[phenixbb] Searchable phenixbb
Mark Collins
mcollins at convex.hhmi.columbia.edu
Fri Apr 11 12:49:12 PDT 2008
Ok first of all, DOH! I always forget I can do that in google. But as
Pavel suggests I put in my questions anyway, here it goes....
>From the Yeates twinning server and xtriage my data seems to be twinned
at approx 22-25%, the log is attached.
I have an MR solution from a related MAD structure I solved and Arp/Warp
rebuilt 99% of this structure without any account for twinning.
Upon refinement with twinning I get what I think are overly good (refined)
R/Rf values (particularily with waters = refine 3). And refinement
without twining gives R/Rf on the bad side for my resolution (2A) but not
so terrible. And these improve to "reasonable" R/Rf with the inclusion of
TLS and waters (= refine 5). I have looked at the structures and maps for
both refine3-twin and refine5-notwin and see little differences but
nothing major. So my dilemma is which structure to continue refiniing the
twinned or not twinned+TLS, how do I know which is correct?
My other questions alternate conformations, is it possible to
refine the occupancy?
Thanks Mark
On Fri, 11 Apr 2008, Francis E Reyes wrote:
> http://www.google.com/search?hl=en&q=phenixbb+site%3Aphenix-online.org&btnG=Search
>
>
> Google seems to be indexing it.
>
> On Apr 11, 2008, at 12:33 PM, Mark Collins wrote:
>
> > Hi phenix community
> > Is there a search function for this bb, as there is for the ccp4bb? I
> > have some questions about twinning, TLS and alternate conformations in
> > phenix.refine. I hate repeating questions that have been answered
> > previously but going thru the Archives month by month is proving to
> > be a
> > little slow.
> > Thanks Mark Collins
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
-------------- next part --------------
#############################################################
## 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 2008-04-08 Time 07:38:20 EDT -0400 (1207654700.68 s)
##-------------------------------------------##
## WARNING: ##
## Number of residues unspecified ##
##-------------------------------------------##
##-------------------------------------------##
## Unit cell defined manually, will ignore
## specification in reflection file:
## From file : (71.651, 71.651, 37.102, 90, 90, 90)
## From input: (71.651, 71.651, 37.103, 90, 90, 90)
##-------------------------------------------##
##-------------------------------------------##
## Space group defined manually, will ignore
## specification in reflection file:
## From file : P 43
## From input: P 43
##-------------------------------------------##
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 = "twin.log"
ccp4_style_graphs = True
}
}
xray_data {
file_name = "output-horiz.sca"
obs_labels = None
calc_labels = None
unit_cell = 71.651 71.651 37.103 90 90 90
space_group = "P 43"
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: output-horiz.sca:i_obs,sigma
Observation type: xray.amplitude
Type of data: double, size=12606
Type of sigmas: double, size=12606
Number of Miller indices: 12606
Anomalous flag: False
Unit cell: (71.651, 71.651, 37.103, 90, 90, 90)
Space group: P 43 (No. 78)
Systematic absences: 0
Centric reflections: 952
Resolution range: 29.9345 2.01276
Completeness in resolution range: 0.989171
Completeness with d_max=infinity: 0.988706
##----------------------------------------------------##
## Basic statistics ##
##----------------------------------------------------##
Number of residues unknown, assuming 50% solvent content
----------------------------------------------------------------
| Best guess : 174 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 |
----------------------------------------------------------------------------------------
| 29.94 - 4.96 | 95.8% | 95.8% | 95.8% | 95.8% | 95.1% | 94.2% |
| 4.96 - 3.94 | 98.1% | 98.1% | 98.1% | 98.1% | 97.7% | 97.2% |
| 3.94 - 3.44 | 98.9% | 98.9% | 98.9% | 98.9% | 97.8% | 96.4% |
| 3.44 - 3.13 | 99.4% | 99.3% | 98.9% | 98.5% | 96.7% | 94.5% |
| 3.13 - 2.90 | 99.2% | 98.6% | 98.4% | 97.5% | 96.1% | 91.5% |
| 2.90 - 2.73 | 99.4% | 99.3% | 98.8% | 97.6% | 92.0% | 83.3% |
| 2.73 - 2.59 | 99.6% | 99.1% | 98.0% | 95.1% | 88.3% | 76.9% |
| 2.59 - 2.48 | 99.4% | 98.9% | 97.8% | 93.4% | 82.0% | 65.1% |
| 2.48 - 2.39 | 99.4% | 98.3% | 96.7% | 91.7% | 76.4% | 58.5% |
| 2.39 - 2.30 | 99.0% | 98.1% | 95.5% | 89.5% | 68.2% | 46.1% |
| 2.30 - 2.23 | 98.8% | 96.3% | 93.4% | 87.0% | 64.9% | 44.0% |
| 2.23 - 2.17 | 99.2% | 97.2% | 94.2% | 86.9% | 59.3% | 36.9% |
| 2.17 - 2.11 | 99.4% | 97.9% | 93.9% | 83.3% | 56.3% | 35.4% |
| 2.11 - 2.06 | 98.7% | 95.1% | 90.1% | 76.7% | 39.8% | 22.6% |
----------------------------------------------------------------------------------------
The completeness of data for which I/sig(I)>3.00, exceeds 85% for
for resolution ranges lower than 2.06A.
