##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: #phil __ON__ scaling { input { asu_contents { sequence_file = None n_residues = None n_bases = None n_copies_per_asu = 2 } xray_data { file_name = "/net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz" obs_labels = "F-obs" calc_labels = None unit_cell = 40.862 46.758 283.125 90 90 90 space_group = "P 2 2 21" high_resolution = 2.18 low_resolution = None reference { data { file_name = None labels = None unit_cell = None space_group = None } structure { file_name = None } } } parameters { reporting { verbose = 1 log = "/net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz_xtriage.log" loggraphs = False } merging { n_bins = 10 skip_merging = False } misc_twin_parameters { missing_symmetry { sigma_inflation = 1.25 } twinning_with_ncs { perform_analyses = False n_bins = 7 } twin_test_cuts { low_resolution = 10 high_resolution = None isigi_cut = 3 completeness_cut = 0.85 } apply_basic_filters_prior_to_twin_analysis = True } } optional { hklout = None hklout_type = mtz sca *Auto label_extension = "massaged" aniso { action = *remove_aniso None final_b = *eigen_min eigen_mean user_b_iso b_iso = None } outlier { action = *extreme basic beamstop None parameters { basic_wilson { level = 1e-06 } extreme_wilson { level = 0.01 } beamstop { level = 0.001 d_min = 10 } } } symmetry { action = detwin twin *None twinning_parameters { twin_law = None fraction = None } } } } gui { result_file = None output_dir = None job_title = None } } #phil __END__ Symmetry, cell and reflection file content summary Miller array info: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz:F-obs,SIGF-obs Observation type: xray.amplitude Type of data: double, size=27157 Type of sigmas: double, size=27157 Number of Miller indices: 27157 Anomalous flag: False Unit cell: (40.862, 46.758, 283.125, 90, 90, 90) Space group: P 2 2 21 (No. 17) Systematic absences: 0 Centric reflections: 4004 Resolution range: 47.1875 2.18069 Completeness in resolution range: 0.920389 Completeness with d_max=infinity: 0.920327 Wavelength: 1.0000 ################################################################################ # Basic statistics # ################################################################################ =================== Solvent content and Matthews coefficient ================== Number of residues unknown, assuming 50% solvent content Best guess : 495 residues in the ASU Caution: this estimate is based on the distribution of solvent content across structures in the PDB, but it does not take into account the resolution of the data (which is strongly correlated with solvent content) or the physical properties of the model (such as oligomerization state, et cetera). If you encounter problems with molecular replacement and/or refinement, you may need to consider the possibility that the ASU contents are different than expected. Number of copies per asymmetric unit provided Will use user specified value of 2.0 ======================== Data strength and completeness ======================= ----------Completeness at I/sigma cutoffs---------- The following table lists the completeness in various resolution ranges, after applying a I/sigI cut. Miller indices for which individual I/sigI values are larger than the value specified in the top row of the table, are retained, while other intensities are discarded. The