.284, 2.845 +4: 2.845, 2.545 +5: 2.545, 2.323 +6: 2.323, 2.151 +7: 2.151, 2.012 +8: 2.012, 1.897 +9: 1.897, 1.800 + +# Datasets: 4 +# Reflections: 212648 +# Unique: 34076 +CC 1/2 mean: 99.263 +CC 1/2 excluding dataset 0: 99.264 +CC 1/2 excluding dataset 1: 99.236 +CC 1/2 excluding dataset 2: 99.199 +CC 1/2 excluding dataset 3: 99.224 +Dataset: 0, Delta CC 1/2: -0.001 +Dataset: 1, Delta CC 1/2: 0.027 +Dataset: 3, Delta CC 1/2: 0.039 +Dataset: 2, Delta CC 1/2: 0.064 +Writing table to delta_cchalf.dat + +mean delta_cc_half 0.0323083071378 +stddev delta_cc_half 0.0235618260127 +cutoff value: -0.0619389969129 + +Saving 306137 reflections to filtered.refl +Saving the experiments to filtered.expt diff --git a/tutorial_data/master/multi_crystal/dials.cosym.cmd b/tutorial_data/master/multi_crystal/dials.cosym.cmd new file mode 100644 index 000000000..c01944462 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.cosym.cmd @@ -0,0 +1 @@ +dials.cosym /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_0.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_1.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_2.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_3.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_0.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_1.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_2.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_3.refl \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.cosym.html b/tutorial_data/master/multi_crystal/dials.cosym.html new file mode 100644 index 000000000..a38f45b19 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.cosym.html @@ -0,0 +1,934 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Symmetry analysis +

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Scoring individual symmetry operations

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likelihoodZ-CCCCOperator
0.9449.860.99*** 4^-1 |(0, 0, 1)
0.9449.870.99*** 2 |(0, 1, 0)
0.9439.840.98*** 2 |(-1, 1, 0)
0.9429.830.98*** 2 |(0, 0, 1)
0.9459.890.99*** 2 |(1, 1, 0)
0.9419.810.98*** 4 |(0, 0, 1)
0.9429.830.98*** 2 |(1, 0, 0)
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Scoring all possible subgroups

