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Hi Lucas,<br>
<br>
Your P21 just looks twinned. Have a look at the last section of the
xtriage output:<br>
<br>
<br>
-------------------------------------------------------------------------------<br>
Twinning and intensity statistics summary (acentric data):<br>
<br>
Statistics independent of twin laws<br>
- <I^2>/<I>^2 : 1.915<br>
- <F>^2/<F^2> : 0.821<br>
- <|E^2-1|> : 0.677<br>
- <|L|>, <L^2>: 0.442, 0.267<br>
Multivariate Z score L-test: 3.623<br>
The multivariate Z score is a quality measure of the given<br>
spread in intensities. Good to reasonable data is expected<br>
to have a Z score lower than 3.5.<br>
Large values can indicate twinning, but small values do not<br>
neccesarily exclude it.<br>
<br>
<br>
Statistics depending on twin laws<br>
------------------------------------------------------------------<br>
| Operator | type | R obs. | Britton alpha | H alpha | ML alpha |<br>
------------------------------------------------------------------<br>
| h,-k,-h-l | PM | 0.090 | 0.406 | 0.417 | 0.370 |<br>
------------------------------------------------------------------<br>
<br>
Patterson analyses<br>
- Largest peak height : 6.379<br>
(correpsonding p value : 6.273e-01)<br>
<br>
<br>
The largest off-origin peak in the Patterson function is 6.38% of the<br>
height of the origin peak. No significant pseudotranslation is detected.<br>
<br>
The results of the L-test indicate that the intensity statistics<br>
are significantly different then is expected from good to reasonable,<br>
untwinned data.<br>
As there are twin laws possible given the crystal symmetry, twinning
could<br>
be the reason for the departure of the intensity statistics from
normality.<br>
It might be worthwhile carrying out refinement with a twin specific
target function.<br>
<br>
-------------------------------------------------------------------------------<br>
<br>
You might have NCS parallel to the twin axis. If you run
mmtbx.xtwin_map_utils on your P21 data, you get a mtzfile called
obs_and_calc.mtz <br>
push that through xtriage (make sure to specify labels for observed and
calculated data) to get the RvsR statistic. When you do that, please
also provide the keyword <br>
'perform=True' on the xtriage command line for my pleasure and send me
the resulting log file.<br>
<br>
I guess the twin refinement will push the r values down a bit.<br>
<br>
Note that for futurte reference, xtriage produces a logfile as well,
usually named logfile.log unless you ask it to be a different name.
logfile.log contains some ccp4 style graphs you can view with loggraph
(such as the L, NZ, Britton and H curves).<br>
<br>
If the above is too cryptic and you need more info, please let me know.<br>
<br>
HTH<br>
<br>
Peter<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Lucas Bleicher wrote:
<blockquote cite="mid69208.91476.qm@web31104.mail.mud.yahoo.com"
type="cite">
<pre wrap="">Hi, Peter!
I am sending the xtriage output for both space groups.
So, the correct approach would be to use the MTZ
processed in P21 with the twin law from the xtriage
output from this MTZ file?