resulting completeness profiles are an indication of the strength of the data. **********WARNING********** Please be aware that the input data were given as amplitudes and squared for the purposes of this analysis, therefore the numbers displayed here are less reliable than the values calculated from the raw intensities. ---------------------------------------------------------------------------------------- | Completeness and data strength | |--------------------------------------------------------------------------------------| | Res. range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | |--------------------------------------------------------------------------------------| | 47.20 - 5.38 | 96.5 | 93.3 | 92.7 | 89.8 | 74.8 | 35.5 | | 5.38 - 4.27 | 95.1 | 89.2 | 87.8 | 84.4 | 68.2 | 31.9 | | 4.27 - 3.73 | 94.9 | 84.9 | 83.2 | 78.3 | 59.5 | 22.8 | | 3.73 - 3.39 | 95.2 | 81.2 | 78.1 | 70.4 | 51.7 | 23.8 | | 3.39 - 3.14 | 95.4 | 72.1 | 67.1 | 59.7 | 41.8 | 20.5 | | 3.14 - 2.96 | 94.5 | 63.0 | 58.3 | 50.4 | 36.2 | 19.4 | | 2.96 - 2.81 | 94.3 | 58.0 | 53.0 | 44.9 | 30.9 | 17.1 | | 2.81 - 2.69 | 91.4 | 49.9 | 44.9 | 37.2 | 23.9 | 11.3 | | 2.69 - 2.59 | 87.9 | 43.8 | 38.8 | 31.7 | 19.6 | 9.3 | | 2.59 - 2.50 | 85.8 | 39.1 | 34.0 | 26.4 | 15.6 | 8.8 | | 2.50 - 2.42 | 83.0 | 35.1 | 30.3 | 23.2 | 13.4 | 6.8 | | 2.42 - 2.35 | 81.0 | 34.9 | 30.1 | 23.1 | 12.2 | 6.3 | | 2.35 - 2.29 | 79.6 | 29.3 | 24.5 | 17.3 | 10.9 | 7.2 | | 2.29 - 2.23 | 76.2 | 28.2 | 24.5 | 18.5 | 11.2 | 7.4 | ---------------------------------------------------------------------------------------- The completeness of data for which I/sig(I)>3.00, exceeds 85 % for resolution ranges lower than 4.27A. As we do not want to throw away too much data, the resolution for analyzing the intensity statistics will be limited to 3.50A. ----------Low resolution completeness analyses---------- The following table shows the completeness of the data to 5.0 A. Poor low-resolution completeness often leads to map distortions and other difficulties, and is typically caused by problems with the crystal orientation during data collection, overexposure of frames, interference with the beamstop, or omission of reflections by data-processing software. --------------------------------------------------------- | Resolution range | N(obs)/N(possible) | Completeness | --------------------------------------------------------- | 47.1896 - 10.7349 | [311/314] | 0.990 | | 10.7349 - 8.5371 | [274/275] | 0.996 | | 8.5371 - 7.4628 | [278/281] | 0.989 | | 7.4628 - 6.7826 | [237/239] | 0.992 | | 6.7826 - 6.2977 | [284/285] | 0.996 | | 6.2977 - 5.9271 | [245/246] | 0.996 | | 5.9271 - 5.6308 | [261/264] | 0.989 | | 5.6308 - 5.3860 | [264/266] | 0.992 | | 5.3860 - 5.1790 | [231/233] | 0.991 | | 5.1790 - 5.0004 | [272/275] | 0.989 | --------------------------------------------------------- ----------Completeness (log-binning)---------- The table below presents an alternative overview of data completeness, using the entire resolution range but on a logarithmic scale. This is more sensitive to missing low-resolution data (and is complementary to the separate table showing low-resolution completeness only). -------------------------------------------------- | Resolution | Reflections | Completeness | -------------------------------------------------- | 47.1875 - 16.0889 | 100/100 | 100.0% | | 16.0883 - 12.5655 | 