#############################################################
##                        mmtbx.xtriage                    ##
##                                                         ##
##      P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams     ##
##                                                         ##
#############################################################
Date 2006-07-10 Time 13:37:54 PDT -0700


##-------------------------------------------##
## WARNING:                                  ##
## Number of residues unspecified            ##
##-------------------------------------------##


Effective parameters: 
scaling.input {
  parameters {
    asu_contents {
      n_residues = None
      n_bases = None
      n_copies_per_asu = None
    }
    misc_twin_parameters {
      missing_symmetry {
        tanh_location = 0.08
        tanh_slope = 50
      }
      twinning_with_ncs {
        perform_analyses = True
        n_bins = 7
      }
      twin_test_cuts {
        low_resolution = 10
        high_resolution = None
        isigi_cut = 3
        completeness_cut = 0.85
      }
    }
    reporting {
      verbose = 1
      log = "logfile.log"
      ccp4_style_graphs = True
    }
  }
  xray_data {
    file_name = "1p7g.mtz"
    obs_labels = None
    calc_labels = None
    unit_cell = 163.4290009 163.4290009 172.1690063 90 90 120
    space_group = "P 32"
    high_resolution = 4
    low_resolution = None
  }
}


Symmetry, cell and reflection file content summary

Miller array info: 1p7g.mtz:FOBS,SIGFOBS
Observation type: xray.amplitude
Type of data: double, size=42963
Type of sigmas: double, size=42963
Number of Miller indices: 42963
Anomalous flag: False
Unit cell: (163.429, 163.429, 172.169, 90, 90, 120)
Space group: P 32 (No. 145)
Systematic absences: 0
Centric reflections: 0
Resolution range: 36.4443 4.00004
Completeness in resolution range: 0.990273
Completeness with d_max=infinity: 0.988951

##----------------------------------------------------##
##                    Basic statistics                ##
##----------------------------------------------------##


Matthews coefficient and Solvent content statistics

Number of residues unknown, assuming 50% solvent content

----------------------------------------------------------------
|              Best guess : 4857  residues in the asu          |
----------------------------------------------------------------


Completeness and data strength analyses 

  The following table lists the completeness in various resolution
  ranges, after applying a I/sigI cut. Miller indices for which
  individual I/sigI values are larger than the value specified in
  the top row of the table, are retained, while other intensities
  are discarded. The resulting completeness profiles are an indication
  of the strength of the data.

----------------------------------------------------------------------------------------
| Res. Range   | I/sigI>1  | I/sigI>2  | I/sigI>3  | I/sigI>5  | I/sigI>10 | I/sigI>15 |
----------------------------------------------------------------------------------------
| 36.45 - 9.80 | 91.1%     | 89.6%     | 87.6%     | 83.4%     | 75.0%     | 63.5%     |
|  9.80 - 7.81 | 97.5%     | 97.4%     | 96.6%     | 94.6%     | 88.9%     | 78.9%     |
|  7.81 - 6.83 | 99.2%     | 98.8%     | 97.3%     | 94.7%     | 88.5%     | 78.1%     |
|  6.83 - 6.21 | 99.8%     | 99.3%     | 97.6%     | 95.2%     | 88.8%     | 79.9%     |
|  6.21 - 5.76 | 99.7%     | 99.2%     | 97.8%     | 95.2%     | 88.4%     | 78.2%     |
|  5.76 - 5.43 | 99.7%     | 99.0%     | 98.2%     | 96.2%     | 90.7%     | 82.5%     |
|  5.43 - 5.15 | 99.8%     | 99.5%     | 98.4%     | 97.5%     | 93.7%     | 86.8%     |
|  5.15 - 4.93 | 99.8%     | 99.7%     | 99.2%     | 97.9%     | 93.9%     | 87.2%     |
|  4.93 - 4.74 | 99.7%     | 99.5%     | 99.1%     | 97.8%     | 93.9%     | 87.9%     |
|  4.74 - 4.58 | 99.8%     | 99.6%     | 99.2%     | 98.3%     | 95.1%     | 88.6%     |
|  4.58 - 4.44 | 99.9%     | 99.8%     | 99.4%     | 98.7%     | 95.5%     | 90.1%     |
|  4.44 - 4.31 | 99.7%     | 99.6%     | 99.4%     | 98.8%     | 95.8%     | 90.6%     |
|  4.31 - 4.20 | 99.9%     | 99.5%     | 99.0%     | 98.2%     | 94.8%     | 88.8%     |
|  4.20 - 4.09 | 99.9%     | 99.6%     | 98.9%     | 97.7%     | 94.2%     | 88.6%     |
----------------------------------------------------------------------------------------



Maximum likelihood isotropic Wilson scaling 
ML estimate of overall B value of 1p7g.mtz:FOBS,SIGFOBS:
 5.54 A**(-2)
Estimated -log of scale factor of 1p7g.mtz:FOBS,SIGFOBS:
 0.29


Maximum likelihood anisotropic Wilson scaling 
ML estimate of overall B_cart value of 1p7g.mtz:FOBS,SIGFOBS:
 6.17,  0.00,  0.00
        6.17,  0.00
               4.33
Equivalent representation as U_cif: 
 0.08,  0.04, -0.00
        0.08,  0.00
               0.05

ML estimate of  -log of scale factor of 1p7g.mtz:FOBS,SIGFOBS:
 0.29
Correcting for anisotropy in the data

Some basic intensity statistics follow.



