#############################################################
##                     phenix.xtriage                      ##
##                                                         ##
##     P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams      ##
##                                                         ##
#############################################################
#phil __OFF__
  This cryptic code, together with the tags __ON__ and __OFF__
  allows one to use the log file as an input file for xtriage.
  Try : phenix.xtriage  <logfile> to give it a try!

Date 2008-01-16 Time 00:20:46 PST -0800 (1200471646.65 s)


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


Effective parameters: 
#phil __ON__
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 = False
        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 = "model_refine_data.mtz"
    obs_labels = None
    calc_labels = None
    unit_cell = 69.54750061 46.46070099 85.69889832 90 90 90
    space_group = "P 21 21 21"
    high_resolution = None
    low_resolution = None
    reference {
      data {
        file_name = None
        labels = None
        unit_cell = None
        space_group = None
      }
    }
  }
}
#phil __END__


Symmetry, cell and reflection file content summary

Miller array info: model_refine_data.mtz:F-obs,SIGF-obs
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 85.6989, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8521 1.98003
Completeness in resolution range: 0.983729
Completeness with d_max=infinity: 0.980578

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

Number of residues unknown, assuming 50% solvent content

----------------------------------------------------------------
|              Best guess :  253  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 |
----------------------------------------------------------------------------------------
| 14.85 - 4.83 | 98.3%     | 97.4%     | 96.9%     | 95.8%     | 92.7%     | 87.3%     |
|  4.83 - 3.86 | 98.3%     | 97.5%     | 97.2%     | 96.4%     | 94.5%     | 92.8%     |
|  3.86 - 3.38 | 98.5%     | 97.9%     | 97.5%     | 96.5%     | 94.1%     | 91.4%     |
|  3.38 - 3.07 | 98.2%     | 97.4%     | 96.3%     | 95.0%     | 90.7%     | 82.9%     |
|  3.07 - 2.85 | 98.6%     | 97.8%     | 97.1%     | 95.8%     | 91.9%     | 84.9%     |
|  2.85 - 2.68 | 97.9%     | 97.3%     | 96.7%     | 95.2%     | 92.4%     | 88.4%     |
|  2.68 - 2.55 | 97.9%     | 96.6%     | 96.0%     | 94.6%     | 91.3%     | 87.1%     |
|  2.55 - 2.44 | 99.3%     | 98.3%     | 98.0%     | 96.2%     | 93.0%     | 89.3%     |
|  2.44 - 2.35 | 97.5%     | 96.1%     | 95.5%     | 94.2%     | 90.1%     | 84.4%     |
|  2.35 - 2.27 | 97.5%     | 96.3%     | 95.7%     | 94.4%     | 90.5%     | 84.8%     |
|  2.27 - 2.20 | 98.0%     | 96.5%     | 95.3%     | 92.9%     | 87.7%     | 82.7%     |
|  2.20 - 2.13 | 98.1%     | 96.2%     | 95.3%     | 93.2%     | 87.7%     | 81.9%     |
|  2.13 - 2.08 | 96.6%     | 95.4%     | 94.6%     | 92.6%     | 87.4%     | 81.1%     |
|  2.08 - 2.03 | 98.9%     | 97.2%     | 96.4%     | 95.1%     | 87.6%     | 79.7%     |
----------------------------------------------------------------------------------------

  The completeness of data for which I/sig(I)>3.00, exceeds  85% for
  for resolution ranges lower than 2.03A.
  The data are cut at this resolution for the potential twin tests 
  and intensity statistics.
ML estimate of overall B_cart value of None:
10.95,  0.00,  0.00
       11.85,  0.00
              11.95
Equivalent representation as U_cif: 
 0.14, -0.00, -0.00
        0.15,  0.00
               0.15

Eigen analyses of B-cart:
                 Value   Vector
Eigenvector 1 :  11.950  ( 0.00,  0.00,  1.00)
Eigenvector 2 :  11.849  ( 0.00,  1.00, -0.00)
Eigenvector 3 :  10.955  ( 1.00, -0.00, -0.00)