Thanks in advance,
Lucas
Alertas do Yahoo! Mail em seu celular. Saiba mais em <a class="moz-txt-link-freetext" href="http://br.mobile.yahoo.com/mailalertas/">http://br.mobile.yahoo.com/mailalertas/</a></pre>
<pre wrap="">
<hr size="4" width="90%">
#############################################################
## mmtbx.xtriage ##
## ##
## P.H. Zwart, R.W. Grosse-Kunstleve & P.D. Adams ##
## ##
#############################################################
Date 2007-07-31 Time 16:43:49 BRT -0300
##-------------------------------------------##
## 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 = 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 = "LamNatP1High_scala1.mtz"
obs_labels = "MEAN_lnls,SIGIMEAN_lnls"
calc_labels = None
unit_cell = 52.16379929 64.59190369 108.2256012 89.99259949 89.99089813 \
66.10500336
space_group = "P 1"
high_resolution = None
low_resolution = None
}
}
<scitbx_array_family_flex_ext.double object at 0xb5e96dac>
Symmetry, cell and reflection file content summary
Miller array info: LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls
Observation type: xray.amplitude
Type of data: double, size=94082
Type of sigmas: double, size=94082
Number of Miller indices: 94082
Anomalous flag: False
Unit cell: (52.1638, 64.5919, 108.226, 89.9926, 89.9909, 66.105)
Space group: P 1 (No. 1)
Systematic absences: 0
Centric reflections: 0
Resolution range: 26.0819 1.85
Completeness in resolution range: 0.854134
Completeness with d_max=infinity: 0.853839
##----------------------------------------------------##
## Basic statistics ##
##----------------------------------------------------##
Matthews coefficient and Solvent content statistics
Number of residues unknown, assuming 50% solvent content
----------------------------------------------------------------
| Best guess : 1220 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 |
----------------------------------------------------------------------------------------
| 26.08 - 4.55 | 97.0% | 96.3% | 95.5% | 93.5% | 87.3% | 80.3% |
| 4.55 - 3.62 | 96.5% | 96.1% | 95.4% | 93.8% | 87.8% | 81.2% |
| 3.62 - 3.16 | 95.7% | 94.5% | 93.2% | 89.4% | 78.1% | 66.3% |
| 3.16 - 2.87 | 93.1% | 90.7% | 87.1% | 79.1% | 60.8% | 44.5% |
| 2.87 - 2.67 | 88.4% | 84.0% | 78.5% | 66.7% | 44.0% | 27.9% |
| 2.67 - 2.51 | 85.5% | 78.6% | 71.1% | 57.7% | 32.6% | 17.9% |
| 2.51 - 2.38 | 82.4% | 74.1% | 65.3% | 49.3% | 24.8% | 12.2% |
| 2.38 - 2.28 | 81.6% | 72.3% | 62.4% | 46.0% | 20.4% | 9.0% |
| 2.28 - 2.19 | 78.5% | 67.6% | 55.1% | 37.2% | 14.8% | 5.7% |
| 2.19 - 2.12 | 75.5% | 61.9% | 49.0% | 30.7% | 9.9% | 3.5% |
| 2.12 - 2.05 | 72.1% | 55.6% | 41.8% | 23.7% | 6.3% | 1.9% |
| 2.05 - 1.99 | 68.6% | 50.2% | 35.8% | 17.9% | 4.1% | 1.0% |
| 1.99 - 1.94 | 63.2% | 42.9% | 28.5% | 13.7% | 3.1% | 0.5% |
| 1.94 - 1.89 | 56.6% | 36.7% | 23.2% | 10.4% | 1.7% | 0.3% |
----------------------------------------------------------------------------------------
The completeness of data for which I/sig(I)>3.00, exceeds 85% for
for resolution ranges lower than 2.87A.
The data is cut at this resolution for the potential twin tests
and intensity statistics.
Maximum likelihood isotropic Wilson scaling
ML estimate of overall B value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls:
15.59 A**(-2)
Estimated -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls:
-2.45
Maximum likelihood anisotropic Wilson scaling
ML estimate of overall B_cart value of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls:
15.61, 1.39, -1.33
11.40, 0.27
21.10
Equivalent representation as U_cif:
0.18, -0.04, -0.02
0.14, 0.00
0.27
ML estimate of -log of scale factor of LamNatP1High_scala1.mtz:IMEAN_lnls,SIGIMEAN_lnls:
-2.45
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: - 26.0822 [ 0/38 ] 0.000
bin 1: 26.0822 - 10.5555 [528/541] 0.976
bin 2: 10.5555 - 8.4726 [551/564] 0.977
bin 3: 8.4726 - 7.4299 [530/547] 0.969
bin 4: 7.4299 - 6.7636 [568/582] 0.976
bin 5: 6.7636 - 6.2860 [525/540] 0.972
bin 6: 6.2860 - 5.9200 [547/559] 0.979
bin 7: 5.9200 - 5.6266 [530/546] 0.971
bin 8: 5.6266 - 5.3839 [519/532] 0.976
bin 9: 5.3839 - 5.1783 [568/584] 0.973
bin 10: 5.1783 - 5.0009 [516/532] 0.970
unused: 5.0009 - [ 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> |
------------------------------------------------
| 9.993 | 7.15 | 0.97 | 0.426 |
| 8.448 | 7.29 | 0.98 | 0.559 |
| 7.451 | 6.09 | 0.97 | 0.676 |
| 4.303 | 4.64 | 0.97 | 1.223 |
| 3.410 | 4.52 | 0.96 | 1.176 |
| 3.333 | 6.63 | 0.96 | 1.262 |
| 3.261 | 5.36 | 0.96 | 1.205 |
| 3.194 | 5.48 | 0.96 | 1.203 |
| 3.071 | 4.87 | 0.94 | 1.183 |
| 2.962 | 6.43 | 0.94 | 1.245 |
| 2.911 | 4.61 | 0.93 | 1.160 |
| 2.454 | 4.96 | 0.87 | 0.872 |
| 2.425 | 6.89 | 0.87 | 0.825 |
| 2.397 | 4.68 | 0.87 | 0.873 |
| 2.182 | 6.79 | 0.84 | 0.830 |
| 2.142 | 5.54 | 0.84 | 0.856 |
| 1.870 | 5.46 | 0.60 | 1.205 |
| 1.857 | 11.65 | 0.54 | 1.570 |
------------------------------------------------
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) |
-----------------------------------------------------------------
| 2.114 | -18, -9, 35 | 3.79 | 5.57e-07 | 5.08e-02 |
| 3.066 | -16, -8, 12 | 3.93 | 1.90e-07 | 1.77e-02 |
| 3.066 | 16, 8, 12 | 3.95 | 1.69e-07 | 1.57e-02 |
| 2.115 | 18, 9, 35 | 3.79 | 5.65e-07 | 5.15e-02 |
-----------------------------------------------------------------
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 : 3.46
( rms deviation : 1.89 )
mean bin completeness : 0.89
( rms deviation : 0.09 )
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 | 0.51 | 0.97 | 1.000 |
| 3.669 | 1.87 | 0.97 | 0.750 |
| 3.441 | 4.52 | 0.96 | 0.530 |
| 2.671 | 3.84 | 0.89 | 0.170 |
| 2.249 | 3.61 | 0.87 | 0.390 |
| 2.072 | 3.23 | 0.82 | 0.300 |
| 1.948 | 0.62 | 0.76 | 0.040 |
| 1.918 | 0.44 | 0.73 | 0.180 |
| 1.883 | 5.46 | 0.60 | 0.030 |
------------------------------------------------
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 2.87 Angstrom.
Determining possible twin laws.
The following twin laws have been found:
---------------------------------------------------------------------------------
| Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law |
---------------------------------------------------------------------------------
| PM | 2-fold | 0.009 | 0.010 | 0.000 | -h,-k,l |
| PM | 2-fold | 0.090 | 0.079 | 0.001 | -h,-h+k,-l |
| PM | 2-fold | 0.099 | 0.080 | 0.001 | h,h-k,-l |
---------------------------------------------------------------------------------
M: Merohedral twin law
PM: Pseudomerohedral twin law
0 merohedral twin operators found
3 pseudo-merohedral twin operators found
In total, 3 twin operator were found
Number of centrics : 0
Number of acentrics : 27599
Largest patterson peak with length larger then 15 Angstrom
Frac. coord. : 0.119 -0.276 -0.000
Distance to origin : 16.337
Height (origin=100) : 5.893
p_value(height) : 7.365e-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 7.365e-01
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.
