***** XSCALE ***** (VERSION January 10, 2014 BUILT=20140307) 15-May-2014 Author: Wolfgang Kabsch Copy licensed until 31-Dec-2014 to academic users for non-commercial applications No redistribution. ****************************************************************************** CONTROL CARDS ****************************************************************************** MAXIMUM_NUMBER_OF_PROCESSORS=16 SPACE_GROUP_NUMBER=21 UNIT_CELL_CONSTANTS= 83.09 96.79 57.95 90.00 90.00 90.00 MINIMUM_I/SIGMA=3.0 OUTPUT_FILE=SAD.HKL FRIEDEL'S_LAW=FALSE MERGE=FALSE STRICT_ABSORPTION_CORRECTION=TRUE INPUT_FILE=SAD_SWEEP1.HKL XDS_ASCII INCLUDE_RESOLUTION_RANGE= 50.38 1.90 CORRECTIONS= DECAY MODULATION ABSORPTION THE DATA COLLECTION STATISTICS REPORTED BELOW ASSUMES: SPACE_GROUP_NUMBER= 21 UNIT_CELL_CONSTANTS= 83.09 96.79 57.95 90.000 90.000 90.000 ***** 8 EQUIVALENT POSITIONS IN SPACE GROUP # 21 ***** If x',y',z' is an equivalent position to x,y,z, then x'=x*ML(1)+y*ML( 2)+z*ML( 3)+ML( 4)/12.0 y'=x*ML(5)+y*ML( 6)+z*ML( 7)+ML( 8)/12.0 z'=x*ML(9)+y*ML(10)+z*ML(11)+ML(12)/12.0 # 1 2 3 4 5 6 7 8 9 10 11 12 1 1 0 0 0 0 1 0 0 0 0 1 0 2 -1 0 0 0 0 -1 0 0 0 0 1 0 3 1 0 0 0 0 -1 0 0 0 0 -1 0 4 -1 0 0 0 0 1 0 0 0 0 -1 0 5 1 0 0 6 0 1 0 6 0 0 1 0 6 -1 0 0 6 0 -1 0 6 0 0 1 0 7 1 0 0 6 0 -1 0 6 0 0 -1 0 8 -1 0 0 6 0 1 0 6 0 0 -1 0 ALL DATA SETS WILL BE SCALED TO SAD_SWEEP1.HKL ****************************************************************************** READING INPUT REFLECTION DATA FILES ****************************************************************************** NUMBER OF UNIQUE REFLECTIONS IN FILE "REMOVE.HKL" 4985 DATA MEAN REFLECTIONS INPUT FILE NAME SET# INTENSITY ACCEPTED REJECTED 1 0.1323E+03 125179 56 SAD_SWEEP1.HKL ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & RESOLUTION ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: SAD.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW=FALSE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 720 DEGREES OF FREEDOM OF CHI^2 FIT 50346.0 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.990 NUMBER OF CYCLES CARRIED OUT 4 CORRECTION FACTORS for visual inspection by XDS-Viewer DECAY_001.cbf XMIN= 0.4 XMAX= 1799.7 NXBIN= 36 YMIN= 0.00055 YMAX= 0.27701 NYBIN= 20 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 71432 ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF X (fast) & Y(slow) IN THE DETECTOR PLANE ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: SAD.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW=FALSE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 1444 DEGREES OF FREEDOM OF CHI^2 FIT 50271.8 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.986 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer MODPIX_001.cbf XMIN= 149.1 XMAX= 1316.9 NXBIN= 38 YMIN= 253.6 YMAX= 1424.7 NYBIN= 38 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 71432 ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & DETECTOR SURFACE POSITION ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: SAD.