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Patterson groupLikelihoodNetZccZcc+Zcc-deltaReindex operator
P 4/m m m***1.000 9.85 9.85 0.000.0-a,b,-c
C m m m0.000 0.01 9.85 9.840.0a-b,a+b,c
P m m m0.000-0.01 9.84 9.850.0-a,b,-c
P 4/m0.000-0.02 9.84 9.860.0-a,b,-c
C 1 2/m 10.000 0.04 9.89 9.840.0a-b,a+b,c
P 1 2/m 10.000 0.02 9.87 9.840.0-a,b,-c
C 1 2/m 10.000-0.01 9.84 9.850.0a+b,-a+b,c
P 1 2/m 10.000-0.02 9.83 9.850.0-a,-c,-b
P 1 2/m 10.000-0.02 9.83 9.850.0-b,-a,-c
P -10.000-9.85 0.00 9.850.0-a,b,-c
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Best solutionP 4/m m m
Unit cell68.360 68.360 103.953 90.0 90.0 90.0
Reindex operator-x,y,-z
Laue group probability1.000
Laue group confidence1.000
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+ + + + diff --git a/tutorial_data/master/multi_crystal/dials.cosym.log b/tutorial_data/master/multi_crystal/dials.cosym.log new file mode 100644 index 000000000..5ebf4ddcb --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.cosym.log @@ -0,0 +1,198 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +input { + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_0.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_1.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_2.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_3.expt + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_0.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_1.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_2.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_3.refl +} + +Hierarchical clustering of unit cells +Using Andrews-Bernstein distance from Andrews & Bernstein J Appl Cryst 47:346 (2014) +Distances have been calculated + Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90) + +0 singletons: + +Point group a b c alpha beta gamma + +1 cluster: + +Cluster_id N_xtals Med_a Med_b Med_c Med_alpha Med_beta Med_gamma Delta(deg) +4 in P422. +cluster_1 4 68.36 (0.01 ) 68.36 (0.01 ) 103.95(0.02 ) 90.00 (0.00) 90.00 (0.00) 90.00 (0.00) + P 4/m m m (No. 123) 68.36 68.36 103.95 90.00 90.00 90.00 0.0 + + +Standard deviations are in brackets. +Each cluster: +Input lattice count, with integration Bravais setting space group. +Cluster median with Niggli cell parameters (std dev in brackets). +Highest possible metric symmetry and unit cell using LePage (J Appl Cryst 1982, 15:255) method, maximum delta 3deg. +Filtering reflections for dataset 0 +Read 76079 predicted reflections +Selected 54367 reflections integrated by profile and summation methods +Combined 1127 partial reflections with other partial reflections +Removed 491 reflections below partiality threshold +Removed 0 intensity.sum.value reflections with I/Sig(I) < -5 +Removed 12 intensity.prf.value reflections with I/Sig(I) < -5 +Filtering reflections for dataset 1 +Read 75607 predicted reflections +Selected 54845 reflections integrated by profile and summation methods +Combined 1284 partial reflections with other partial reflections +Removed 554 reflections below partiality threshold +Removed 0 intensity.sum.value reflections with I/Sig(I) < -5 +Removed 10 intensity.prf.value reflections with I/Sig(I) < -5 +Filtering reflections for dataset 2 +Read 77983 predicted reflections +Selected 54461 reflections integrated by profile and summation methods +Combined 1404 partial reflections with other partial reflections +Removed 541 reflections below partiality threshold +Removed 0 intensity.sum.value reflections with I/Sig(I) < -5 +Removed 7 intensity.prf.value reflections with I/Sig(I) < -5 +Filtering reflections for dataset 3 +Read 76468 predicted reflections +Selected 53877 reflections integrated by profile and summation methods +Combined 1062 partial reflections with other partial reflections +Removed 514 reflections below partiality threshold +Removed 0 intensity.sum.value reflections with I/Sig(I) < -5 +Removed 3 intensity.prf.value reflections with I/Sig(I) < -5 +Patterson group: P 4/m m m + +-------------------------------------------------------------------------------- + +Normalising intensities for dataset 1 + +ML estimate of overall B value: + 13.46 A**2 +ML estimate of -log of scale factor: + -3.04 + +-------------------------------------------------------------------------------- + +Normalising intensities for dataset 2 + +ML estimate of overall B value: + 11.06 A**2 +ML estimate of -log of scale factor: + -3.50 + +-------------------------------------------------------------------------------- + +Normalising intensities for dataset 3 + +ML estimate of overall B value: + 11.45 A**2 +ML estimate of -log of scale factor: + -2.96 + +-------------------------------------------------------------------------------- + +Normalising intensities for dataset 4 + +ML estimate of overall B value: + 12.14 A**2 +ML estimate of -log of scale factor: + -2.67 + +-------------------------------------------------------------------------------- + +Estimation of resolution for Laue group analysis + +Resolution estimate from / > 4.0 : 2.07 +Resolution estimate from CC1/2 > 0.60: 1.80 +High resolution limit set to: 1.80 +Selecting 188689 reflections with d > 1.80 +Using 8 dimensions for analysis +Using 1 dimensions for analysis +Functional: 14.5344 +Principal component analysis: +Explained variance: 8.3e-05 +Explained variance ratio: 1 +Using 2 dimensions for analysis +Functional: 15.6782 +Principal component analysis: +Explained variance: 0.025, 9.6e-05 +Explained variance ratio: 1, 0.0039 +Using 3 dimensions for analysis +Functional: 14.6072 +Principal component analysis: +Explained variance: 0.0014, 0.00087, 7.5e-05 +Explained variance ratio: 0.6, 0.37, 0.032 +Using 4 dimensions for analysis +Functional: 15.0484 +Principal component analysis: +Explained variance: 0.0065, 0.006, 0.0033, 7.1e-05 +Explained variance ratio: 0.41, 0.38, 0.21, 0.0044 +Using 5 dimensions for analysis +Functional: 14.8964 +Principal component analysis: +Explained variance: 0.0025, 0.0018, 0.00077, 0.00056, 9.2e-05 +Explained variance ratio: 0.44, 0.31, 0.14, 0.097, 0.016 +Using 6 dimensions for analysis +Functional: 14.7407 +Principal component analysis: +Explained variance: 0.0016, 0.0012, 0.0011, 0.00082, 0.00074, 0.00011 +Explained variance ratio: 0.29, 0.22, 0.19, 0.15, 0.13, 0.02 +Using 7 dimensions for analysis +Functional: 14.8194 +Principal component analysis: +Explained variance: 0.0019, 0.0017, 0.0016, 0.0013, 0.0012, 0.0012, 7.7e-05 +Explained variance ratio: 0.21, 0.19, 0.18, 0.14, 0.14, 0.13, 0.0085 +Using 8 dimensions for analysis +Functional: 14.8284 +Principal component analysis: +Explained variance: 0.0031, 0.0011, 0.00064, 0.00052, 0.00048, 0.00035, 0.00032, 4.4e-05 +Explained variance ratio: 0.48, 0.16, 0.098, 0.079, 0.074, 0.054, 0.049, 0.0068 +Best number of dimensions: 3 +Using 3 dimensions for analysis +Principal component analysis: +Explained variance: 0.0082, 0.0052, 8.2e-05 +Explained variance ratio: 0.61, 0.39, 0.0061 +Scoring individual symmetry elements +--------------------------------------------- +likelihood Z-CC CC Operator +--------------------------------------------- +0.944 9.86 0.99 *** 4^-1 |(0, 0, 1) +0.944 9.87 0.99 *** 2 |(0, 1, 0) +0.943 9.84 0.98 *** 2 |(-1, 1, 0) +0.942 9.83 0.98 *** 2 |(0, 0, 1) +0.945 9.89 0.99 *** 2 |(1, 1, 0) +0.941 9.81 0.98 *** 4 |(0, 0, 1) +0.942 9.83 0.98 *** 2 |(1, 0, 0) +--------------------------------------------- +Scoring all possible sub-groups +------------------------------------------------------------------------------- +Patterson group Likelihood NetZcc Zcc+ Zcc- delta Reindex operator +------------------------------------------------------------------------------- +P 4/m m m *** 1.000 9.85 9.85 0.00 0.0 -a,b,-c +C m m m 0.000 0.01 9.85 9.84 0.0 a-b,a+b,c +P m m m 0.000 -0.01 9.84 9.85 0.0 -a,b,-c +P 4/m 0.000 -0.02 9.84 9.86 0.0 -a,b,-c +C 1 2/m 1 0.000 0.04 9.89 9.84 0.0 a-b,a+b,c +P 1 2/m 1 0.000 0.02 9.87 9.84 0.0 -a,b,-c +C 1 2/m 1 0.000 -0.01 9.84 9.85 0.0 a+b,-a+b,c +P 1 2/m 1 0.000 -0.02 9.83 9.85 0.0 -a,-c,-b +P 1 2/m 1 0.000 -0.02 9.83 9.85 0.0 -b,-a,-c +P -1 0.000 -9.85 0.00 9.85 0.0 -a,b,-c +------------------------------------------------------------------------------- +Best solution: P 4/m m m +Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90) +Reindex operator: -a,b,-c +Laue group probability: 1.000 +Laue group confidence: 1.000 +Space groups: +P 4 2 2 +[0, 1, 2, 3] +Reindexing operators: +x,y,z +[0, 1, 2, 3] +Writing html report to: dials.cosym.html +Writing json to: dials.cosym.json +Saving reindexed experiments to symmetrized.expt +Saving reindexed reflections to symmetrized.refl diff --git a/tutorial_data/master/multi_crystal/dials.merge.cmd b/tutorial_data/master/multi_crystal/dials.merge.cmd new file mode 100644 index 000000000..ea7e277b4 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.merge.cmd @@ -0,0 +1 @@ +dials.merge symmetrized.expt symmetrized.refl \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.merge.log b/tutorial_data/master/multi_crystal/dials.merge.log new file mode 100644 index 000000000..ad3cf135f --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.merge.log @@ -0,0 +1,284 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +input { + experiments = symmetrized.expt + reflections = symmetrized.refl +} + + +Merging scaled reflection data + +Read 306137 predicted reflections +Selected 212642 scaled reflections +Combined 68 partial reflections with other partial reflections +Combined 77 partial reflections with other partial reflections +Combined 106 partial reflections with other partial reflections +Combined 69 partial reflections with other partial reflections +Removed 4080 reflections below partiality threshold +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) +Running systematic absences check +Laue group: P 4/m m m +--------------------------------------------------------------------------------------------------------------- +| Screw axis | Score | No. present | No. absent | present | absent | present | absent | +--------------------------------------------------------------------------------------------------------------- +| 41c | 1.000 | 11 | 33 | 728.990 | 0.128 | 32.486 | 0.382 | +| 21a | 1.000 | 14 | 14 | 957.612 | 0.523 | 21.366 | 0.970 | +| 42c | 1.000 | 22 | 22 | 364.336 | 0.351 | 16.558 | 0.257 | +--------------------------------------------------------------------------------------------------------------- +------------------------ +| Space group | score | +------------------------ +| P 4 2 2 | 0.0000 | +| P 4 21 2 | 0.0000 | +| P 41 2 2 | 0.0000 | +| P 42 2 2 | 0.0000 | +| P 41 21 2 | 1.0000 | +| P 42 21 2 | 0.0000 | +------------------------ +Recommended space group: P 41 21 2 +Space group with equivalent score (enantiomorphic pair): P 43 21 2 + +Scaling input intensities via French-Wilson Method +Total number of rejected intensities 0 + +===================== Absolute scaling and Wilson analysis ==================== + + + ----------Maximum likelihood isotropic Wilson scaling---------- + + ML estimate of overall B value: + 12.77 A**2 + Estimated -log of scale factor: + -2.83 + The overall B value ("Wilson B-factor", derived from the Wilson plot) gives + an isotropic approximation for the falloff of intensity as a function of + resolution. Note that this approximation may be misleading for anisotropic + data (where the crystal is poorly ordered along an axis). The Wilson B is + strongly correlated with refined atomic B-factors but these may differ by + a significant amount, especially if anisotropy is present. + + ----------Maximum likelihood anisotropic Wilson scaling---------- + +ML estimate of overall B_cart value: + 11.99, 0.00, 0.00 + 11.99, 0.00 + 14.07 + +Equivalent representation as U_cif: + 0.15, -0.00, -0.00 + 0.15, 0.00 + 0.18 + +Eigen analyses of B-cart: + ------------------------------------------------- + | Eigenvector | Value | Vector | + ------------------------------------------------- + | 1 | 14.066 | ( 0.00, 0.00, 1.00) | + | 2 | 11.992 | (-0.71, 0.71, -0.00) | + | 3 | 11.992 | ( 0.71, 0.71, -0.00) | + ------------------------------------------------- +ML estimate of -log of scale factor: + -2.83 + + ----------Anisotropy analyses---------- + + + For the resolution shell spanning between 1.95 - 1.80 Angstrom, + the mean I/sigI is equal to 4.00. 