ML estimate of  -log of scale factor of None:
 0.67


Low resolution completeness analyses 

 The following table shows the completeness
 of the data to 5 Angstrom.
unused:         - 14.8522 [  0/64 ] 0.000
bin  1: 14.8522 -  9.7635 [130/137] 0.949
bin  2:  9.7635 -  8.1553 [138/142] 0.972
bin  3:  8.1553 -  7.2604 [130/132] 0.985
bin  4:  7.2604 -  6.6620 [124/125] 0.992
bin  5:  6.6620 -  6.2221 [131/131] 1.000
bin  6:  6.2221 -  5.8794 [122/122] 1.000
bin  7:  5.8794 -  5.6015 [132/133] 0.992
bin  8:  5.6015 -  5.3697 [120/120] 1.000
bin  9:  5.3697 -  5.1720 [127/127] 1.000
bin 10:  5.1720 -  5.0006 [120/122] 0.984
unused:  5.0006 -         [  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> |
------------------------------------------------
     None
------------------------------------------------

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

 Acentric reflections:

            None 

 Centric reflections:

            None 


Ice ring related problems

 The following statistics were obtained from ice-ring 
 insensitive resolution ranges 
  mean bin z_score      : 1.47
      ( rms deviation   : 1.03 )
  mean bin completeness : 0.98
     ( rms deviation   : 0.02 )

 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. |
------------------------------------------------
|    3.897  |   0.70  |   0.98 |     1.000     |
|    3.669  |   3.58  |   0.97 |     0.750     |
|    3.441  |   4.16  |   1.00 |     0.530     |
|    2.671  |   0.10  |   1.00 |     0.170     |
|    2.249  |   1.12  |   1.00 |     0.390     |
|    2.072  |   1.52  |   1.00 |     0.300     |
------------------------------------------------

 Abnormalities in mean intensity or completeness at
 resolution ranges with a relative ice ring intensity
 lower than 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 






$TABLE: Intensity plots:
$GRAPHS
:Intensity plots 
:A:1,2,3,4:
$$
1/resol^2   <I>_smooth_approximation   <I>_via_binning   <I>_expected   $$ 
$$
0.010022   90280.727953   87772.658324   103893.101848
0.014022   70797.795124   80728.050933   81767.319631
0.018022   55298.211937   47275.015698   60061.988852
0.022022   48023.039712   47110.865653   51501.970327
0.026022   47425.671164   48603.634196   51499.880050
0.030022   52097.054070   48871.494720   56697.843500
0.034022   61202.267703   67718.403920   68899.980225
0.038022   73845.049640   84772.594893   88292.337930
0.042022   88529.950047   96913.530166   110224.508872
0.046022   103102.522998   101002.170063   128208.640731
0.050022   115255.003860   120851.511357   138263.205914
0.054022   123290.943011   108537.843515   140585.802352
0.058022   126634.832826   123641.763824   138215.896603
0.062022   125801.025938   119894.636797   134553.260691
0.066022   121952.334243   137988.386054   131573.866246
0.070022   116381.535648   114939.218742   129448.444010
0.074022   110158.079654   117236.017856   127223.761351
0.078022   103992.888337   100135.114031   123812.155012
0.082022   98256.431164   95041.510084   118683.245753
0.086022   93065.046515   88429.159878   112037.304682
0.090022   88378.331448   93242.640164   104571.289700
0.094022   84082.002436   79631.757697   97093.307183
0.098022   80049.416378   83738.712241   90211.768720
0.102022   76182.061959   82703.864261   84207.151149
0.106022   72430.828811   74031.729053   79074.933759
0.110022   68800.381775   70747.346429   74659.606966
0.114022   65340.244422   65346.300254   70790.824149
0.118022   62127.749427   56478.984921   67364.516633
0.122022   59248.624081   57503.754517   64355.766963
0.126022   56780.000056   54082.185000   61783.950000
0.130022   54778.464390   59079.903598   59664.062155
0.134022   53273.434111   53026.159876   57972.887311
0.138022   52264.570077   54066.892396   56643.086128
0.142022   51721.525178   55263.793362   55582.009177
0.146022   51584.882741   49076.480128   54701.753313
0.150022   51768.220234   52459.259126   53945.027400
0.154022   52162.286172   54628.602087   53296.233105
0.158022   52642.778817   54295.822888   52775.153123
0.162022   53082.747769   56423.108760   52417.954969
0.166022   53369.092596   55055.032096   52254.283622
0.170022   53420.448276   47087.427208   52289.260218
0.174022   53201.957551   54737.582882   52496.061112
0.178022   52732.214639   47578.865005   52820.174463
0.182022   52079.537404   50749.811639   53192.279599
0.186022   51347.964678   48091.965915   53544.292079
0.190022   50656.327955   51106.980190   53822.939961
0.194022   50114.927764   53268.210586   53996.939881
0.198022   49803.486738   51149.522349   54056.541140
0.202022   49752.272478   55036.171914   54006.865037
0.206022   49927.358271   47530.744837   53858.247079
0.210022   50222.289373   48251.123761   53617.272797
0.214022   50461.908265   52626.228191   53281.435765
0.218022   50427.385748   49645.049283   52838.763884
0.222022   49909.671843   50082.534096   52271.964664
0.226022   48786.736115   51670.707338   51565.213054
0.230022   47100.034937   48271.298283   50711.033789
0.234022   45091.746349   46186.457122   49714.924521
0.238022   43173.961330   44964.223880   48596.266762
0.242022   41829.879783   40575.996869   47385.332694
0.246022   41452.813505   40221.348296   46117.406855
0.250022   42051.074729   42936.617228   44825.852353
0.255067   42374.334701   43125.469882   43201.538802
$$