101/103 | 98.1% | | 12.4994 - 9.8148 | 204/205 | 99.5% | | 9.7995 - 7.6667 | 388/391 | 99.2% | | 7.6643 - 5.9875 | 794/799 | 99.4% | | 5.9854 - 4.6758 | 1606/1624 | 98.9% | | 4.6750 - 3.6523 | 3318/3354 | 98.9% | | 3.6518 - 2.8524 | 6883/6912 | 99.6% | | 2.8521 - 2.1807 | 13763/16017 | 85.9% | -------------------------------------------------- ----------Analysis of resolution limits---------- Your data have been examined to determine the resolution limits of the data along the reciprocal space axes (a*, b*, and c*). These are expected to vary slightly depending on unit cell parameters and overall resolution, but should never be significantly different for complete data. (This is distinct from the amount of anisotropy present in the data, which changes the effective resolution but does not actually exclude reflections.) overall d_min = 2.181 d_min along a* = 2.270 d_min along b* = 2.227 d_min along c* = 2.212 max. difference between axes = 0.058 Resolution limits are within expected tolerances. ===================== Absolute scaling and Wilson analysis ==================== ----------Maximum likelihood isotropic Wilson scaling---------- ML estimate of overall B value of /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz:F-obs,SIGF-obs: 33.95 A**(-2) Estimated -log of scale factor of /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz:F-obs,SIGF-obs: -0.12 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: 38.49, 0.00, 0.00 65.54, 0.00 16.70 Equivalent representation as U_cif: 0.49, -0.00, -0.00 0.83, 0.00 0.21 Eigen analyses of B-cart: ------------------------------------------------- | Eigenvector | Value | Vector | ------------------------------------------------- | 1 | 65.544 | ( 0.00, 1.00, 0.00) | | 2 | 38.491 | ( 1.00, -0.00, 0.00) | | 3 | 16.702 | (-0.00, -0.00, 1.00) | ------------------------------------------------- ML estimate of -log of scale factor: -0.17 ----------Anisotropy analyses---------- For the resolution shell spanning between 2.26 - 2.18 Angstrom, the mean I/sigI is equal to 3.88. 26.5 % 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 : 4.81e+00 Fraction of I/sigI > 3 : 3.48e-01 ( Z = 4.21 ) The quarter of Intensities *most* affected by the anisotropy correction show : 1.12e+00 Fraction of I/sigI > 3 : 1.60e-02 ( Z = 12.62 ) 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: ----------------------------------------------------------------- | Mean intensity by shell (outliers) | |---------------------------------------------------------------| | d_spacing | z_score | completeness | / | |---------------------------------------------------------------| | 9.991 | 5.52 | 1.00 | 1.819 | | 8.446 | 5.66 | 0.99 | 1.703 | | 7.450 | 7.20 | 0.99 | 1.875 | | 6.739 | 4.78 | 1.00 | 1.419 | | 3.580 | 5.61 | 0.99 | 0.782 | | 3.492 | 10.45 | 1.00 | 0.642 | | 3.410 | 11.14 | 1.00 | 0.638 | | 3.333 | 10.81 | 1.00 | 0.653 | | 3.261 | 8.89 | 0.99 | 0.703 | | 3.194 | 10.05 | 1.00 | 0.671 | | 3.131 | 9.79 | 1.00 | 0.678 | | 3.071 | 11.34 | 1.00 | 0.646 | | 3.015 | 6.89 | 1.00 | 0.756 | | 2.911 | 5.84 | 0.99 | 0.799 | | 2.773 | 6.86 | 0.99 | 0.769 | | 2.732 | 6.19 | 0.93 | 0.787 | | 2.692 | 5.22 | 0.94 | 0.816 | | 2.654 | 6.61 | 0.93 | 0.770 | | 2.617 | 7.52 | 0.94 | 0.744 | | 2.425 | 5.76 | 0.86 | 1.314 | | 2.397 | 4.74 | 0.85 | 1.242 | | 2.319 | 8.14 | 0.83 | 1.504 | | 2.294 | 8.37 | 0.82 | 1.521 | | 2.270 | 8.97 | 0.80 | 1.576 | | 2.247 | 12.32 | 0.83 | 1.970 | | 2.225 | 10.97 | 0.77 | 1.823 | | 2.203 | 13.04 | 0.76 | 2.087 | | 2.181 | 5.15 | 0.41 | 1.608 | ----------------------------------------------------------------- Possible reasons for the presence of the reported unexpected low or elevated mean intensity in a given resolution bin are : - missing overloaded or weak reflections - suboptimal data processing - satellite (ice) crystals - NCS - translational pseudo symmetry (detected elsewhere) - outliers (detected elsewhere) - ice rings (detected elsewhere) - other problems Note that the presence of abnormalities in a certain region of reciprocal space might confuse the data validation algorithm throughout a large region of reciprocal space, even though the data are acceptable in those areas. ----------Possible outliers---------- Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: ----------------------------------------------------------------------------------------------------- | Acentric reflections | |---------------------------------------------------------------------------------------------------| | d_spacing | H K L | |E| | p(wilson) | p(extreme) | |---------------------------------------------------------------------------------------------------| | 4.589 | 1, 1, 61 | 3.79 | 5.83e-07 | 1.33e-02 | | 2.233 | 1, 20, 37 | 4.43 | 3.06e-09 | 7.06e-05 | | 2.211 | 1, 20, 41 | 4.60 | 6.33e-10 | 1.46e-05 | | 4.648 | 2, 1, 59 | 4.00 | 1.13e-07 | 2.61e-03 | | 4.803 | 2, 2, 56 | 3.93 | 1.89e-07 | 4.34e-03 | | 4.727 | 2, 2, 57 | 3.65 | 1.68e-06 | 3.80e-02 | | 2.694 | 2, 17, 16 | 4.22 | 1.89e-08 | 4.36e-04 | | 2.518 | 2, 18, 24 | 3.72 | 9.79e-07 | 2.23e-02 | | 2.268 | 3, 20, 22 | 5.40 | 2.10e-13 | 4.83e-09 | | 2.211 | 3, 20, 36 | 6.21 | 0.00e+00 | 0.00e+00 | | 2.775 | 4, 1, 98 | 3.52 | 4.11e-06 | 9.04e-02 | | 4.845 | 4, 2, 50 | 3.65 | 1.64e-06 | 3.71e-02 | | 3.012 | 4, 2, 89 | 3.72 | 9.50e-07 | 2.16e-02 | | 4.655 | 4, 3, 51 | 4.18 | 2.51e-08 | 5.78e-04 | | 2.596 | 4, 17, 23 | 4.42 | 3.32e-09 | 7.63e-05 | | 2.517 | 4, 18, 3 | 5.20 | 1.85e-12 | 4.26e-08 | | 2.432 | 4, 18, 30 | 7.01 | 0.00e+00 | 0.00e+00 | | 2.223 | 4, 20, 28 | 4.03 | 8.79e-08 | 2.02e-03 | | 2.806 | 5, 2, 94 | 3.79 | 5.62e-07 | 1.28e-02 | | 2.475 | 5, 18, 3 | 6.45 | 0.00e+00 | 0.00e+00 | | 2.257 | 5, 19, 36 | 3.51 | 4.35e-06 | 9.52e-02 | | 2.211 | 5, 20, 23 | 7.49 | 0.00e+00 | 0.00e+00 | | 2.192 | 6, 20, 17 | 3.65 | 1.63e-06 | 3.69e-02 | | 2.253 | 8, 18, 29 | 6.02 | 2.22e-16 | 5.11e-12 | | 2.244 | 8, 18, 31 | 3.59 | 2.47e-06 | 5.53e-02 | | 2.327 | 9, 17, 18 | 5.74 | 5.11e-15 | 1.18e-10 | | 2.280 | 12, 15, 16 | 3.73 | 9.32e-07 | 2.12e-02 | | 2.375 | 17, 3, 1 | 4.00 | 1.11e-07 | 2.56e-03 | ----------------------------------------------------------------------------------------------------- p(wilson) : 1-(1-exp[-|E|^2]) p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed if it were selected at random 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. Centric reflections: ----------------------------------------------------------------------------------------------------- | Centric reflections | |---------------------------------------------------------------------------------------------------| | d_spacing | H K L | |E| | p(wilson) | p(extreme) | |---------------------------------------------------------------------------------------------------| | 4.424 | 0, 0, 64 | 