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW=FALSE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 468 DEGREES OF FREEDOM OF CHI^2 FIT 50346.0 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.982 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer ABSORP_001.cbf XMIN= 0.4 XMAX= 1799.7 NXBIN= 36 DETECTOR_SURFACE_POSITION= 733 839 DETECTOR_SURFACE_POSITION= 931 1038 DETECTOR_SURFACE_POSITION= 535 1038 DETECTOR_SURFACE_POSITION= 535 640 DETECTOR_SURFACE_POSITION= 931 640 DETECTOR_SURFACE_POSITION= 1182 1026 DETECTOR_SURFACE_POSITION= 919 1289 DETECTOR_SURFACE_POSITION= 547 1289 DETECTOR_SURFACE_POSITION= 284 1026 DETECTOR_SURFACE_POSITION= 284 653 DETECTOR_SURFACE_POSITION= 547 389 DETECTOR_SURFACE_POSITION= 919 389 DETECTOR_SURFACE_POSITION= 1182 653 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 71432 ****************************************************************************** CORRECTION PARAMETERS FOR THE STANDARD ERROR OF REFLECTION INTENSITIES ****************************************************************************** The variance v0(I) of the intensity I obtained from counting statistics is replaced by v(I)=a*(v0(I)+b*I^2). The model parameters a, b are chosen to minimize the discrepancies between v(I) and the variance estimated from sample statistics of symmetry related reflections. This model implicates an asymptotic limit ISa=1/SQRT(a*b) for the highest I/Sigma(I) that the experimental setup can produce (Diederichs (2010) Acta Cryst D66, 733-740). Often the value of ISa is reduced from the initial value ISa0 due to systematic errors showing up by comparison with other data sets in the scaling procedure. (ISa=ISa0=-1 if v0 is unknown for a data set.) a b ISa ISa0 INPUT DATA SET 1.004E+00 1.729E-03 24.00 25.70 SAD_SWEEP1.HKL FACTOR TO PLACE ALL DATA SETS TO AN APPROXIMATE ABSOLUTE SCALE 0.821642E+03 (ASSUMING A PROTEIN WITH 50% SOLVENT) ****************************************************************************** STATISTICS OF SCALED OUTPUT DATA SET : SAD.HKL FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=FALSE 6 OUT OF 125179 REFLECTIONS REJECTED 125173 REFLECTIONS ON OUTPUT FILE ****************************************************************************** DEFINITIONS: R-FACTOR observed = (SUM(ABS(I(h,i)-I(h))))/(SUM(I(h,i))) expected = expected R-FACTOR derived from Sigma(I) COMPARED = number of reflections used for calculating R-FACTOR I/SIGMA = mean of intensity/Sigma(I) of unique reflections (after merging symmetry-related observations) Sigma(I) = standard deviation of reflection intensity I estimated from sample statistics R-meas = redundancy independent R-factor (intensities) Diederichs & Karplus (1997), Nature Struct. Biol. 4, 269-275. CC(1/2) = percentage of correlation between intensities from random half-datasets. Correlation significant at the 0.1% level is marked by an asterisk. Karplus & Diederichs (2012), Science 336, 1030-33 Anomal = percentage of correlation between random