Low resolution completeness analyses 

 The following table shows the completeness
 of the data to 5 Angstrom.
unused:         - 36.4452 [   0/58  ] 0.000
bin  1: 36.4452 - 10.6901 [2012/2219] 0.907
bin  2: 10.6901 -  8.5207 [2109/2210] 0.954
bin  3:  8.5207 -  7.4541 [2182/2214] 0.986
bin  4:  7.4541 -  6.7774 [2207/2219] 0.995
bin  5:  6.7774 -  6.2943 [2215/2219] 0.998
bin  6:  6.2943 -  5.9248 [2215/2224] 0.996
bin  7:  5.9248 -  5.6292 [2223/2226] 0.999
bin  8:  5.6292 -  5.3850 [2209/2216] 0.997
bin  9:  5.3850 -  5.1783 [2214/2218] 0.998
bin 10:  5.1783 -  5.0001 [2230/2234] 0.998
unused:  5.0001 -         [   0/0   ]



Mean intensity analyses 
 Analyses of the mean intensity. 
 Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59.
 The following resolution shells are worrisome: 
------------------------------------------------
| d_spacing | z_score | compl. | <Iobs>/<Iexp> |
------------------------------------------------
|    9.995  |   4.97  |   0.94 |     0.607     |
|    6.740  |   4.55  |   1.00 |     1.174     |
|    6.201  |   5.78  |   1.00 |     1.225     |
------------------------------------------------

 Possible reasons for the presence of the reported
 unexpected low or elevated mean intensity in
 a given resolution bin are : 
 - missing overloaded or weak reflections
 - suboptimal data processing
 - satelite (ice) crystals
 - NCS
 - translational pseudo symmetry (detected elsewhere)
 - outliers (detected elsewhere)
 - ice rings (detected elsewhere)
 - other problems
 Note that the presence of abnormalities 
 in a certain region of reciprocal space might
 confuse the data validation algorithm throughout
 a large region of reciprocal space, even though
 the data is acceptable in those areas. 


Possible outliers 
  Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764

 Acentric reflections:

-----------------------------------------------------------------
| d_space |      H     K     L |  |E|  | p(wilson) | p(extreme) |
-----------------------------------------------------------------
|   9.790 |      0,    6,   16 |  4.27 |  1.18e-08 |   4.86e-04 |
|   5.579 |      0,   24,  -10 |  4.42 |  3.41e-09 |   1.40e-04 |
|   4.995 |      1,   16,  -28 |  4.43 |  3.00e-09 |   1.23e-04 |
|   5.379 |      2,    8,  -30 |  3.80 |  5.33e-07 |   2.17e-02 |
|   5.760 |      2,   11,   26 |  4.12 |  4.09e-08 |   1.68e-03 |
|   5.141 |      2,   14,  -28 |  3.66 |  1.53e-06 |   6.12e-02 |
|   5.616 |      3,    3,   30 |  4.22 |  1.78e-08 |   7.32e-04 |
|   6.655 |      3,    6,  -24 |  3.77 |  6.57e-07 |   2.67e-02 |
|   7.192 |      3,    9,  -20 |  3.66 |  1.53e-06 |   6.10e-02 |
|   4.752 |      3,   15,  -30 |  3.66 |  1.51e-06 |   6.03e-02 |
|   5.750 |      3,   18,   18 |  3.83 |  4.20e-07 |   1.72e-02 |
|   8.292 |      4,    1,   20 |  3.78 |  6.15e-07 |   2.50e-02 |
|   7.363 |      4,   13,   14 |  3.79 |  5.75e-07 |   2.34e-02 |
|   5.657 |      4,   19,   16 |  4.09 |  5.39e-08 |   2.22e-03 |
|   4.029 |      4,   19,   34 |  3.78 |  6.33e-07 |   2.58e-02 |
|   6.137 |      5,    5,  -26 |  4.21 |  1.94e-08 |   8.01e-04 |
|   6.569 |      5,    5,  -24 |  4.35 |  5.97e-09 |   2.46e-04 |
|   6.655 |      6,    3,  -24 |  3.75 |  8.08e-07 |   3.28e-02 |
|   7.752 |      6,    3,  -20 |  4.16 |  3.11e-08 |   1.28e-03 |
|   6.785 |      6,    6,  -22 |  3.62 |  2.08e-06 |   8.22e-02 |
|   7.277 |      6,    6,   20 |  4.03 |  8.70e-08 |   3.58e-03 |
|   4.403 |      6,    6,   37 |  3.86 |  3.31e-07 |   1.35e-02 |
|   7.399 |      7,    7,   18 |  3.79 |  5.59e-07 |   2.28e-02 |
|   6.709 |      7,    7,   21 |  3.97 |  1.41e-07 |   5.80e-03 |
|   6.953 |      7,   10,   17 |  3.60 |  2.40e-06 |   9.42e-02 |
|   5.379 |      8,    2,  -30 |  3.88 |  2.99e-07 |   1.23e-02 |
|   7.192 |      9,    3,  -20 |  3.75 |  8.05e-07 |   3.26e-02 |
|   6.561 |      9,   15,   -6 |  3.85 |  3.55e-07 |   1.45e-02 |
|   5.927 |     10,   10,  -20 |  4.34 |  6.41e-09 |   2.64e-04 |
|   6.353 |     10,   13,  -12 |  3.85 |  3.77e-07 |   1.54e-02 |
|   5.760 |     11,    2,   26 |  4.25 |  1.47e-08 |   6.05e-04 |
|   7.192 |     11,   11,   -6 |  3.67 |  1.40e-06 |   5.62e-02 |
|   6.359 |     11,   14,   -6 |  3.66 |  1.49e-06 |   5.95e-02 |
|   5.141 |     14,    2,  -28 |  3.76 |  7.11e-07 |   2.89e-02 |
|   4.752 |     15,    3,  -30 |  3.67 |  1.39e-06 |   5.57e-02 |
|   6.977 |     15,    3,   14 |  3.61 |  2.15e-06 |   8.49e-02 |
|   4.995 |     16,    1,  -28 |  4.17 |  2.92e-08 |   1.20e-03 |
|   5.750 |     18,    3,   18 |  3.80 |  5.21e-07 |   2.12e-02 |
|   5.657 |     19,    4,   16 |  4.35 |  6.26e-09 |   2.58e-04 |
|   5.017 |     25,    4,    9 |  3.88 |  2.89e-07 |   1.18e-02 |
|   4.961 |     26,    2,   11 |  4.12 |  4.34e-08 |   1.79e-03 |
-----------------------------------------------------------------

 p(wilson)  : 1-(1-exp[-|E|^2]) 
 p(extreme) : 1-(1-exp[-|E|^2])^(n_acentrics)
 p(wilson) is the probability that an E-value of the specified
 value would be observed when it would selected at random from
 the given data set.
 p(extreme) is the probability that the largest |E| value is 
 larger or equal then the observed largest |E| value.

