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Thank you Dr. Murshudov for the information. But please I still need help. In restrained refinement, I could not find where to enter the residues I want to restrict from moving much. I was only able to find that in rigid body refinement, so I tried it and got a higher R factor than the initial file (before refinement). Is it normal to get a higher R factor when doing rigid body refinement? if not, any suggestion regarding what could be wrong? Is there a way to restrict one chain or part of a chain from moving much while doing restrained refinement? Thank you for any input, Remie On Aug 13, 2014, at 10:48 AM, Garib Murshudov <[log in to unmask]> wrote: > Hi Remie, > > You can add harmonic restraints for parts you do not want to move too much. Instructions could be found here: > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Harmonic > > > Regards > Garib > > > On 13 Aug 2014, at 15:44, Remie Fawaz-Touma <[log in to unmask]> wrote: > >> Hi everyone, >> >> Does anyone know of a way to refine with CCP4 - Refmac5 (restrained refinement is what I do) fixing a part of the the ligand? >> >> Thank you very much for your input, >> >> Remie > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > >