Well, as no one else has come back to you, I wouldn't say 10 % difference between R and R-free is 'bad' and it's certainly not super-bad! It's a bit high, but if you look at the papers by Ian Tickle from the late 90's and others I think you can be reasonably happy with it. I've been told that A N other well-known protein crystallography suite gives a lower difference for the same structure, so you could always try that ;-)
Jon Cooper
On 6 Mar 2020 13:36, M T <michel...@gmail.com> 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
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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