50.9 % of these intensities have + an I/sigI > 3. When sorting these intensities by their anisotropic + correction factor and analysing the I/sigI behavior for this ordered + list, we can gauge the presence of 'anisotropy induced noise amplification' + in reciprocal space. + + The quarter of Intensities *least* affected by the anisotropy correction show + + : 4.28e+00 + Fraction of I/sigI > 3 : 5.49e-01 ( Z = 1.77 ) + The quarter of Intensities *most* affected by the anisotropy correction show + + : 3.15e+00 + Fraction of I/sigI > 3 : 3.90e-01 ( Z = 5.32 ) + Z-scores are computed on the basis of a Bernoulli model assuming independence + of weak reflections with respect to anisotropy. + + ----------Wilson plot---------- + + The Wilson plot shows the falloff in intensity as a function in resolution; + this is used to calculate the overall B-factor ("Wilson B-factor") for the + data shown above. The expected plot is calculated based on analysis of + macromolecule structures in the PDB, and the distinctive appearance is due to + the non-random arrangement of atoms in the crystal. Some variation is + natural, but major deviations from the expected plot may indicate pathological + data (including ice rings, detector problems, or processing errors). + + ----------Mean intensity analyses---------- + + Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. + The following resolution shells are worrisome: + *** None *** + + ----------Possible outliers---------- + + Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 + +Acentric reflections: + None + +Centric reflections: + ----------------------------------------------------------------------------------------------------- + | Centric reflections | + |---------------------------------------------------------------------------------------------------| + | d_spacing | H K L | |E| | p(wilson) | p(extreme) | + |---------------------------------------------------------------------------------------------------| + | 2.628 | 26, 0, 1 | 4.28 | 1.83e-05 | 4.92e-02 | + ----------------------------------------------------------------------------------------------------- + + + + p(wilson) : 1-(erf[|E|/sqrt(2)]) + p(extreme) : 1-(erf[|E|/sqrt(2)])^(n_acentrics) + + + p(wilson) is the probability that an E-value of the specified + value would be observed when it would selected at random from + the given data set. + p(extreme) is the probability that the largest |E| value is + larger or equal than the observed largest |E| value. + + Both measures can be used for outlier detection. p(extreme) + takes into account the size of the dataset. + + + ----------Ice ring related problems---------- + + The following statistics were obtained from ice-ring insensitive resolution + ranges: + + mean bin z_score : 1.37 + ( rms deviation : 1.10 ) + mean bin completeness : 0.86 + ( rms deviation : 0.28 ) + + The following table shows the Wilson plot Z-scores and completeness for + observed data in ice-ring sensitive areas. The expected relative intensity + is the theoretical intensity of crystalline ice at the given resolution. + Large z-scores and high completeness in these resolution ranges might + be a reason to re-assess your data processsing if ice rings were present. + + ------------------------------------------------------------- + | d_spacing | Expected rel. I | Data Z-score | Completeness | + ------------------------------------------------------------- + | 3.897 | 1.000 | 2.86 | 1.00 | + | 3.669 | 0.750 | 1.17 | 1.00 | + | 3.441 | 0.530 | 3.42 | 0.99 | + | 2.671 | 0.170 | 1.09 | 1.00 | + | 2.249 | 0.390 | 1.39 | 0.97 | + | 2.072 | 0.300 | 1.03 | 0.77 | + | 1.948 | 0.040 | 1.51 | 0.43 | + | 1.918 | 0.180 | 0.17 | 0.31 | + | 1.883 | 0.030 | 0.56 | 0.24 | + ------------------------------------------------------------- + Abnormalities in mean intensity or completeness at resolution ranges with a + relative ice ring intensity lower than 0.10 will be ignored. + No ice ring related problems detected. + If ice rings were present, the data does not look worse at ice ring related + d_spacings as compared to the rest of the data set. + + + ----------Merging statistics---------- + +Resolution: 68.36 - 1.80 +Observations: 208242 +Unique reflections: 20132 +Redundancy: 10.3 +Completeness: 85.61% +Mean intensity: 152.3 +Mean I/sigma(I): 27.0 +R-merge: 0.056 +R-meas: 0.059 +R-pim: 0.016 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 68.41 4.89 20284 1334 15.21 100.00 318.2 52.2 0.047 0.049 0.012 0.998* -0.091 + 4.89 3.88 20000 1244 16.08 100.00 481.2 55.5 0.045 0.047 0.011 0.999* -0.049 + 3.88 3.39 19496 1208 16.14 100.00 369.3 51.3 0.048 0.050 0.012 0.999* -0.040 + 3.39 3.08 19560 1189 16.45 100.00 260.5 46.1 0.053 0.055 0.013 0.999* -0.069 + 3.08 2.86 19749 1185 16.67 100.00 180.8 40.1 0.060 0.062 0.015 0.999* -0.087 + 2.86 2.69 19922 1191 16.73 100.00 146.2 37.1 0.066 0.068 0.016 0.998* -0.160 + 2.69 2.55 19694 1172 16.80 100.00 115.0 31.8 0.075 0.078 0.019 0.998* 0.013 + 2.55 2.44 15819 1167 13.56 100.00 104.0 27.0 0.078 0.081 0.022 0.997* -0.139 + 2.44 2.35 11841 1162 10.19 100.00 90.5 22.4 0.082 0.086 0.027 0.996* -0.002 + 2.35 2.27 9896 1180 8.39 100.00 89.3 20.0 0.083 0.088 0.030 0.995* -0.082 + 2.27 2.20 8269 1150 7.19 99.91 76.6 16.9 0.090 0.097 0.036 0.990* -0.223 + 2.20 2.13 6811 1164 5.85 98.98 69.2 13.9 0.093 0.102 0.041 0.993* -0.065 + 2.13 2.08 5282 1115 4.74 97.13 60.2 11.1 0.098 0.110 0.048 0.990* -0.102 + 2.08 2.03 4005 1056 3.79 91.43 53.4 9.2 0.102 0.117 0.056 0.985* -0.076 + 2.03 1.98 3058 999 3.06 85.97 45.2 7.4 0.108 0.129 0.068 0.981* -0.014 + 1.98 1.94 2052 895 2.29 77.89 42.7 6.1 0.102 0.127 0.074 0.975* -0.061 + 1.94 1.90 1161 699 1.66 60.99 36.5 4.6 0.117 0.152 0.096 0.963* 0.000 + 1.90 1.86 748 530 1.41 46.17 31.8 3.7 0.113 0.153 0.102 0.968* 0.000 + 1.86 1.83 463 365 1.27 31.82 29.0 3.3 0.111 0.153 0.105 0.964* 0.000 + 1.83 1.80 132 127 1.04 11.08 24.9 2.6 0.417 0.589 0.417 -0.368 0.000 + 68.36 1.80 208242 20132 10.34 85.61 152.3 27.0 0.056 0.059 0.016 0.999* -0.086 + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.800 + based on CC(1/2) >= 0.33 : 1.831 + based on mean(I/sigma) >= 2.0 : 1.831 + based on R-merge < 0.5 : 1.831 + based on R-meas < 0.5 : 1.831 + based on completeness >= 90% : 2.028 + based on completeness >= 50% : 1.901 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + + +Writing reflections to merged.mtz +Title: From dials.merge +Space group symbol from file: P41212 +Space group number from file: 92 +Space group from matrices: P 41 21 2 (No. 92) +Point group symbol from file: 422 +Number of crystals: 1 +Number of Miller indices: 20132 +Resolution range: 68.3603 1.80033 +History: + From DIALS 2.dev.1062-gb01dfcdc9, run on 2019-11-13 at 17:53:15 GMT +Crystal 1: + Name: XTAL + Project: AUTOMATIC + Id: 1 + Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90) + Number of datasets: 1 + Dataset 1: + Name: NATIVE + Id: 1 + Wavelength: 0.979493 + Number of columns: 17 + label #valid %valid min max type + H 20132 100.00% 0.00 36.00 H: index h,k,l + K 20132 100.00% 0.00 24.00 H: index h,k,l + L 20132 100.00% 0.00 56.00 H: index h,k,l + IMEAN 20132 100.00% -12.16 6226.60 J: intensity + SIGIMEAN 20132 100.00% 0.17 216.08 Q: standard deviation + I(+) 19874 98.72% -12.16 6226.60 K: I(+) or I(-) + SIGI(+) 19874 98.72% 0.17 216.08 M: standard deviation + I(-) 14163 70.35% -7.90 4100.76 K: I(+) or I(-) + SIGI(-) 14163 70.35% 0.48 96.38 M: standard deviation + N(+) 19874 98.72% 2.00 8.00 I: integer + N(-) 14163 70.35% 8.00 8.00 I: integer + F 20132 100.00% 0.37 78.55 F: amplitude + SIGF 20132 100.00% 0.05 1.68 Q: standard deviation + F(+) 19874 98.72% 0.37 78.55 G: F(+) or F(-) + SIGF(+) 19874 98.72% 0.05 1.68 L: standard deviation + F(-) 14163 70.35% 1.00 63.99 G: F(+) or F(-) + SIGF(-) 14163 70.35% 0.07 1.53 L: standard deviation + diff --git a/tutorial_data/master/multi_crystal/dials.resolutionizer.cmd b/tutorial_data/master/multi_crystal/dials.resolutionizer.cmd new file mode 100644 index 000000000..b0e3032ab --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.resolutionizer.cmd @@ -0,0 +1 @@ +dials.resolutionizer scaled.expt scaled.refl \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.resolutionizer.log b/tutorial_data/master/multi_crystal/dials.resolutionizer.log new file mode 100644 index 000000000..4dd8b96f9 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.resolutionizer.log @@ -0,0 +1,27 @@ +The following parameters have been modified: + +input { + experiments = scaled.expt + reflections = scaled.refl +} + +DIALS 2.dev.1062-gb01dfcdc9 +Detected existence of a multi-dataset reflection table +containing 4 datasets. + +Read 76079 predicted reflections +Selected 53255 scaled reflections +Combined 68 partial reflections with other partial reflections +Read 75607 predicted reflections +Selected 53558 scaled reflections +Combined 77 partial reflections with other partial reflections +Read 77983 predicted reflections +Selected 53084 scaled reflections +Combined 106 partial reflections with other partial reflections +Read 76468 predicted reflections +Selected 52808 scaled reflections +Combined 69 partial reflections with other partial reflections +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) +Resolution cc_half: 1.80 +Resolution I/sig: 1.80 +Resolution Mn(I/sig): 1.80 diff --git a/tutorial_data/master/multi_crystal/dials.scale.cmd b/tutorial_data/master/multi_crystal/dials.scale.cmd new file mode 100644 index 000000000..311e172a2 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale.cmd @@ -0,0 +1 @@ +dials.scale symmetrized.expt symmetrized.refl \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.scale.log b/tutorial_data/master/multi_crystal/dials.scale.log new file mode 100644 index 000000000..d12ba410c --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale.log @@ -0,0 +1,621 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +input { + experiments = symmetrized.expt + reflections = symmetrized.refl +} + +Checking for the existence of a reflection table +containing multiple datasets + +Detected existence of a multi-dataset reflection table +containing 4 datasets. + +Found 4 reflection tables & 4 experiments in total. + +Dataset unique identifiers are ['0', '1', '2', '3'] + +Space group being used