 Both measures can be used for outlier detection. p(extreme)
 takes into account the size of the dataset.


 Centric reflections:

            None 


Ice ring related problems

 The following statistics were obtained from ice-ring 
 insensitive resolution ranges 
  mean bin z_score      : 2.24
      ( rms deviation   : 1.64 )
  mean bin completeness : 0.99
     ( rms deviation   : 0.01 )

 The following table shows the z-scores 
 and completeness in ice-ring sensitive areas.
 Large z-scores and high completeness in these 
 resolution ranges might be a reason to re-assess
 your data processsing if ice rings were present.

------------------------------------------------
| d_spacing | z_score | compl. | Rel. Ice int. |
------------------------------------------------
------------------------------------------------

 Abnormalities in mean intensity or completeness at
 resolution ranges with a relative ice ring intensity
 lower then 0.10 will be ignored.

 No ice ring related problems detected.
 If ice rings were present, the data does not look
 worse at ice ring related d_spacings as compared
 to the rest of the data set 




Basic analyses completed

##----------------------------------------------------##
##                   Twinning Analyses                ##
##----------------------------------------------------##



Using data between 10.00 to 4.09 Angstrom.

Determining possible twin laws.

The following twin laws have been found:

--------------------------------------------------------------------------------
| Type | Axis   | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law  |
--------------------------------------------------------------------------------
|   M  | 2-fold | 0.000        | 0.000           | 0.000           | -h-k,k,-l |
|   M  | 2-fold | 0.000        | 0.000           | 0.000           | -h,-k,l   |
|   M  | 2-fold | 0.000        | 0.000           | 0.000           | h+k,-k,-l |
--------------------------------------------------------------------------------
M:  Merohedral twin law
PM: Pseudomerohedral twin law

  3 merohedral twin operators found
  0 pseudo-merohedral twin operators found
In total,   3 twin operator were found


Number of centrics  : 0
Number of acentrics : 37503

 Largest patterson peak with length larger then 15 Angstrom 

 Frac. coord.        :   0.332   -0.334   -0.000
 Distance to origin  :  94.277
 Height (origin=100) :  65.792
 p_value(height)     :   6.698e-06

   The reported p_value has the following meaning: 
     The probability that a peak of the specified height 
     or larger is found in a Patterson function of a 
     macro molecule that does not have any translational
     pseudo symmetry is equal to  6.698e-06 
     p_values smaller then 0.05 might indicate 
     weak translation pseudo symmetry, or the self vector of 
     a large anomalous scatterer such as Hg, whereas values 
     smaller then 1e-3 are a very strong indication for 
     the presence of translational pseudo symmetry.


The full list of patterson peaks is: 

  x      y      z            height   p-value(height)
( 0.332,-0.334,-0.000 ) :   65.792   (6.698e-06)
( 0.000, 0.000, 0.500 ) :   16.688   (2.096e-02)
( 0.332,-0.334,-0.500 ) :   15.700   (2.708e-02)
( 0.000, 0.010, 0.500 ) :   11.006   (1.113e-01)


Wilson ratio and moments 

Acentric reflections 
   <I^2>/<I>^2    :3.730   (untwinned: 2.000; perfect twin 1.500)
   <F>^2/<F^2>    :0.626   (untwinned: 0.785; perfect twin 0.885)
   <|E^2 - 1|>    :1.044   (untwinned: 0.736; perfect twin 0.541)



NZ test (0<=z<1) to detect twinning and possible translational NCS


-----------------------------------------------
|  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
-----------------------------------------------
| 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
| 0.1 |   0.193 |    0.095 |  0.000 |   0.248 |
| 0.2 |   0.341 |    0.181 |  0.000 |   0.345 |
| 0.3 |   0.446 |    0.259 |  0.000 |   0.419 |
| 0.4 |   0.528 |    0.330 |  0.000 |   0.474 |
| 0.5 |   0.588 |    0.394 |  0.000 |   0.520 |
| 0.6 |   0.633 |    0.451 |  0.000 |   0.561 |
| 0.7 |   0.670 |    0.503 |  0.000 |   0.597 |
| 0.8 |   0.701 |    0.551 |  0.000 |   0.629 |
| 0.9 |   0.726 |    0.593 |  0.000 |   0.657 |
| 1.0 |   0.746 |    0.632 |  0.000 |   0.683 |
-----------------------------------------------
| Maximum deviation acentric      :  0.198    |
| Maximum deviation centric       :  0.683    |
|                                             |
| <NZ(obs)-NZ(twinned)>_acentric  : +0.144    |
| <NZ(obs)-NZ(twinned)>_centric   : -0.467    |
-----------------------------------------------


 L test for acentric data

 using difference vectors (dh,dk,dl) of the form: 
(3hp,3kp,2lp)
  where hp, kp, and lp are random signed integers such that 
  2 <= |dh| + |dk| + |dl| <= 8 

  Mean |L|   :0.480  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.310  (untwinned: 0.333; perfect twin: 0.200)

  The distribution of |L| values indicates a twin fraction of
  0.02. Note that this estimate is not as reliable as obtained
  via a Britton plot or H-test if twin laws are available. 



---------------------------------------------
 Analysing possible twin law :  -h-k,k,-l
---------------------------------------------


Results of the H-test on a-centric data: 

 (Only 50.0% of the strongest twin pairs were used)

mean |H| : 0.464   (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.306   (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.036
Estimation of twin fraction via cum. dist. of H: 0.033



Britton analyses

  Extrapolation performed on  0.00 < alpha < 0.495 
  Estimated twin fraction: 0.014
  Correlation: 0.9997

R vs R statistic:
  R_abs_twin = <|I1-I2|>/<|I1+I2|>
  Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

   R_abs_twin observed data   : 0.473

  R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
   R_sq_twin observed data    : 0.283
  No calculated data available.
  R_twin for calculated data not determined.


Maximum Likelihood twin fraction determination
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.


   The estimated twin fraction is equal to 0.022


Estimation of twin fraction, while taking into account the
effects of possible NCS parallel to the twin axis.
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.

