Dear Eleanor and Eric Thanks for your replies.
Yes indeed when we looked at the plots e.g. R factor vs resln there was a sharp peak near 3.6 - 3.8 A which is where we visibly saw an ice ring on the image. Thus our first thought was to remove the ic ring. (either reprocess or can we bypass this resolution range during refinement?) The protein is 50 kDa, two molecule in the ASU, seemingly no obvious density was unassigned. We got ~30000 total observations, ~15000 unique observations. NCS restraints was applied. Best regards Sam On Thu, 4 Apr 2019 at 08:57, Eric Montemayor <montemayor.e...@gmail.com> wrote: > That’s a rather large gap between Rwork and Rfree. I suspect you have > mis-assigned your space group and as a result have a large number of copies > in your asymmetric unit. Any structure can be solved in P1, but that does > not mean the true space group is indeed P1. If you use P1 when it’s not > actually P1, you will have an unnecessarily overparamerized model, hence > the large gap between Rwork and Rfree. > > Questions: > 1- how many copies in your asymmetric unit in P1? > 2- how many atoms in your model vs number of unique reflections? > 3- if more than one copy per asymmetric unit, are you imposing NCS > restraints during refinement? > > -Eric > > > > On Wed, Apr 3, 2019 at 1:41 PM Sam Tang <samtys0...@gmail.com> wrote: > >> Hi everyone again >> >> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However >> after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The >> structure was solved by MR and current model seems to fit density well. In >> Refmac log I found that at the resolution corresponding to high R there may >> be a solvent/ice ring. Since imosflm should be able to exclude ice rings, I >> am not 100% sure whether it's the cause to high R. But if this is actually >> the case, is there a way I can exclude certain resolution bins during >> Refmac (and is it an appropriate way to do so?) >> >> PS - the data is not affected by twining or pseudosymmetry as checked by >> Xtriage. >> >> Many thanks! >> >> Sam >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> 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
