***** XSCALE ***** (VERSION Jun 1, 2017 BUILT=20170923) 8-Nov-2017 Author: Wolfgang Kabsch Copy licensed until 31-Mar-2018 to academic users for non-commercial applications No redistribution. ****************************************************************************** CONTROL CARDS ****************************************************************************** MAXIMUM_NUMBER_OF_PROCESSORS=4 SPACE_GROUP_NUMBER=89 UNIT_CELL_CONSTANTS= 73.92 73.92 110.00 90.00 90.00 90.00 MINIMUM_I/SIGMA=3.0 OUTPUT_FILE=NATIVE.HKL FRIEDEL'S_LAW=TRUE MERGE=FALSE INPUT_FILE=NATIVE_SWEEP1.HKL XDS_ASCII INCLUDE_RESOLUTION_RANGE= 34.48 1.65 CORRECTIONS= DECAY MODULATION ABSORPTION THE DATA COLLECTION STATISTICS REPORTED BELOW ASSUMES: SPACE_GROUP_NUMBER= 89 UNIT_CELL_CONSTANTS= 73.92 73.92 110.00 90.000 90.000 90.000 ***** 8 EQUIVALENT POSITIONS IN SPACE GROUP # 89 ***** 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 0 -1 0 0 -1 0 0 0 0 0 -1 0 6 0 1 0 0 1 0 0 0 0 0 -1 0 7 0 1 0 0 -1 0 0 0 0 0 1 0 8 0 -1 0 0 1 0 0 0 0 0 1 0 ALL DATA SETS WILL BE SCALED TO NATIVE_SWEEP1.HKL ****************************************************************************** READING INPUT REFLECTION DATA FILES ****************************************************************************** NUMBER OF UNIQUE REFLECTIONS IN FILE "REMOVE.HKL" 936 DATA MEAN REFLECTIONS INPUT FILE NAME SET# INTENSITY ACCEPTED REJECTED 1 0.9438E+03 429943 89 NATIVE_SWEEP1.HKL ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & RESOLUTION ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: NATIVE.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW= TRUE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 680 DEGREES OF FREEDOM OF CHI^2 FIT 174499.8 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 1.091 NUMBER OF CYCLES CARRIED OUT 4 CORRECTION FACTORS for visual inspection by XDS-Viewer DECAY_001.cbf XMIN= 0.6 XMAX= 1684.0 NXBIN= 34 YMIN= 0.00092 YMAX= 0.36731 NYBIN= 20 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 195145 ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF X (fast) & Y(slow) IN THE DETECTOR PLANE ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: NATIVE.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW= TRUE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 3906 DEGREES OF FREEDOM OF CHI^2 FIT 174197.3 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 1.088 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer MODPIX_001.cbf XMIN= 5.2 XMAX= 2457.5 NXBIN= 62 YMIN= 4.5 YMAX= 2522.3 NYBIN= 63 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 195145 ****************************************************************************** CORRECTION FACTORS AS FUNCTION OF IMAGE NUMBER & DETECTOR SURFACE POSITION ****************************************************************************** RECIPROCAL CORRECTION FACTORS FOR INPUT DATA SETS MERGED TO OUTPUT FILE: NATIVE.HKL THE