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