$TABLE: Z scores and completeness:
$GRAPHS
:Data sanity and completeness check 
:A:1,2,3:
$$
1/resol^2   Z_score   Completeness   $$ 
$$
0.010022   1.361662   0.971429
0.014022   0.120026   0.975410
0.018022   2.610179   0.977941
0.022022   1.059423   1.000000
0.026022   0.697780   1.000000
0.030022   1.881808   0.994286
0.034022   0.212690   1.000000
0.038022   0.533440   0.989796
0.042022   1.739233   1.000000
0.046022   3.323253   0.975728
0.050022   1.894599   1.000000
0.054022   3.820447   0.995305
0.058022   1.649238   0.978355
0.062022   1.783277   1.000000
0.066022   0.698886   0.976000
0.070022   1.903196   1.000000
0.074022   1.248666   1.000000
0.078022   3.580962   0.970696
0.082022   3.864017   0.996416
0.086022   4.157501   1.000000
0.090022   1.885964   0.970370
0.094022   3.553096   1.000000
0.098022   1.275998   1.000000
0.102022   0.298463   1.000000
0.106022   1.117992   0.964286
0.110022   0.919248   1.000000
0.114022   1.393451   1.000000
0.118022   3.227852   0.968454
0.122022   2.120494   0.988406
0.126022   2.496742   1.000000
0.130022   0.175639   1.000000
0.134022   1.606277   0.960843
0.138022   0.844689   0.991304
0.142022   0.102775   1.000000
0.146022   2.011243   1.000000
0.150022   0.509639   0.967213
0.154022   0.444674   0.980769
0.158022   0.515196   1.000000
0.162022   1.336462   1.000000
0.166022   0.938328   0.986264
0.170022   2.052151   0.949367
0.174022   0.765986   1.000000
0.178022   2.052480   1.000000
0.182022   0.895058   1.000000
0.186022   2.087883   0.957500
0.190022   1.016420   0.976134
0.194022   0.253570   0.997340
0.198022   1.120098   1.000000
0.202022   0.354385   1.000000
0.206022   2.574686   0.949192
0.210022   2.157560   0.967213
0.214022   0.243561   1.000000
0.218022   1.264475   1.000000
0.222022   0.854118   1.000000
0.226022   0.039245   0.946512
0.230022   0.998849   0.960526
0.234022   1.523839   0.997773
0.238022   1.560973   1.000000
0.242022   3.385458   1.000000
0.246022   2.894545   0.964758
0.250022   0.866386   0.949002
0.255067   0.029985   0.878873
$$


