Agreed, and this is ongoing work. Yet it is not trivial to get better resolution than this for small (in the world of EM) samples either. ________________________________________ Von: Mark van Raaij [mjvanra...@cnb.csic.es] Gesendet: Donnerstag, 27. Oktober 2016 22:08 An: Hillen, Hauke Betreff: Re: [ccp4bb] AW: [ccp4bb] intensity statistics and twinning
Another option might be to go full cryo-EM Mark J van Raaij CNB-CSIC www.cnb.csic.es/~mjvanraaijOn 27 Oct 2016 21:37, "Hillen, Hauke" <hauke.hil...@mpibpc.mpg.de> wrote: > > Dear Mark, > > Thanks for your reply. Unfortunately, I have already spent a lot of time > trying to do exactly this. I do think some biologically relevant questions > can be answered by architecture at this resolution, so I would like to try to > get the most out of these datasets I can. > > Best wishes, > Hauke > > > ________________________________________ > Von: Mark van Raaij [mjvanra...@cnb.csic.es] > Gesendet: Donnerstag, 27. Oktober 2016 21:29 > An: Hillen, Hauke > Betreff: Re: [ccp4bb] intensity statistics and twinning > > I'd say intensity statistics at this resolution at not reliable and your > crystal are most likely not twinned. > Unless you think you can answer any interesting biological question at this > resolution, I'd forget about these datasets and spend all my efforts at > getting better diffracting ones. Even if this means going back to cloning or > working on a different species...although lysine methylation, limited > proteolysis etc. might also be tried if you haven't done so already. > A slightly different crystal contact might make the difference and yield much > better diffraction. > > Mark J van Raaij > CNB-CSIC > www.cnb.csic.es/~mjvanraaij > > On 27 Oct 2016 21:11, "Hillen, Hauke" <hauke.hil...@mpibpc.mpg.de> wrote: > Dear ccp4 community, > > I am currently working on some low resolution datasets (around 4.5A). The > space group seems to be P21, as suggested by XDS and pointless. I have > collected many datasets of these crystals, both native as well as > SeMet-labeled. Using MR-SAD I have been able to obtain a clearly > interpretable electron density map for all features I expect and heavy atom > sites that make sense for both the model used in MR and the yet unmodeled > components. So far, so good. > > While routinely analyzing my datasets with Phenix Xtriage, I have noticed > that the intensity statistics for all of these datasets look unusual. In > fact, Xtriage complains about this with the message: „The intensity > statistics look unusual, but twinning is not indicated or possible in the > given space group“ when processed in P21. > The occurence of this message depends somewhat on the typ of input file I use > for the same dataset as well as the input parameters (high resolution > cut-off). If I use XDSCONV to convert the intensities to amplitudes for > phenix, this message appears. If I use the output of XSCALE directly as > intensities, this message does not appear, yet the actual statistics are > somewhat similar. I have attached the log file output for four scenarios at > the end of this message (P21 intensities, P21 amplitudes, P1 intensities, P1 > amplitudes). > These results got me questioning whether the true space group is really P21, > or whether it could be that it is P1 with some twinning issue. Since the > Xtriage output regarding the „normality“ of the intensity statistics varies > upon the input format, I assume that this case may be somewhat borderline. > Since I have very little experience both with low-resolution crystals as well > as with twinning, I am a bit unsure how to proceed with this data. > How can I distinguish between a partially twinned P1 crystal and an untwinned > P21 crystal? It is my impression from previous discussions here that > distinguishing twinned from untwinned data simply by comparing refinement > results with and without twin laws is not always conclusive, as the R-factors > are not directly comparable. If the crystal is truly P21, could these issues > arise from intensity to amplitude conversion problems? (Xtriage also suggests > this as a possibility) If so, can these be overcome? Or could the deviation > from ideal intensities simply originate from the low quality (= resolution) > of the data and are within the range of tolerance for such a dataset? Could > this be some type of pseudosymmetry issue? And finally, what > > I would be very grateful for any advice on how to proceed with these data! > > > Kind regards, > Hauke > > > > Processed as P21, intensity input: > > =============== Diagnostic tests for twinning and pseudosymmetry > ============== > > Using data between 10.00 to 3.50 Angstrom. > > ----------Patterson analyses---------- > > Largest Patterson peak with length larger than 15 Angstrom: > Frac. coord. : 0.164 0.000 -0.021 > Distance to origin : 17.720 > Height relative to origin : 3.072 % > p_value(height) : 1.000e+00 > > Explanation > The p-value, the probability that a peak of the specified height or larger > is found in a Patterson function of a macromolecule that does not have any > translational pseudo-symmetry, is equal to 1.000e+00. 