  A parameters D_ncs will be estimated as a function of resolution,
  together with a global twin fraction.
  D_ncs is an estimate of the correlation coefficient between
  untwinned, error-free, twin related, normalized intensities.
  Large values (0.95) could indicate an incorrect point group.
  Value of D_ncs larger than say, 0.5, could indicate the presence
  of NCS. The twin fraction should be smaller or similar to other
  estimates given elsewhere.

  The refinement can take some time. 
  For numerical stability issues, D_ncs is limited between 0 and 0.95.
  The twin fraction is allowed to vary between 0 and 0.45.
  Refinement cycle numbers are printed out to keep you entertained.

. . . .   5  . . . .  10  . . . .  15  . . . .  20  . . . .  25  . . . .  30 
. . . .  35  . . . .  40  . . . .  45  . . . .  50  . . . .  55  . . .

  Cycle :  58
  -----------
  Log[likelihood]:      304293.536
  twin fraction: 0.001
  D_ncs in resolution ranges: 
     9.9935 -- 6.9787 :: 0.688
     6.9787 -- 5.8946 :: 0.635
     5.8946 -- 5.2724 :: 0.615
     5.2724 -- 4.8504 :: 0.574
     4.8504 -- 4.5376 :: 0.580
     4.5376 -- 4.2925 :: 0.605
     4.2925 -- 4.0930 :: 0.569


---------------------------------------------
 Analysing possible twin law :  -h,-k,l
---------------------------------------------


Results of the H-test on a-centric data: 

 (Only 50.0% of the strongest twin pairs were used)

mean |H| : 0.466   (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.306   (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.034
Estimation of twin fraction via cum. dist. of H: 0.032



Britton analyses

  Extrapolation performed on  0.00 < alpha < 0.495 
  Estimated twin fraction: 0.015
  Correlation: 0.9995

R vs R statistic:
  R_abs_twin = <|I1-I2|>/<|I1+I2|>
  Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

   R_abs_twin observed data   : 0.460

  R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
   R_sq_twin observed data    : 0.277
  No calculated data available.
  R_twin for calculated data not determined.


Maximum Likelihood twin fraction determination
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.


   The estimated twin fraction is equal to 0.022


Estimation of twin fraction, while taking into account the
effects of possible NCS parallel to the twin axis.
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.

  A parameters D_ncs will be estimated as a function of resolution,
  together with a global twin fraction.
  D_ncs is an estimate of the correlation coefficient between
  untwinned, error-free, twin related, normalized intensities.
  Large values (0.95) could indicate an incorrect point group.
  Value of D_ncs larger than say, 0.5, could indicate the presence
  of NCS. The twin fraction should be smaller or similar to other
  estimates given elsewhere.

  The refinement can take some time. 
  For numerical stability issues, D_ncs is limited between 0 and 0.95.
  The twin fraction is allowed to vary between 0 and 0.45.
  Refinement cycle numbers are printed out to keep you entertained.

. . . .   5  . . . .  10  . . . .  15  . . . .  20  . . . .  25  . . . .  30 
. . . .  35  . . . .  40  . . . .  45  . . . .  50  . . . .  55  . . . .  60 
. . . .  65  . . . .

  Cycle :  69
  -----------
  Log[likelihood]:      304212.311
  twin fraction: 0.001
  D_ncs in resolution ranges: 
     9.9935 -- 6.9787 :: 0.689
     6.9787 -- 5.8946 :: 0.635
     5.8946 -- 5.2724 :: 0.615
     5.2724 -- 4.8504 :: 0.573
     4.8504 -- 4.5376 :: 0.579
     4.5376 -- 4.2925 :: 0.604
     4.2925 -- 4.0930 :: 0.568


---------------------------------------------
 Analysing possible twin law :  h+k,-k,-l
---------------------------------------------


Results of the H-test on a-centric data: 

 (Only 50.0% of the strongest twin pairs were used)

mean |H| : 0.035   (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.003   (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.465
Estimation of twin fraction via cum. dist. of H: 0.469



Britton analyses

  Extrapolation performed on  0.46 < alpha < 0.495 
  Estimated twin fraction: 0.438
  Correlation: 0.9916

R vs R statistic:
  R_abs_twin = <|I1-I2|>/<|I1+I2|>
  Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

   R_abs_twin observed data   : 0.028

  R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
   R_sq_twin observed data    : 0.001
  No calculated data available.
  R_twin for calculated data not determined.


Maximum Likelihood twin fraction determination
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.


   The estimated twin fraction is equal to 0.436


Estimation of twin fraction, while taking into account the
effects of possible NCS parallel to the twin axis.
    Zwart, Read, Grosse-Kunstleve & Adams, to be published.

  A parameters D_ncs will be estimated as a function of resolution,
  together with a global twin fraction.
  D_ncs is an estimate of the correlation coefficient between
  untwinned, error-free, twin related, normalized intensities.
  Large values (0.95) could indicate an incorrect point group.
  Value of D_ncs larger than say, 0.5, could indicate the presence
  of NCS. The twin fraction should be smaller or similar to other
  estimates given elsewhere.

  The refinement can take some time. 
  For numerical stability issues, D_ncs is limited between 0 and 0.95.
  The twin fraction is allowed to vary between 0 and 0.45.
  Refinement cycle numbers are printed out to keep you entertained.

. . . .   5  . . . .  10  . . . .  15  . . . .  20  . . . .  25  . . . .  30 
. . . .  35  . . . .  40  . . . .  45  . . . .  50  . . . .  55  . . . .  60 
. . . .  65  . . . .  70  .

  Cycle :  71
  -----------
  Log[likelihood]:      218846.714
  twin fraction: 0.385
  D_ncs in resolution ranges: 
     9.9935 -- 6.9787 :: 0.950
     6.9787 -- 5.8946 :: 0.950
     5.8946 -- 5.2724 :: 0.950
     5.2724 -- 4.8504 :: 0.950
     4.8504 -- 4.5376 :: 0.950
     4.5376 -- 4.2925 :: 0.950
     4.2925 -- 4.0930 :: 0.950



Exploring higher metric symmetry

The point group of data as dictated by the space group is P 3
  the point group in the niggli setting is P 3
The point group of the lattice is P 6 2 2
A summary of R values for various possible point groups follow.