during scaling is P 4 2 2 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Scaling models have been initialised for all experiments. + +================================================================================ + +The experiment identifier for this dataset is 0 +Preprocessing data for scaling. The id assigned to this +dataset is 0, and the scaling model type being applied is physical. + +22812/76079 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 21712 +criterion: not integrated by any method, reflections: 17194 +criterion: user excluded, reflections: 13615 +criterion: bad d-value, reflections: 8461 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +A round of outlier rejection has been performed, +3331 outliers have been identified. + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 1 +Preprocessing data for scaling. The id assigned to this +dataset is 1, and the scaling model type being applied is physical. + +22041/75607 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 20762 +criterion: not integrated by any method, reflections: 16091 +criterion: user excluded, reflections: 13153 +criterion: bad d-value, reflections: 7556 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +A round of outlier rejection has been performed, +257 outliers have been identified. + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 2 +Preprocessing data for scaling. The id assigned to this +dataset is 2, and the scaling model type being applied is physical. + +24878/77983 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 23522 +criterion: not integrated by any method, reflections: 18787 +criterion: user excluded, reflections: 15433 +criterion: bad d-value, reflections: 9985 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +A round of outlier rejection has been performed, +976 outliers have been identified. + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 3 +Preprocessing data for scaling. The id assigned to this +dataset is 3, and the scaling model type being applied is physical. + +23620/76468 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 22591 +criterion: not integrated by any method, reflections: 17982 +criterion: user excluded, reflections: 13932 +criterion: bad d-value, reflections: 8998 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +A round of outlier rejection has been performed, +6234 outliers have been identified. + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +Configuring a MultiScaler to handle the individual Scalers. + +Determining symmetry equivalent reflections across datasets. + + +Determining highly connected reflections across datasets for scaling model +minimisation. Prefiltering for symmetry groups that have reflections with +multiplicity of at least 2 with > 1.0. This leaves 197826 out of 212786 reflections +to potentially use for scaling model minimisation based on cross-dataset +connectedness (these belong to 16683 symmetry groups). + +Attempting to choose at least 5357 reflections from each dataset, +with a total number between 21428 and 64284.0. + +Choosing 35270 cross-dataset connected reflections from 1487 symmetry groups for minimisation. + +Summary of reflections chosen for minimisation from each dataset: +---------------------------------------------------------------------- +| Dataset id | reflections | reflections | combined number | +| | connected to | highly connected | of reflections | +| | other datasets | within dataset | | +---------------------------------------------------------------------- +| 0 | 5358 | 4824 | 9675 | +| 1 | 10014 | 4512 | 13305 | +| 2 | 9278 | 4237 | 12651 | +| 3 | 10620 | 4704 | 14013 | +---------------------------------------------------------------------- +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 26.8514351845 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 46103 | 10.096 | +| 1 | 46103 | 6.7123 | +| 2 | 46103 | 5.81 | +| 3 | 46103 | 5.1394 | +| 4 | 46103 | 4.9349 | +| 5 | 46103 | 4.454 | +| 6 | 46103 | 4.3004 | +| 7 | 46103 | 4.1537 | +| 8 | 46103 | 4.0248 | +| 9 | 46103 | 3.8459 | +| 10 | 46103 | 3.7613 | +| 11 | 46103 | 3.3909 | +| 12 | 46103 | 3.0947 | +| 13 | 46103 | 2.9884 | +| 14 | 46103 | 2.7563 | +| 15 | 46103 | 2.5926 | +| 16 | 46103 | 2.4217 | +| 17 | 46103 | 2.2852 | +| 18 | 46103 | 2.1683 | +| 19 | 46103 | 2.0754 | +| 20 | 46103 | 2.0484 | +| 21 | 46103 | 2.0168 | +| 22 | 46103 | 2.0049 | +| 23 | 46103 | 1.9912 | +| 24 | 46103 | 1.986 | +| 25 | 46103 | 1.9768 | +| 26 | 46103 | 1.9628 | +| 27 | 46103 | 1.9365 | +| 28 | 46103 | 1.9255 | +| 29 | 46103 | 1.9047 | +| 30 | 46103 | 1.8982 | +| 31 | 46103 | 1.8941 | +| 32 | 46103 | 1.8901 | +| 33 | 46103 | 1.886 | +| 34 | 46103 | 1.8812 | +| 35 | 46103 | 1.8789 | +| 36 | 46103 | 1.8773 | +| 37 | 46103 | 1.8765 | +| 38 | 46103 | 1.8754 | +| 39 | 46103 | 1.8746 | +| 40 | 46103 | 1.8735 | +| 41 | 46103 | 1.8729 | +| 42 | 46103 | 1.8722 | +| 43 | 46103 | 1.8714 | +| 44 | 46103 | 1.871 | +| 45 | 46103 | 1.8705 | +| 46 | 46103 | 1.87 | +| 47 | 46103 | 1.8692 | +| 48 | 46103 | 1.8679 | +| 49 | 46103 | 1.8668 | +| 50 | 46103 | 1.8655 | +| 51 | 46103 | 1.8643 | +| 52 | 46103 | 1.8631 | +| 53 | 46103 | 1.8615 | +| 54 | 46103 | 1.8591 | +| 55 | 46103 | 1.8583 | +| 56 | 46103 | 1.8576 | +| 57 | 46103 | 1.8567 | +| 58 | 46103 | 1.8564 | +| 59 | 46103 | 1.8549 | +| 60 | 46103 | 1.8542 | +| 61 | 46103 | 1.8526 | +| 62 | 46103 | 1.8507 | +| 63 | 46103 | 1.8497 | +| 64 | 46103 | 1.8487 | +| 65 | 46103 | 1.8481 | +| 66 | 46103 | 1.8472 | +| 67 | 46103 | 1.8453 | +| 68 | 46103 | 1.8431 | +| 69 | 46103 | 1.8416 | +| 70 | 46103 | 1.8408 | +| 71 | 46103 | 1.8399 | +| 72 | 46103 | 1.8383 | +| 73 | 46103 | 1.8366 | +| 74 | 46103 | 1.8355 | +| 75 | 46103 | 1.8336 | +| 76 | 46103 | 1.8323 | +| 77 | 46103 | 1.8312 | +| 78 | 46103 | 1.8302 | +| 79 | 46103 | 1.8284 | +| 80 | 46103 | 1.8277 | +| 81 | 46103 | 1.8261 | +| 82 | 46103 | 1.8259 | +| 83 | 46103 | 1.8236 | +| 84 | 46103 | 1.8228 | +| 85 | 46103 | 1.8221 | +| 86 | 46103 | 1.821 | +| 87 | 46103 | 1.8203 | +| 88 | 46103 | 1.819 | +| 89 | 46103 | 1.8186 | +| 90 | 46103 | 1.8177 | +| 91 | 46103 | 1.8173 | +| 92 | 46103 | 1.8165 | +| 93 | 46103 | 1.8162 | +| 94 | 46103 | 1.8158 | +| 95 | 46103 | 1.8153 | +| 96 | 46103 | 1.8145 | +| 97 | 46103 | 1.8139 | +| 98 | 46103 | 1.8131 | +| 99 | 46103 | 1.812 | +| 100 | 46103 | 1.8116 | +| 101 | 46103 | 1.8105 | +| 102 | 46103 | 1.81 | +| 103 | 46103 | 1.8092 | +| 104 | 46103 | 1.8085 | +| 105 | 46103 | 1.8075 | +| 106 | 46103 | 1.8067 | +| 107 | 46103 | 1.8059 | +| 108 | 46103 | 1.8045 | +| 109 | 46103 | 1.8037 | +| 110 | 46103 | 1.8014 | +| 111 | 46103 | 1.8002 | +| 112 | 46103 | 1.7989 | +| 113 | 46103 | 1.7976 | +| 114 | 46103 | 1.7962 | +| 115 | 46103 | 1.7949 | +| 116 | 46103 | 1.7937 | +| 117 | 46103 | 1.7924 | +| 118 | 46103 | 1.7907 | +| 119 | 46103 | 1.7895 | +| 120 | 46103 | 1.7879 | +| 121 | 46103 | 1.7874 | +| 122 | 46103 | 1.7867 | +| 123 | 46103 | 1.7857 | +| 124 | 46103 | 1.785 | +| 125 | 46103 | 1.7842 | +| 126 | 46103 | 1.7835 | +| 127 | 46103 | 1.7829 | +| 128 | 46103 | 1.7824 | +| 129 | 46103 | 1.7818 | +| 130 | 46103 | 1.7814 | +| 131 | 46103 | 1.7811 | +| 132 | 46103 | 1.7808 | +| 133 | 46103 | 1.7804 | +| 134 | 46103 | 1.7797 | +| 135 | 46103 | 1.7795 | +| 136 | 46103 | 1.779 | +| 137 | 46103 | 1.7788 | +| 138 | 46103 | 1.7786 | +| 139 | 46103 | 1.7782 | +| 140 | 46103 | 1.7778 | +| 141 | 46103 | 1.7776 | +| 142 | 46103 | 1.7774 | +| 143 | 46103 | 1.7772 | +| 144 | 46103 | 1.7768 | +| 145 | 46103 | 1.7764 | +| 146 | 46103 | 1.7759 | +| 147 | 46103 | 1.7758 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +4814 outliers have been identified. + +Performing multi-dataset profile/summation intensity optimisation. +--------------------------------------- +| Combination | CC1/2 | Rmeas | +--------------------------------------- +| prf only | 0.9981 | 0.06924 | +| sum only | 0.99786 | 0.07595 | +| Imid = 872.14 | 0.99456 | 0.18672 | +| Imid = 11217.96 | 0.95211 | 0.30229 | +| Imid = 1121.8 | 0.9933 | 0.20882 | +| Imid = 112.18 | 0.99774 | 0.08437 | +--------------------------------------- +Profile intensities determined to be best for scaling. + +Combined outlier rejection has been performed across multiple datasets, +4814 outliers have been identified. + +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 5.04790091515 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 48281 | 1.9137 | +| 1 | 48281 | 1.9078 | +| 2 | 48281 | 1.9048 | +| 3 | 48281 | 1.8982 | +| 4 | 48281 | 1.8938 | +| 5 | 48281 | 1.8831 | +| 6 | 48281 | 1.8809 | +| 7 | 48281 | 1.8768 | +| 8 | 48281 | 1.874 | +| 9 | 48281 | 1.8733 | +| 10 | 48281 | 1.8703 | +| 11 | 48281 | 1.8694 | +| 12 | 48281 | 1.8684 | +| 13 | 48281 | 1.867 | +| 14 | 48281 | 1.8659 | +| 15 | 48281 | 1.8648 | +| 16 | 48281 | 1.8645 | +| 17 | 48281 | 1.8642 | +| 18 | 48281 | 1.864 | +| 19 | 48281 | 1.8637 | +| 20 | 48281 | 1.8634 | +| 21 | 48281 | 1.8631 | +| 22 | 48281 | 1.8629 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +3799 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139234 | 0.39929 | +| 1 | 139234 | 0.24955 | +| 2 | 139234 | 0.17073 | +| 3 | 139234 | 0.16895 | +| 4 | 139234 | 0.16791 | +| 5 | 139234 | 0.1678 | +| 6 | 139234 | 0.16762 | +| 7 | 139234 | 0.16762 | +-------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00195, b = 0.05880 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 16.975 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10139.49 - 1812.32 | 1392 | 20.979 | 0.546 | +| 1812.32 - 1390.96 | 1392 | 15.242 | 0.664 | +| 1390.96 - 1168.43 | 1392 | 14.623 | 0.802 | +| 1168.43 - 917.91 | 2714 | 12.854 | 0.875 | +| 917.91 - 503.50 | 12044 | 9.351 | 1.039 | +| 503.50 - 276.18 | 20641 | 6.073 | 1.21 | +| 276.18 - 151.49 | 28388 | 3.824 | 1.339 | +| 151.49 - 83.10 | 30896 | 2.361 | 1.258 | +| 83.10 - 45.58 | 25424 | 1.582 | 1.088 | +| 45.58 - 24.99 | 14951 | 1.059 | 0.845 | +------------------------------------------------------------------------------- + +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 16.4332590103 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48599 | 0.86564 | +| 1 | 48599 | 0.8276 | +| 2 | 48599 | 0.82156 | +| 3 | 48599 | 0.81275 | +| 4 | 48599 | 0.80569 | +| 5 | 48599 | 0.80329 | +| 6 | 48599 | 0.8029 | +| 7 | 48599 | 0.80278 | +| 8 | 48599 | 0.80275 | +-------------------------- +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 3.5609228611 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48599 | 0.80275 | +| 1 | 48599 | 0.80275 | +-------------------------- +RMSD no longer decreasing + +================================================================================ + +Calculating error estimates of inverse scale factors. + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +81 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139413 | 0.37073 | +| 1 | 139413 | 0.16198 | +| 2 | 139413 | 0.13004 | +| 3 | 139413 | 0.12929 | +| 4 | 139413 | 0.1289 | +| 5 | 139413 | 0.12845 | +-------------------------------- +lbfgs error: Line search failed: Rounding errors prevent further progress. There may not be a step which satisfies the sufficient decrease and curvature conditions. Tolerances may be too small. + +Error model details: + Type: basic + Current parameters: a = 1.00068, b = 0.04882 