############################################################# ## phenix.xtriage ## ## ## ## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ## ## ## ############################################################# #phil __OFF__ This cryptic code, together with the tags __ON__ and __OFF__ allows one to use the log file as an input file for xtriage. Try : phenix.xtriage to give it a try! Date 2008-06-09 Time 18:36:33 CEST +0200 ##-------------------------------------------## ## WARNING: ## ## Number of residues unspecified ## ##-------------------------------------------## Effective parameters: #phil __ON__ scaling.input { parameters { asu_contents { n_residues = None n_bases = None n_copies_per_asu = None } misc_twin_parameters { missing_symmetry { tanh_location = 0.08 tanh_slope = 50 } 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 } } reporting { verbose = 1 log = "logfile.log" ccp4_style_graphs = True } } xray_data { file_name = "x003_P3112_2.mtz" obs_labels = "IMEAN_native,SIGIMEAN_native" calc_labels = None unit_cell = 92.44480133 92.44480133 135.645401 90 90 120 space_group = "P 31 1 2" high_resolution = None low_resolution = None reference { data { file_name = None labels = None unit_cell = None space_group = None } } } } #phil __END__ Symmetry, cell and reflection file content summary Miller array info: x003_P3112_2.mtz:IMEAN_native,SIGIMEAN_native Observation type: xray.amplitude Type of data: double, size=33419 Type of sigmas: double, size=33419 Number of Miller indices: 33419 Anomalous flag: False Unit cell: (92.4448, 92.4448, 135.645, 90, 90, 120) Space group: P 31 1 2 (No. 151) Systematic absences: 0 Centric reflections: 1857 Resolution range: 29.5337 2.20006 Completeness in resolution range: 0.985986 Completeness with d_max=infinity: 0.985462 ##----------------------------------------------------## ## Basic statistics ## ##----------------------------------------------------## Number of residues unknown, assuming 50% solvent content ---------------------------------------------------------------- | Best guess : 612 residues in the asu | ---------------------------------------------------------------- Completeness and data strength analyses 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. ---------------------------------------------------------------------------------------- | Res. Range | I/sigI>1 | I/sigI>2 | I/sigI>3 | I/sigI>5 | I/sigI>10 | I/sigI>15 | ---------------------------------------------------------------------------------------- | 29.54 - 5.42 | 94.2% | 92.5% | 91.1% | 88.0% | 59.3% | 19.5% | | 5.42 - 4.30 | 97.9% | 97.1% | 96.2% | 93.5% | 62.0% | 19.7% | | 4.30 - 3.76 | 99.1% | 97.9% | 96.0% | 92.3% | 59.4% | 19.0% | | 3.76 - 3.42 | 98.8% | 97.6% | 94.7% | 88.7% | 51.4% | 17.9% | | 3.42 - 3.17 | 98.2% | 95.1% | 90.8% | 81.5% | 43.2% | 13.7% | | 3.17 - 2.99 | 