Well - there are several possible reasons for that . The least pleasing is that you have built the ligand in the wrong place, but leaving that aside.
When you add something to your model the coordinates are rather approximate and the B factors are usually set to some quite arbitrary value, so it takes several cycles of refinement for these to be corrected. Then you have probably only added a small percentage of the model, so the R factors will not change very much.. The best check is to re-inspect the map after refinement and see if the ligand fits snugly into the density. Good luck Eleanor On Wed, 20 Jan 2021 at 18:10, Pavel Afonine <[email protected]> wrote: > Hi Wajahat, > > first off, there is a dedicated mailing list for Phenix specific questions > (http://phenix-online.org/). > > You need to run more than one refinement cycle before you try making sense > of R factors. > > Pavel > > On Wed, Jan 20, 2021 at 10:05 AM Wajahat ali khan <[email protected]> > wrote: > >> Dear all, >> >> >> I have just started with X-ray diffraction. >> I would appreciate any ideas as to why after one cycle of phenix.refine , >> the Rfree value increased for my ligand fitted model molecular replacement >> solution model. >> >> Thanks >> >> Wajahat >> >> ######################################################################## >> >> 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 > ######################################################################## 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/