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 20.470 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10328.65 - 1822.77 | 1394 | 19.764 | 0.734 | +| 1822.77 - 1396.16 | 1394 | 14.359 | 0.856 | +| 1396.16 - 1176.94 | 1394 | 13.065 | 0.97 | +| 1176.94 - 928.14 | 2608 | 10.911 | 0.994 | +| 928.14 - 508.17 | 11907 | 7.65 | 1.11 | +| 508.17 - 278.23 | 20560 | 4.691 | 1.178 | +| 278.23 - 152.33 | 28153 | 2.908 | 1.196 | +| 152.33 - 83.40 | 30857 | 1.807 | 1.074 | +| 83.40 - 45.66 | 25547 | 1.277 | 0.944 | +| 45.66 - 24.99 | 15599 | 0.917 | 0.775 | +------------------------------------------------------------------------------- + + +The reflection table variances have been adjusted to account for the +uncertainty in the scaling models for all datasets +0 reflections set as outliers: scale factor < 0.001 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Total time taken: 58.9131s + +================================================================================ + +Warning: Over half (55.36%) of model parameters have signficant +uncertainty (sigma/abs(parameter) > 0.5), which could indicate a +poorly-determined scaling problem or overparameterisation. + +Summary of dataset partialities +---------------------------- +| Partiality (p) | n_refl | +---------------------------- +| all reflections | 306137 | +| p > 0.99 | 244580 | +| 0.5 < p < 0.99 | 4670 | +| 0.01 < p < 0.5 | 10499 | +| p < 0.01 | 46388 | +---------------------------- + +Reflections below a partiality_cutoff of 0.4 are not considered for any +part of the scaling analysis or for the reporting of merging statistics. +Additionally, if applicable, only reflections with a min_partiality > 0.95 +were considered for use when refining the scaling model. + + + ----------Merging statistics---------- + +Resolution: 68.36 - 1.80 +Observations: 212705 +Unique reflections: 20144 +Redundancy: 10.6 +Completeness: 84.99% +Mean intensity: 150.0 +Mean I/sigma(I): 27.5 +R-merge: 0.058 +R-meas: 0.060 +R-pim: 0.016 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 68.41 4.88 20827 1342 15.52 100.00 317.5 52.9 0.048 0.050 0.013 0.998* -0.077 + 4.88 3.87 20554 1245 16.51 100.00 472.7 56.5 0.047 0.048 0.012 0.999* -0.062 + 3.87 3.38 19998 1212 16.50 100.00 363.4 52.3 0.049 0.051 0.012 0.999* -0.081 + 3.38 3.07 20405 1207 16.91 100.00 253.9 47.2 0.055 0.057 0.014 0.999* -0.075 + 3.07 2.85 20416 1190 17.16 100.00 176.6 41.3 0.061 0.063 0.015 0.999* -0.002 + 2.85 2.68 20326 1186 17.14 100.00 142.1 38.2 0.067 0.069 0.016 0.999* -0.175 + 2.68 2.55 20303 1179 17.22 100.00 113.4 32.9 0.076 0.078 0.019 0.998* -0.046 + 2.55 2.44 16103 1181 13.64 100.00 102.2 27.6 0.080 0.083 0.022 0.997* -0.016 + 2.44 2.35 12112 1177 10.29 99.92 87.8 22.8 0.084 0.089 0.027 0.995* -0.027 + 2.35 2.26 9988 1170 8.54 99.91 86.5 20.4 0.087 0.093 0.032 0.994* -0.028 + 2.26 2.19 8336 1170 7.12 99.57 75.5 16.8 0.089 0.097 0.036 0.991* -0.164 + 2.19 2.13 6735 1162 5.80 99.06 66.8 13.6 0.094 0.103 0.041 0.992* -0.122 + 2.13 2.07 5246 1111 4.72 96.78 59.9 11.2 0.097 0.109 0.048 0.991* -0.220 + 2.07 2.02 4025 1081 3.72 91.30 52.1 9.0 0.103 0.119 0.058 0.986* -0.192 + 2.02 1.98 2944 981 3.00 85.16 44.9 7.3 0.107 0.128 0.068 0.981* 0.075 + 1.98 1.94 2003 887 2.26 76.40 41.1 5.9 0.104 0.130 0.076 0.973* -0.157 + 1.94 1.90 1112 686 1.62 59.70 35.1 4.4 0.116 0.152 0.096 0.964* 0.000 + 1.90 1.86 735 526 1.40 45.34 31.4 3.8 0.110 0.149 0.099 0.966* 0.000 + 1.86 1.83 430 346 1.24 29.60 28.5 3.2 0.114 0.158 0.110 0.968* 0.000 + 1.83 1.80 107 105 1.02 9.23 23.6 2.5 0.412 0.582 0.412 -1.000 0.000 + 68.36 1.80 212705 20144 10.56 84.99 150.0 27.5 0.058 0.060 0.016 0.999* -0.106 + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.797 + based on CC(1/2) >= 0.33 : 1.828 + based on mean(I/sigma) >= 2.0 : 1.828 + based on R-merge < 0.5 : 1.828 + based on R-meas < 0.5 : 1.828 + based on completeness >= 90% : 2.024 + based on completeness >= 50% : 1.897 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + +Writing html report to: scaling.html + +================================================================================ + +Saving the experiments to scaled.expt +Time taken: 0.435127 +Saving the scaled reflections to scaled.refl +Time taken: 1.49411 +See dials.github.io/dials_scale_user_guide.html for more info on scaling options diff --git a/tutorial_data/master/multi_crystal/dials.scale_cut.cmd b/tutorial_data/master/multi_crystal/dials.scale_cut.cmd new file mode 100644 index 000000000..da16b8a90 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale_cut.cmd @@ -0,0 +1 @@ +dials.scale scaled.expt scaled.refl d_min=1.80 \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.scale_cut.log b/tutorial_data/master/multi_crystal/dials.scale_cut.log new file mode 100644 index 000000000..3ac2549bf --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale_cut.log @@ -0,0 +1,487 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +cut_data { + d_min = 1.8 +} +input { + experiments = scaled.expt + reflections = scaled.refl +} + +Checking for the existence of a reflection table +containing multiple datasets + +Detected existence of a multi-dataset reflection table +containing 4 datasets. + +Found 4 reflection tables & 4 experiments in total. + +Dataset unique identifiers are ['0', '1', '2', '3'] + +Space group being used during scaling is P 4 2 2 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Scaling models have been initialised for all experiments. + +================================================================================ + +The experiment identifier for this dataset is 0 +Preprocessing data for scaling. The id assigned to this +dataset is 0, and the scaling model type being applied is physical. + +22812/76079 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 21712 +criterion: not integrated by any method, reflections: 17194 +criterion: user excluded, reflections: 13656 +criterion: bad d-value, reflections: 8461 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 1 +Preprocessing data for scaling. The id assigned to this +dataset is 1, and the scaling model type being applied is physical. + +22043/75607 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 20762 +criterion: not integrated by any method, reflections: 16091 +criterion: user excluded, reflections: 13186 +criterion: bad d-value, reflections: 7556 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 2 +Preprocessing data for scaling. The id assigned to this +dataset is 2, and the scaling model type being applied is physical. + +24879/77983 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 23522 +criterion: not integrated by any method, reflections: 18787 +criterion: user excluded, reflections: 15473 +criterion: bad d-value, reflections: 9985 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 3 +Preprocessing data for scaling. The id assigned to this +dataset is 3, and the scaling model type being applied is physical. + +23621/76468 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 22591 +criterion: not integrated by any method, reflections: 17982 +criterion: user excluded, reflections: 13968 +criterion: bad d-value, reflections: 8998 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +Configuring a MultiScaler to handle the individual Scalers. + +Determining symmetry equivalent reflections across datasets. + + +Determining highly connected reflections across datasets for scaling model +minimisation. Prefiltering for symmetry groups that have reflections with +multiplicity of at least 2 with > 1.0. This leaves 197826 out of 212782 reflections +to potentially use for scaling model minimisation based on cross-dataset +connectedness (these belong to 16683 symmetry groups). + +Attempting to choose at least 5357 reflections from each dataset, +with a total number between 21428 and 64284.0. + +Choosing 35270 cross-dataset connected reflections from 1487 symmetry groups for minimisation. + +Summary of reflections chosen for minimisation from each dataset: +---------------------------------------------------------------------- +| Dataset id | reflections | reflections | combined number | +| | connected to | highly connected | of reflections | +| | other datasets | within dataset | | +---------------------------------------------------------------------- +| 0 | 5358 | 4824 | 9675 | +| 1 | 10014 | 4567 | 13342 | +| 2 | 9278 | 4135 | 12547 | +| 3 | 10620 | 4728 | 14027 | +---------------------------------------------------------------------- +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 7.00125217438 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 49557 | 2.2683 | +| 1 | 49557 | 2.2636 | +| 2 | 49557 | 2.2584 | +| 3 | 49557 | 2.2538 | +| 4 | 49557 | 2.2483 | +| 5 | 49557 | 2.2437 | +| 6 | 49557 | 2.2415 | +| 7 | 49557 | 2.2381 | +| 8 | 49557 | 2.237 | +| 9 | 49557 | 2.2354 | +| 10 | 49557 | 2.234 | +| 11 | 49557 | 2.2329 | +| 12 | 49557 | 2.232 | +| 13 | 49557 | 2.2309 | +| 14 | 49557 | 2.2291 | +| 15 | 49557 | 2.2282 | +| 16 | 49557 | 2.2266 | +| 17 | 49557 | 2.2258 | +| 18 | 49557 | 2.2248 | +| 19 | 49557 | 2.2227 | +| 20 | 49557 | 2.2206 | +| 21 | 49557 | 2.2189 | +| 22 | 49557 | 2.2169 | +| 23 | 49557 | 2.2161 | +| 24 | 49557 | 2.215 | +| 25 | 49557 | 2.2136 | +| 26 | 49557 | 2.213 | +| 27 | 49557 | 2.2122 | +| 28 | 49557 | 2.211 | +| 29 | 49557 | 2.2104 | +| 30 | 49557 | 2.2096 | +| 31 | 49557 | 2.2092 | +| 32 | 49557 | 2.2089 | +| 33 | 49557 | 2.2088 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +2836 outliers have been identified. + +Performing multi-dataset profile/summation intensity optimisation. +--------------------------------------- +| Combination | CC1/2 | Rmeas | +--------------------------------------- +| prf only | 0.99905 | 0.05791 | +| sum only | 0.99873 | 0.06698 | +| Imid = 892.04 | 0.9955 | 0.18369 | +| Imid = 11484.08 | 0.95126 | 0.30286 | +| Imid = 1148.41 | 0.99433 | 0.20716 | +| Imid = 114.84 | 0.9986 | 0.07665 | +--------------------------------------- +Profile intensities determined to be best for scaling. + +Combined outlier rejection has been performed across multiple datasets, +2836 outliers have been identified. + +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 1.88731789589 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 48841 | 1.7985 | +| 1 | 48841 | 1.7977 | +| 2 | 48841 | 1.7972 | +| 3 | 48841 | 1.7966 | +| 4 | 48841 | 1.7959 | +| 5 | 48841 | 1.7955 | +| 6 | 48841 | 1.7953 | +| 7 | 48841 | 1.7951 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +2928 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139591 | 0.36934 | +| 1 | 139591 | 0.16278 | +| 2 | 139591 | 0.13182 | +| 3 | 139591 | 0.13112 | +| 4 | 139591 | 0.13074 | +| 5 | 139591 | 0.13033 | +| 6 | 139591 | 0.13033 | +-------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00079, b = 0.04915 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 20.331 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10158.10 - 1831.05 | 1395 | 20.225 | 0.714 | +| 1831.05 - 1394.55 | 1395 | 14.21 | 0.857 | +| 1394.55 - 1177.87 | 1395 | 12.687 | 0.927 | +| 1177.87 - 918.90 | 2750 | 10.94 | 0.975 | +| 918.90 - 503.94 | 12006 | 7.616 | 1.101 | +| 503.94 - 276.37 | 20607 | 4.759 | 1.192 | +| 276.37 - 151.57 | 28212 | 2.936 | 1.209 | +| 151.57 - 83.12 | 30784 | 1.829 | 1.086 | +| 83.12 - 