----------------------------------------------------------------------------------
| Point group | mean R_used | max R_used | mean R_unused | min R_unused | choice |
----------------------------------------------------------------------------------
| P 3         | None        | None       | 0.251         | 0.028        |        |
| P 6 2 2     | 0.251       | 0.473      | None          | None         |        |
| P 3 2 1     | 0.473       | 0.473      | 0.460         | 0.460        |        |
| P 6         | 0.460       | 0.460      | 0.473         | 0.473        |        |
| P 3 1 2     | 0.028       | 0.028      | 0.473         | 0.473        | <---   |
----------------------------------------------------------------------------------

R_used: mean and maximum R value for symmetry operators *used* in this point group
R_unused: mean and minimum R value for symmetry operators *not used* in this point group
 The likely point group of the data is:  P 3 1 2

Possible space groups in this point groups are:
   Unit cell: (163.429, 163.429, 172.169, 90, 90, 120)
   Space group: P 31 1 2 (No. 151)

   Unit cell: (163.429, 163.429, 172.169, 90, 90, 120)
   Space group: P 32 1 2 (No. 153)

Note that this analyses does not take into account the effects of twinning.
If the data is (allmost) perfectly twinned, the symmetry will appear to be
higher than it actually is.





-------------------------------------------------------------------------------
Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
  - <I^2>/<I>^2 : 3.730
  - <F>^2/<F^2> : 0.626
  - <|E^2-1|>   : 1.044
  - 
, <L^2>: 0.480, 0.310
       Multivariate Z score L-test: 0.872 
       The multivariate Z score is a quality measure of the given
       spread in intensities. Good to reasonable data is expected
       to have a Z score lower than 3.5. 
       Large values can indicate twinning, but small values do not
       neccesarily exclude it. 


Statistics depending on twin laws
------------------------------------------------------------------
| Operator  | type | R obs. | Britton alpha | H alpha | ML alpha |
------------------------------------------------------------------
| -h-k,k,-l |   M  | 0.473  | 0.014         | 0.033   | 0.022    |
| -h,-k,l   |   M  | 0.460  | 0.015         | 0.032   | 0.022    |
| h+k,-k,-l |   M  | 0.028  | 0.438         | 0.469   | 0.436    |
------------------------------------------------------------------

Patterson analyses
  - Largest peak height   : 65.792
   (correpsonding p value : 6.698e-06)


The analyses of the Patterson function reveals a significant off-origin
peak that is 65.79 % of the origin peak, indicating pseudo translational symmetry.
The chance of finding a peak of this or larger height by random in a 
structure without pseudo translational symmetry is equal to the 6.6981e-06.
The detected tranlational NCS is most likely also responsible for the elevated intensity ratio.
See the relevant section of the logfile for more details.
The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.
The symmetry of the lattice and intensity however suggests that the
input space group is too low. See the relevant sections of the log
file for more details on your choice of space groups.
As the symmetry is suspected to be incorrect, it is advicable to reconsider data processing.
 

-------------------------------------------------------------------------------


$TABLE: Intensity plots:
$GRAPHS
:Intensity plots 
:A:1,2,3,4:
$$
1/resol^2   <I>_smooth_approximation   <I>_via_binning   <I>_expected   $$ 
$$
0.010010   881906.015157   908173.285976   1496388.700229
0.014010   1077659.580423   1063961.784598   1178432.954968
0.018010   915257.511971   903996.393926   865439.720512
0.022010   850680.120391   870597.618416   741672.878229
0.026010   907617.330313   908410.487105   741397.108534
0.030010   754361.390210   745154.116608   815990.918055
0.034010   1007939.434003   1030617.763877   991340.154429
0.038010   1326097.878488   1325599.751544   1270315.580075
0.042010   1760106.050742   1765158.314425   1586134.199243
0.046010   1714057.905972   1726157.096258   1845358.446659
0.050010   1932751.793375   1893364.064132   1990492.169387
0.054010   1946296.084811   1998878.685995   2024212.814706
0.058010   1863803.911725   1942977.692658   1990213.820598
0.062499   1618264.013301   1868400.154058   1931429.715934
$$


$TABLE: Z scores and completeness:
$GRAPHS
:Data sanity and completeness check 
:A:1,2,3:
$$
1/resol^2   Z_score   Completeness   $$ 
$$
0.010010   4.972859   0.942459
0.014010   1.655140   0.980779
0.018010   0.892609   0.989737
0.022010   4.550030   0.997972
0.026010   5.783126   0.997052
0.030010   2.320082   0.996545
0.034010   1.109557   0.998021
0.038010   1.275965   0.998485
0.042010   3.153616   0.997358
0.046010   1.837077   0.998030
0.050010   1.425680   0.998135
0.054010   0.395464   0.997678
0.058010   0.846311   0.998998
0.062499   1.182548   0.998841
$$


$TABLE: <I/sigma_I>:
$GRAPHS
:Signal to noise 
:N:1,2:
$$
1/resol^2   <I/sigma_I>;_Signal_to_noise   $$ 
$$
0.002753   15.301805
0.006753   19.929854
0.010753   21.734061
0.014753   21.619718
0.018753   21.590650
0.022753   21.428160
0.026753   21.540278
0.030753   21.810894
0.034753   23.177579
0.038753   23.783444
0.042753   23.993158
0.046753   24.415113
0.050753   24.879861
0.054753   24.711182
0.058753   24.842962
0.062753   24.572436
$$


$TABLE: NZ test:
$GRAPHS
:NZ test, acentric and centric data 
:A:1,2,3,4,5:
$$
z   Acentric_observed   Acentric_untwinned   Centric_observed   Centric_untwinned   $$ 
$$
0.000000   0.000000   0.000000   0.000000   0.000000
0.100000   0.192678   0.095200   0.000000   0.248100
0.200000   0.340559   0.181300   0.000000   0.345300
0.300000   0.445511   0.259200   0.000000   0.418700
0.400000   0.527504   0.329700   0.000000   0.473800
0.500000   0.587553   0.393500   0.000000   0.520500
0.600000   0.633363   0.451200   0.000000   0.561400
0.700000   0.670106   0.503400   0.000000   0.597200
0.800000   0.700904   0.550700   0.000000   0.628900
0.900000   0.726235   0.593400   0.000000   0.657200
1.000000   0.746180   0.632100   0.000000   0.683300
$$