The data are cut at this resolution for the potential twin tests
and intensity statistics.
ML estimate of overall B_cart value of output-horiz.sca:i_obs,sigma:
22.55, 0.00, 0.00
22.55, 0.00
26.87
Equivalent representation as U_cif:
0.29, -0.00, -0.00
0.29, 0.00
0.34
Eigen analyses of B-cart:
Value Vector
Eigenvector 1 : 26.870 ( 0.00, 0.00, 1.00)
Eigenvector 2 : 22.554 (-0.71, 0.71, -0.00)
Eigenvector 3 : 22.554 ( 0.71, 0.71, -0.00)
ML estimate of -log of scale factor of output-horiz.sca:i_obs,sigma:
-1.39
Low resolution completeness analyses
The following table shows the completeness
of the data to 5 Angstrom.
unused: - 29.9350 [ 0/6 ] 0.000
bin 1: 29.9350 - 10.6345 [81/97] 0.835
bin 2: 10.6345 - 8.5046 [74/89] 0.831
bin 3: 8.5046 - 7.4485 [81/82] 0.988
bin 4: 7.4485 - 6.7761 [88/89] 0.989
bin 5: 6.7761 - 6.2953 [84/84] 1.000
bin 6: 6.2953 - 5.9271 [90/91] 0.989
bin 7: 5.9271 - 5.6323 [88/88] 1.000
bin 8: 5.6323 - 5.3886 [77/78] 0.987
bin 9: 5.3886 - 5.1823 [83/85] 0.976
bin 10: 5.1823 - 5.0043 [90/91] 0.989
unused: 5.0043 - [ 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 : 1.14
( rms deviation : 0.73 )
mean bin completeness : 0.98
( rms deviation : 0.04 )
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 | 0.69 | 0.98 | 1.000 |
| 3.669 | 0.01 | 0.99 | 0.750 |
| 3.441 | 0.52 | 0.99 | 0.530 |
| 2.671 | 1.03 | 1.00 | 0.170 |
| 2.249 | 0.19 | 0.99 | 0.390 |
| 2.072 | 1.78 | 0.99 | 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:
$$
1/resol^2 <I>_smooth_approximation <I>_via_binning <I>_expected $$
$$
0.010291 59304.370307 72799.297481 70847.324704
0.014291 44989.568369 47846.761766 55028.923661
0.018291 35096.107360 33339.527411 40629.946375
0.022291 31627.588448 29012.471832 35287.329256
0.026291 33262.095920 31624.557468 35543.988960
0.030291 39236.538585 32025.694596 39388.738906
0.034291 49143.666179 47546.802075 48145.858574
0.038291 62121.563703 66649.910430 61732.181019
0.042291 76324.498727 82510.955555 76767.935842
0.046291 89148.485404 98817.612057 88824.475207
0.050291 98195.075115 90275.505654 95347.661275
0.054291 102274.491540 106124.877180 96650.655573
0.058291 101698.457340 102125.151886 94894.080050
0.062291 97793.063826 90122.172304 92378.658541
0.066291 92141.787920 96062.608875 90377.579015
0.070291 86040.990991 84264.740235 88936.367114
0.074291 80302.658525 87337.560997 87372.464041
0.078291 75295.401823 81291.154240 84952.456348
0.082291 71075.159017 69631.222697 81345.520577
0.086291 67515.976363 73674.274028 76719.564657
0.090291 64411.083445 65634.976745 71567.485252
0.094291 61544.383780 58707.369462 66441.319443
0.098291 58738.991249 57011.899236 61745.601008
0.102291 55886.301964 52529.814029 57658.079223
0.106291 52955.914565 52145.999358 54165.459448
0.110291 49987.334908 49509.437501 51157.447304
0.114291 47067.968810 50316.068440 48518.741277
0.118291 44305.203639 40621.147375 46181.627981
0.122291 41800.764300 40112.346731 44132.004434
0.126291 39632.783778 35739.610444 42384.015343
0.130291 37847.000953 39952.634621 40946.744762
0.134291 36455.345677 40429.911655 39802.090824
0.138291 35438.954272 34119.503846 38902.020380
0.142291 34753.158400 35692.053257 38182.363807
0.146291 34333.327237 34901.534966 37583.608592
0.150291 34101.712236 33202.236165 37068.177552
0.154291 33976.013741 33937.621175 36627.238198
0.158291 33879.982254 32750.876703 36275.628293
0.162291 33755.136687 34431.607117 36038.406405
