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 > <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 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 <michel...@gmail.com > <mailto: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 > <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. > > 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