97.6% | 93.7% | 88.0% | 74.9% | 36.0% | 11.2% | | 2.99 - 2.84 | 96.4% | 88.9% | 80.3% | 65.1% | 25.7% | 7.0% | | 2.84 - 2.71 | 94.9% | 84.3% | 72.3% | 52.6% | 17.4% | 3.7% | | 2.71 - 2.61 | 92.6% | 80.1% | 67.2% | 45.6% | 12.6% | 1.6% | | 2.61 - 2.52 | 89.8% | 73.9% | 58.8% | 37.0% | 9.7% | 1.7% | | 2.52 - 2.44 | 88.2% | 68.0% | 50.7% | 29.3% | 7.0% | 1.4% | | 2.44 - 2.37 | 83.1% | 61.0% | 44.6% | 23.9% | 6.1% | 0.9% | | 2.37 - 2.31 | 81.5% | 56.4% | 38.9% | 19.1% | 4.0% | 0.4% | | 2.31 - 2.25 | 81.8% | 53.7% | 35.9% | 16.2% | 3.2% | 0.3% | ---------------------------------------------------------------------------------------- The completeness of data for which I/sig(I)>3.00, exceeds 85% for for resolution ranges lower than 2.99A. The data are cut at this resolution for the potential twin tests and intensity statistics. ML estimate of overall B_cart value of x003_P3112_2.mtz:IMEAN_native,SIGIMEAN_native: 38.12, -0.00, 0.00 38.12, -0.00 22.50 Equivalent representation as U_cif: 0.48, 0.24, -0.00 0.48, 0.00 0.28 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 38.119 ( 0.81, -0.58, 0.00) Eigenvector 2 : 38.119 ( 0.58, 0.81, -0.00) Eigenvector 3 : 22.495 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of x003_P3112_2.mtz:IMEAN_native,SIGIMEAN_native: -1.59 Low resolution completeness analyses The following table shows the completeness of the data to 5 Angstrom. unused: - 29.5342 [ 0/18 ] 0.000 bin 1: 29.5342 - 10.6204 [259/319] 0.812 bin 2: 10.6204 - 8.4958 [267/297] 0.899 bin 3: 8.4958 - 7.4415 [290/304] 0.954 bin 4: 7.4415 - 6.7701 [293/298] 0.983 bin 5: 6.7701 - 6.2898 [300/302] 0.993 bin 6: 6.2898 - 5.9222 [287/288] 0.997 bin 7: 5.9222 - 5.6277 [297/299] 0.993 bin 8: 5.6277 - 5.3843 [285/287] 0.993 bin 9: 5.3843 - 5.1781 [285/286] 0.997 bin 10: 5.1781 - 5.0003 [290/294] 0.986 unused: 5.0003 - [ 0/0 ] Mean intensity analyses Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | / | ------------------------------------------------ | 9.979 | 5.95 | 0.85 | 0.494 | | 5.127 | 6.50 | 0.99 | 1.520 | | 4.877 | 5.09 | 0.99 | 1.357 | | 3.675 | 6.18 | 1.00 | 0.771 | | 3.580 | 6.20 | 1.00 | 0.772 | | 3.333 | 6.58 | 1.00 | 0.773 | | 2.817 | 5.05 | 0.99 | 0.833 | ------------------------------------------------ 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: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 2.879 | 2, 0, 47 | 3.61 | 2.24e-06 | 6.80e-02 | | 3.116 | 4, 0, 43 | 4.84 | 6.85e-11 | 2.15e-06 | | 2.405 | 4, 0, 56 | 4.10 | 5.03e-08 | 1.58e-03 | | 2.392 | 4, 2, -56 | 5.04 | 9.37e-12 | 2.94e-07 | | 2.670 | 4, 2, -50 | 3.66 | 1.54e-06 | 4.73e-02 | | 3.858 | 4, 2, 34 | 4.80 | 9.64e-11 | 3.03e-06 | | 3.088 | 4, 2, 43 | 3.77 | 6.55e-07 | 2.04e-02 | | 3.535 | 6, 0, 37 | 4.99 | 1.53e-11 | 4.79e-07 | | 3.211 | 6, 0, 41 | 3.99 | 1.21e-07 | 3.79e-03 | | 2.765 | 6, 0, 48 | 3.55 | 3.27e-06 | 9.76e-02 | | 2.909 | 6, 2, -45 | 4.06 | 6.75e-08 | 2.11e-03 | | 2.970 | 6, 2, -44 | 3.64 | 1.75e-06 | 5.33e-02 | | 3.319 | 6, 2, -39 | 4.13 | 4.06e-08 | 1.27e-03 | | 3.960 | 6, 2, -32 | 4.03 | 8.88e-08 | 2.78e-03 | | 10.782 | 6, 2, -3 | 3.63 | 1.90e-06 | 5.78e-02 | | 8.591 | 6, 2, 10 | 3.72 | 9.66e-07 | 2.98e-02 | | 7.011 | 6, 2, 15 | 4.01 | 1.03e-07 | 3.24e-03 | | 6.738 | 6, 2, 16 | 4.71 | 2.42e-10 | 7.58e-06 | | 6.479 | 6, 2, 17 | 3.72 | 9.92e-07 | 3.07e-02 | | 3.755 | 6, 2, 34 | 4.85 | 6.00e-11 | 1.88e-06 | | 2.923 | 6, 4, -44 | 4.23 | 1.71e-08 | 5.37e-04 | | 5.283 | 6, 4, 21 | 4.22 | 1.77e-08 | 5.55e-04 | | 5.119 | 6, 4, 22 | 3.64 | 1.73e-06 | 5.28e-02 | | 4.536 | 6, 4, 26 | 4.27 | 1.25e-08 | 3.93e-04 | | 4.056 | 6, 4, 30 | 4.66 | 3.66e-10 | 1.15e-05 | | 3.849 | 6, 4, 32 | 4.02 | 9.88e-08 | 3.10e-03 | | 3.752 | 6, 4, 33 | 4.55 | 1.05e-09 | 3.29e-05 | | 3.181 | 6, 4, 40 | 4.04 | 8.34e-08 | 2.61e-03 | | 6.020 | 8, 0, 18 | 3.97 | 1.41e-07 | 4.43e-03 | | 2.223 | 8, 2, -59 | 3.61 | 2.24e-06 | 6.77e-02 | | 2.849 | 8, 2, -45 | 3.98 | 1.31e-07 | 4.10e-03 | | 3.029 | 8, 2, -42 | 4.08 | 5.95e-08 | 1.87e-03 | | 3.231 | 8, 2, -39 | 5.46 | 1.13e-13 | 3.55e-09 | | 5.357 | 8, 2, -20 | 3.70 | 1.17e-06 | 3.59e-02 | | 2.456 | 8, 2, 53 | 3.60 | 2.28e-06 | 6.91e-02 | | 7.383 | 8, 4, 4 | 3.92 | 2.20e-07 | 6.89e-03 | | 5.339 | 8, 4, 18 | 3.74 | 8.23e-07 | 2.55e-02 | | 3.094 | 8, 4, 40 | 3.83 | 4.15e-07 | 1.29e-02 | | 3.564 | 8, 6, -32 | 4.52 | 1.30e-09 | 4.06e-05 | | 4.499 | 8, 6, -22 | 3.66 | 1.47e-06 | 4.51e-02 | | 6.395 | 8, 6, 5 | 3.62 | 2.06e-06 | 6.25e-02 | | 6.319 | 8, 6, 6 | 3.88 | 2.94e-07 | 9.18e-03 | | 4.957 | 8, 6, 18 | 3.85 | 3.79e-07 | 1.18e-02 | | 2.273 | 8, 6, 56 | 4.32 | 8.10e-09 | 2.54e-04 | | 7.679 | 10, 0, 5 | 3.70 | 1.12e-06 | 3.44e-02 | | 5.027 | 10, 0, 21 | 3.80 | 5.44e-07 | 1.69e-02 | | 4.443 | 10, 2, -24 | 4.14 | 3.59e-08 | 1.12e-03 | | 6.489 | 10, 2, 9 | 3.69 | 1.26e-06 | 3.88e-02 | | 4.680 | 10, 2, 22 | 4.34 | 6.40e-09 | 2.01e-04 | | 3.337 | 10, 2, 36 | 3.61 | 2.24e-06 | 6.79e-02 | | 2.946 | 10, 2, 42 | 3.59 | 2.61e-06 | 7.88e-02 | | 3.057 | 10, 4, -39 | 3.93 | 1.91e-07 | 5.97e-03 | | 3.460 | 10, 4, -33 | 5.41 | 1.88e-13 | 5.91e-09 | | 5.229 | 10, 4, -15 | 4.09 | 5.28e-08 | 1.66e-03 | | 4.770 | 10, 4, 19 | 5.35 | 3.54e-13 | 1.11e-08 | | 4.550 | 10, 4, 21 | 4.10 | 4.98e-08 | 1.56e-03 | | 3.391 | 10, 8, -30 | 4.12 | 4.09e-08 | 1.28e-03 | | 2.964 | 12, 0, 41 | 3.83 | 4.13e-07 | 1.29e-02 | | 4.147 | 12, 2, -24 | 4.58 | 7.56e-10 | 2.37e-05 | | 4.640 | 12, 2, 19 | 4.57 | 8.76e-10 | 2.75e-05 | | 4.241 | 12, 2, 23 | 3.72 | 9.51e-07 | 2.94e-02 | | 3.650 | 12, 4, -28 | 4.18 | 2.62e-08 | 8.23e-04 | | 4.210 | 12, 4, 21 | 4.49 | 1.79e-09 | 5.62e-05 | | 3.303 | 12, 4, 33 | 3.57 | 3.01e-06 | 9.02e-02 | | 3.240 | 12, 4, 34 | 3.88 | 2.85e-07 | 8.91e-03 | | 4.881 | 12, 6, -7 | 3.62 | 2.07e-06 | 6.30e-02 | | 3.115 | 12, 