half-sets Corr of anomalous intensity differences. Correlation significant at the 0.1% level is marked. SigAno = mean anomalous difference in units of its estimated standard deviation (|F(+)-F(-)|/Sigma). F(+), F(-) are structure factor estimates obtained from the merged intensity observations in each parity class. Nano = Number of unique reflections used to calculate Anomal_Corr & SigAno. At least two observations for each (+ and -) parity are required. NOTE: Friedel pairs are treated as different reflections. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 8.50 1512 401 406 98.8% 2.7% 2.9% 1512 42.41 3.2% 99.8* 24 0.901 154 6.01 2813 733 733 100.0% 2.9% 3.1% 2813 37.86 3.4% 99.8* 12 0.864 316 4.91 3493 930 931 99.9% 3.0% 3.1% 3493 36.21 3.5% 99.8* 3 0.861 416 4.25 3323 1112 1133 98.1% 2.8% 3.0% 3286 33.00 3.4% 99.8* 1 0.820 475 3.80 4258 1259 1265 99.5% 2.9% 3.1% 4248 33.91 3.5% 99.8* 8 0.877 569 3.47 4858 1394 1403 99.4% 3.3% 3.3% 4845 32.25 3.9% 99.8* -1 0.816 638 3.21 5411 1510 1510 100.0% 3.7% 3.6% 5408 29.14 4.4% 99.8* 6 0.906 704 3.00 6034 1649 1651 99.9% 4.5% 4.3% 6033 24.48 5.3% 99.7* 1 0.866 771 2.83 6404 1742 1748 99.7% 5.1% 5.0% 6404 20.73 6.0% 99.6* 5 0.854 818 2.69 6755 1824 1827 99.8% 5.9% 5.8% 6754 18.38 6.9% 99.5* 1 0.850 863 2.56 7160 1927 1929 99.9% 7.8% 7.6% 7160 14.24 9.1% 99.3* 0 0.823 913 2.45 5916 1986 2002 99.2% 8.8% 9.0% 5821 10.48 10.8% 99.1* -1 0.784 863 2.36 6820 2098 2122 98.9% 10.7% 10.9% 6740 9.42 12.9% 98.6* 11 0.871 927 2.27 7529 2199 2208 99.6% 13.9% 14.3% 7490 7.69 16.5% 97.8* 3 0.775 1014 2.19 7967 2256 2266 99.6% 17.4% 17.1% 7943 6.53 20.6% 97.4* 5 0.832 1054 2.12 8364 2344 2349 99.8% 19.4% 19.7% 8331 5.69 22.9% 97.2* 3 0.792 1090 2.06 8588 2400 2408 99.7% 25.1% 25.3% 8562 4.49 29.6% 95.6* 5 0.816 1128 2.00 8959 2492 2496 99.8% 33.9% 34.4% 8947 3.40 40.0% 90.1* 0 0.771 1188 1.95 9324 2586 2590 99.8% 45.6% 46.6% 9311 2.50 53.7% 87.0* 4 0.766 1231 1.90 9685 2672 2674 99.9% 63.4% 65.2% 9677 1.82 74.6% 74.2* 2 0.704 1278 total 125173 35514 35651 99.6% 4.8% 4.8% 124778 14.09 5.6% 99.9* 3 0.814 16410 ========== STATISTICS OF INPUT DATA SET ========== R-FACTORS FOR INTENSITIES OF DATA SET SAD_SWEEP1.HKL RESOLUTION R-FACTOR R-FACTOR COMPARED LIMIT observed expected 8.50 2.7% 2.9% 1512 6.01 2.9% 3.1% 2813 4.91 3.0% 3.1% 3493 4.25 2.8% 3.0% 3286 3.80 2.9% 3.1% 4248 3.47 3.3% 3.3% 4845 3.21 3.7% 3.6% 5408 3.00 4.5% 4.3% 6033 2.83 5.1% 5.0% 6404 2.69 5.9% 5.8% 6754 2.56 7.8% 7.6% 7160 2.45 8.8% 9.0% 5821 2.36 10.7% 10.9% 6740 2.27 13.9% 14.3% 7490 2.19 17.4% 17.1% 7943 2.12 19.4% 19.7% 8331 2.06 25.1% 25.3% 8562 2.00 33.9% 34.4% 8947 1.95 45.6% 46.6% 9311 1.90 63.4% 65.2% 9677 total 4.8% 4.8% 124778 ****************************************************************************** WILSON STATISTICS OF SCALED DATA SET: SAD.HKL ****************************************************************************** Data is divided into resolution shells and a straight line A - 2*B*SS is fitted to log, where RES = mean resolution (Angstrom) in