CALCULATIONS ASSUME FRIEDEL'S_LAW= TRUE TOTAL NUMBER OF CORRECTION FACTORS DEFINED 442 DEGREES OF FREEDOM OF CHI^2 FIT 174535.0 CHI^2-VALUE OF FIT OF CORRECTION FACTORS 1.075 NUMBER OF CYCLES CARRIED OUT 3 CORRECTION FACTORS for visual inspection by XDS-Viewer ABSORP_001.cbf XMIN= 0.6 XMAX= 1684.0 NXBIN= 34 DETECTOR_SURFACE_POSITION= 1231 1263 DETECTOR_SURFACE_POSITION= 1648 1691 DETECTOR_SURFACE_POSITION= 815 1691 DETECTOR_SURFACE_POSITION= 815 836 DETECTOR_SURFACE_POSITION= 1648 836 DETECTOR_SURFACE_POSITION= 2174 1664 DETECTOR_SURFACE_POSITION= 1622 2231 DETECTOR_SURFACE_POSITION= 841 2231 DETECTOR_SURFACE_POSITION= 289 1664 DETECTOR_SURFACE_POSITION= 289 863 DETECTOR_SURFACE_POSITION= 841 296 DETECTOR_SURFACE_POSITION= 1622 296 DETECTOR_SURFACE_POSITION= 2174 863 NUMBER OF REFLECTIONS USED FOR DETERMINING CORRECTION FACTORS 195145 ****************************************************************************** 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 1.220E+00 6.185E-03 11.51 13.45 NATIVE_SWEEP1.HKL FACTOR TO PLACE ALL DATA SETS TO AN APPROXIMATE ABSOLUTE SCALE 0.570243E+02 (ASSUMING A PROTEIN WITH 50% SOLVENT) ****************************************************************************** STATISTICS OF SCALED OUTPUT DATA SET : NATIVE.HKL FILE TYPE: XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE 0 OUT OF 429943 REFLECTIONS REJECTED 429943 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. 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 7.38 4980 501 514 97.5% 4.3% 6.6% 4977 34.34 4.5% 99.9* -20 0.500 277 5.22 9151 848 848 100.0% 5.2% 6.7% 9144 35.14 5.4% 99.9* -31 0.545 603 4.26 11493 1051 1054 99.7% 5.6% 6.6% 11491 35.97 5.9% 99.8* -20 0.622 815 3.69 12541 1205 1206 99.9% 6.0% 6.7% 12540 34.72 6.3% 99.8* -24 0.645 966 3.30 15476 1377 1378 99.9% 6.5% 6.7% 15476 34.70 6.7% 99.8* -20 0.755 1132 3.01 17253 1493 1497 99.7% 6.8% 6.9% 17253 32.83 7.1% 99.8* -21 0.735 1254 2.79 17305 1625 1630 99.7% 7.3% 7.2% 17305 28.93 7.7% 99.7* -14 0.807 1383 2.61 20170 1714 1716 99.9% 8.4% 7.9% 20170 27.15 8.8% 99.7* -23 0.748 1476 2.46 21950 1831 1836 99.7% 9.1% 8.5% 21949 25.27 9.5% 99.8* -22 0.732 1596 2.33 23172 1921 1927 99.7% 10.7% 9.9% 23171 22.14 11.2% 99.7* -18 0.753 1686 2.22 22671 2028 2033 99.8% 12.9% 11.8% 22670 18.66 13.5% 99.5* -11 0.795 1784 2.13 25172 2104 2112 99.6% 15.5% 14.7% 25172 16.53 16.2% 99.5* -12 0.744 1872 2.05 26849 2176 2185 99.6% 19.3% 19.2% 26847 13.78 20.1% 99.3* -9 0.732 1937 1.97 28546 2280 2290 99.6% 24.9% 26.1% 28546 11.01 26.0% 98.9* -12 0.712 2041 1.91 27264 2344 2360 99.3% 33.3% 36.2% 27263 8.06 34.8% 97.8* -7 0.704 2116 1.84 28573 2409 2431 99.1% 45.7% 51.1% 28572 5.92 47.7% 95.7* -10 0.654 2175 1.79 30279 2481 2503 99.1% 64.8% 69.8% 30278 4.15 67.6% 90.4* -16 0.682 2245 1.74 31862 2573 2597 99.1% 87.3% 93.4% 31861 2.89 91.0% 82.5* -22 0.649 2335 1.69 31075 2597 2638 98.4% 112.3% 124.5% 31068 2.01 117.2% 