In addition to Sacha’s work there are a few older papers by Ian Tickle & Cie. (summarized in BMC) and a figure of the empirical distributions
http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-24.htm
which are broad and – as mentioned - the actual delta values are context dependent.
Best, BR
From: CCP4 bulletin board <[log in to unmask]> On Behalf Of Andrew Leslie
Sent: Friday, March 6, 2020 08:52
To: [log in to unmask]
Subject: Re: [ccp4bb] Overrefinement considerations and Refmac5.
I would like to add a small caveat to Eleanor’s rule about a 3% difference being too low for a structure refined against 3Å data.
If the 3Å data is for a structure that has already been solved at much higher resolution (e.g. 2Å) and the only difference for the 3Å dataset is a different ligand (say) and the structure is solved by molecular replacement using the high resolution structure as a model, in those circumstances it is possible (and quite acceptable) to have a much lower difference between Rwork and Rfree than one might expect, even at low as 3-4%.
Andrew
On 6 Mar 2020, at 15:22, Eleanor Dodson <[log in to unmask]> wrote:
You dont give the data resolution - that is very important..
I hate this rule bound approach to Rfree - R differences.. but as a guide
No non-crystallographic symmetry.
1A data - you would expect them to be almost equal
3A data - I would expect a difference of at least 10% - once had the pleasure of sendng a paper back as unreasonable when the data was only to 3A and the r factors differed by 3%
Pseudo-symmetry and non-crystallographic symmetry can make things more complicated.
Ideally reflections related by such symmetry should match - either set belong to the Rfree set, or working set.
The best way to get a low Rfactor and a high Rfree is to have virtually no geometric restraints. ie have a very high weighting term.
The auto selection works pretty well in my experience..
Not really an answer but some ideas..
Eleanor
On Fri, 6 Mar 2020 at 13:32, M T <[log in to unmask]> 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.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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