$TABLE: <I/sigma_I>:
$GRAPHS
:Signal to noise 
:N:1,2:
$$
1/resol^2   <I/sigma_I>;_Signal_to_noise   $$ 
$$
0.006533   13.842523
0.010533   20.957704
0.014533   26.607568
0.018533   30.239009
0.022533   31.724815
0.026533   31.137329
0.030533   32.940574
0.034533   35.651508
0.038533   36.552725
0.042533   36.813461
0.046533   37.802745
0.050533   37.669717
0.054533   38.502476
0.058533   38.639259
0.062533   39.240327
0.066533   38.419213
0.070533   38.822325
0.074533   38.768306
0.078533   36.472622
0.082533   34.637552
0.086533   33.716641
0.090533   32.249409
0.094533   26.356585
0.098533   19.441508
0.102533   18.163842
0.106533   18.661484
0.110533   19.604703
0.114533   29.122766
0.118533   31.118588
0.122533   31.367730
0.126533   29.726870
0.130533   30.186327
0.134533   33.059804
0.138533   31.487930
0.142533   32.195366
0.146533   30.861571
0.150533   31.924299
0.154533   29.490356
0.158533   29.774696
0.162533   30.257002
0.166533   30.252353
0.170533   29.228048
0.174533   28.569802
0.178533   29.025464
0.182533   29.357493
0.186533   29.214084
0.190533   28.273021
0.194533   29.237473
0.198533   27.802909
0.202533   27.413851
0.206533   26.098052
0.210533   26.519585
0.214533   26.339743
0.218533   25.766542
0.222533   26.466345
0.226533   26.131958
0.230533   25.444282
0.234533   25.364813
0.238533   24.069252
0.242533   23.587619
0.246533   24.085128
0.250533   23.838024
0.254533   24.053317
$$

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



Using data between 10.00 to 2.03 Angstrom.

Determining possible twin laws.

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


Number of centrics  : 2276
Number of acentrics : 15968

 Largest Patterson peak with length larger than 15 Angstrom 

 Frac. coord.        :   0.500    0.000    0.500
 Distance to origin  :  55.184
 Height (origin=100) :   8.118
 p_value(height)     :   3.238e-01

   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  3.238e-01 
     p_values smaller than 0.05 might indicate 
     weak translational pseudo symmetry, or the self vector of 
     a large anomalous scatterer such as Hg, whereas values 
     smaller than 1e-3 are a very strong indication for 
     the presence of translational pseudo symmetry.



Wilson ratio and moments 

Acentric reflections 
   <I^2>/<I>^2    :1.967   (untwinned: 2.000; perfect twin 1.500)
   <F>^2/<F^2>    :0.792   (untwinned: 0.785; perfect twin 0.885)
   <|E^2 - 1|>    :0.729   (untwinned: 0.736; perfect twin 0.541)


Centric reflections 
   <I^2>/<I>^2    :2.824   (untwinned: 3.000; perfect twin 2.000)
   <F>^2/<F^2>    :0.654   (untwinned: 0.637; perfect twin 0.785)
   <|E^2 - 1|>    :0.921   (untwinned: 0.968; perfect twin 0.736)



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 |   0.087 |    0.095 |  0.236 |   0.248 |
| 0.2 |   0.176 |    0.181 |  0.336 |   0.345 |
| 0.3 |   0.254 |    0.259 |  0.413 |   0.419 |
| 0.4 |   0.326 |    0.330 |  0.477 |   0.474 |
| 0.5 |   0.388 |    0.394 |  0.519 |   0.520 |
| 0.6 |   0.448 |    0.451 |  0.555 |   0.561 |
| 0.7 |   0.502 |    0.503 |  0.599 |   0.597 |
| 0.8 |   0.549 |    0.551 |  0.633 |   0.629 |
| 0.9 |   0.594 |    0.593 |  0.662 |   0.657 |
| 1.0 |   0.633 |    0.632 |  0.690 |   0.683 |
-----------------------------------------------
| Maximum deviation acentric      :  0.008    |
| Maximum deviation centric       :  0.012    |
|                                             |
| <NZ(obs)-NZ(twinned)>_acentric  : -0.003    |
| <NZ(obs)-NZ(twinned)>_centric   : -0.001    |
-----------------------------------------------


 L test for acentric data

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

  Mean |L|   :0.490  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.323  (untwinned: 0.333; perfect twin: 0.200)

