How very odd!
I have no ideas on the Zn phenonema - what do the R factor plots look
like against resolution - is there some aberrant reflection which was
part of the FreeR set? The theory is that excluding 5% of the data
should not affect the model seriously at all..
Re the 2nd point. Two things - I would first check that the occupancy is
actually correct in the file - I have messed that up at times..
And then maps do sometimes have weird pits and peaks - presumably
related to missing data or imperfect scaling - I guess that could cause
such a problem in one region of the map..
Eleanor
On 05/26/2011 11:11 AM, Petr Kolenko wrote:
> Dear colleagues,
>
> I have two problems in two structure refinements using REFMAC5.
>
> 1) 1.8A resolution, zinc in the active site. Refinement using work
> reflections - ADP for Zinc was about 14. Final refinement including
> all reflections increase ADP to 20 or even higher values - followed by
> very high positive difference density in position of the zinc. I have
> tried also PHENIX, the same thing. I changed ADP manually to 14 and
> only calculated maps (no refinement) look good. May I deposit the
> structure using "manually" fixed ADP according to the best agreement
> to the observed and difference electron density? By the way, it is
> clear that this is zinc.
>
> 2) 1.9A resolution, about 600AA, all of them OK in electron density.
> But, somehow, about ten atoms give very strong positive electron
> density suggesting they are not taken into account in refinement. On
> the other hand, ADPs are reasonable and seem to be refined. All of
> these atoms are fully occupied. I tried to omit whole residues and
> build them again, but the maxima appeared again. Using of PHENIX
> resulted in no difference electron density for these atoms. I have
> also tried to take PHENIX output to REFMAC, but the maxima are there
> again. It is always one or two atoms from the same residues -
> sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but
> still on the same five residues. Does anyone have any idea how to
> solve this problem?
>
> Many thanks for any response.
>
> Petr
>
>
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