$TABLE: L test,acentric data:
$GRAPHS
:L test, acentric data 
:A:1,2,3,4:
$$
|l|   Observed   Acentric_theory   Acentric_theory,_perfect_twin   $$ 
$$
0.000000   0.000245   0.000000   0.000000
0.020000   0.022866   0.020000   0.029996
0.040000   0.044876   0.040000   0.059968
0.060000   0.066612   0.060000   0.089892
0.080000   0.086054   0.080000   0.119744
0.100000   0.106138   0.100000   0.149500
0.120000   0.128393   0.120000   0.179136
0.140000   0.147438   0.140000   0.208628
0.160000   0.168837   0.160000   0.237952
0.180000   0.189716   0.180000   0.267084
0.200000   0.211085   0.200000   0.296000
0.220000   0.232147   0.220000   0.324676
0.240000   0.253485   0.240000   0.353088
0.260000   0.273508   0.260000   0.381212
0.280000   0.294999   0.280000   0.409024
0.300000   0.314319   0.300000   0.436500
0.320000   0.335993   0.320000   0.463616
0.340000   0.357117   0.340000   0.490348
0.360000   0.377904   0.360000   0.516672
0.380000   0.399395   0.380000   0.542564
0.400000   0.420335   0.400000   0.568000
0.420000   0.440542   0.420000   0.592956
0.440000   0.461146   0.440000   0.617408
0.460000   0.481047   0.460000   0.641332
0.480000   0.501528   0.480000   0.664704
0.500000   0.523172   0.500000   0.687500
0.520000   0.543134   0.520000   0.709696
0.540000   0.564288   0.540000   0.731268
0.560000   0.585290   0.560000   0.752192
0.580000   0.605160   0.580000   0.772444
0.600000   0.626956   0.600000   0.792000
0.620000   0.648294   0.620000   0.810836
0.640000   0.669754   0.640000   0.828928
0.660000   0.689869   0.660000   0.846252
0.680000   0.710473   0.680000   0.862784
0.700000   0.730619   0.700000   0.878500
0.720000   0.751009   0.720000   0.893376
0.740000   0.770573   0.740000   0.907388
0.760000   0.790046   0.760000   0.920512
0.780000   0.810375   0.780000   0.932724
0.800000   0.829879   0.800000   0.944000
0.820000   0.850208   0.820000   0.954316
0.840000   0.869467   0.840000   0.963648
0.860000   0.887809   0.860000   0.971972
0.880000   0.908382   0.880000   0.979264
0.900000   0.926938   0.900000   0.985500
0.920000   0.944791   0.920000   0.990656
0.940000   0.961237   0.940000   0.994708
0.960000   0.977470   0.960000   0.997632
0.980000   0.992235   0.980000   0.999404
$$


$TABLE: Britton plot for twin law -h-k,k,-l:
$GRAPHS
:percentage negatives 
:A:1,2,3:
$$
alpha   percentage_negatives   fit   $$ 
$$
0.000000   0.000000   0.000000
0.009901   0.003724   0.000000
0.019802   0.010797   0.005787
0.029703   0.018246   0.015256
0.039604   0.026417   0.024726
0.049505   0.034294   0.034196
0.059406   0.042412   0.043665
0.069307   0.051281   0.053135
0.079208   0.060953   0.062604
0.089109   0.070678   0.072074
0.099010   0.080779   0.081543
0.108911   0.089112   0.091013
0.118812   0.098007   0.100483
0.128713   0.107920   0.109952
0.138614   0.117565   0.119422
0.148515   0.126273   0.128891
0.158416   0.135784   0.138361
0.168317   0.145295   0.147830
0.178218   0.154699   0.157300
0.188119   0.164425   0.166770
0.198020   0.174258   0.176239
0.207921   0.185055   0.185709
0.217822   0.194781   0.195178
0.227723   0.204721   0.204648
0.237624   0.213964   0.214117
0.247525   0.223208   0.223587
0.257426   0.231647   0.233057
0.267327   0.239872   0.242526
0.277228   0.249196   0.251996
0.287129   0.258815   0.261465
0.297030   0.269023   0.270935
0.306931   0.279231   0.280404
0.316832   0.289037   0.289874
0.326733   0.298334   0.299344
0.336634   0.307389   0.308813
0.346535   0.317061   0.318283
0.356436   0.326224   0.327752
0.366337   0.335763   0.337222
0.376238   0.345890   0.346691
0.386139   0.354999   0.356161
0.396040   0.364457   0.365631
0.405941   0.373915   0.375100
0.415842   0.384310   0.384570
0.425743   0.393848   0.394039
0.435644   0.404190   0.403509
0.445545   0.415309   0.412978
0.455446   0.426267   0.422448
0.465347   0.437627   0.431918
0.475248   0.447969   0.441387
0.485149   0.457588   0.450857
$$


