On 11/2/2020 2:26 AM, Nika Žibrat wrote: > > Hello, > > > > I am trying to solve an X-ray structure of a protein of which the > structure is already known. My aim is to only seek for ligands (soaking) > and interpret any conformational changes. Since I am using a model with > 100% sequence identity from PDB I am not doing Autobuild after Molecular > phasing and continue directly with phenix.refine according to > reccomendations (10 rounds). In accordance with X-triage I am also using > NCS default settings in the refinement. > > > > This refinement produces solid R free and R work values around 0.29 and > 0.22. The problem becomes when I want to manually edit the structure, > correct the loops which are changed upon binding of the ligand, and > correct any outliers. This results in R free slightly lower than R work. > Upon refining, R work drops normally while R free rises significantly > (for 0.2 -0.3). I have been trying to crack this for a few days with no > success. > > > > I read that slightly lower R free can be normal in such cases but > nevertheless both R values should drop, and haven’t found anything about > the big rise of this value after refinement. It feels like I am missing > something, since this is my first time solving a structure. Any advice?
This is not normal behavior at all. Rwrk and Rfree will be roughly equal only before you perform any refinement. The R's you report before your model building sound quite reasonable. When you manually change the model you will likely cause both to increase, but you would have to perform massive changes to get them to equalize at some larger value. The only thing I can think of that would cause this is for your second refinement to be working with a newly created test set. It is possible that somehow you have reset your R free flags? In an MTZ the full data set is divided into twenty subsets -- one is the test set while the other nineteen are the working set. When you ran Refmac the second time could you have told it to use a different segment as the test set? Dale Tronrud > > > > Thank you, > > Nika > > > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