45.59 | 25575 | 1.302 | 0.961 | +| 45.59 - 24.99 | 15472 | 0.917 | 0.778 | +------------------------------------------------------------------------------- + +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 7.23849201202 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48832 | 0.89684 | +| 1 | 48832 | 0.87606 | +| 2 | 48832 | 0.87591 | +| 3 | 48832 | 0.87588 | +-------------------------- +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 3.54379796982 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48832 | 0.87588 | +| 1 | 48832 | 0.87588 | +-------------------------- +RMSD no longer decreasing + +================================================================================ + +Calculating error estimates of inverse scale factors. + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +132 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139403 | 0.36497 | +| 1 | 139403 | 0.15434 | +| 2 | 139403 | 0.12918 | +| 3 | 139403 | 0.12857 | +| 4 | 139403 | 0.12808 | +| 5 | 139403 | 0.12773 | +| 6 | 139403 | 0.12773 | +-------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00071, b = 0.04838 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 20.656 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10298.08 - 1828.14 | 1394 | 19.978 | 0.746 | +| 1828.14 - 1397.23 | 1394 | 13.906 | 0.857 | +| 1397.23 - 1176.87 | 1394 | 12.333 | 0.926 | +| 1176.87 - 926.49 | 2632 | 10.891 | 1.003 | +| 926.49 - 507.41 | 11942 | 7.48 | 1.096 | +| 507.41 - 277.90 | 20540 | 4.637 | 1.185 | +| 277.90 - 152.20 | 28106 | 2.886 | 1.202 | +| 152.20 - 83.35 | 30818 | 1.808 | 1.08 | +| 83.35 - 45.65 | 25548 | 1.279 | 0.948 | +| 45.65 - 24.99 | 15635 | 0.918 | 0.777 | +------------------------------------------------------------------------------- + + +The reflection table variances have been adjusted to account for the +uncertainty in the scaling models for all datasets +0 reflections set as outliers: scale factor < 0.001 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Total time taken: 26.2374s + +================================================================================ + +Warning: Over half (55.36%) of model parameters have signficant +uncertainty (sigma/abs(parameter) > 0.5), which could indicate a +poorly-determined scaling problem or overparameterisation. + +Summary of dataset partialities +---------------------------- +| Partiality (p) | n_refl | +---------------------------- +| all reflections | 306137 | +| p > 0.99 | 244580 | +| 0.5 < p < 0.99 | 4670 | +| 0.01 < p < 0.5 | 10499 | +| p < 0.01 | 46388 | +---------------------------- + +Reflections below a partiality_cutoff of 0.4 are not considered for any +part of the scaling analysis or for the reporting of merging statistics. +Additionally, if applicable, only reflections with a min_partiality > 0.95 +were considered for use when refining the scaling model. + + + ----------Merging statistics---------- + +Resolution: 68.36 - 1.80 +Observations: 212648 +Unique reflections: 20140 +Redundancy: 10.6 +Completeness: 85.42% +Mean intensity: 152.6 +Mean I/sigma(I): 27.7 +R-merge: 0.057 +R-meas: 0.060 +R-pim: 0.016 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 68.41 4.89 20729 1334 15.54 100.00 319.6 53.3 0.048 0.050 0.012 0.999* -0.036 + 4.89 3.88 20469 1244 16.45 100.00 483.2 56.8 0.046 0.048 0.011 0.999* -0.135 + 3.88 3.39 19974 1208 16.53 100.00 370.6 52.7 0.049 0.050 0.012 0.999* -0.049 + 3.39 3.08 20078 1189 16.89 100.00 261.0 47.6 0.054 0.056 0.014 0.999* -0.044 + 3.08 2.86 20273 1185 17.11 100.00 181.1 41.5 0.060 0.062 0.015 0.999* -0.086 + 2.86 2.69 20469 1191 17.19 100.00 146.4 38.6 0.066 0.068 0.016 0.998* -0.131 + 2.69 2.55 20173 1172 17.21 100.00 115.0 33.1 0.076 0.078 0.019 0.998* 0.011 + 2.55 2.44 16110 1167 13.80 100.00 103.7 27.8 0.080 0.083 0.022 0.997* -0.103 + 2.44 2.35 12117 1162 10.43 99.91 90.2 23.2 0.083 0.088 0.027 0.996* -0.028 + 2.35 2.27 10135 1180 8.59 99.92 88.8 20.7 0.086 0.092 0.031 0.994* 0.086* + 2.27 2.20 8323 1150 7.24 99.65 76.7 17.0 0.090 0.097 0.036 0.994* -0.202 + 2.20 2.13 6830 1165 5.86 99.06 69.4 13.9 0.093 0.102 0.041 0.993* -0.061 + 2.13 2.08 5300 1116 4.75 97.04 60.4 11.2 0.098 0.110 0.048 0.990* -0.249 + 2.08 2.03 4021 1056 3.81 91.27 53.5 9.3 0.102 0.117 0.056 0.986* -0.103 + 2.03 1.98 3076 1001 3.07 86.14 45.4 7.4 0.108 0.129 0.068 0.982* 0.120 + 1.98 1.94 2060 896 2.30 77.85 42.9 6.1 0.102 0.127 0.074 0.975* -0.130 + 1.94 1.90 1163 700 1.66 61.03 36.7 4.6 0.118 0.153 0.096 0.962* 0.000 + 1.90 1.86 751 531 1.41 46.21 31.8 3.8 0.113 0.153 0.101 0.967* 0.000 + 1.86 1.83 464 366 1.27 31.88 29.1 3.3 0.110 0.153 0.105 0.965* 0.000 + 1.83 1.80 133 127 1.05 11.07 25.0 2.6 0.373 0.528 0.373 -0.318 0.000 + 68.36 1.80 212648 20140 10.56 85.42 152.6 27.7 0.057 0.060 0.016 0.999* -0.099 + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.800 + based on CC(1/2) >= 0.33 : 1.831 + based on mean(I/sigma) >= 2.0 : 1.831 + based on R-merge < 0.5 : 1.831 + based on R-meas < 0.5 : 1.831 + based on completeness >= 90% : 2.028 + based on completeness >= 50% : 1.901 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + +Writing html report to: scaling.html + +================================================================================ + +Saving the experiments to scaled.expt +Time taken: 0.339957 +Saving the scaled reflections to scaled.refl +Time taken: 1.47307 +See dials.github.io/dials_scale_user_guide.html for more info on scaling options diff --git a/tutorial_data/master/multi_crystal/dials.scale_exclude.cmd b/tutorial_data/master/multi_crystal/dials.scale_exclude.cmd new file mode 100644 index 000000000..da16b8a90 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale_exclude.cmd @@ -0,0 +1 @@ +dials.scale scaled.expt scaled.refl d_min=1.80 \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.scale_exclude.log b/tutorial_data/master/multi_crystal/dials.scale_exclude.log new file mode 100644 index 000000000..73a9fce3e --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.scale_exclude.log @@ -0,0 +1,466 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +cut_data { + d_min = 1.8 +} +input { + experiments = scaled.expt + reflections = scaled.refl +} + +Checking for the existence of a reflection table +containing multiple datasets + +Detected existence of a multi-dataset reflection table +containing 4 datasets. + +Found 4 reflection tables & 4 experiments in total. + +Dataset unique identifiers are ['0', '1', '2', '3'] + +Space group being used during scaling is P 4 2 2 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Scaling models have been initialised for all experiments. + +================================================================================ + +The experiment identifier for this dataset is 0 +Preprocessing data for scaling. The id assigned to this +dataset is 0, and the scaling model type being applied is physical. + +22812/76079 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 21712 +criterion: not integrated by any method, reflections: 17194 +criterion: user excluded, reflections: 13656 +criterion: bad d-value, reflections: 8461 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 1 +Preprocessing data for scaling. The id assigned to this +dataset is 1, and the scaling model type being applied is physical. + +22043/75607 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 20762 +criterion: not integrated by any method, reflections: 16091 +criterion: user excluded, reflections: 13186 +criterion: bad d-value, reflections: 7556 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 2 +Preprocessing data for scaling. The id assigned to this +dataset is 2, and the scaling model type being applied is physical. + +24879/77983 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 23522 +criterion: not integrated by any method, reflections: 18787 +criterion: user excluded, reflections: 15473 +criterion: bad d-value, reflections: 9985 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +The experiment identifier for this dataset is 3 +Preprocessing data for scaling. The id assigned to this +dataset is 3, and the scaling model type being applied is physical. + +23621/76468 reflections not suitable for scaling +Reflections passing individual criteria: +criterion: excluded for scaling, reflections: 22591 +criterion: not integrated by any method, reflections: 17982 +criterion: user excluded, reflections: 13968 +criterion: bad d-value, reflections: 8998 + +The following corrections will be applied to this dataset: + +----------------------------- +| correction | n_parameters | +----------------------------- +| scale | 10 | +| decay | 8 | +| absorption | 24 | +----------------------------- +Using previously determined optimal intensity choice: profile intensities + +Completed preprocessing and initialisation for this dataset. + +================================================================================ + +Configuring a MultiScaler to handle the individual Scalers. + +Determining symmetry equivalent reflections across datasets. + + +Determining highly connected reflections across datasets for scaling model +minimisation. Prefiltering for symmetry groups that have reflections with +multiplicity of at least 2 with > 1.0. This leaves 197826 out of 212782 reflections +to potentially use for scaling model minimisation based on cross-dataset +connectedness (these belong to 16683 symmetry groups). + +Attempting to choose at least 5357 reflections from each dataset, +with a total number between 21428 and 64284.0. + +Choosing 35270 cross-dataset connected reflections from 1487 symmetry groups for minimisation. + +Summary of reflections chosen for minimisation from each dataset: +---------------------------------------------------------------------- +| Dataset id | reflections | reflections | combined number | +| | connected to | highly connected | of reflections | +| | other datasets | within dataset | | +---------------------------------------------------------------------- +| 0 | 5358 | 4824 | 9675 | +| 1 | 10014 | 4567 | 13342 | +| 2 | 9278 | 4135 | 12547 | +| 3 | 10620 | 4728 | 14027 | +---------------------------------------------------------------------- +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 2.86744880676 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 49544 | 2.1939 | +| 1 | 49544 | 2.1903 | +| 2 | 49544 | 2.188 | +| 3 | 49544 | 2.1847 | +| 4 | 49544 | 2.1831 | +| 5 | 49544 | 2.1813 | +| 6 | 49544 | 2.1802 | +| 7 | 49544 | 2.1793 | +| 8 | 49544 | 2.1788 | +| 9 | 49544 | 2.1781 | +| 10 | 49544 | 2.1777 | +| 11 | 49544 | 2.1771 | +| 12 | 49544 | 2.1769 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +2859 outliers have been identified. + +Performing multi-dataset profile/summation intensity optimisation. +--------------------------------------- +| Combination | CC1/2 | Rmeas | +--------------------------------------- +| prf only | 0.99902 | 0.05804 | +| sum only | 0.99869 | 0.0671 | +| Imid = 894.05 | 0.9954 | 0.18389 | +| Imid = 11987.04 | 0.95007 | 0.30105 | +| Imid = 1198.7 | 0.99396 | 0.21123 | +| Imid = 119.87 | 0.99856 | 0.07759 | +--------------------------------------- +Profile intensities determined to be best for scaling. + +Combined outlier rejection has been performed across multiple datasets, +2859 outliers have been