0.166291 33571.259520 34504.897277 35935.148682
0.170291 33332.631658 36035.022955 35967.968004
0.174291 33077.654511 31216.796275 36116.962314
0.178291 32871.388377 30913.107256 36343.632758
0.182291 32792.553660 37871.114491 36600.015005
0.186291 32917.479032 31642.315171 36839.714377
0.190291 33302.920663 32769.336089 37027.013224
0.194291 33968.417933 37134.462723 37141.457992
0.198291 34878.556235 37626.978914 37177.210229
0.202291 35927.865171 35642.704152 37138.249296
0.206291 36936.544344 35488.701600 37031.684404
0.210291 37671.045770 36732.951621 36861.703761
0.214291 37902.327246 38408.355759 36626.115209
0.218291 37497.711153 37703.785030 36316.320824
0.222291 36512.227404 37465.360508 35920.338747
0.226291 35226.026718 32835.429898 35427.532446
0.230291 34093.227199 37558.215581 34833.285631
0.234291 33608.078548 30734.674423 34142.032591
0.238291 34077.081294 34408.981855 33367.698305
0.242291 35123.844658 35386.942314 32531.476427
0.246841 34148.215121 34397.373415 31535.794714
$$
$TABLE: Z scores and completeness:
$GRAPHS
:Data sanity and completeness check
:A:1,2,3:
$$
1/resol^2 Z_score Completeness $$
$$
0.010291 0.170280 0.784615
0.014291 1.153337 0.950617
0.018291 1.878039 0.989362
0.022291 1.979913 0.989474
0.026291 1.209403 0.990826
0.030291 2.224799 1.000000
0.034291 0.129937 0.991597
0.038291 0.775620 0.975610
0.042291 0.739272 1.000000
0.046291 1.141931 0.965986
0.050291 0.627402 0.972789
0.054291 0.990219 1.000000
0.058291 0.851566 0.993590
0.062291 0.309147 0.964497
0.066291 0.692212 0.979452
0.070291 0.702867 0.994220
0.074291 0.005034 0.988304
0.078291 0.584270 0.989071
0.082291 2.160853 0.994444
0.086291 0.517234 0.988024
0.090291 1.240041 0.990099
0.094291 1.723036 1.000000
0.098291 1.126140 0.994898
0.102291 1.328955 0.994975
0.106291 0.552420 0.995434
0.110291 0.442383 1.000000
0.114291 0.520767 1.000000
0.118291 1.906709 0.990338
0.122291 1.433283 1.000000
0.126291 2.719174 1.000000
0.130291 0.365829 1.000000
0.134291 0.231340 0.995708
0.138291 2.011878 1.000000
0.142291 1.031530 0.995745
0.146291 1.174919 1.000000
0.150291 1.685430 1.000000
0.154291 1.226896 0.996094
0.158291 1.594210 0.995690
0.162291 0.708721 1.000000
0.166291 0.664632 1.000000
0.170291 0.029349 1.000000
0.174291 2.440256 0.996169
0.178291 2.631060 0.991837
0.182291 0.533744 1.000000
0.186291 2.530037 0.996169
0.190291 2.113598 0.993151
0.194291 0.002932 1.000000
0.198291 0.191488 0.992674
0.202291 0.692537 1.000000
0.206291 0.670588 1.000000
0.210291 0.057707 0.996516
0.214291 0.777167 0.993289
0.218291 0.613548 1.000000
0.222291 0.660533 1.000000
0.226291 1.334900 1.000000
0.230291 1.176940 0.996429
0.234291 1.782104 0.992908
0.238291 0.521323 0.993730
0.242291 1.371325 0.990260
0.246841 1.062292 0.796209
$$
$TABLE: <I/sigma_I>:
$GRAPHS
:Signal to noise
:N:1,2:
$$
1/resol^2 <I/sigma_I>;_Signal_to_noise $$
$$
0.003116 39.980122
0.007116 43.438170
0.011116 45.532318
0.015116 46.271691
0.019116 46.891170
0.023116 44.532734
0.027116 42.983361
0.031116 44.553802
0.035116 47.030992
0.039116 46.126212
0.043116 47.263481
0.047116 47.087297
0.051116 45.935808
0.055116 40.874920
0.059116 40.571599
0.063116 40.006688
0.067116 39.536607
0.071116 38.956572
0.075116 39.211404
0.079116 38.891205
0.083116 36.879987
0.087116 31.141866
0.091116 30.842580
0.095116 29.441717
0.099116 29.536389
0.103116 28.509638
0.107116 28.316964
0.111116 25.845431
0.115116 25.391718
0.119116 23.366596
0.123116 23.515599
