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CORRECT.LP

3,241 bytes added, 20:42, 4 September 2012
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== Statistics of reflections ==
 
Near the top of CORRECT.LP we find:
531781 REFLECTIONS ON FILE "INTEGRATE.HKL"
0 CORRUPTED REFLECTION RECORDS (IGNORED)
0 REFLECTIONS INCOMPLETE OR OUTSIDE IMAGE RANGE 1 ... 1799
0 OVERLOADED REFLECTIONS (IGNORED)
81 REFLECTIONS OUTSIDE ACCEPTED RESOLUTION RANGES
OR TOO CLOSE TO ROTATION AXIS (IGNORED)
531700 REFLECTIONS ACCEPTED
 
== Statistics of observations ==
 
XDS, like SCALA and d*TREK, gives statistics about unaveraged and averaged quantities, but in different tables.
The unaveraged values are in a table that is fine-grained in terms of resolution, at the beginning of CORRECT.LP. The Sigma values in that table are corrected to match the RMS scatter.
observed expected
3948.660 268 1917.587 853 89.23 63 0.96 97 65.36 06 76.12 10 929 865 940 75868 44 1917.587 853 13.079 10.02 0.97 5.22 6.14 1301 1305 81 13.079 10.780 812 79.83 1.10 5.56 5.94 1374 1388 99 10.39 812 09.423 9.88 1.09 5.94 32 6.03 1820 1825 108 9.423 8.460 9.56 1.07 6.03 76.46 21 1956 2087 1959 2101 66167
.... (many resolution shells deleted for brevity)
== Statistics of unique reflections ==
----Later tables talk about the averaged intensities:
and later it gives the table for the averaged intensities with heading
R-FACTOR
R-meas = redundancy independent R-factor (intensities)
Rmrgd-F = quality of amplitudes (F) of this data set
For definition of R-meas and Rmrgd-F see
Diederichs & Karplus (1997), Nature Struct. Biol. 4, 269-275.
CC(rest 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 heading deleted unique reflections used to calculate Anomal_Corr & SigAno. At least two observations for brevityeach (+ and -)parity are required.
and the table itself is
 
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 Rmrgd-F CC(1/2) Anomal SigAno Nano
LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr
65.66 72 12698 23750 5958 10069 7284 7488 97.3% 6.6% 6.6% 23666 14.59 7.29% 99.3* 33* 1.043 3033 4.06 541574 12997 13384 97.1% 10.0% 8.3% 41476 11.40 12.1% 98.3* 45* 1.341 5775 3.32 56679 16961 17336 97.8% 16.8% 15.4% 56494 6.749 20.1% 11577 97.9* 31* 101.079 7697 2.55 88 67173 20272 620497 98.9% 38.84% 539.50% -2766875 2.91 45.9% 93.1* 19* 0.740 527840 9333 42.74 57 22569 79365 11140 23100 17519 23197 6399.6% 77.6% 7 85.3% 779063 1.46 92.81% 19592 75.3* 5 80.701 10761 2.24 35 86431 25554 925631 99.57% 128.9% 146.17% -2586014 0.86 153.2% 54.7* 3 0.734 629633 11894 32.88 18 28199 83863 14683 27529 22445 27946 6598.45% 7 197.90% 7230.70% 23437 81669 70.88 1049 237.37% 1031.6% * -31% 1 0.769 449575 11422 32.37 04 34407 51338 17986 23815 26530 29966 6779.85% 12 286.32% 12 343.0% 28131 43478 50.25 1626 361.1% 2015.6% -19% 1* 0 0.777 351526 5523 31.01 92 39636 25803 20921 15877 29958 31898 6949.8% 22 483.3% 577.75% 17026 0.12 23635.3% 3.8 2 31896 0.519 1856 total 515976 173389 3197343 87.9% 27.08 8% 29.83% 495761 422.689 33.5% -12% 98.2* 19* 0.644 211781 67294 NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 531700 NUMBER OF REJECTED MISFITS 15698 NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 NUMBER OF ACCEPTED OBSERVATIONS 516002 NUMBER OF UNIQUE ACCEPTED REFLECTIONS 173398 Why is there a discrepancy between "total 515976 173389" ''versus'' "NUMBER OF ACCEPTED OBSERVATIONS 516002", and "NUMBER OF UNIQUE ACCEPTED REFLECTIONS 173398" ?? The reason is that the higher numbers ''include'' even those reflections with I<3*sigma(I), whereas the numbers in the table refer only to those reflections which should be used downstream (rest deleted for brevityphasing and refinement). Indeed, XDSCONV filters out observations with I<-3*sigma(I).
At the bottom of CORRECT.LP we find:
 
NUMBER OF UNIQUE ALIEN REFLECTIONS WITH A Z-SCORE ABOVE LIMIT 162
(ALIENS ABOVE LIMIT (REJECT_ALIEN= 20.0) ARE MARKED INVALID)
NUMBER OF REFLECTION RECORDS ON OUTPUT FILE "XDS_ASCII.HKL" 531700
NUMBER OF ACCEPTED OBSERVATIONS (INCLUDING SYSTEMATIC ABSENCES) 515712
NUMBER OF REJECTED MISFITS & ALIENS (marked by -1*SIGMA(IOBS)) 15988
So, the program indicates quite clearly what the statistics refer toThe file XDS_ASCII.HKL actually has all 531700 reflections.
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