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 <[email protected]>
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 <[email protected]>
> wrote:
>
>> Can you attach the refinement log?
>>
>> Eleanor
>>
>> On 10 August 2018 at 16:57, Marcelo Liberato <[email protected]>
>> 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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