0.127116 21.801842
0.131116 22.701323
0.135116 21.578436
0.139116 20.475213
0.143116 20.542375
0.147116 20.508356
0.151116 19.158601
0.155116 18.606461
0.159116 18.219011
0.163116 18.062354
0.167116 16.696900
0.171116 17.010934
0.175116 15.343091
0.179116 14.174736
0.183116 14.753399
0.187116 12.977454
0.191116 13.060987
0.195116 15.186243
0.199116 13.837175
0.203116 14.280917
0.207116 12.436064
0.211116 13.090369
0.215116 14.609062
0.219116 14.005402
0.223116 12.076580
0.227116 11.425280
0.231116 10.714408
0.235116 9.530683
0.239116 9.250195
0.243116 7.046011
0.247116 5.585173
$$
##----------------------------------------------------##
## Twinning Analyses ##
##----------------------------------------------------##
Using data between 10.00 to 2.06 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,-l |
-------------------------------------------------------------------------------
M: Merohedral twin law
PM: Pseudomerohedral twin law
1 merohedral twin operators found
0 pseudo-merohedral twin operators found
In total, 1 twin operator were found
Number of centrics : 877
Number of acentrics : 10821
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord. : 0.355 -0.373 0.500
Distance to origin : 41.271
Height (origin=100) : 5.776
p_value(height) : 7.629e-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 7.629e-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 :1.695 (untwinned: 2.000; perfect twin 1.500)
<F>^2/<F^2> :0.854 (untwinned: 0.785; perfect twin 0.885)
<|E^2 - 1|> :0.612 (untwinned: 0.736; perfect twin 0.541)
Centric reflections
<I^2>/<I>^2 :2.741 (untwinned: 3.000; perfect twin 2.000)
<F>^2/<F^2> :0.720 (untwinned: 0.637; perfect twin 0.785)
<|E^2 - 1|> :0.890 (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 | 0.027 | 0.095 | 0.119 | 0.248 |
| 0.2 | 0.086 | 0.181 | 0.241 | 0.345 |
| 0.3 | 0.159 | 0.259 | 0.325 | 0.419 |
| 0.4 | 0.235 | 0.330 | 0.396 | 0.474 |
| 0.5 | 0.313 | 0.394 | 0.465 | 0.520 |
| 0.6 | 0.387 | 0.451 | 0.515 | 0.561 |
| 0.7 | 0.457 | 0.503 | 0.562 | 0.597 |
| 0.8 | 0.521 | 0.551 | 0.603 | 0.629 |
| 0.9 | 0.578 | 0.593 | 0.641 | 0.657 |
| 1.0 | 0.625 | 0.632 | 0.667 | 0.683 |
-----------------------------------------------
| Maximum deviation acentric : 0.101 |
| Maximum deviation centric : 0.130 |
| |
| <NZ(obs)-NZ(twinned)>_acentric : -0.055 |
| <NZ(obs)-NZ(twinned)>_centric : -0.055 |
-----------------------------------------------
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| :0.407 (untwinned: 0.500; perfect twin: 0.375)
Mean L^2 :0.232 (untwinned: 0.333; perfect twin: 0.200)
The distribution of |L| values indicates a twin fraction of
0.19. 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:
$$
z Acentric_observed Acentric_untwinned Centric_observed Centric_untwinned $$
$$
0.000000 0.000000 0.000000 0.000000 0.000000
0.100000 0.026985 0.095200 0.118586 0.248100
0.200000 0.085574 0.181300 0.240593 0.345300
0.300000 0.158581 0.259200 0.324971 0.418700
0.400000 0.235468 0.329700 0.395667 0.473800
0.500000 0.312540 0.393500 0.465222 0.520500
0.600000 0.386748 0.451200 0.515393 0.561400
0.700000 0.456612 0.503400 0.562144 0.597200
0.800000 0.521209 0.550700 0.603193 0.628900
0.900000 0.577765 0.593400 0.640821 0.657200
1.000000 0.625173 0.632100 0.667047 0.683300
$$
$TABLE: L test,acentric data:
$GRAPHS
:L test, acentric data
:A:1,2,3,4:
$$
|l| Observed Acentric_theory Acentric_theory,_perfect_twin $$
$$
0.000000 0.004958 0.000000 0.000000