$TABLE: H test for possible twin law -h-k,k,-l:
$GRAPHS
:H test for Acentric data 
:A:1,2,3:
$$
H   Observed_S(H)   Fitted_S(H)   $$ 
$$
0.000000   0.045333   0.000000
0.020000   0.069982   0.021412
0.040000   0.090451   0.042824
0.060000   0.109742   0.064235
0.080000   0.130533   0.085647
0.100000   0.154110   0.107059
0.120000   0.176830   0.128471
0.140000   0.198907   0.149882
0.160000   0.217876   0.171294
0.180000   0.236952   0.192706
0.200000   0.256457   0.214118
0.220000   0.273818   0.235529
0.240000   0.293752   0.256941
0.260000   0.312614   0.278353
0.280000   0.330833   0.299765
0.300000   0.351088   0.321176
0.320000   0.369199   0.342588
0.340000   0.385811   0.364000
0.360000   0.402744   0.385412
0.380000   0.421605   0.406824
0.400000   0.443468   0.428235
0.420000   0.461044   0.449647
0.440000   0.480977   0.471059
0.460000   0.499946   0.492471
0.480000   0.518058   0.513882
0.500000   0.536170   0.535294
0.520000   0.552138   0.556706
0.540000   0.569500   0.578118
0.560000   0.587718   0.599529
0.580000   0.607223   0.620941
0.600000   0.629193   0.642353
0.620000   0.647948   0.663765
0.640000   0.667560   0.685176
0.660000   0.685457   0.706588
0.680000   0.704319   0.728000
0.700000   0.726182   0.749412
0.720000   0.745151   0.770824
0.740000   0.763262   0.792235
0.760000   0.782124   0.813647
0.780000   0.800450   0.835059
0.800000   0.818240   0.856471
0.820000   0.841818   0.877882
0.840000   0.862716   0.899294
0.860000   0.885114   0.920706
0.880000   0.904298   0.942118
0.900000   0.920802   0.963529
0.920000   0.935913   0.984941
0.940000   0.953167   1.000000
0.960000   0.970957   1.000000
0.980000   0.987675   1.000000
$$


$TABLE: Likelihood based twin fraction estimation for possible twin law -h-k,k,-l:
$GRAPHS
:Likelihood based twin fraction estimate 
:A:1,2:
$$
alpha   NLL_(acentric_data)   $$ 
$$
0.021739   97933.883881
0.043478   152373.014844
0.065217   217009.482730
0.086957   292261.163725
0.108696   380187.466859
0.130435   473517.708338
0.152174   568248.492979
0.173913   661741.257083
0.195652   757562.463117
0.217391   860795.820691
0.239130   965597.187013
0.260870   1071707.850959
0.282609   1183630.108845
0.304348   1290739.787732
0.326087   1395541.647175
0.347826   1505495.785493
0.369565   1617856.397583
0.391304   1730544.257308
0.413043   1845779.173740
0.434783   1959407.734552
0.456522   2077153.045151
0.478261   2193493.638532
$$


$TABLE: Britton plot for twin law -h,-k,l:
$GRAPHS
:percentage negatives 
:A:1,2,3:
$$
alpha   percentage_negatives   fit   $$ 
$$
0.000000   0.000000   0.000000
0.009901   0.003832   0.000000
0.019802   0.010933   0.005025
0.029703   0.018355   0.014560
0.039604   0.026421   0.024094
0.049505   0.034620   0.033628
0.059406   0.042632   0.043163
0.069307   0.051556   0.052697
0.079208   0.061175   0.062231
0.089109   0.070607   0.071766
0.099010   0.079879   0.081300
0.108911   0.088588   0.090835
0.118812   0.098395   0.100369
0.128713   0.107881   0.109903
0.138614   0.116563   0.119438
0.148515   0.126182   0.128972
0.158416   0.136579   0.138506
0.168317   0.146038   0.148041
0.178218   0.154586   0.157575
0.188119   0.164313   0.167109
0.198020   0.174388   0.176644
0.207921   0.183660   0.186178
0.217822   0.195396   0.195712
0.227723   0.204909   0.205247
0.237624   0.214100   0.214781
0.247525   0.222916   0.224315
0.257426   0.231973   0.233850
0.267327   0.241700   0.243384
0.277228   0.250703   0.252918
0.287129   0.259680   0.262453
0.297030   0.270023   0.271987
0.306931   0.279482   0.281521
0.316832   0.287923   0.291056
0.326733   0.297838   0.300590
0.336634   0.307886   0.310125
0.346535   0.317425   0.319659
0.356436   0.326107   0.329193
0.366337   0.336075   0.338728
0.376238   0.346151   0.348262
0.386139   0.355663   0.357796
0.396040   0.365069   0.367331
0.405941   0.374688   0.376865
0.415842   0.384389   0.386399
0.425743   0.394464   0.395934
0.435644   0.405638   0.405468
0.445545   0.417535   0.415002
0.455446   0.429379   0.424537
0.465347   0.442000   0.434071
0.475248   0.454353   0.443605
0.485149   0.466760   0.453140
$$


$TABLE: H test for possible twin law -h,-k,l:
$GRAPHS
:H test for Acentric data 
:A:1,2,3:
$$
H   Observed_S(H)   Fitted_S(H)   $$ 
$$
0.000000   0.013934   0.000000
0.020000   0.054344   0.021366
0.040000   0.078675   0.042732
0.060000   0.103864   0.064098
0.080000   0.124605   0.085464
0.100000   0.149686   0.106830
0.120000   0.175411   0.128196
0.140000   0.197599   0.149562
0.160000   0.216785   0.170928
0.180000   0.237151   0.192295
0.200000   0.257731   0.213661
0.220000   0.275202   0.235027
0.240000   0.294818   0.256393
0.260000   0.311967   0.277759
0.280000   0.330082   0.299125
0.300000   0.348197   0.320491
0.320000   0.365346   0.341857
0.340000   0.384962   0.363223
0.360000   0.404577   0.384589
0.380000   0.421727   0.405955
0.400000   0.441020   0.427321
0.420000   0.460850   0.448687
0.440000   0.478857   0.470053
0.460000   0.498794   0.491419
0.480000   0.518088   0.512785
0.500000   0.536310   0.534152
0.520000   0.550458   0.555518
0.540000   0.566429   0.576884
0.560000   0.586151   0.598250
0.580000   0.608339   0.619616
0.600000   0.628062   0.640982
0.620000   0.649392   0.662348
0.640000   0.667935   0.683714
0.660000   0.685085   0.705080
0.680000   0.703735   0.726446
0.700000   0.725602   0.747812
0.720000   0.745753   0.769178
0.740000   0.762045   0.790544
0.760000   0.781446   0.811910
0.780000   0.802240   0.833276
0.800000   0.820248   0.854642
0.820000   0.841578   0.876009
0.840000   0.862801   0.897375
0.860000   0.884238   0.918741
0.880000   0.903639   0.940107
0.900000   0.920467   0.961473
0.920000   0.936331   0.982839
0.940000   0.953267   1.000000
0.960000   0.970631   1.000000
0.980000   0.987352   1.000000
$$