71.5* -13 0.629 2359 1.65 24154 2571 2720 94.5% 151.4% 176.7% 24107 1.22 160.1% 51.2* 0 0.643 2183 total 429936 37129 37475 99.1% 7.8% 8.5% 429860 15.96 8.1% 99.9* -14 0.700 32235 ========== STATISTICS OF INPUT DATA SET ========== R-FACTORS FOR INTENSITIES OF DATA SET NATIVE_SWEEP1.HKL RESOLUTION R-FACTOR R-FACTOR COMPARED LIMIT observed expected 7.38 4.3% 6.6% 4977 5.22 5.2% 6.7% 9144 4.26 5.6% 6.6% 11491 3.69 6.0% 6.7% 12540 3.30 6.5% 6.7% 15476 3.01 6.8% 6.9% 17253 2.79 7.3% 7.2% 17305 2.61 8.4% 7.9% 20170 2.46 9.1% 8.5% 21949 2.33 10.7% 9.9% 23171 2.22 12.9% 11.8% 22670 2.13 15.5% 14.7% 25172 2.05 19.3% 19.2% 26847 1.97 24.9% 26.1% 28546 1.91 33.3% 36.2% 27263 1.84 45.7% 51.1% 28572 1.79 64.8% 69.8% 30278 1.74 87.3% 93.4% 31861 1.69 112.3% 124.5% 31068 1.65 151.4% 176.7% 24107 total 7.8% 8.5% 429860 ****************************************************************************** WILSON STATISTICS OF SCALED DATA SET: NATIVE.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= 13.394 B= 36.958 CORRELATION= 0.99 # RES SS log() BO 582 9.174 0.003 4.2867E+05 12.968 71.7 912 5.741 0.008 2.0392E+05 12.226 77.0 1127 4.499 0.012 3.7836E+05 12.844 22.3 1322 3.818 0.017 2.6301E+05 12.480 26.7 1471 3.374 0.022 1.7541E+05 12.075 30.0 1613 3.055 0.027 9.6674E+04 11.479 35.8 1746 2.813 0.032 5.4645E+04 10.909 39.3 1853 2.620 0.036 3.6180E+04 10.496 39.8 1960 2.463 0.041 2.8806E+04 10.268 37.9 2080 2.331 0.046 2.1048E+04 9.955 37.4 2176 2.217 0.051 1.6628E+04 9.719 36.1 2264 2.119 0.056 1.2608E+04 9.442 35.5 2365 2.033 0.061 9.0044E+03 9.105 35.4 2426 1.956 0.065 5.9204E+03 8.686 36.0 2521 1.888 0.070 3.8866E+03 8.265 36.6 2604 1.826 0.075 2.3088E+03 7.745 37.7 2651 1.770 0.080 1.5768E+03 7.363 37.8 2768 1.719 0.085 1.1333E+03 7.033 37.6 2687 1.672 0.089 8.3968E+02 6.733 37.2 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF CENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 3**2 15**3 105**4 251 9.174 0.825 0.645 0.432 249 5.741 0.948 0.863 0.732 248 4.499 0.815 0.700 0.543 255 3.818 0.925 0.859 0.748 251 3.374 1.249 1.957 3.223 249 3.055 1.303 1.680 2.240 248 2.813 1.044 0.997 0.829 250 2.620 1.101 1.195 1.176 239 2.463 0.720 0.597 0.457 249 2.331 0.998 1.036 0.952 251 2.217 1.129 1.226 1.189 237 2.119 1.110 1.051 0.897 253 2.033 0.899 0.823 0.666 230 1.956 1.127 1.370 1.528 237 1.888 0.762 0.580 0.401 242 1.826 0.914 0.705 0.470 223 1.770 1.070 1.004 0.890 241 1.719 1.068 1.115 1.112 199 1.672 1.600 1.742 1.833 4602 overall 1.026 1.055 1.065 HIGHER ORDER MOMENTS OF WILSON DISTRIBUTION OF ACENTRIC DATA AS COMPARED WITH THEORETICAL VALUES. (EXPECTED: 1.00) # RES / / / 2**2 6**3 24**4 331 9.174 1.228 1.546 1.929 663 5.741 1.013 1.039 1.027 879 4.499 1.071 1.098 1.069 1067 3.818 1.019 1.064 1.172 1220 3.374 1.052 1.190 1.441 1364 3.055 0.983 0.964 0.915 1498 2.813 1.099 1.310 1.642 1603 2.620 1.089 1.244 1.436 1721 2.463 1.225 1.551 1.916 1831 2.331 1.132 1.316 