0.020000 0.028996 0.020000 0.029996
0.040000 0.054112 0.040000 0.059968
0.060000 0.082031 0.060000 0.089892
0.080000 0.109734 0.080000 0.119744
0.100000 0.136467 0.100000 0.149500
0.120000 0.160397 0.120000 0.179136
0.140000 0.187345 0.140000 0.208628
0.160000 0.213862 0.160000 0.237952
0.180000 0.238331 0.180000 0.267084
0.200000 0.266897 0.200000 0.296000
0.220000 0.294276 0.220000 0.324676
0.240000 0.321225 0.240000 0.353088
0.260000 0.345801 0.260000 0.381212
0.280000 0.370271 0.280000 0.409024
0.300000 0.394416 0.300000 0.436500
0.320000 0.420610 0.320000 0.463616
0.340000 0.446157 0.340000 0.490348
0.360000 0.470950 0.360000 0.516672
0.380000 0.496497 0.380000 0.542564
0.400000 0.519133 0.400000 0.568000
0.420000 0.542740 0.420000 0.592956
0.440000 0.567101 0.440000 0.617408
0.460000 0.591032 0.460000 0.641332
0.480000 0.612914 0.480000 0.664704
0.500000 0.636089 0.500000 0.687500
0.520000 0.659588 0.520000 0.709696
0.540000 0.678129 0.540000 0.731268
0.560000 0.697747 0.560000 0.752192
0.580000 0.717150 0.580000 0.772444
0.600000 0.738924 0.600000 0.792000
0.620000 0.758758 0.620000 0.810836
0.640000 0.774927 0.640000 0.828928
0.660000 0.792282 0.660000 0.846252
0.680000 0.812547 0.680000 0.862784
0.700000 0.834106 0.700000 0.878500
0.720000 0.850490 0.720000 0.893376
0.740000 0.869570 0.740000 0.907388
0.760000 0.883799 0.760000 0.920512
0.780000 0.899429 0.780000 0.932724
0.800000 0.913442 0.800000 0.944000
0.820000 0.928533 0.820000 0.954316
0.840000 0.943408 0.840000 0.963648
0.860000 0.955589 0.860000 0.971972
0.880000 0.966692 0.880000 0.979264
0.900000 0.975962 0.900000 0.985500
0.920000 0.983292 0.920000 0.990656
0.940000 0.990622 0.940000 0.994708
0.960000 0.995042 0.960000 0.997632
0.980000 0.998383 0.980000 0.999404
$$
---------------------------------------------
Analysing possible twin law : h,-k,-l
---------------------------------------------
Results of the H-test on acentric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.267 (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.103 (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.233
Estimation of twin fraction via cum. dist. of H: 0.227
Britton analyses
Extrapolation performed on 0.18 < alpha < 0.495
Estimated twin fraction: 0.200
Correlation: 0.9962
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 : 0.286
R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data : 0.103
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 0.204
$TABLE: Britton plot for twin law h,-k,-l:
$GRAPHS
:percentage negatives
:A:1,2,3:
$$
alpha percentage_negatives fit $$
$$
0.000000 0.000000 0.000000
0.009901 0.000000 0.000000
0.019802 0.000000 0.000000
0.029703 0.000000 0.000000
0.039604 0.000000 0.000000
0.049505 0.000000 0.000000
0.059406 0.000000 0.000000
0.069307 0.000000 0.000000
0.079208 0.000000 0.000000
0.089109 0.000185 0.000000
0.099010 0.000463 0.000000
0.108911 0.000463 0.000000
0.118812 0.000833 0.000000
0.128713 0.000926 0.000000
0.138614 0.001018 0.000000
0.148515 0.001574 0.000000
0.158416 0.002314 0.000000
0.168317 0.003518 0.000000
0.178218 0.004814 0.000000
0.188119 0.007684 0.000000
0.198020 0.012775 0.000000
0.207921 0.018423 0.011311
0.217822 0.025088 0.026268
0.227723 0.036845 0.041226
0.237624 0.048880 0.056183
0.247525 0.060637 0.071141
0.257426 0.072672 0.086098
0.267327 0.087669 0.101056
0.277228 0.102481 0.116013
0.287129 0.115719 0.130971
0.297030 0.130717 0.145928