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




$TABLE: NZ test:
$GRAPHS
:NZ test, acentric and centric data 
:A:1,2,3,4,5:
$$
z   Acentric_observed   Acentric_untwinned   Centric_observed   Centric_untwinned   $$ 
$$
0.000000   0.000000   0.000000   0.000000   0.000000
0.100000   0.086861   0.095200   0.236380   0.248100
0.200000   0.175539   0.181300   0.336116   0.345300
0.300000   0.253820   0.259200   0.412566   0.418700
0.400000   0.325526   0.329700   0.477153   0.473800
0.500000   0.387963   0.393500   0.519332   0.520500
0.600000   0.447833   0.451200   0.554921   0.561400
0.700000   0.502067   0.503400   0.599297   0.597200
0.800000   0.549161   0.550700   0.632689   0.628900
0.900000   0.593625   0.593400   0.662127   0.657200
1.000000   0.633329   0.632100   0.690246   0.683300
$$


$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   0.008384   0.000000   0.000000
0.020000   0.028288   0.020000   0.029996
0.040000   0.049140   0.040000   0.059968
0.060000   0.067367   0.060000   0.089892
0.080000   0.085812   0.080000   0.119744
0.100000   0.107539   0.100000   0.149500
0.120000   0.127297   0.120000   0.179136
0.140000   0.150190   0.140000   0.208628
0.160000   0.169364   0.160000   0.237952
0.180000   0.188539   0.180000   0.267084
0.200000   0.206839   0.200000   0.296000
0.220000   0.226961   0.220000   0.324676
0.240000   0.244824   0.240000   0.353088
0.260000   0.264363   0.260000   0.381212
0.280000   0.284558   0.280000   0.409024
0.300000   0.304024   0.300000   0.436500
0.320000   0.323564   0.320000   0.463616
0.340000   0.344269   0.340000   0.490348
0.360000   0.364246   0.360000   0.516672
0.380000   0.384223   0.380000   0.542564
0.400000   0.406095   0.400000   0.568000
0.420000   0.425124   0.420000   0.592956
0.440000   0.446923   0.440000   0.617408
0.460000   0.468139   0.460000   0.641332
0.480000   0.487824   0.480000   0.664704
0.500000   0.509697   0.500000   0.687500
0.520000   0.531059   0.520000   0.709696
0.540000   0.551837   0.540000   0.731268
0.560000   0.573345   0.560000   0.752192
0.580000   0.594342   0.580000   0.772444
0.600000   0.615704   0.600000   0.792000
0.620000   0.635025   0.620000   0.810836
0.640000   0.654272   0.640000   0.828928
0.660000   0.675634   0.660000   0.846252
0.680000   0.695611   0.680000   0.862784
0.700000   0.715296   0.700000   0.878500
0.720000   0.733815   0.720000   0.893376
0.740000   0.751385   0.740000   0.907388
0.760000   0.773039   0.760000   0.920512
0.780000   0.792286   0.780000   0.932724
0.800000   0.812628   0.800000   0.944000
0.820000   0.831146   0.820000   0.954316
0.840000   0.852873   0.840000   0.963648
0.860000   0.872849   0.860000   0.971972
0.880000   0.893555   0.880000   0.979264
0.900000   0.913386   0.900000   0.985500
0.920000   0.932633   0.920000   0.990656
0.940000   0.950058   0.940000   0.994708
0.960000   0.970181   0.960000   0.997632
0.980000   0.986731   0.980000   0.999404
$$




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Twinning and intensity statistics summary (acentric data):

Statistics independent of twin laws
  - <I^2>/<I>^2 : 1.967
  - <F>^2/<F^2> : 0.792
  - <|E^2-1|>   : 0.729
  - 
, <L^2>: 0.490, 0.323
       Multivariate Z score L-test: 0.448 
       The multivariate Z score is a quality measure of the given
       spread in intensities. Good to reasonable data are expected
       to have a Z score lower than 3.5. 
       Large values can indicate twinning, but small values do not
       necessarily exclude it. 


No (pseudo)merohedral twin laws were found.


Patterson analyses
  - Largest peak height   : 8.118
   (corresponding p value : 0.32380)


The largest off-origin peak in the Patterson function is 8.12% of the 
height of the origin peak. No significant pseudotranslation is detected.

The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.

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