Yes, as Dale says when the FreeR goes up after minor rebuilding you have usually somehow picked up a different FreeR set.. This is almost certainly what causes this to happen - you say
*This results in R free slightly lower than R work.* Small changes in a well refined structure dont change r factors very much! Eleanor On Mon, 2 Nov 2020 at 10:57, Dale Tronrud <de...@daletronrud.com> wrote: > 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/ > ######################################################################## 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/