0.306931 0.146825 0.160886
0.316832 0.164599 0.175843
0.326733 0.181726 0.190801
0.336634 0.199315 0.205758
0.346535 0.217089 0.220715
0.356436 0.232087 0.235673
0.366337 0.247732 0.250630
0.376238 0.264858 0.265588
0.386139 0.281892 0.280545
0.396040 0.299111 0.295503
0.405941 0.315219 0.310460
0.415842 0.330772 0.325418
0.425743 0.345954 0.340375
0.435644 0.360489 0.355333
0.445545 0.375301 0.370290
0.455446 0.388909 0.385248
0.465347 0.405388 0.400205
0.475248 0.422700 0.415163
0.485149 0.440567 0.430120
$$
$TABLE: H test for possible twin law h,-k,-l:
$GRAPHS
:H test for Acentric data
:A:1,2,3:
$$
H Observed_S(H) Fitted_S(H) $$
$$
0.000000 0.064803 0.000000
0.020000 0.094612 0.036600
0.040000 0.132383 0.073199
0.060000 0.164969 0.109799
0.080000 0.203481 0.146399
0.100000 0.236808 0.182998
0.120000 0.267543 0.219598
0.140000 0.299759 0.256197
0.160000 0.323829 0.292797
0.180000 0.356415 0.329397
0.200000 0.389372 0.365996
0.220000 0.424181 0.402596
0.240000 0.456767 0.439196
0.260000 0.493057 0.475795
0.280000 0.530457 0.512395
0.300000 0.565266 0.548995
0.320000 0.602296 0.585594
0.340000 0.632290 0.622194
0.360000 0.667839 0.658793
0.380000 0.708943 0.695393
0.400000 0.740418 0.731993
0.420000 0.769672 0.768592
0.440000 0.795964 0.805192
0.460000 0.823366 0.841792
0.480000 0.857064 0.878391
0.500000 0.880763 0.914991
0.520000 0.904092 0.951590
0.540000 0.924458 0.988190
0.560000 0.951861 1.000000
0.580000 0.970746 1.000000
0.600000 0.980744 1.000000
0.620000 0.990002 1.000000
0.640000 0.995927 1.000000
0.660000 0.998148 1.000000
0.680000 0.999259 1.000000
0.700000 0.999630 1.000000
0.720000 0.999630 1.000000
0.740000 0.999630 1.000000
0.760000 1.000000 1.000000
0.780000 1.000000 1.000000
0.800000 1.000000 1.000000
0.820000 1.000000 1.000000
0.840000 1.000000 1.000000
0.860000 1.000000 1.000000
0.880000 1.000000 1.000000
0.900000 1.000000 1.000000
0.920000 1.000000 1.000000
0.940000 1.000000 1.000000
0.960000 1.000000 1.000000
0.980000 1.000000 1.000000
$$
$TABLE: Likelihood based twin fraction estimation for possible twin law h,-k,-l:
$GRAPHS
:Likelihood based twin fraction estimate
:A:1,2:
$$
alpha NLL_(acentric_data) $$
$$
0.021739 21096.787205
0.043478 20601.003576
0.065217 20081.199221
0.086957 19539.259430
0.108696 18973.200772
0.130435 18384.984419
0.152174 17785.633772
0.173913 17214.808548
0.195652 16826.958052
0.217391 17167.862655
0.239130 19991.133768
0.260870 28618.042986
0.282609 45755.817655
0.304348 69403.554438
0.326087 101966.619711
0.347826 140358.993897
0.369565 184324.570511
0.391304 229975.931849
0.413043 278281.458194
0.434783 328009.127298
0.456522 384028.198951
0.478261 434226.735780
$$
Exploring higher metric symmetry
The point group of data as dictated by the space group is P 4
the point group in the niggli setting is P 4 (c,a,b)
The point group of the lattice is P 4 2 2 (c,a,b)
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 4 2 2 (c,a,b) | 0.286 | 0.286 | None | None | |
| P 4 (c,a,b) | None | None | 0.286 | 0.286 | <--- |
--------------------------------------------------------------------------------------
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 4 (c,a,b)
Possible space groups in this point groups are:
Unit cell: (71.651, 71.651, 37.103, 90, 90, 90)
Space group: P 41 (No. 76)
Unit cell: (71.651, 71.651, 37.103, 90, 90, 90)
Space group: P 43 (No. 78)
Note that this analysis does not take into account the effects of twinning.