$TABLE: Likelihood based twin fraction estimation for possible twin law -h,-k,l:
$GRAPHS
:Likelihood based twin fraction estimate 
:A:1,2:
$$
alpha   NLL_(acentric_data)   $$ 
$$
0.021739   97799.697896
0.043478   152878.486469
0.065217   216126.922861
0.086957   292454.221691
0.108696   380180.010101
0.130435   474147.507283
0.152174   568274.145705
0.173913   661188.053208
0.195652   758623.059399
0.217391   858120.415041
0.239130   960624.001444
0.260870   1071307.489082
0.282609   1179590.651832
0.304348   1290058.259902
0.326087   1397387.067193
0.347826   1506066.983539
0.369565   1619174.320085
0.391304   1731092.488385
0.413043   1845924.141075
0.434783   1958670.709839
0.456522   2072811.209908
0.478261   2197408.726453
$$


$TABLE: Britton plot for twin law h+k,-k,-l:
$GRAPHS
:percentage negatives 
:A:1,2,3:
$$
alpha   percentage_negatives   fit   $$ 
$$
0.000000   0.000000   0.000000
0.009901   0.000000   0.000000
0.019802   0.000000   0.000000
0.029703   0.000000   0.000000
0.039604   0.000000   0.000000
0.049505   0.000000   0.000000
0.059406   0.000000   0.000000
0.069307   0.000000   0.000000
0.079208   0.000000   0.000000
0.089109   0.000000   0.000000
0.099010   0.000027   0.000000
0.108911   0.000053   0.000000
0.118812   0.000053   0.000000
0.128713   0.000080   0.000000
0.138614   0.000080   0.000000
0.148515   0.000080   0.000000
0.158416   0.000107   0.000000
0.168317   0.000134   0.000000
0.178218   0.000134   0.000000
0.188119   0.000160   0.000000
0.198020   0.000187   0.000000
0.207921   0.000187   0.000000
0.217822   0.000321   0.000000
0.227723   0.000428   0.000000
0.237624   0.000454   0.000000
0.247525   0.000641   0.000000
0.257426   0.000748   0.000000
0.267327   0.000989   0.000000
0.277228   0.001176   0.000000
0.287129   0.001496   0.000000
0.297030   0.001817   0.000000
0.306931   0.002244   0.000000
0.316832   0.002699   0.000000
0.326733   0.003340   0.000000
0.336634   0.004008   0.000000
0.346535   0.004596   0.000000
0.356436   0.005691   0.000000
0.366337   0.007455   0.000000
0.376238   0.009779   0.000000
0.386139   0.012612   0.000000
0.396040   0.016673   0.000000
0.405941   0.021776   0.000000
0.415842   0.029525   0.000000
0.425743   0.040453   0.000000
0.435644   0.055576   0.000000
0.445545   0.078769   0.045101
0.455446   0.109443   0.102685
0.465347   0.153075   0.160268
0.475248   0.209614   0.217851
0.485149   0.284107   0.275435
$$


$TABLE: H test for possible twin law h+k,-k,-l:
$GRAPHS
:H test for Acentric data 
:A:1,2,3:
$$
H   Observed_S(H)   Fitted_S(H)   $$ 
$$
0.000000   0.038262   0.000000
0.020000   0.467589   0.317778
0.040000   0.678833   0.635556
0.060000   0.800353   0.953333
0.080000   0.881900   1.000000
0.100000   0.930636   1.000000
0.120000   0.964089   1.000000
0.140000   0.982045   1.000000
0.160000   0.991557   1.000000
0.180000   0.995297   1.000000
0.200000   0.997221   1.000000
0.220000   0.998076   1.000000
0.240000   0.998611   1.000000
0.260000   0.999252   1.000000
0.280000   0.999572   1.000000
0.300000   0.999572   1.000000
0.320000   0.999679   1.000000
0.340000   0.999679   1.000000
0.360000   0.999786   1.000000
0.380000   0.999786   1.000000
0.400000   0.999893   1.000000
0.420000   0.999893   1.000000
0.440000   0.999893   1.000000
0.460000   0.999893   1.000000
0.480000   1.000000   1.000000
0.500000   1.000000   1.000000
0.520000   1.000000   1.000000
0.540000   1.000000   1.000000
0.560000   1.000000   1.000000
0.580000   1.000000   1.000000
0.600000   1.000000   1.000000
0.620000   1.000000   1.000000
0.640000   1.000000   1.000000
0.660000   1.000000   1.000000
0.680000   1.000000   1.000000
0.700000   1.000000   1.000000
0.720000   1.000000   1.000000
0.740000   1.000000   1.000000
0.760000   1.000000   1.000000
0.780000   1.000000   1.000000
0.800000   1.000000   1.000000
0.820000   1.000000   1.000000
0.840000   1.000000   1.000000
0.860000   1.000000   1.000000
0.880000   1.000000   1.000000
0.900000   1.000000   1.000000
0.920000   1.000000   1.000000
0.940000   1.000000   1.000000
0.960000   1.000000   1.000000
0.980000   1.000000   1.000000
$$


$TABLE: Likelihood based twin fraction estimation for possible twin law h+k,-k,-l:
$GRAPHS
:Likelihood based twin fraction estimate 
:A:1,2:
$$
alpha   NLL_(acentric_data)   $$ 
$$
0.021739   72478.831201
0.043478   70740.713639
0.065217   68918.193181
0.086957   67004.374511
0.108696   64989.221001
0.130435   62864.377241
0.152174   60616.351726
0.173913   58233.780398
0.195652   55703.950678
0.217391   53003.758595
0.239130   50154.918618
0.260870   47126.338741
0.282609   43776.404287
0.304348   40131.920147
0.326087   36257.058668
0.347826   31966.432839
0.369565   27448.796451
0.391304   22545.612664
0.413043   17949.168528
0.434783   13852.843115
0.456522   14392.410776
0.478261   26821.320562
$$