Dear Eleanor, dear Michel (?), A while ago we statistically analysed the distribution of R, Rfree and of their difference as a function of the logarithm of resolution (Urzhumtsev et al., 2009, Acta Cryst, D65, 1283-1291). In this log-scale, the mode values for all three are nearly linear functions (see Figs. 4 and 5 and equations (11) and (12) ).
At 3A resolution, indeed, 3% difference is too small but anyhow 10% seems to be not common; just from pure statistics, its mode is rather closer to 5%. At 1A, the mode of Rfree-R distribution is near 2%. With best wishes, Sacha Urzhumtsev ----- Le 6 Mar 20, à 16:22, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit : > 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 < [ mailto:michel...@gmail.com | > 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. >> To unsubscribe from the CCP4BB list, click the following link: >> [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