If the data are (almost) 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 : 1.695
- <F>^2/<F^2> : 0.854
- <|E^2-1|> : 0.612
- <|L|>, <L^2>: 0.407, 0.232
Multivariate Z score L-test: 7.603
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.
Statistics depending on twin laws
-----------------------------------------------------------------
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |
-----------------------------------------------------------------
| h,-k,-l | M | 0.286 | 0.200 | 0.227 | 0.204 |
-----------------------------------------------------------------
Patterson analyses
- Largest peak height : 5.776
(corresponding p value : 0.76286)
The largest off-origin peak in the Patterson function is 5.78% of the
height of the origin peak. No significant pseudotranslation is detected.
The results of the L-test indicate that the intensity statistics
are significantly different than is expected from good to reasonable,
untwinned data.
As there are twin laws possible given the crystal symmetry, twinning could
be the reason for the departure of the intensity statistics from normality.
It might be worthwhile carrying out refinement with a twin specific target function.
-------------------------------------------------------------------------------
-------------- next part --------------
refine1: twin, 25 individual sites ml, 25 individual adp, 10 cycles
r_work = 0.1840 r_free = 0.2188 bonds = 0.009 angles = 1.119
refine1-NT: no twin ==
r_work = 0.2327 r_free = 0.2873 bonds = 0.008 angles = 1.066
refine2: twin, sim ann 4k first, 25 individual sites ml, 25 individual adp, 10 cycles
r_work = 0.1846 r_free = 0.2207 bonds = 0.006 angles = 0.841
refine3: twin, ordered water, 25 individual sites ml, 25 individual adp, 10 cycles
r_work = 0.1555 r_free = 0.1907 bonds = 0.005 angles = 0.848
refine3-NT: no twin ==
r_work = 0.1985 r_free = 0.2558 bonds = 0.006 angles = 0.942
refine4: twin, tls(A+B), 25 individual sites ml, 25 individual adp, 5 cycles
r_work = 0.1698 r_free = 0.2066 bonds = 0.009 angles = 1.086
refine4-NT: no twin ==
r_work = 0.2209 r_free = 0.2787 bonds = 0.008 angles = 1.073
refine5: twin, tls(A+B), ordered water, 25 individual sites ml, 25 individual adp, 5 cycles
r_work = 0.1428 r_free = 0.1770 bonds = 0.006 angles = 0.909
refine5-NT: no twin ==
r_work = 0.1922 r_free = 0.2435 bonds = 0.005 angles = 0.872
SUMMARY:
No twin (Rw/Rf) Twinned (Rw/Rf)
refine1 0.2327 / 0.2873 0.1840 / 0.2188
(-TLS-H2O)
refine2 -------------- 0.1846 / 0.2207
(-TLS-H2O+1st SA 4k)
refine3 0.1985 / 0.2558 0.1555 / 0.1907 ***
(-TLS+H2O)
refine4 0.2209 / 0.2787 0.1698 / 0.2066
(+TLS-H2O)
refine5 0.1922 / 0.2435 *** 0.1428 / 0.1770
(+TLS+H2O)
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