Dear Nika, XDS probably did what you asked it to do ;-)
This is, however, not a problem. You only need to refine for a couple of rounds longer to gain independence of your Rfree set. No need to reassign them. Depending on the refinement program, it may take many rounds. With Refmac (or shelxl), it does not take very long. Wenn you plot the LLgain, listed at the end of the refmac log-file, and its curve flattens out, your Rfree reflections should be independent and not model-biased anymore. Best regards, Tim On Wed, 4 Nov 2020 13:18:06 +0000 Nika Žibrat <nika.zib...@ki.si> wrote: > Hello, > > Two days ago I was asking about R free rising. The problem was xds > adds R free flags already and then re-introduced them in Phenix, > causing R free to rise. I would like to thank you for your answers, > they were most helpful. > > Best, > Nika > > > From: Nika Žibrat > Sent: ponedeljek, 02. november 2020 11:26 > To: ccp4bb@jiscmail.ac.uk > Subject: R free rising > > > 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? > > > > 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 > > 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/ -- -- 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/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/
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