shell SS = mean of (sin(THETA)/LAMBDA)**2 in shell = mean reflection intensity in shell BO = (A - log)/(2*SS) # = number of reflections in resolution shell WILSON LINE (using all data) : A= 13.140 B= 40.039 CORRELATION= 0.99 # RES SS log() BO 279 10.612 0.002 4.1204E+05 12.929 47.5 445 6.647 0.006 1.7185E+05 12.054 95.9 569 5.195 0.009 1.8486E+05 12.127 54.7 651 4.401 0.013 2.3890E+05 12.384 29.3 744 3.886 0.017 2.1376E+05 12.273 26.2 799 3.519 0.020 1.6486E+05 12.013 27.9 883 3.240 0.024 9.3835E+04 11.449 35.5 924 3.018 0.027 5.7643E+04 10.962 39.7 977 2.838 0.031 3.9093E+04 10.574 41.3 1058 2.685 0.035 2.8647E+04 10.263 41.5 1114 2.553 0.038 1.9119E+04 9.858 42.8 1117 2.440 0.042 1.5572E+04 9.653 41.5 1189 2.341 0.046 1.1407E+04 9.342 41.6 1228 2.253 0.049 1.0401E+04 9.250 39.5 1288 2.174 0.053 8.2456E+03 9.017 39.0 1297 2.103 0.057 6.0875E+03 8.714 39.2 1367 2.039 0.060 4.2791E+03 8.361 39.7 1401 1.980 0.064 2.8248E+03 7.946 40.7 1456 1.925 0.067 2.0981E+03 7.649 40.7 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF CENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 3**2 15**3 105**4 103 10.612 0.831 0.775 0.617 104 6.647 0.716 0.461 0.243 107 5.195 0.696 0.588 0.420 100 4.401 1.150 0.922 0.631 106 3.886 0.817 0.559 0.323 102 3.519 1.344 1.452 1.409 106 3.240 1.078 0.882 0.615 101 3.018 1.338 1.503 1.418 104 2.838 1.461 1.537 1.377 107 2.685 1.164 1.515 1.797 113 2.553 1.456 2.236 3.146 95 2.440 1.538 2.146 2.753 98 2.341 0.840 0.775 0.652 105 2.253 1.549 1.863 1.989 108 2.174 3.248 7.940 16.910 102 2.103 2.340 3.508 4.576 104 2.039 2.925 6.640 13.518 107 1.980 0.941 0.818 0.632 107 1.925 1.937 3.177 4.684 1979 overall 1.443 2.081 3.071 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF ACENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 2**2 6**3 24**4 176 10.612 1.038 0.911 0.743 341 6.647 1.183 1.381 1.536 462 5.195 1.058 1.005 0.882 551 4.401 0.961 0.960 0.929 638 3.886 0.998 0.976 0.932 697 3.519 0.964 0.959 0.947 777 3.240 0.981 0.973 0.921 823 3.018 1.029 1.109 1.180 873 2.838 0.985 1.028 1.078 951 2.685 1.069 1.143 1.164 1001 2.553 1.137 1.407 1.775 1022 2.440 1.064 1.227 1.454 1091 2.341 1.137 1.326 1.492 1123 2.253 1.169 1.432 1.761 1180 2.174 1.257 1.991 3.301 1195 2.103 1.217 1.705 2.362 1263 2.039 1.180 1.510 1.950 1294 1.980 1.457 2.492 4.988 1349 1.925 1.320 1.726 2.247 16807 overall 1.147 1.436 1.910 ======= CUMULATIVE INTENSITY DISTRIBUTION ======= DEFINITIONS: = mean reflection intensity Na(Z)exp = expected number of acentric reflections with I <= Z* Na(Z)obs = observed number of acentric reflections with I <= Z* Nc(Z)exp = expected number of centric reflections with I <= Z* Nc(Z)obs = observed number of centric reflections with I <= Z* Nc(Z)obs/Nc(Z)exp versus resolution and Z (0.1-1.0) # RES 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 103 10.612 1.25 1.10 1.05 1.09 1.12 1.11 1.11 1.13 1.11 1.10 104 6.647 1.08 1.11 1.18 1.12 1.11 1.10 1.03 1.01 1.02 1.06 107 5.195 1.17 1.19 1.17 1.20 1.20 1.20 