***** 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= 83.50 96.74 57.97 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= 52.33 2.04 CORRECTIONS= DECAY MODULATION ABSORPTION THE DATA COLLECTION STATISTICS REPORTED BELOW ASSUMES: SPACE_GROUP_NUMBER= 21 UNIT_CELL_CONSTANTS= 83.50 96.74 57.97 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" 37 DATA MEAN REFLECTIONS INPUT FILE NAME SET# INTENSITY ACCEPTED REJECTED 1 0.2669E+02 99053 181 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 36391.3 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.995 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer DECAY_001.cbf XMIN= 0.3 XMAX= 1799.3 NXBIN= 36 YMIN= 0.00072 YMAX= 0.24027 NYBIN= 20 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 52272 ****************************************************************************** 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 1024 DEGREES OF FREEDOM OF CHI^2 FIT 36322.4 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.991 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer MODPIX_001.cbf XMIN= 196.0 XMAX= 1270.6 NXBIN= 32 YMIN= 300.8 YMAX= 1378.8 NYBIN= 32 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 52272 ****************************************************************************** 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 36396.0 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 0.984 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer ABSORP_001.cbf XMIN= 0.3 XMAX= 1799.3 NXBIN= 36 DETECTOR_SURFACE_POSITION= 733 840 DETECTOR_SURFACE_POSITION= 916 1023 DETECTOR_SURFACE_POSITION= 551 1023 DETECTOR_SURFACE_POSITION= 551 657 DETECTOR_SURFACE_POSITION= 916 657 DETECTOR_SURFACE_POSITION= 1146 1011 DETECTOR_SURFACE_POSITION= 904 1254 DETECTOR_SURFACE_POSITION= 562 1254 DETECTOR_SURFACE_POSITION= 320 1011 DETECTOR_SURFACE_POSITION= 320 668 DETECTOR_SURFACE_POSITION= 562 425 DETECTOR_SURFACE_POSITION= 904 425 DETECTOR_SURFACE_POSITION= 1146 668 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 52272 ****************************************************************************** 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 9.777E-01 2.692E-03 19.49 21.65 SAD_SWEEP1.HKL FACTOR TO PLACE ALL DATA SETS TO AN APPROXIMATE ABSOLUTE SCALE 0.550108E+04 (ASSUMING A PROTEIN WITH 50% SOLVENT) ****************************************************************************** STATISTICS OF SCALED OUTPUT DATA SET : SAD.HKL FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=FALSE 0 OUT OF 99053 REFLECTIONS REJECTED 99053 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 9.12 1246 325 332 97.9% 2.8% 3.7% 1246 32.83 3.2% 99.9* -1 0.614 121 6.45 2264 589 589 100.0% 3.5% 4.1% 2264 28.19 4.1% 99.8* 13 0.775 253 5.27 2972 772 772 100.0% 4.1% 4.4% 2972 24.91 4.8% 99.8* 7 0.810 340 4.56 2719 839 893 94.0% 4.1% 4.3% 2644 23.87 4.9% 99.6* -6 0.804 337 4.08 3328 1035 1047 98.9% 3.9% 4.2% 3323 23.38 4.7% 99.7* 17* 0.913 466 3.72 3718 1112 1132 98.2% 4.5% 4.4% 3709 23.05 5.4% 99.6* 39* 1.151 497 3.45 4053 1218 1230 99.0% 5.0% 4.8% 4034 20.79 6.0% 99.6* 32* 1.144 546 3.23 4630 1316 1326 99.2% 6.1% 5.6% 4630 18.45 7.2% 99.4* 26* 1.065 613 3.04 5019 1394 1403 