4.21 | 2.52e-05 | 9.26e-02 | | 2.949 | 0, 0, 96 | 4.83 | 1.35e-06 | 5.18e-03 | | 2.722 | 0, 0, 104 | 4.22 | 2.49e-05 | 9.14e-02 | | 4.473 | 0, 1, 63 | 5.85 | 4.99e-09 | 1.92e-05 | | 2.231 | 0, 20, 38 | 6.42 | 1.38e-10 | 5.30e-07 | | 4.612 | 1, 0, 61 | 4.95 | 7.34e-07 | 2.82e-03 | | 4.467 | 1, 0, 63 | 4.84 | 1.33e-06 | 5.11e-03 | | 2.882 | 1, 0, 98 | 4.67 | 2.97e-06 | 1.14e-02 | | 2.297 | 11, 16, 0 | 4.37 | 1.22e-05 | 4.60e-02 | | 3.261 | 12, 0, 25 | 4.56 | 5.21e-06 | 1.99e-02 | | 3.239 | 12, 0, 27 | 4.72 | 2.37e-06 | 9.07e-03 | ----------------------------------------------------------------------------------------------------- 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 : 4.74 ( rms deviation : 3.31 ) mean bin completeness : 0.93 ( rms deviation : 0.11 ) 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 | 3.68 | 0.99 | | 3.669 | 0.750 | 5.61 | 0.99 | | 3.441 | 0.530 | 11.14 | 1.00 | | 2.671 | 0.170 | 6.61 | 0.93 | | 2.249 | 0.390 | 12.32 | 0.83 | ------------------------------------------------------------- Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower than 0.10 will be ignored. At 3.44 A the z-score is more than 4.00 times the standard deviation of all z-scores, while at the same time, the occupancy does not go down. At 2.25 A the z-score is more than 4.00 times the standard deviation of all z-scores, while at the same time, the occupancy does not go down. There were 2 ice ring related warnings. This could indicate the presence of ice rings. ################################################################################ # Twinning and symmetry analyses # ################################################################################ ============================= Systematic absences ============================= ----------Table of systematic absence rules---------- The following table gives information about systematic absences allowed for the specified intensity point group. For each operator, the reflections are split in three classes: Absent : Reflections that are absent for this operator. Non Absent: Reflection of the same type (i.e. (0,0,l)) as above, but they should be present. Complement: All other reflections. For each class, the is reported, as well as the number of 'violations'. A 'violation' is designated as a reflection for which a I/sigI criterion is not met. The criteria are: Absent violation : I/sigI > 3.0 Non Absent violation : I/sigI < 3.0 Complement violation : I/sigI < 3.0 Operators with low associated violations for *both* absent and non absent reflections, are likely to be true screw axis or glide planes. Both the number of violations and their percentages are given. The number of violations within the 'complement' class, can be used as a comparison for the number of violations in the non-absent class. --------------------------------------------------------------------------------------------------------------------------------------- | Operator | # absent | (violations) | # not absent | (violations) | # complete | (violations) | Score | --------------------------------------------------------------------------------------------------------------------------------------- | 2_0 (a) | 0 | 0.00 (0, 0.0%) | 7 | 8.26 (1, 14.3%) | 6986 | 11.51 (889, 12.7%) | 1.89e+00 | | 2_1 (a) | 4 | 7.32 (3, 75.0%) | 3 | 9.51 (0, 0.0%) | 6986 | 11.51 (889, 12.7%) | 1.24e+01 | | 2_0 (b) | 0 | 0.00 (0, 