This MR looks good to me, but there are serious flaws with the data. Your
secon moment plot from the aimless log has most spectacular spikes which
are always a BAD THING, and the Wilson plot is not very smooth either..

As Randy says, try to sort those problems out first.

Then you have this message:


TRANSLATIONAL NCS:

Translational NCS has been detected at ( 0.000,  0.500,  0.125).
A translation of 0.5 along B will generate pseudo-absences along b so you
can be sure whether there is a scre axis or not..

The space group is most likely orthorhombic - these indicators are pretty
convincing for P2/mmm - so I dont know why you have chosen P21 as the
spacegroup?


Scores for each symmetry element

Nelmt  Lklhd  Z-cc    CC        N  Rmeas    Symmetry & operator (in Lattice
Cell)

  1   *0.917 *  8.18   0.82   61009  0.298     identity
  2  * 0.883*   7.85   0.78  100711  0.381 **  2-fold l ( 0 0 1) {-h,-k,l},
along original k
  3   *0.921*   8.39   0.84   99542  0.355 *** 2-fold k ( 0 1 0) {-h,k,-l},
along original l
  4   *0.920*   8.26   0.83   99218  0.320 *** 2-fold h ( 1 0 0) {h,-k,-l},
along original h

So my suggestions:
Sort out data problems

Merge as P2/mmm

Let MR search select the most likely spacegroup of the 8 possible.

You cant even limit the b axis to be a screw axis .

Your refinement behavior looks OK, but the maps will look bad with spurious
reflections in the list..

Eleanor





On 10 August 2018 at 19:02, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:

> Actually Marcelo - Refinement to an R of 41% is pretty good for an MR
> solution!
>
>
>
> On 10 August 2018 at 18:42, Eleanor Dodson <eleanor.dod...@york.ac.uk>
> wrote:
>
>> Can you attach the refinement log?
>>
>> Eleanor
>>
>> On 10 August 2018 at 16:57, Marcelo Liberato <marcelovliber...@gmail.com>
>> wrote:
>>
>>> Dear Randy,
>>>
>>> Thank you very much for answering. I followed your suggestions but,
>>> unfortunately, I couldn't get a reasonable electron density map after MR
>>> and refinement.
>>>
>>>
>>> First I would look at the data to see if you have ice rings, because the
>>>> peak in mean intensity and second moment of the intensity at about 2.25A
>>>> resolution suggests an ice ring problem.  If so, you should make sure you
>>>> don't contaminate the data with spurious large intensities.
>>>>
>>>> Indeed, the data has ice rings. At first, I required imosflm to remove
>>> ice rings, but it didn't happened. So, I re-processed the data in different
>>> space groups removing the ice rings.
>>>
>>> Second, the statistics (e.g. the second moments plot after tNCS
>>>> correction in Phaser) would be consistent with a scenario in which you have
>>>> pseudosymmetry along with a twin operator that parallels the
>>>> pseudosymmetry.  If that's true, it's hard to be sure of the symmetry.  For
>>>> instance, if the structure really is monoclinic, can you be sure you chose
>>>> the correct axis to be the 2-fold?
>>>>
>>>
>>> I am not sure. However, I tried two possible axis to be the 2-fold and
>>> none of them gave me reasonable maps after MR and refinement.
>>>
>>>
>>>>
>>>> Since you have a good model that gives clear MR solutions even in P21,
>>>> you can probably process the data in P1 and solve it with 8 copies in the
>>>> unit cell.  Then you can look at the symmetry of the MR solution (e.g. in
>>>> Zanuda) and see whether it obeys any higher symmetry than P1.
>>>>
>>>
>>> I processed data in P1. After MR (with 8 copies in the ASU), it
>>> resulted in TFZ=11.6 and LLG=1434. But the map is still bad and high
>>> Rwork and Rfree.
>>> According to Zanuda, the data should be P21:
>>>
>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>>
>>>    | >>   4   | P 1 21 1   | 68.6868  |  0.6289  |  0.5487  |  0.5523  |
>>>
>>>    ---------------------------------------------------------------------
>>>
>>>    |      1   | P 1        | 69.4151  |  0.6171  |  0.5471  |  0.5559  |
>>>
>>>    |      4   | P 1 21 1   | 69.3810  |    --    |  0.5482  |  0.5442  |
>>>
>>>    |     11   | P 21 21 21 | 52.0271  |    --    |  0.6107  |  0.6178  |
>>>
>>>    ---------------------------------------------------------------------
>>>
>>>    | <<   4   | P 1 21 1   | 69.3810  |    --    |  0.5482  |  0.5442  |
>>>
>>>    ---------------------------------------------------------------------
>>>
>>> I processed in P21 using two different unit cells, and MR resulted in
>>> TFZ=20.8 and LLG=511, and TFZ=56 and LLG=2867. However, again, no good
>>> maps and statistics.
>>>
>>> Best regards
>>>
>>> Marcelo Liberato
>>>
>>> ------------------------------
>>>
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>>
>>
>

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