identified. + +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 2.12460398674 + +Refinement steps: +------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +------------------------- +| 0 | 48821 | 1.7898 | +| 1 | 48821 | 1.7891 | +| 2 | 48821 | 1.7882 | +| 3 | 48821 | 1.7873 | +| 4 | 48821 | 1.7867 | +| 5 | 48821 | 1.7861 | +| 6 | 48821 | 1.7858 | +| 7 | 48821 | 1.7855 | +| 8 | 48821 | 1.7854 | +------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +================================================================================ + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +2922 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139578 | 0.36978 | +| 1 | 139578 | 0.16278 | +| 2 | 139578 | 0.13176 | +| 3 | 139578 | 0.13105 | +| 4 | 139578 | 0.13067 | +| 5 | 139578 | 0.13025 | +| 6 | 139578 | 0.13025 | +-------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00076, b = 0.04909 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 20.355 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10187.12 - 1829.11 | 1395 | 20.076 | 0.718 | +| 1829.11 - 1395.43 | 1395 | 13.917 | 0.838 | +| 1395.43 - 1177.32 | 1395 | 12.83 | 0.95 | +| 1177.32 - 920.52 | 2711 | 10.928 | 0.977 | +| 920.52 - 504.69 | 12019 | 7.68 | 1.105 | +| 504.69 - 276.71 | 20605 | 4.76 | 1.193 | +| 276.71 - 151.71 | 28190 | 2.92 | 1.205 | +| 151.71 - 83.18 | 30832 | 1.822 | 1.081 | +| 83.18 - 45.60 | 25545 | 1.295 | 0.956 | +| 45.60 - 24.99 | 15491 | 0.915 | 0.776 | +------------------------------------------------------------------------------- + +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 4.49458599091 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48794 | 0.8922 | +| 1 | 48794 | 0.87581 | +| 2 | 48794 | 0.87578 | +-------------------------- +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 2.92792606354 + +Refinement steps: +-------------------------- +| Step | Nref | RMSD_I | +| | | (a.u) | +-------------------------- +| 0 | 48794 | 0.87578 | +| 1 | 48794 | 0.87578 | +-------------------------- +RMSD no longer decreasing + +================================================================================ + +Calculating error estimates of inverse scale factors. + +Scale factors determined during minimisation have now been +applied to all datasets. + +Combined outlier rejection has been performed across multiple datasets, +131 outliers have been identified. + +Performing a round of error model refinement. + +Refinement steps: +-------------------------------- +| Step | Nref | RMSD_deltahl | +| | | (a.u) | +-------------------------------- +| 0 | 139407 | 0.36619 | +| 1 | 139407 | 0.15606 | +| 2 | 139407 | 0.12953 | +| 3 | 139407 | 0.1289 | +| 4 | 139407 | 0.12844 | +| 5 | 139407 | 0.12807 | +| 6 | 139407 | 0.12807 | +-------------------------------- +RMSD no longer decreasing +lbfgs minimizer stop: callback_after_step is True + +Error model details: + Type: basic + Current parameters: a = 1.00070, b = 0.04850 + Error model formula: σ'² = a²(σ² + (bI)²) + estimated I/sigma asymptotic limit: 20.603 + +Results of error model refinement. Uncorrected and corrected variances +of normalised intensity deviations for given intensity ranges. Variances +are expected to be ~1.0 for reliable errors (sigmas). +------------------------------------------------------------------------------- +| Intensity range () | n_refl | Uncorrected variance | Corrected variance | +------------------------------------------------------------------------------- +| 10305.07 - 1826.98 | 1394 | 19.843 | 0.736 | +| 1826.98 - 1397.21 | 1394 | 13.791 | 0.844 | +| 1397.21 - 1177.13 | 1394 | 12.625 | 0.952 | +| 1177.13 - 926.85 | 2627 | 10.947 | 1.009 | +| 926.85 - 507.57 | 11944 | 7.5 | 1.097 | +| 507.57 - 277.96 | 20540 | 4.644 | 1.183 | +| 277.96 - 152.22 | 28111 | 2.891 | 1.201 | +| 152.22 - 83.36 | 30824 | 1.809 | 1.078 | +| 83.36 - 45.65 | 25544 | 1.28 | 0.948 | +| 45.65 - 24.99 | 15635 | 0.918 | 0.776 | +------------------------------------------------------------------------------- + + +The reflection table variances have been adjusted to account for the +uncertainty in the scaling models for all datasets +0 reflections set as outliers: scale factor < 0.001 +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) + +Total time taken: 18.7017s + +================================================================================ + +Warning: Over half (55.36%) of model parameters have signficant +uncertainty (sigma/abs(parameter) > 0.5), which could indicate a +poorly-determined scaling problem or overparameterisation. + +Summary of dataset partialities +---------------------------- +| Partiality (p) | n_refl | +---------------------------- +| all reflections | 306137 | +| p > 0.99 | 244580 | +| 0.5 < p < 0.99 | 4670 | +| 0.01 < p < 0.5 | 10499 | +| p < 0.01 | 46388 | +---------------------------- + +Reflections below a partiality_cutoff of 0.4 are not considered for any +part of the scaling analysis or for the reporting of merging statistics. +Additionally, if applicable, only reflections with a min_partiality > 0.95 +were considered for use when refining the scaling model. + + + ----------Merging statistics---------- + +Resolution: 68.36 - 1.80 +Observations: 212642 +Unique reflections: 20140 +Redundancy: 10.6 +Completeness: 85.42% +Mean intensity: 152.1 +Mean I/sigma(I): 27.6 +R-merge: 0.057 +R-meas: 0.060 +R-pim: 0.016 + + +Statistics by resolution bin: + d_max d_min #obs #uniq mult. %comp r_mrg r_meas r_pim cc1/2 cc_ano + 68.41 4.89 20727 1334 15.54 100.00 318.6 53.2 0.048 0.050 0.012 0.999* -0.033 + 4.89 3.88 20468 1244 16.45 100.00 481.8 56.7 0.046 0.048 0.011 0.999* -0.131 + 3.88 3.39 19972 1208 16.53 100.00 369.5 52.6 0.049 0.050 0.012 0.999* -0.050 + 3.39 3.08 20077 1189 16.89 100.00 260.3 47.5 0.054 0.056 0.014 0.999* -0.042 + 3.08 2.86 20273 1185 17.11 100.00 180.6 41.5 0.060 0.062 0.015 0.999* -0.086 + 2.86 2.69 20469 1191 17.19 100.00 146.0 38.5 0.066 0.068 0.016 0.998* -0.131 + 2.69 2.55 20173 1172 17.21 100.00 114.6 33.0 0.076 0.078 0.019 0.998* 0.012 + 2.55 2.44 16110 1167 13.80 100.00 103.4 27.8 0.080 0.083 0.022 0.997* -0.103 + 2.44 2.35 12117 1162 10.43 99.91 89.9 23.2 0.083 0.088 0.027 0.996* -0.029 + 2.35 2.27 10135 1180 8.59 99.92 88.5 20.6 0.086 0.092 0.031 0.994* 0.084* + 2.27 2.20 8323 1150 7.24 99.65 76.5 17.0 0.090 0.097 0.036 0.994* -0.204 + 2.20 2.13 6830 1165 5.86 99.06 69.2 13.9 0.093 0.102 0.041 0.993* -0.062 + 2.13 2.08 5300 1116 4.75 97.04 60.3 11.2 0.098 0.110 0.048 0.990* -0.248 + 2.08 2.03 4021 1056 3.81 91.27 53.4 9.3 0.102 0.118 0.056 0.986* -0.104 + 2.03 1.98 3076 1001 3.07 86.14 45.2 7.4 0.108 0.129 0.068 0.982* 0.126 + 1.98 1.94 2060 896 2.30 77.85 42.7 6.1 0.102 0.127 0.074 0.975* -0.130 + 1.94 1.90 1163 700 1.66 61.03 36.6 4.6 0.117 0.152 0.096 0.962* 0.000 + 1.90 1.86 751 531 1.41 46.21 31.7 3.7 0.113 0.152 0.101 0.967* 0.000 + 1.86 1.83 464 366 1.27 31.88 29.0 3.3 0.111 0.153 0.105 0.964* 0.000 + 1.83 1.80 133 127 1.05 11.07 24.9 2.6 0.373 0.528 0.373 -0.317 0.000 + 68.36 1.80 212642 20140 10.56 85.42 152.1 27.6 0.057 0.060 0.016 0.999* -0.077 + + + + + ----------Resolution cutoff estimates---------- + + resolution of all data : 1.800 + based on CC(1/2) >= 0.33 : 1.831 + based on mean(I/sigma) >= 2.0 : 1.831 + based on R-merge < 0.5 : 1.831 + based on R-meas < 0.5 : 1.831 + based on completeness >= 90% : 2.028 + based on completeness >= 50% : 1.901 + +NOTE: we recommend using all data out to the CC(1/2) limit +for refinement. + +Writing html report to: scaling.html + +================================================================================ + +Saving the experiments to scaled.expt +Time taken: 0.4271 +Saving the scaled reflections to scaled.refl +Time taken: 2.05826 +See dials.github.io/dials_scale_user_guide.html for more info on scaling options diff --git a/tutorial_data/master/multi_crystal/dials.symmetry.cmd b/tutorial_data/master/multi_crystal/dials.symmetry.cmd new file mode 100644 index 000000000..002b3c057 --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.symmetry.cmd @@ -0,0 +1 @@ +dials.symmetry scaled.expt scaled.refl laue_group=None \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/dials.symmetry.log b/tutorial_data/master/multi_crystal/dials.symmetry.log new file mode 100644 index 000000000..7a81083ac --- /dev/null +++ b/tutorial_data/master/multi_crystal/dials.symmetry.log @@ -0,0 +1,62 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +laue_group = None +input { + experiments = scaled.expt + reflections = scaled.refl +} + +Detected existence of a multi-dataset reflection table +containing 4 datasets. + +================================================================================ + +Analysing systematic absences + +Read 76079 predicted reflections +Selected 53251 scaled reflections +Combined 68 partial reflections with other partial reflections +Read 75607 predicted reflections +Selected 53545 scaled reflections +Combined 77 partial reflections with other partial reflections +Read 77983 predicted reflections +Selected 53065 scaled reflections +Combined 106 partial reflections with other partial reflections +Read 76468 predicted reflections +Selected 52781 scaled reflections +Combined 69 partial reflections with other partial reflections +Using median unit cell across experiments : (68.3603, 68.3603, 103.953, 90, 90, 90) +Resolution estimate from / > 4.0 : 1.80 +Resolution estimate from CC1/2 > 0.60: 1.80 +Performing systematic absence checks on scaled data +Read 306137 predicted reflections +Selected 212642 scaled reflections +Removed 1 reflections with d < 1.80 +Combined 68 partial reflections with other partial reflections +Combined 77 partial reflections with other partial reflections +Combined 106 partial reflections with other partial reflections +Combined 69 partial reflections with other partial reflections +Removed 4080 reflections below partiality threshold +Laue group: P 4/m m m +--------------------------------------------------------------------------------------------------------------- +| Screw axis | Score | No. present | No. absent | present | absent | present | absent | +--------------------------------------------------------------------------------------------------------------- +| 41c | 1.000 | 11 | 33 | 728.990 | 0.128 | 32.486 | 0.382 | +| 21a | 1.000 | 14 | 14 | 957.612 | 0.523 | 21.366 | 0.970 | +| 42c | 1.000 | 22 | 22 | 364.336 | 0.351 | 16.558 | 0.257 | +--------------------------------------------------------------------------------------------------------------- +------------------------ +| Space group | score | +------------------------ +| P 4 2 2 | 0.0000 | +| P 4 21 2 | 0.0000 | +| P 41 2 2 | 0.0000 | +| P 42 2 2 | 0.0000 | +| P 41 21 2 | 1.0000 | +| P 42 21 2 | 0.0000 | +------------------------ +Recommended space group: P 41 21 2 +Space group with equivalent score (enantiomorphic pair): P 43 21 2 +Saving reindexed experiments to symmetrized.expt +Saving 306137 reindexed reflections to symmetrized.refl diff --git a/tutorial_data/master/multi_crystal/scaling.html b/tutorial_data/master/multi_crystal/scaling.html new file mode 100644 index 000000000..d73bdf684 --- /dev/null +++ b/tutorial_data/master/multi_crystal/scaling.html @@ -0,0 +1,2919 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+