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 :1.935 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.805 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.696 (untwinned: 0.736; perfect twin 0.541) > > Centric reflections: > > > <I^2>/<I>^2 :2.431 (untwinned: 3.000; perfect twin 2.000) > <F>^2/<F^2> :0.733 (untwinned: 0.637; perfect twin 0.785) > <|E^2 - 1|> :0.812 (untwinned: 0.968; perfect twin 0.736) > > > ----------NZ test for twinning and TNCS---------- > > > The NZ test is diagnostic for both twinning and translational NCS. Note > however that if both are present, the effects may cancel each other out, > therefore the results of the Patterson analysis and L-test also need to be > considered. > > > Maximum deviation acentric : 0.028 > Maximum deviation centric : 0.103 > > <NZ(obs)-NZ(twinned)>_acentric : -0.009 > <NZ(obs)-NZ(twinned)>_centric : -0.061 > > > ----------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| :0.471 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.301 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.00. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > Reference: > J. Padilla & T. O. Yeates. A statistic for local intensity differences: > robustness to anisotropy and pseudo-centering and utility for detecting > twinning. Acta Crystallogr. D59, 1124-30, 2003. > > > ================================== Twin laws > ================================== > > > ----------Twin law identification---------- > > > No twin laws are possible for this crystal lattice. > > > ================== Twinning and intensity statistics summary > ================== > > > ----------Final verdict---------- > > > The largest off-origin peak in the Patterson function is 3.07% 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. > > ----------Statistics independent of twin laws---------- > > <I^2>/<I>^2 : 1.935 (untwinned: 2.0, perfect twin: 1.5) > <F>^2/<F^2> : 0.805 (untwinned: 0.785, perfect twin: 0.885) > <|E^2-1|> : 0.696 (untwinned: 0.736, perfect twin: 0.541) > <|L|> : 0.471 (untwinned: 0.500; perfect twin: 0.375) > <L^2> : 0.301 (untwinned: 0.333; perfect twin: 0.200) > Multivariate Z score L-test: 1.292 > > > 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. Note that the expected values for perfect twinning > are for merohedrally twinned structures, and deviations from untwinned will > be larger for perfect higher-order twinning. > > > No (pseudo)merohedral twin laws were found. > > > Data processed P21, amplitudes as input: > > =============== Diagnostic tests for twinning and pseudosymmetry > ============== > > Using data between 10.00 to 3.50 Angstrom. > > ----------Patterson analyses---------- > > Largest Patterson peak with length larger than 15 Angstrom: > Frac. coord. : 0.162 0.000 -0.020 > Distance to origin : 17.554 > Height relative to origin : 2.975 % > p_value(height) : 1.000e+00 > > Explanation > The p-value, the probability that a peak of the specified height or larger > is found in a Patterson function of a macromolecule that does not have any > translational pseudo-symmetry, is equal to 1.000e+00. 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 :1.974 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.816 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.689 (untwinned: 0.736; perfect twin 0.541) > > Centric reflections: > > > <I^2>/<I>^2 :2.817 (untwinned: 3.000; perfect twin 2.000) > <F>^2/<F^2> :0.691 (untwinned: 0.637; perfect twin 0.785) > <|E^2 - 1|> :0.832 (untwinned: 0.968; perfect twin 0.736) > > > ----------NZ test for twinning and TNCS---------- > > > The NZ test is diagnostic for both twinning and translational NCS. Note > however that if both are present, the effects may cancel each other out, > therefore the results of the Patterson analysis and L-test also need to be > considered. > > > Maximum deviation acentric : 0.061 > Maximum deviation centric : 0.060 > > <NZ(obs)-NZ(twinned)>_acentric : -0.011 > <NZ(obs)-NZ(twinned)>_centric : +0.017 > > > ----------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| :0.435 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.262 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.00. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > Reference: > J. Padilla & T. O. Yeates. A statistic for local intensity differences: > robustness to anisotropy and pseudo-centering and utility for detecting > twinning. Acta Crystallogr. D59, 1124-30, 2003. > > > ================================== Twin laws > ================================== > > > ----------Twin law identification---------- > > > No twin laws are possible for this crystal lattice. > > > ================== Twinning and intensity statistics summary > ================== > > > ----------Final verdict---------- > > > The largest off-origin peak in the Patterson function is 2.98% 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 no twin laws possible given the crystal symmetry, there could be > a number of reasons for the departure of the intensity statistics from > normality. Overmerging pseudo-symmetric or twinned data, intensity to > amplitude conversion problems as well as bad data quality might be possible > reasons. It could be worthwhile considering reprocessing the data. > > ----------Statistics independent of twin laws---------- > > <I^2>/<I>^2 : 1.974 (untwinned: 2.0, perfect twin: 1.5) > <F>^2/<F^2> : 0.816 (untwinned: 0.785, perfect twin: 0.885) > <|E^2-1|> : 0.689 (untwinned: 0.736, perfect twin: 0.541) > <|L|> : 0.435 (untwinned: 0.500; perfect twin: 0.375) > <L^2> : 0.262 (untwinned: 0.333; perfect twin: 0.200) > Multivariate Z score L-test: 4.774 > > > 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. Note that the expected values for perfect twinning > are for merohedrally twinned structures, and deviations from untwinned will > be larger for perfect higher-order twinning. > > > No (pseudo)merohedral twin laws were found. > > > Data processed as P1, intensities as input: > =============== Diagnostic tests for twinning and pseudosymmetry > ============== > > Using data between 10.00 to 3.50 Angstrom. > > ----------Patterson analyses---------- > > Largest Patterson peak with length larger than 15 Angstrom: > Frac. coord. : 0.109 -0.092 0.018 > Distance to origin : 18.636 > Height relative to origin : 3.518 % > p_value(height) : 9.999e-01 > > Explanation > The p-value, the probability that a peak of the specified height or larger > is found in a Patterson function of a macromolecule that does not have any > translational pseudo-symmetry, is equal to 9.999e-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 :1.916 (untwinned: 2.000; perfect twin 1.500) > <F>^2/<F^2> :0.809 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.704 (untwinned: 0.736; perfect twin 0.541) > > > ----------NZ test for twinning and TNCS---------- > > > The NZ test is diagnostic for both twinning and translational NCS. Note > however that if both are present, the effects may cancel each other out, > therefore the results of the Patterson analysis and L-test also need to be > considered. > > > Maximum deviation acentric : 0.043 > Maximum deviation centric : 0.683 > > <NZ(obs)-NZ(twinned)>_acentric : -0.026 > <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| :0.466 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.296 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.00. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > Reference: > J. Padilla & T. O. Yeates. A statistic for local intensity differences: > robustness to anisotropy and pseudo-centering and utility for detecting > twinning. Acta Crystallogr. D59, 1124-30, 2003. > > > ================================== Twin laws > ================================== > > > ----------Twin law identification---------- > > Possible twin laws: > ------------------------------------------------------------------------------- > | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law > | > ------------------------------------------------------------------------------- > | PM | 2-fold | 0.053 | 0.035 | 0.000 | -h,-k,l > | > ------------------------------------------------------------------------------- > > 0 merohedral twin operators found > 1 pseudo-merohedral twin operators found > In total, 1 twin operators were found > > Please note that the possibility of twin laws only means that the lattice > symmetry permits twinning; it does not mean that the data are actually > twinned. You should only treat the data as twinned if the intensity > statistics are abnormal. > > ----------Twin law-specific tests---------- > > The following tests analyze the input data with each of the possible twin > laws applied. If twinning is present, the most appropriate twin law will > usually have a low R_abs_twin value and a consistent estimate of the twin > fraction (significantly above 0) from each test. The results are also > compiled in the summary section. > > WARNING: please remember that the possibility of twin laws, and the results > of the specific tests, does not guarantee that twinning is actually present > in the data. Only the presence of abnormal intensity statistics (as judged > by the Wilson moments, NZ-test, and L-test) is diagnostic for twinning. > > > ----------Analysis of twin law -h,-k,l---------- > > H-test on acentric data > Only 50.0 % of the strongest twin pairs were used. > > mean |H| : 0.239 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.116 (0.33: untwinned; 0.0: 50% twinned) > > Estimation of twin fraction via mean |H|: 0.261 > Estimation of twin fraction via cum. dist. of H: 0.278 > > Britton analyses > > Extrapolation performed on 0.45 < alpha < 0.495 > Estimated twin fraction: 0.337 > Correlation: 0.9951 > > R vs R statistics > R_abs_twin = <|I1-I2|>/<|I1+I2|> > (Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95) > R_abs_twin observed data : 0.236 > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.096 > No calculated data available. > R_twin for calculated data not determined. > > ======================= 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 P 1 1 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 | BIC > | choice | > ---------------------------------------------------------------------------------------------- > | P 1 | None | None | 0.236 | 0.236 | > 5.792e+05 | | > | P 1 1 2 | 0.236 | 0.236 | None | None | > 3.867e+05 | | > ---------------------------------------------------------------------------------------------- > > 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 > > > An automated point group suggestion is made on the basis of the BIC (Bayesian > information criterion). > > The likely point group of the data is: P 1 1 2 > > Possible space groups in this point group are: > Unit cell: (103.91, 197.01, 137.2, 90, 99.873, 90) > Space group: P 1 2 1 (No. 3) > > Unit cell: (103.91, 197.01, 137.2, 90, 99.873, 90) > Space group: P 1 21 1 (No. 4) > > > 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 > ================== > > > ----------Final verdict---------- > > > The largest off-origin peak in the Patterson function is 3.52% 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. > The symmetry of the lattice and intensity however suggests that the input > 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 advisable to reconsider > data processing. > > ----------Statistics independent of twin laws---------- > > <I^2>/<I>^2 : 1.916 (untwinned: 2.0, perfect twin: 1.5) > <F>^2/<F^2> : 0.809 (untwinned: 0.785, perfect twin: 0.885) > <|E^2-1|> : 0.704 (untwinned: 0.736, perfect twin: 0.541) > <|L|> : 0.466 (untwinned: 0.500; perfect twin: 0.375) > <L^2> : 0.296 (untwinned: 0.333; perfect twin: 0.200) > Multivariate Z score L-test: 1.670 > > > 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. Note that the expected values for perfect twinning > are for merohedrally twinned structures, and deviations from untwinned will > be larger for perfect higher-order twinning. > > > ----------Statistics depending on twin laws---------- > > ----------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ----------------------------------------------------------------- > | -h,-k,l | PM | 0.236 | 0.337 | 0.278 | 0.348 | > ———————————————————————————————— > > > Data processed as P1, amplitudes as input: > > =============== Diagnostic tests for twinning and pseudosymmetry > ============== > > Using data between 10.00 to 3.50 Angstrom. > > ----------Patterson analyses---------- > > Largest Patterson peak with length larger than 15 Angstrom: > Frac. coord. : 0.109 -0.091 0.018 > Distance to origin : 18.517 > Height relative to origin : 3.198 % > p_value(height) : 1.000e+00 > > Explanation > The p-value, the probability that a peak of the specified height or larger > is found in a Patterson function of a macromolecule that does not have any > translational pseudo-symmetry, is equal to 1.000e+00. 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> :0.821 (untwinned: 0.785; perfect twin 0.885) > <|E^2 - 1|> :0.690 (untwinned: 0.736; perfect twin 0.541) > > > ----------NZ test for twinning and TNCS---------- > > > The NZ test is diagnostic for both twinning and translational NCS. Note > however that if both are present, the effects may cancel each other out, > therefore the results of the Patterson analysis and L-test also need to be > considered. > > > Maximum deviation acentric : 0.077 > Maximum deviation centric : 0.683 > > <NZ(obs)-NZ(twinned)>_acentric : -0.022 > <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| :0.427 (untwinned: 0.500; perfect twin: 0.375) > Mean L^2 :0.254 (untwinned: 0.333; perfect twin: 0.200) > > The distribution of |L| values indicates a twin fraction of > 0.00. Note that this estimate is not as reliable as obtained > via a Britton plot or H-test if twin laws are available. > > Reference: > J. Padilla & T. O. Yeates. A statistic for local intensity differences: > robustness to anisotropy and pseudo-centering and utility for detecting > twinning. Acta Crystallogr. D59, 1124-30, 2003. > > > ================================== Twin laws > ================================== > > > ----------Twin law identification---------- > > Possible twin laws: > ------------------------------------------------------------------------------- > | Type | Axis | R metric (%) | delta (le Page) | delta (Lebedev) | Twin law > | > ------------------------------------------------------------------------------- > | PM | 2-fold | 0.053 | 0.035 | 0.000 | -h,-k,l > | > ------------------------------------------------------------------------------- > > 0 merohedral twin operators found > 1 pseudo-merohedral twin operators found > In total, 1 twin operators were found > > Please note that the possibility of twin laws only means that the lattice > symmetry permits twinning; it does not mean that the data are actually > twinned. You should only treat the data as twinned if the intensity > statistics are abnormal. > > ----------Twin law-specific tests---------- > > The following tests analyze the input data with each of the possible twin > laws applied. If twinning is present, the most appropriate twin law will > usually have a low R_abs_twin value and a consistent estimate of the twin > fraction (significantly above 0) from each test. The results are also > compiled in the summary section. > > WARNING: please remember that the possibility of twin laws, and the results > of the specific tests, does not guarantee that twinning is actually present > in the data. Only the presence of abnormal intensity statistics (as judged > by the Wilson moments, NZ-test, and L-test) is diagnostic for twinning. > > > ----------Analysis of twin law -h,-k,l---------- > > H-test on acentric data > Only 50.0 % of the strongest twin pairs were used. > > mean |H| : 0.213 (0.50: untwinned; 0.0: 50% twinned) > mean H^2 : 0.082 (0.33: untwinned; 0.0: 50% twinned) > > Estimation of twin fraction via mean |H|: 0.287 > Estimation of twin fraction via cum. dist. of H: 0.288 > > Britton analyses > > Extrapolation performed on 0.44 < alpha < 0.495 > Estimated twin fraction: 0.337 > Correlation: 0.9956 > > R vs R statistics > R_abs_twin = <|I1-I2|>/<|I1+I2|> > (Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95) > R_abs_twin observed data : 0.219 > R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> > R_sq_twin observed data : 0.093 > No calculated data available. > R_twin for calculated data not determined. > > ======================= 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 P 1 1 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 | BIC > | choice | > ---------------------------------------------------------------------------------------------- > | P 1 | None | None | 0.219 | 0.219 | > 3.436e+05 | | > | P 1 1 2 | 0.219 | 0.219 | None | None | > 2.188e+05 | | > ---------------------------------------------------------------------------------------------- > > 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 > > > An automated point group suggestion is made on the basis of the BIC (Bayesian > information criterion). > > The likely point group of the data is: P 1 1 2 > > Possible space groups in this point group are: > Unit cell: (103.91, 197.01, 137.2, 90, 99.873, 90) > Space group: P 1 2 1 (No. 3) > > Unit cell: (103.91, 197.01, 137.2, 90, 99.873, 90) > Space group: P 1 21 1 (No. 4) > > > 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 > ================== > > > ----------Final verdict---------- > > > The largest off-origin peak in the Patterson function is 3.20% 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. > > Please note however that R-factors from twinned refinement cannot be directly > compared to R-factors without twinning, as they will always be lower when a > twin law is used. You should also use caution when interpreting the maps from > refinement, as they will have significantly more model bias. > > > Note that the symmetry of the intensities suggest that the assumed space group > is too low. As twinning is however suspected, it is not immediately clear if > this is the case. Careful reprocessing and (twin)refinement for all cases > might resolve this question. > > ----------Statistics independent of twin laws---------- > > <I^2>/<I>^2 : 1.967 (untwinned: 2.0, perfect twin: 1.5) > <F>^2/<F^2> : 0.821 (untwinned: 0.785, perfect twin: 0.885) > <|E^2-1|> : 0.690 (untwinned: 0.736, perfect twin: 0.541) > <|L|> : 0.427 (untwinned: 0.500; perfect twin: 0.375) > <L^2> : 0.254 (untwinned: 0.333; perfect twin: 0.200) > Multivariate Z score L-test: 5.697 > > > 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. Note that the expected values for perfect twinning > are for merohedrally twinned structures, and deviations from untwinned will > be larger for perfect higher-order twinning. > > > ----------Statistics depending on twin laws---------- > > ----------------------------------------------------------------- > | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | > ----------------------------------------------------------------- > | -h,-k,l | PM | 0.219 | 0.337 | 0.288 | 0.307 | > -----------------------------------------------------------------
