Dear TO,
at medium to poor resolution, I prefer to set the weighting myself rather than
use the automatic weighting. At 3'ish A resolution, I would start with 0.01 or
0.005 with many more than the default 10 cycles, maybe 50 or 100. The numbers
you list below go in the other direction (>4).
Best,
Tim
On Friday, March 6, 2020 2:36:01 PM CET M T wrote:
> Dear BBers,
>
> I am trying to refine a structure using COOT and Refmac5 and I have some
> concerns about overrefinement and x-ray term weight in Refmac5, based on
> the fact that during refinement to let R factor to drift too far from Rfree
> is not good...
>
> So... First question about that : what is too far ? I have some values in
> mind like 6% of difference is OK, 10% is not... But is there a relation in
> between resolution of the structure and this difference? Should it be
> higher at lower resolution, or always around 6-7% independently of the
> resolution?
>
> Second question is, ok, I have a too big difference, lets say 9-10%... What
> could be the reason of that and on what to play to reduce this difference?
>
> One way I choose is to look at the x-ray term weight (even if I am totally
> sure that Refmac5 is doing things better than me), because I saw that the
> final rms on BondLength were to constraint (I have in mind that this value
> should stays in between 0.02 and 0.01).
> So I looked into Refmac log to know where was the starting point and I
> found 8.75.
> Then I tried several tests and here are the results:
> *************************************************************************
>
> R factor
>
> Rfree
> BondLength
>
> BondAngle
>
> ChirVolume
>
> Auto weighting and experimental sigmas boxes checked
>
> 0.1932
> 0.2886
>
> 0.0072
>
> 1.6426
>
> 0.1184
>
> Weighting term at 4 and experimental sigmas box checked
>
> 0.1780
> 0.3159
>
> 0.1047
>
> 8.1929
>
> 0.5937
>
> Weighting term at 4
>
> 0.1792
> 0.3143
>
> 0.1008
>
> 7.8200
>
> 0.5667
>
> Weighting term at 15 and experimental sigmas box checked
>
> 0.1783
> 0.3272
>
> 0.2020
>
> 1.6569
>
> 0.9745
>
> Weighting term at 15
>
> 0.1801
> 0.3279
>
> 0.2022
>
> 12.5748
>
> 0.9792
>
> Weighting term at 8.75
>
> 0.1790
> 0.3235
>
> 0.1545
>
> 10.5118
>
> 0.7909
>
> Auto weighting box checked
>
> 0.1948
> 0.2880
>
> 0.0076
>
> 1.6308
>
> 0.1176
>
>
>
> *Refinement Parameters*
> [image: image.png]
>
> So like nothing looks satisfying I decided to ask my questions here...
>
> What do you recommend to fix my problem, which is a too large difference
> between R and Rfree?
>
> Thank you for answers.
>
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>
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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
GPG Key ID = A46BEE1A
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