Wilson ratio and moments
Acentric reflections
<I^2>/<I>^2 :1.932 (untwinned: 2.000; perfect twin 1.500)
<F>^2/<F^2> :0.820 (untwinned: 0.785; perfect twin 0.885)
<|E^2 - 1|> :0.678 (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 | 0.046 | 0.095 | 0.000 | 0.248 |
| 0.2 | 0.127 | 0.181 | 0.000 | 0.345 |
| 0.3 | 0.210 | 0.259 | 0.000 | 0.419 |
| 0.4 | 0.287 | 0.330 | 0.000 | 0.474 |
| 0.5 | 0.361 | 0.394 | 0.000 | 0.520 |
| 0.6 | 0.427 | 0.451 | 0.000 | 0.561 |
| 0.7 | 0.486 | 0.503 | 0.000 | 0.597 |
| 0.8 | 0.544 | 0.551 | 0.000 | 0.629 |
| 0.9 | 0.597 | 0.593 | 0.000 | 0.657 |
| 1.0 | 0.643 | 0.632 | 0.000 | 0.683 |
-----------------------------------------------
| Maximum deviation acentric : 0.055 |
| Maximum deviation centric : 0.683 |
| |
| <NZ(obs)-NZ(twinned)>_acentric : -0.024 |
| <NZ(obs)-NZ(twinned)>_centric : -0.467 |
-----------------------------------------------
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| :0.441 (untwinned: 0.500; perfect twin: 0.375)
Mean L^2 :0.267 (untwinned: 0.333; perfect twin: 0.200)
The distribution of |L| values indicates a twin fraction of
0.08. 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,l
---------------------------------------------
Results of the H-test on a-centric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.053 (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.005 (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.447
Estimation of twin fraction via cum. dist. of H: 0.449
Britton analyses
Extrapolation performed on 0.47 < alpha < 0.495
Estimated twin fraction: 0.442
Correlation: 0.9953
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 : 0.054
R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data : 0.004
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 0.415
---------------------------------------------
Analysing possible twin law : -h,-h+k,-l
---------------------------------------------
Results of the H-test on a-centric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.093 (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.015 (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.407
Estimation of twin fraction via cum. dist. of H: 0.407
Britton analyses
Extrapolation performed on 0.44 < alpha < 0.495
Estimated twin fraction: 0.399
Correlation: 0.9959
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 : 0.093
R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data : 0.011
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 0.361
---------------------------------------------
Analysing possible twin law : h,h-k,-l
---------------------------------------------
Results of the H-test on a-centric data:
(Only 50.0% of the strongest twin pairs were used)
mean |H| : 0.085 (0.50: untwinned; 0.0: 50% twinned)
mean H^2 : 0.013 (0.33: untwinned; 0.0: 50% twinned)
Estimation of twin fraction via mean |H|: 0.415
Estimation of twin fraction via cum. dist. of H: 0.417
Britton analyses
Extrapolation performed on 0.46 < alpha < 0.495
Estimated twin fraction: 0.411
Correlation: 0.9961
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 : 0.086
R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2>
R_sq_twin observed data : 0.009
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 0.350
Exploring higher metric symmetry
The point group of data as dictated by the space group is P 1
the point group in the niggli setting is P 1
The point group of the lattice is Hall: C 2 2 (x+y,2*y,z)
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 |
-----------------------------------------------------------------------------------------------
| Hall: C 2y (x-y,2*x,z) | 0.086 | 0.086 | 0.054 | 0.054 | |
| P 1 | None | None | 0.070 | 0.054 | |
| Hall: C 2y (x+y,2*y,z) | 0.093 | 0.093 | 0.054 | 0.054 | |
| Hall: C 2 2 (x+y,2*y,z) | 0.070 | 0.086 | None | None | |
| P 1 1 2 | 0.054 | 0.054 | 0.093 | 0.093 | <--- |
-----------------------------------------------------------------------------------------------
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 1 1 2
Possible space groups in this point groups are:
Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90)
Space group: P 1 2 1 (No. 3)
Unit cell: (52.1638, 108.226, 64.5258, 90, 113.762, 90)
Space group: P 1 21 1 (No. 4)
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 : 1.932
- <F>^2/<F^2> : 0.820
- <|E^2-1|> : 0.678
- <|L|>, <L^2>: 0.441, 0.267
Multivariate Z score L-test: 3.807
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,l | PM | 0.054 | 0.442 | 0.449 | 0.415 |
| -h,-h+k,-l | PM | 0.093 | 0.399 | 0.407 | 0.361 |
| h,h-k,-l | PM | 0.086 | 0.411 | 0.417 | 0.350 |
-------------------------------------------------------------------
Patterson analyses
- Largest peak height : 5.893
(correpsonding p value : 7.365e-01)
The largest off-origin peak in the Patterson function is 5.89% 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 then 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 refinement with a twin specific target function.
Note that the symmetry of the intensities suggest that the assumed space group
is too low. As twinning is however suspected, it is not immediuatly clear if this
is the case. Carefull reprocessing and (twin)refinement for all cases might resolve
this question.
-------------------------------------------------------------------------------</pre>
</blockquote>
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