8, -32 | 3.80 | 5.30e-07 | 1.65e-02 | | 3.666 | 12, 10, -18 | 3.55 | 3.30e-06 | 9.85e-02 | | 4.887 | 14, 4, 1 | 3.60 | 2.31e-06 | 6.98e-02 | | 4.328 | 16, 2, 12 | 3.55 | 3.29e-06 | 9.81e-02 | | 4.073 | 18, 2, 8 | 3.89 | 2.75e-07 | 8.60e-03 | | 3.842 | 18, 4, 8 | 3.94 | 1.78e-07 | 5.56e-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: ----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 3.439 | 2, 2, 39 | 6.15 | 7.64e-10 | 1.39e-06 | | 2.412 | 4, 4, -55 | 4.99 | 6.15e-07 | 1.12e-03 | | 3.254 | 4, 4, -40 | 4.58 | 4.60e-06 | 8.31e-03 | | 4.755 | 4, 4, 26 | 4.95 | 7.45e-07 | 1.35e-03 | | 3.980 | 4, 4, 32 | 5.78 | 7.69e-09 | 1.40e-05 | | 3.385 | 6, 6, -36 | 5.35 | 8.63e-08 | 1.57e-04 | | 5.236 | 6, 6, -19 | 4.05 | 5.20e-05 | 9.01e-02 | | 5.236 | 6, 6, 19 | 4.96 | 7.23e-07 | 1.31e-03 | | 4.683 | 6, 6, 23 | 4.61 | 4.02e-06 | 7.27e-03 | | 3.385 | 6, 6, 36 | 4.37 | 1.25e-05 | 2.25e-02 | | 2.862 | 6, 6, 44 | 4.11 | 3.98e-05 | 6.97e-02 | | 5.651 | 8, 8, 5 | 5.24 | 1.59e-07 | 2.88e-04 | | 3.232 | 10, 10, -30 | 4.26 | 2.01e-05 | 3.58e-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 : 2.34 ( rms deviation : 1.76 ) mean bin completeness : 0.98 ( rms deviation : 0.03 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. 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 | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 0.69 | 1.00 | 1.000 | | 3.669 | 6.20 | 1.00 | 0.750 | | 3.441 | 0.21 | 1.00 | 0.530 | | 2.671 | 0.38 | 1.00 | 0.170 | | 2.249 | 2.06 | 0.98 | 0.390 | ------------------------------------------------ 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 ##----------------------------------------------------## ## Twinning Analyses ## ##----------------------------------------------------## Using data between 10.00 to 2.99 Angstrom. Determining possible twin laws. The following twin laws have been found: ------------------------------------------------------------------------------- | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law | ------------------------------------------------------------------------------- | M | 6-fold | 0.000 | 0.000 | 0.000 | h+k,-h,l | ------------------------------------------------------------------------------- M: Merohedral twin law PM: Pseudomerohedral twin law 1 merohedral twin operators found 0 pseudo-merohedral twin operators found In total, 1 twin operator were found Number of centrics : 923 Number of acentrics : 12209 Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.000 0.500 0.000 Distance to origin : 46.222 Height (origin=100) : 78.342 p_value(height) : 7.057e-07 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 7.057e-07 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. The full list of Patterson peaks is: x y z height p-value(height) ( 0.000, 0.500, 0.000 ) : 78.342 (7.057e-07) (-0.001,-0.500, 0.053 ) : 10.373 (1.389e-01)