1.16 1.13 1.17 1.14 100 4.401 0.89 0.87 0.84 0.89 0.92 0.87 0.85 0.84 0.90 0.89 106 3.886 0.99 0.96 0.91 0.96 0.98 0.94 0.93 0.93 0.96 0.95 102 3.519 0.91 0.91 0.99 0.95 0.96 0.94 0.94 0.97 0.96 0.96 106 3.240 0.95 0.93 0.88 0.92 0.85 0.82 0.87 0.89 0.88 0.90 101 3.018 0.96 1.00 1.00 1.05 1.14 1.15 1.13 1.07 1.07 1.06 104 2.838 1.08 0.95 0.97 0.91 0.96 0.98 0.95 0.95 0.94 0.92 107 2.685 0.75 0.81 0.92 0.91 0.93 1.02 1.02 1.03 1.07 1.08 113 2.553 1.00 1.18 1.15 1.10 1.10 1.14 1.14 1.10 1.08 1.05 95 2.440 0.81 1.00 0.96 0.91 0.93 0.98 0.95 0.97 0.96 0.99 98 2.341 0.95 1.00 1.05 1.10 1.08 1.07 1.06 1.04 1.03 1.02 105 2.253 0.92 0.91 0.98 1.03 1.06 1.03 1.04 1.06 1.04 1.02 108 2.174 1.19 1.02 1.07 1.02 1.01 1.04 1.05 1.02 1.00 0.99 102 2.103 1.07 0.96 1.06 1.08 1.02 0.98 0.95 0.94 0.93 0.92 104 2.039 0.93 0.92 0.95 1.00 0.98 0.98 1.01 1.02 1.02 1.01 107 1.980 1.13 1.00 0.94 0.93 0.97 1.03 1.00 0.98 1.00 1.00 107 1.925 1.28 0.97 1.01 0.93 0.93 0.93 0.92 0.98 1.02 1.00 1979 overall 1.02 0.99 1.00 1.00 1.01 1.02 1.01 1.00 1.01 1.00 Na(Z)obs/Na(Z)exp versus resolution and Z (0.1-1.0) # RES 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 176 10.612 0.78 0.75 0.79 0.83 0.84 0.86 0.84 0.85 0.88 0.87 341 6.647 1.17 1.10 1.07 1.06 1.06 1.04 1.04 1.03 1.00 1.01 462 5.195 0.82 0.92 0.86 0.88 0.92 0.94 0.92 0.95 0.94 0.98 551 4.401 1.11 1.08 1.08 1.07 1.07 1.03 1.05 1.02 1.05 1.04 638 3.886 0.92 0.96 0.99 1.02 1.02 1.01 1.00 1.02 1.01 1.00 697 3.519 1.07 1.04 1.09 1.03 1.01 1.00 1.01 1.02 1.03 1.01 777 3.240 0.87 0.91 0.97 1.04 1.06 1.07 1.05 1.05 1.04 1.03 823 3.018 1.12 1.05 1.02 1.02 1.01 0.99 1.01 1.00 1.01 1.03 873 2.838 0.94 0.97 1.01 1.04 1.05 1.06 1.05 1.05 1.05 1.03 951 2.685 0.95 1.06 1.12 1.10 1.06 1.06 1.04 1.03 1.02 1.03 1001 2.553 1.00 1.04 1.10 1.08 1.07 1.08 1.08 1.08 1.06 1.06 1022 2.440 1.13 1.18 1.07 1.03 1.07 1.06 1.04 1.04 1.04 1.05 1091 2.341 1.18 1.12 1.11 1.07 1.08 1.05 1.03 1.02 1.02 1.00 1123 2.253 1.63 1.30 1.27 1.22 1.18 1.15 1.11 1.09 1.08 1.07 1180 2.174 1.21 1.28 1.27 1.25 1.21 1.17 1.13 1.12 1.10 1.08 1195 2.103 1.42 1.25 1.24 1.22 1.18 1.16 1.14 1.14 1.11 1.10 1263 2.039 1.55 1.29 1.21 1.19 1.17 1.17 1.15 1.11 1.10 1.08 1294 1.980 2.03 1.44 1.28 1.21 1.17 1.14 1.11 1.09 1.07 1.05 1349 1.925 2.22 1.49 1.24 1.17 1.11 1.07 1.04 1.04 1.03 1.01 16807 overall 1.32 1.17 1.14 1.11 1.10 1.08 1.06 1.06 1.05 1.04 List of 3 reflections *NOT* obeying Wilson distribution (Z> 10.0) h k l RES Z Intensity Sigma 6 10 28 2.00 16.26 0.9187E+05 0.3214E+04 "alien" 4 24 22 2.19 10.92 0.1801E+06 0.4661E+04 "alien" 2 24 22 2.20 10.05 0.1658E+06 0.3797E+04 "alien" List of 3 reflections *NOT* obeying Wilson distribution (sorted by resolution) Ice rings could occur at (Angstrom): 3.897,3.669,3.441, 2.671,2.249,2.072, 1.948,1.918,1.883,1.721 h k l RES Z Intensity Sigma 6 10 28 2.00 16.26 0.9187E+05 0.3214E+04 4 24 22 2.19 10.92 0.1801E+06 0.4661E+04 2 24 22 2.20 10.05 0.1658E+06 0.3797E+04 cpu time used by XSCALE 21.7 sec elapsed wall-clock time 3.6 sec