If you are using TLS refinement the please check TLS definitions.It may be that atoms for which you have positive density are not in TLS definitions. Try to use without TLS.
regards Garib On 26 May 2011, at 11:11, Petr Kolenko wrote: > Dear colleagues, > > I have two problems in two structure refinements using REFMAC5. > > 1) 1.8A resolution, zinc in the active site. Refinement using work > reflections - ADP for Zinc was about 14. Final refinement including > all reflections increase ADP to 20 or even higher values - followed by > very high positive difference density in position of the zinc. I have > tried also PHENIX, the same thing. I changed ADP manually to 14 and > only calculated maps (no refinement) look good. May I deposit the > structure using "manually" fixed ADP according to the best agreement > to the observed and difference electron density? By the way, it is > clear that this is zinc. > > 2) 1.9A resolution, about 600AA, all of them OK in electron density. > But, somehow, about ten atoms give very strong positive electron > density suggesting they are not taken into account in refinement. On > the other hand, ADPs are reasonable and seem to be refined. All of > these atoms are fully occupied. I tried to omit whole residues and > build them again, but the maxima appeared again. Using of PHENIX > resulted in no difference electron density for these atoms. I have > also tried to take PHENIX output to REFMAC, but the maxima are there > again. It is always one or two atoms from the same residues - > sometimes Calpha, sometimes Cbeta, sometimes C, sometimes NH1, but > still on the same five residues. Does anyone have any idea how to > solve this problem? > > Many thanks for any response. > > Petr > > > -- > Petr Kolenko > petr.kole...@biochemtech.uni-halle.de > http://kolda.webz.cz