1.502 1925 2.217 1.124 1.300 1.451 2027 2.119 1.051 1.164 1.268 2112 2.033 1.101 1.291 1.530 2196 1.956 1.066 1.213 1.421 2284 1.888 1.047 1.086 1.150 2362 1.826 1.036 1.061 1.068 2428 1.770 1.040 1.022 0.988 2527 1.719 1.064 1.025 0.937 2488 1.672 1.270 1.433 1.660 32526 overall 1.091 1.198 1.325 ======= 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 1.0 251 9.174 1.06 1.00 0.99 1.01 1.07 1.05 1.05 1.07 1.06 1.05 249 5.741 0.94 0.89 0.91 0.92 0.93 0.94 0.95 0.96 0.97 1.01 248 4.499 1.10 1.04 1.02 1.03 1.02 1.02 1.04 1.05 1.04 1.05 255 3.818 1.11 1.05 1.03 1.04 1.05 1.09 1.05 1.06 1.04 1.02 251 3.374 1.09 1.11 1.07 1.09 1.08 1.04 1.03 1.05 1.05 1.02 249 3.055 1.03 0.96 0.98 1.00 0.96 0.97 0.98 0.96 0.96 0.98 248 2.813 1.07 1.10 1.02 0.99 1.01 1.01 1.03 1.02 1.01 1.01 250 2.620 0.92 1.03 1.07 1.01 1.01 1.00 0.99 0.99 1.00 1.03 239 2.463 0.96 0.93 0.92 1.04 1.01 1.04 1.02 1.04 1.04 1.05 249 2.331 0.97 1.08 1.10 1.10 1.10 1.10 1.07 1.06 1.05 1.05 251 2.217 1.09 1.14 1.08 1.04 1.01 1.04 1.04 1.06 1.05 1.06 237 2.119 0.75 0.84 0.91 0.88 0.87 0.87 0.93 0.96 0.95 0.99 253 2.033 0.91 0.99 1.05 1.06 1.05 1.04 1.05 1.08 1.08 1.09 230 1.956 0.89 0.96 1.03 1.06 1.03 1.03 1.03 1.04 1.04 1.03 237 1.888 0.93 0.93 0.96 1.02 1.05 1.07 1.09 1.04 1.02 1.01 242 1.826 0.73 0.72 0.74 0.79 0.85 0.85 0.90 0.93 0.95 0.98 223 1.770 0.92 0.88 0.97 0.96 0.97 0.99 0.98 0.99 0.99 0.97 241 1.719 0.99 0.92 0.85 0.85 0.89 0.89 0.97 0.97 0.99 1.00 199 1.672 1.34 0.99 0.88 0.86 0.82 0.80 0.82 0.85 0.88 0.88 4602 overall 0.99 0.98 0.98 0.99 0.99 0.99 1.00 1.01 1.01 1.02 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 1.0 331 9.174 0.95 0.93 0.91 0.92 1.01 1.02 1.03 1.03 1.02 1.02 663 5.741 1.05 1.02 1.07 1.00 0.99 1.00 0.97 0.98 1.00 1.00 879 4.499 0.86 1.04 1.00 0.99 1.01 1.03 1.00 0.99 0.99 1.00 1067 3.818 0.89 0.89 0.93 0.96 0.99 1.00 1.01 1.00 1.00 0.99 1220 3.374 0.90 0.97 1.01 1.01 1.02 1.02 1.02 1.03 1.02 1.01 1364 3.055 1.21 1.11 1.08 1.09 1.04 1.02 1.03 1.03 1.01 1.02 1498 2.813 1.02 1.16 1.11 1.10 1.07 1.05 1.05 1.05 1.02 1.01 1603 2.620 1.17 1.15 1.12 1.07 1.08 1.07 1.06 1.04 1.03 1.02 1721 2.463 1.22 1.18 1.18 1.16 1.13 1.10 1.07 1.05 1.05 1.05 1831 2.331 1.06 1.11 1.14 1.13 1.10 1.09 1.07 1.05 1.03 1.02 1925 2.217 1.11 1.15 1.11 1.09 1.09 1.10 1.09 1.08 1.07 1.05 2027 2.119 0.88 0.99 1.05 1.06 1.05 1.06 1.07 1.06 1.04 1.03 2112 2.033 0.89 0.94 0.97 1.02 1.02 1.02 1.03 1.04 1.03 1.03 2196 1.956 0.93 0.93 0.98 1.02 1.02 1.01 1.01 1.02 1.02 1.01 2284 1.888 1.19 0.99 0.96 0.98 0.99 0.98 0.99 1.00 0.99 0.99 2362 1.826 1.36 1.07 1.00 1.00 0.99 1.00 0.99 1.00 1.00 0.99 2428 1.770 1.47 1.10 1.02 0.97 0.98 0.99 0.99 0.99 0.99 0.98 2527 1.719 1.66 1.18 1.02 0.98 0.96 0.96 0.96 0.96 0.96 0.96 2488 1.672 2.28 1.40 1.15 1.06 0.99 0.95 0.94 0.94 0.95 0.94 32526 overall 1.23 1.09 1.05 1.04 1.03 1.02 1.02 1.02 1.01 1.00 cpu time used by XSCALE 14.4 sec elapsed wall-clock time 10.6 sec