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. > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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