99.4% 7.4% 6.9% 5016 15.19 8.7% 99.3* 16* 0.993 642 2.89 5348 1488 1496 99.5% 8.6% 8.2% 5339 12.81 10.1% 99.1* 19* 0.991 687 2.75 5734 1577 1582 99.7% 10.4% 10.0% 5723 10.87 12.2% 98.7* 15* 0.980 734 2.63 6009 1635 1641 99.6% 12.2% 11.8% 6001 9.22 14.3% 98.4* 10 0.920 763 2.53 5853 1687 1699 99.3% 15.7% 15.7% 5827 6.75 18.6% 97.6* 7 0.865 776 2.44 5038 1745 1791 97.4% 19.0% 19.8% 4821 5.09 23.1% 96.2* 12 0.865 679 2.36 5969 1846 1854 99.6% 22.4% 22.3% 5929 4.59 26.9% 94.7* 5 0.841 840 2.28 6337 1886 1898 99.4% 26.4% 26.5% 6305 4.00 31.4% 92.2* 5 0.819 866 2.21 6778 1951 1960 99.5% 30.9% 31.1% 6755 3.45 36.6% 91.4* 6 0.826 912 2.15 7133 2029 2040 99.5% 37.2% 37.7% 7101 2.85 43.9% 90.8* 8 0.828 936 2.09 7257 2058 2085 98.7% 47.3% 48.1% 7229 2.27 55.8% 81.0* 7 0.804 960 2.04 7648 2139 2151 99.4% 57.9% 59.5% 7617 1.83 68.2% 78.7* 2 0.751 996 total 99053 28641 28921 99.0% 7.3% 7.3% 98485 10.33 8.6% 99.8* 13* 0.891 12964 ========== STATISTICS OF INPUT DATA SET ========== R-FACTORS FOR INTENSITIES OF DATA SET SAD_SWEEP1.HKL RESOLUTION R-FACTOR R-FACTOR COMPARED LIMIT observed expected 9.12 2.8% 3.7% 1246 6.45 3.5% 4.1% 2264 5.27 4.1% 4.4% 2972 4.56 4.1% 4.3% 2644 4.08 3.9% 4.2% 3323 3.72 4.5% 4.4% 3709 3.45 5.0% 4.8% 4034 3.23 6.1% 5.6% 4630 3.04 7.4% 6.9% 5016 2.89 8.6% 8.2% 5339 2.75 10.4% 10.0% 5723 2.63 12.2% 11.8% 6001 2.53 15.7% 15.7% 5827 2.44 19.0% 19.8% 4821 2.36 22.4% 22.3% 5929 2.28 26.4% 26.5% 6305 2.21 30.9% 31.1% 6755 2.15 37.2% 37.7% 7101 2.09 47.3% 48.1% 7229 2.04 57.9% 59.5% 7617 total 7.3% 7.3% 98485 ****************************************************************************** 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= 13.145 B= 38.103 CORRELATION= 0.98 # RES SS log() BO 233 11.259 0.002 4.1985E+05 12.948 49.9 376 7.072 0.005 1.8967E+05 12.153 99.2 458 5.549 0.008 1.6688E+05 12.025 68.9 508 4.714 0.011 2.4341E+05 12.402 33.0 599 4.169 0.014 2.3196E+05 12.354 27.5 657 3.777 0.018 2.3818E+05 12.381 21.8 713 3.476 0.021 1.7128E+05 12.051 26.4 770 3.237 0.024 1.0933E+05 11.602 32.3 801 3.043 0.027 6.9843E+04 11.154 36.9 850 2.880 0.030 5.1567E+04 10.851 38.1 884 2.741 0.033 4.0604E+04 10.612 38.0 940 2.620 0.036 2.6536E+04 10.186 40.6 943 2.513 0.040 2.0550E+04 9.931 40.6 1007 2.418 0.043 1.7481E+04 9.769 39.5 1035 2.334 0.046 1.2710E+04 9.450 40.2 1070 2.258 0.049 1.1906E+04 9.385 38.3 1090 2.189 0.052 1.0180E+04 9.228 37.5 1124 2.126 0.055 7.4645E+03 8.918 38.2 1177 2.067 0.058 5.9181E+03 8.686 38.1 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF CENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 3**2 15**3 105**4 91 11.259 0.892 1.036 1.093 93 7.072 0.783 0.573 0.363 91 5.549 0.609 0.530 0.421 75 4.714 0.816 0.532 0.299 92 4.169 1.072 0.891 0.656 92 3.777 0.913 0.721 0.504 93 3.476 1.068 0.993 0.799 92 3.237 1.022 0.770 0.499 93 3.043 1.318 1.412 1.250 86 2.880 1.593 1.842 1.764 91 2.741 1.343 1.425 1.298 89 2.620 0.896 0.846 0.698 78 2.513 2.473 5.002 8.987 93 2.418 0.814 0.574 0.346 91 2.334 0.705 0.583 0.441 87 2.258 1.456 1.975 2.453 94 2.189 4.334 11.780 27.427 85 2.126 1.896 2.278 2.358 92 2.067 3.227 6.446 10.686 1698 overall 1.433 2.123 3.308 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF ACENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 2**2 6**3 24**4 142 11.259 1.041 0.869 0.656 283 7.072 1.091 1.121 1.065 367 5.549 1.139 1.191 1.189 433 4.714 0.951 0.909 0.866 507 4.169 1.001 1.030 1.023 565 3.777 0.953 0.879 0.783 620 3.476 1.056 1.131 1.169 678 3.237 0.938 0.879 0.798 708 3.043 0.996 1.029 1.056 764 2.880 0.964 0.958 0.947 793 2.741 1.052 1.225 1.515 851 2.620 1.137 1.391 1.746 865 2.513 1.057 1.169 1.229 914 2.418 1.155 1.434 1.816 944 2.334 1.143 1.313 1.466 983 2.258 1.187 1.453 1.745 996 2.189 1.156 1.684 2.538 1039 2.126 1.067 1.180 1.282 1085 2.067 1.116 1.362 1.659 13537 overall 1.075 1.224 1.409 ======= 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 91 11.259 1.28 1.08 1.13 1.16 1.14 1.12 1.12 1.15 1.12 1.10 93 7.072 1.21 1.18 1.21 1.16 1.16 1.11 1.06 1.04 1.03 1.04 91 5.549 1.19 1.24 1.21 1.23 1.29 1.21 1.16 1.15 1.14 1.18 75 4.714 0.91 0.85 0.86 0.87 0.90 0.93 0.89 0.89 0.87 0.92 92 4.169 0.96 0.85 0.89 0.85 0.88 0.95 0.93 0.90 0.91 0.96 92 3.777 0.88 0.88 0.97 0.94 0.94 0.95 0.98 0.97 0.98 1.00 93 3.476 1.00 0.96 0.98 1.09 1.07 1.13 1.10 1.04 1.00 0.98 92 3.237 0.74 0.82 0.89 0.87 0.81 0.83 0.86 0.85 0.88 0.91 93 3.043 1.08 1.12 1.06 1.05 1.07 1.09 1.10 1.06 1.06 1.06 86 2.880 0.84 1.04 1.06 0.96 0.98 0.99 0.95 1.00 0.99 0.97 91 2.741 0.71 0.92 0.95 0.93 1.01 1.02 1.05 1.08 1.07 1.05 89 2.620 0.90 0.94 1.00 1.02 1.06 1.08 1.05 1.07 1.15 1.10 78 2.513 0.88 0.96 0.92 0.92 0.99 0.98 0.97 1.00 0.98 0.98 93 2.418 0.82 0.87 0.96 0.95 1.01 1.02 0.95 0.96 0.95 0.96 91 2.334 0.88 0.99 1.16 1.14 1.16 1.14 1.16 1.14 1.09 1.06 87 2.258 1.02 0.96 0.97 0.95 0.93 1.04 1.08 1.08 1.10 1.08 94 2.189 0.90 0.92 0.82 0.85 0.98 0.95 0.98 1.02 1.00 0.98 85 2.126 0.85 0.82 0.79 0.82 0.86 0.92 0.91 0.92 0.93 0.93 92 2.067 0.83 0.75 0.73 0.76 0.73 0.85 0.87 0.92 0.93 0.99 1698 overall 0.94 0.96 0.98 0.98 1.00 1.02 1.01 1.01 1.01 1.01 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 1.0 142 11.259 0.89 0.85 0.76 0.81 0.81 0.83 0.80 0.83 0.83 0.84 283 7.072 0.85 0.96 0.93 1.01 1.04 1.02 1.00 1.02 1.01 1.00 367 5.549 0.94 0.95 0.90 0.92 0.93 0.92 0.91 0.93 0.94 0.96 433 4.714 0.80 0.87 0.92 0.95 0.98 0.97 0.99 1.00 0.98 0.99 507 4.169 1.04 1.02 1.05 1.09 1.06 1.04 1.05 1.03 1.06 1.05 565 3.777 1.02 0.97 0.94 1.00 0.99 0.95 0.95 0.96 0.98 1.00 620 3.476 0.98 1.17 1.13 1.09 1.08 1.04 1.02 1.02 1.02 1.03 678 3.237 0.79 0.98 0.99 1.00 1.00 1.02 1.01 1.02 1.02 1.01 708 3.043 0.99 0.99 0.95 1.02 1.00 1.00 0.98 1.02 0.99 1.01 764 2.880 1.02 1.04 1.03 1.05 1.03 1.03 1.03 1.03 1.03 1.04 793 2.741 0.83 1.04 1.09 1.07 1.10 1.07 1.07 1.05 1.04 1.02 851 2.620 1.12 1.09 1.07 1.03 1.05 1.02 1.02 1.01 1.01 1.03 865 2.513 1.13 1.11 1.07 1.10 1.10 1.10 1.09 1.07 1.07 1.07 914 2.418 1.17 1.21 1.15 1.11 1.09 1.06 1.06 1.06 1.04 1.03 944 2.334 1.27 1.15 1.11 1.09 1.05 1.04 1.03 0.99 0.99 0.99 983 2.258 1.31 1.27 1.26 1.20 1.20 1.18 1.15 1.11 1.09 1.06 996 2.189 1.18 1.19 1.22 1.19 1.19 1.15 1.14 1.13 1.11 1.10 1039 2.126 1.30 1.06 1.04 1.05 1.07 1.07 1.11 1.09 1.08 1.06 1085 2.067 1.63 1.24 1.11 1.05 1.06 1.07 1.08 1.09 1.08 1.07 13537 overall 1.13 1.10 1.07 1.07 1.07 1.05 1.05 1.05 1.04 1.03 cpu time used by XSCALE 16.4 sec elapsed wall-clock time 2.6 sec