0.0%) | 9 | 3.47 (4, 44.4%) | 6984 | 11.52 (886, 12.7%) | 2.58e-01 | | 2_1 (b) | 5 | 2.45 (2, 40.0%) | 4 | 4.75 (1, 25.0%) | 6984 | 11.52 (886, 12.7%) | 1.45e+00 | | 2_0 (c) | 0 | 0.00 (0, 0.0%) | 25 | 8.76 (1, 4.0%) | 6968 | 11.52 (889, 12.8%) | 1.58e+00 | | 2_1 (c) | 0 | 0.00 (0, 0.0%) | 25 | 8.76 (1, 4.0%) | 6968 | 11.52 (889, 12.8%) | 1.58e+00 | --------------------------------------------------------------------------------------------------------------------------------------- ----------Space group identification---------- Analyses of the absences table indicates a number of likely space group candidates, which are listed below. For each space group, the number of absent violations are listed under the '+++' column. The number of present violations (weak reflections) are listed under '---'. The last column is a likelihood based score for the particular space group. Note that enantiomorphic spacegroups will have equal scores. Also, if absences were removed while processing the data, they will be regarded as missing information, rather then as enforcing that absence in the space group choices. ----------------------------------------------------------------------------------- | space group | n absent | _absent | _absent | +++ | --- | score | ----------------------------------------------------------------------------------- | P 2 2 2 | 0 | 0.00 | 0.00 | 0 | 6 | 0.000e+00 | | P 2 2 21 | 0 | 0.00 | 0.00 | 0 | 6 | 0.000e+00 | | P 2 21 2 | 5 | 0.15 | 2.45 | 2 | 3 | 1.194e+00 | | P 2 21 21 | 5 | 0.15 | 2.45 | 2 | 3 | 1.194e+00 | | P 21 2 2 | 4 | 1.45 | 7.32 | 3 | 5 | 1.053e+01 | | P 21 2 21 | 4 | 1.45 | 7.32 | 3 | 5 | 1.053e+01 | | P 21 21 2 | 9 | 0.73 | 4.61 | 5 | 2 | 1.173e+01 | | P 21 21 21 | 9 | 0.73 | 4.61 | 5 | 2 | 1.173e+01 | ----------------------------------------------------------------------------------- ----------List of individual systematic absences---------- Note: this analysis uses the original input data rather than the filtered data used for twinning detection; therefore, the results shown here may include more reflections than shown above. Also note that the input data were amplitudes, which means that weaker reflections may have been modified by French-Wilson treatment or discarded altogether, and the original intensities will not be recovered. P 2 2 2: no systematic absences possible P 2 2 21 (input space group): no absences found P 21 2 2 ( 1, 0, 0): i/sigi = 8.3 ( 3, 0, 0): i/sigi = 0.7 ( 5, 0, 0): i/sigi = 9.8 ( 7, 0, 0): i/sigi = 0.7 ( 9, 0, 0): i/sigi = 8.7 ( 11, 0, 0): i/sigi = 9.2 ( 13, 0, 0): i/sigi = 10.2 ( 15, 0, 0): i/sigi = 0.8 ( 17, 0, 0): i/sigi = 8.2 P 2 21 2 ( 0, 1, 0): i/sigi = 6.5 ( 0, 3, 0): i/sigi = 6.8 ( 0, 5, 0): i/sigi = 0.8 ( 0, 7, 0): i/sigi = 5.2 ( 0, 9, 0): i/sigi = 1.0 ( 0, 11, 0): i/sigi = 0.7 ( 0, 13, 0): i/sigi = 3.5 ( 0, 15, 0): i/sigi = 0.9 P 21 21 2 ( 0, 1, 0): i/sigi = 6.5 ( 0, 3, 0): i/sigi = 6.8 ( 0, 5, 0): i/sigi = 0.8 ( 0, 7, 0): i/sigi = 5.2 ( 0, 9, 0): i/sigi = 1.0 ( 0, 11, 0): i/sigi = 0.7 ( 0, 13, 0): i/sigi = 3.5 ( 0, 15, 0): i/sigi = 0.9 ( 1, 0, 0): i/sigi = 8.3 ( 3, 0, 0): i/sigi = 0.7 ( 5, 0, 0): i/sigi = 9.8 ( 7, 0, 0): i/sigi = 0.7 ( 9, 0, 0): i/sigi = 8.7 ( 11, 0, 0): i/sigi = 9.2 ( 13, 0, 0): i/sigi = 10.2 ( 15, 0, 0): i/sigi = 0.8 ( 17, 0, 0): i/sigi = 8.2 P 2 21 21 ( 0, 1, 0): i/sigi = 6.5 ( 0, 3, 0): i/sigi = 6.8 ( 0, 5, 0): i/sigi = 0.8 ( 0, 7, 0): i/sigi = 5.2 ( 0, 9, 0): i/sigi = 1.0 ( 0, 11, 0): i/sigi = 0.7 ( 0, 13, 0): i/sigi = 3.5 ( 0, 15, 0): i/sigi = 0.9 P 21 2 21 ( 1, 0, 0): i/sigi = 8.3 ( 3, 0, 0): i/sigi = 0.7 ( 5, 0, 0): i/sigi = 9.8 ( 7, 0, 0): i/sigi = 0.7 ( 9, 0, 0): i/sigi = 8.7 ( 11, 0, 0): i/sigi = 9.2 ( 13, 0, 0): i/sigi = 10.2 ( 15, 0, 0): i/sigi = 0.8 ( 17, 0, 0): i/sigi = 8.2 P 21 21 21 ( 0, 1, 0): i/sigi = 6.5 ( 0, 3, 0): i/sigi = 6.8 ( 0, 5, 0): i/sigi = 0.8 ( 0, 7, 0): i/sigi = 5.2 ( 0, 9, 0): i/sigi = 1.0 ( 0, 11, 0): i/sigi = 0.7 ( 0, 13, 0): i/sigi = 3.5 ( 0, 15, 0): i/sigi = 0.9 ( 1, 0, 0): i/sigi = 8.3 ( 3, 0, 0): i/sigi = 0.7 ( 5, 0, 0): i/sigi = 9.8 ( 7, 0, 0): i/sigi = 0.7 ( 9, 0, 0): i/sigi = 8.7 ( 11, 0, 0): i/sigi = 9.2 ( 13, 0, 0): i/sigi = 10.2 ( 15, 0, 0): i/sigi = 0.8 ( 17, 0, 0): i/sigi = 8.2 =============== Diagnostic tests for twinning and pseudosymmetry ============== Using data between 10.00 to 3.50 Angstrom. ----------Patterson analyses---------- Largest Patterson peak with length larger than 15 Angstrom: Frac. coord. : 0.000 0.000 0.095 Distance to origin : 27.013 Height relative to origin : 7.722 % p_value(height) : 3.779e-01 Explanation The p-value, the probability that a peak of the specified height or larger is found in a Patterson function of a macromolecule that does not have any translational pseudo-symmetry, is equal to 3.779e-01. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. ----------Wilson ratio and moments---------- Acentric reflections: /^2 :2.657 (untwinned: 2.000; perfect twin 1.500) ^2/ :0.696 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.854 (untwinned: 0.736; perfect twin 0.541) Centric reflections: /^2 :3.983 (untwinned: 3.000; perfect twin 2.000) ^2/ :0.550 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :1.309 (untwinned: 0.968; perfect twin 0.736) ----------NZ test for twinning and TNCS---------- The NZ test is diagnostic for both twinning and translational NCS. Note however that if both are present, the effects may cancel each other out, therefore the results of the Patterson analysis and L-test also need to be considered. Maximum deviation acentric : 0.104 Maximum deviation centric : 0.034 _acentric : +0.079 _centric : +0.020 ----------L test for acentric data---------- Using difference vectors (dh,dk,dl) of the form: (2hp, 2kp, 2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.535 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.382 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. Reference: J. Padilla & T. O. Yeates. A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr. D59, 1124-30, 2003. ================================== Twin laws ================================== ----------Twin law identification---------- No twin laws are possible for this crystal lattice. ================== Twinning and intensity statistics summary ================== ----------Final verdict---------- The largest off-origin peak in the Patterson function is 7.72% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics show more centric character than is expected for acentric data. ----------Statistics independent of twin laws---------- /^2 : 2.657 (untwinned: 2.0, perfect twin: 1.5) ^2/ : 0.696 (untwinned: 0.785, perfect twin: 0.885) <|E^2-1|> : 0.854 (untwinned: 0.736, perfect twin: 0.541) <|L|>, : 0.535, 0.382 Multivariate Z score L-test: 7.137 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found.