DIALS scaling report

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Summary of merging statistics

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OverallLow resolutionHigh resolution
Resolution (Å)68.36 - 1.8068.41 - 4.891.83 - 1.80
Observations21264220727133
Unique reflections201401334127
Multiplicity10.615.51.0
Completeness85.42%100.00%11.07%
Mean I/sigma(I)27.653.22.6
Rmerge0.0570.0480.373
Rmeas0.0600.0500.528
Rpim0.0160.0120.373
CC1/20.9990.999-0.317
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Merging statistics by resolution bin

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Resolution (Å)N(obs)N(unique)MultiplicityCompletenessMean(I)Mean(I/sigma)RmergeRmeasRpimCC1/2CCano
68.41 - 4.8920727133415.54100.00318.653.20.0480.0500.0120.999*-0.033
4.89 - 3.8820468124416.45100.00481.856.70.0460.0480.0110.999*-0.131
3.88 - 3.3919972120816.53100.00369.552.60.0490.0500.0120.999*-0.050
3.39 - 3.0820077118916.89100.00260.347.50.0540.0560.0140.999*-0.042
3.08 - 2.8620273118517.11100.00180.641.50.0600.0620.0150.999*-0.086
2.86 - 2.6920469119117.19100.00146.038.50.0660.0680.0160.998*-0.131
2.69 - 2.5520173117217.21100.00114.633.00.0760.0780.0190.998*0.012
2.55 - 2.4416110116713.80100.00103.427.80.0800.0830.0220.997*-0.103
2.44 - 2.3512117116210.4399.9189.923.20.0830.0880.0270.996*-0.029
2.35 - 2.271013511808.5999.9288.520.60.0860.0920.0310.994*0.084*
2.27 - 2.20832311507.2499.6576.517.00.0900.0970.0360.994*-0.204
2.20 - 2.13683011655.8699.0669.213.90.0930.1020.0410.993*-0.062
2.13 - 2.08530011164.7597.0460.311.20.0980.1100.0480.990*-0.248
2.08 - 2.03402110563.8191.2753.49.30.1020.1180.0560.986*-0.104
2.03 - 1.98307610013.0786.1445.27.40.1080.1290.0680.982*0.126
1.98 - 1.9420608962.3077.8542.76.10.1020.1270.0740.975*-0.130
1.94 - 1.9011637001.6661.0336.64.60.1170.1520.0960.962*0.000
1.90 - 1.867515311.4146.2131.73.70.1130.1520.1010.967*0.000
1.86 - 1.834643661.2731.8829.03.30.1110.1530.1050.964*0.000
1.83 - 1.801331271.0511.0724.92.60.3730.5280.373-0.3170.000
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+ + + + diff --git a/tutorial_data/master/multi_crystal/xia2.multiplex.cmd b/tutorial_data/master/multi_crystal/xia2.multiplex.cmd new file mode 100644 index 000000000..e7590389e --- /dev/null +++ b/tutorial_data/master/multi_crystal/xia2.multiplex.cmd @@ -0,0 +1 @@ +xia2.multiplex /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_0.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_1.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_2.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_3.expt /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_0.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_1.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_2.refl /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_3.refl \ No newline at end of file diff --git a/tutorial_data/master/multi_crystal/xia2.multiplex.html b/tutorial_data/master/multi_crystal/xia2.multiplex.html new file mode 100644 index 000000000..67b3671c4 --- /dev/null +++ b/tutorial_data/master/multi_crystal/xia2.multiplex.html @@ -0,0 +1,3186 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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xia2.multiplex report

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Cosym Analysis

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+ Symmetry analysis +

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Scoring individual symmetry operations

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likelihoodZ-CCCCOperator
0.9449.860.99*** 4^-1 |(0, 0, 1)
0.9449.870.99*** 2 |(0, 1, 0)
0.9439.840.98*** 2 |(-1, 1, 0)
0.9429.830.98*** 2 |(0, 0, 1)
0.9459.880.99*** 2 |(1, 1, 0)
0.9419.820.98*** 4 |(0, 0, 1)
0.9429.830.98*** 2 |(1, 0, 0)
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Scoring all possible subgroups

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Patterson groupLikelihoodNetZccZcc+Zcc-deltaReindex operator
P 4/m m m***1.000 9.85 9.85 0.000.0-a,-b,c
C m m m0.000 0.01 9.85 9.840.0a+b,-a+b,c
P m m m0.000-0.01 9.84 9.850.0-a,-b,c
P 4/m0.000-0.02 9.84 9.860.0-a,-b,c
C 1 2/m 10.000 0.04 9.88 9.840.0a-b,a+b,c
P 1 2/m 10.000 0.02 9.87 9.840.0-a,-b,c
C 1 2/m 10.000-0.00 9.84 9.850.0a+b,-a+b,c
P 1 2/m 10.000-0.02 9.83 9.850.0-a,-c,-b
P 1 2/m 10.000-0.02 9.83 9.850.0-b,-a,-c
P -10.000-9.85 0.00 9.850.0-a,-b,c
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Best solutionP 4/m m m
Unit cell68.360 68.360 103.953 90.0 90.0 90.0
Reindex operator-x,-y,z
Laue group probability1.000
Laue group confidence1.000
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+ + +
+ + + +
+ + + + +
+ + +
+ + +
+ + + +
+ + + +
+
+
+
+ +
+
+

+ Unit cell analysis +

+
+
+
+
+ + +
+ + +
+ + +
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+ + + + +
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+ + +
+ + + +
+ + + + +
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+
+
+
+ +
+
+

+ Orientation analysis +

+
+
+
+
+ + +
+ + +
+ + +
+ + + +
+ + + + +
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+ + +
+ + + +
+ + + + +
+ + +
+ + +
+ + + +
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+
+
+
+ +
+
+

+ Intensity clustering +

+
+
+
+ +
+
+

+ Correlation coefficient clustering +

+
+
+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ClusterNo. datasetsDatasetsHeightMultiplicityCompleteness
12 0 30.00283.40.68
22 1 20.00385.70.79
34 0 1 2 30.00458.20.83
+
+
+ + +
+ + +
+ + + +
+ +
+
+
+
+ +
+
+

+ Cos angle clustering +

+
+
+
+ +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ClusterNo. datasetsDatasetsHeightMultiplicityCompleteness
12 1 21e-055.70.79
23 1 2 30.00935.70.79
34 0 1 2 30.0328.20.83
+
+
+ + +
+ + +
+ + + +
+ +
+ + + +
+ + +
+ + +
+ + + +
+ + + + +
+ + +
+ + +
+ + + +
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+
+
+ +
+
+
+ +
+ +
+ + + +
+ +
+

Detailed statistics for dataset All data

+ +
+ +
+
+

+ Overall +

+
+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OverallLow resolutionHigh resolution
Resolution (Å)68.36 - 1.8068.41 - 4.891.83 - 1.80
Observations21266820739133
Unique reflections201401334127
Multiplicity10.615.51.0
Completeness85.43%100.00%11.07%
Mean I/sigma(I)26.850.92.6
Rmerge0.0600.0500.345
Rmeas0.0630.0520.488
Rpim0.0170.0130.345
CC1/20.9990.999-0.418
+
+
+
+
+
+ +
+
+

+ Resolution shells +

+
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Resolution (Å)N(obs)N(unique)MultiplicityCompletenessMean(I)Mean(I/sigma)RmergeRmeasRpimCC1/2CCano
68.41 - 4.8920739133415.55100.00292.450.90.0500.0520.0130.999*-0.122
4.89 - 3.8820474124416.46100.00441.654.20.0470.0480.0120.999*-0.103
3.88 - 3.3919974120816.53100.00338.150.50.0500.0520.0130.999*-0.092
3.39 - 3.0820085118916.89100.00238.045.80.0570.0590.0140.999*-0.058
3.08 - 2.8620273118517.11100.00165.040.20.0650.0670.0160.999*-0.099
2.86 - 2.6920468119117.19100.00133.537.50.0710.0740.0170.998*-0.150
2.69 - 2.5520172117217.21100.00104.732.20.0810.0830.0200.998*-0.087
2.55 - 2.4416109116713.80100.0094.627.10.0860.0890.0240.996*-0.067
2.44 - 2.3512118116210.4399.9182.422.70.0900.0940.0290.995*-0.053
2.35 - 2.271013511808.5999.9281.220.20.0940.1000.0340.994*-0.012
2.27 - 2.20832211507.2499.6570.316.70.0960.1040.0380.992*-0.135
2.20 - 2.13683111655.8699.0663.613.60.1020.1120.0440.991*-0.066
2.13 - 2.08530011164.7597.0455.611.00.1050.1180.0520.988*-0.015
2.08 - 2.03402110563.8191.2749.19.20.1070.1220.0590.986*-0.055
2.03 - 1.98307610013.0786.1441.77.30.1150.1370.0730.976*0.036
1.98 - 1.9420608962.3077.8539.46.10.1110.1390.0810.966*0.027
1.94 - 1.9011637001.6661.0334.04.60.1290.1680.1050.955*0.000
1.90 - 1.867515311.4146.2129.43.70.1270.1710.1130.960*0.000
1.86 - 1.834643661.2731.8826.93.30.1200.1670.1150.956*0.000
1.83 - 1.801331271.0511.0723.22.60.3450.4880.345-0.4180.000
+
+ *significant at p=0.01 +
+
+
+ +
+ +
+ +
+

Analysis plots

+ +
+
+
+

+ Analysis by resolution +

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+

+ Analysis by batch +

+
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+ + +
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+
+
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+
+
+

+ Miscellaneous +

+
+
+
+
+ + + + + + + + + + + + + +
+
+
+
+
+ +
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+ +
+ + + + + + diff --git a/tutorial_data/master/multi_crystal/xia2.multiplex.log b/tutorial_data/master/multi_crystal/xia2.multiplex.log new file mode 100644 index 000000000..58707f2e1 --- /dev/null +++ b/tutorial_data/master/multi_crystal/xia2.multiplex.log @@ -0,0 +1,57 @@ +DIALS 2.dev.1062-gb01dfcdc9 +The following parameters have been modified: + +input { + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_0.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_1.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_2.expt + experiments = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/experiments_3.expt + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_0.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_1.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_2.refl + reflections = /dls/science/users/hko55533/software/cctbx/build/dials_data/vmxi_proteinase_k_sweeps/reflections_3.refl +} + +Selecting 4 experiments with profile-fitted reflections +Selecting 4 experiments with refined reflections + Unit cell: (68.3603, 68.3603, 103.953, 90, 90, 90) + +0 singletons: + +Point group a b c alpha beta gamma + +1 cluster: + +Cluster_id N_xtals Med_a Med_b Med_c Med_alpha Med_beta Med_gamma Delta(deg) +4 in P422. +cluster_1 4 68.36 (0.01 ) 68.36 (0.01 ) 103.95(0.02 ) 90.00 (0.00) 90.00 (0.00) 90.00 (0.00) + P 4/m m m (No. 123) 68.36 68.36 103.95 90.00 90.00 90.00 0.0 + + +Standard deviations are in brackets. +Each cluster: +Input lattice count, with integration Bravais setting space group. +Cluster median with Niggli cell parameters (std dev in brackets). +Highest possible metric symmetry and unit cell using LePage (J Appl Cryst 1982, 15:255) method, maximum delta 3deg. +Using all data sets for subsequent analysis +Laue group determined by dials.cosym: P 4 2 2 +Resolution limit: 1.80 (cc_half > 0.3) +Space group determined by dials.symmetry: P 41 21 2 + +Intensity correlation clustering summary: +========= ============== ========== ======== ============== ============== + Cluster No. datasets Datasets Height Multiplicity Completeness +========= ============== ========== ======== ============== ============== + 1 2 0 3 0.0028 3.4 0.68 + 2 2 1 2 0.0038 5.7 0.79 + 3 4 0 1 2 3 0.0045 8.2 0.83 +========= ============== ========== ======== ============== ============== + +Cos(angle) clustering summary: +========= ============== ========== ======== ============== ============== + Cluster No. datasets Datasets Height Multiplicity Completeness +========= ============== ========== ======== ============== ============== + 1 2 1 2 1e-05 5.7 0.79 + 2 3 1 2 3 0.0093 5.7 0.79 + 3 4 0 1 2 3 0.032 8.2 0.83 +========= ============== ========== ======== ============== ==============