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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.
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.
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.
Line 29: Line 42:
                                   observed  expected
                                   observed  expected
   
   
   39.660 19.587     8.23   0.96     6.36     7.12     929     940    75
   48.268 17.853     9.63   0.97     5.06     6.10     865     868      44
   19.587 14.780     7.39   0.88      5.94     7.46   1956   1959     66
   17.853 13.079    10.02  0.97      5.22      6.14   1301    1305      81
  13.079  10.812     9.83  1.10      5.56      5.94    1374    1388      99
  10.812   9.423    9.88   1.09     5.32      6.03    1820    1825    108
    9.423  8.460    9.56  1.07      6.03     6.21   2087   2101     167
  .... (many resolution shells deleted for brevity)
  .... (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-FACTOR
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  R-meas  = redundancy independent R-factor (intensities)
  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.
             Diederichs & Karplus (1997), Nature Struct. Biol. 4, 269-275.
  (rest of heading deleted for brevity)
   
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.


and the table itself is
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
  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  Anomal  SigAno  
  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
   LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
   
   
     6.66       12698   5958    10069       59.2%      5.3%    6.7%    11577   10.55     6.8%    5.5%    -27%    0.740    527
     5.72       23750   7284      7488      97.3%       6.6%      6.6%    23666  14.59     7.9%   99.3*    33*  1.043    3033
     4.74       22569   11140     17519       63.6%       7.3%    7.8%    19592   8.24     9.5%    9.1%    -25%    0.734    629
    4.06       41574  12997    13384      97.1%      10.0%      8.3%    41476  11.40    12.1%    98.3*    45*  1.341    5775
     3.88       28199   14683     22445       65.4%       7.9%    7.7%    23437   7.88    10.3%    10.6%   -31%   0.769    449
    3.32      56679  16961    17336      97.8%      16.8%    15.4%   56494   6.49    20.1%    97.9*    31*   1.079    7697
     3.37       34407   17986     26530       67.8%     12.3%   12.0%    28131   5.25    16.1%    20.6%    -19%   0.777    351
    2.88      67173  20272     20497      98.9%      38.4%    39.0%    66875    2.91    45.9%    93.1*    19*  0.840    9333
     3.01       39636   20921     29958       69.8%     22.7%  23.3%    31896   3.08    29.8%    42.6%    -12%   0.644    211
     2.57       79365   23100     23197       99.6%      77.6%     85.3%    79063    1.46    92.1%    75.3*    5   0.701  10761
  (rest deleted for brevity)
    2.35      86431  25554     25631      99.7%    128.9%    146.7%    86014    0.86  153.2%   54.7*    3   0.633  11894
     2.18       83863   27529     27946       98.5%     197.0%    230.0%    81669   0.49  237.7%    31.6*   -1   0.575  11422
     2.04       51338   23815     29966       79.5%     286.2%   343.0%    43478   0.26  361.1%    15.1*    0   0.526    5523
     1.92       25803   15877     31898       49.8%     483.3%    577.5%   17026    0.12   635.3%     3.8      2   0.519    1856
    total      515976  173389   197343      87.9%      27.8%    29.3%   495761   2.89    33.5%    98.2*   19*  0.781  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 (for phasing 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 to.
The file XDS_ASCII.HKL actually has all 531700 reflections.
Kay
Bureaucrats
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