Hi Joe, at 1.45A resolution it is most likely the best to refine individual anisotropic ADPs using phenix.refine (anisotropic for macro-molecule and isotropic for the solvent). In that case the "local sphere restraints" are not used ("local sphere restraints" are used in individual isotropic ADP refinement only). All the relevant details are here: see "On atomic displacement parameters (ADP) and their parametrization in PHENIX" article: http://www.phenix-online.org/newsletter/ I'm almost sure that refining isotropic ADPs instead of anisotropic causes these residual densities around atoms. It's known effect and I recall seeing it in at least two papers. Another things to check: - is it Met, or Se-Met? - radiation damage? Try refining occupancies of S. Although you said it's not only S, so may be not. Good luck! Pavel.
I am refining a very well ordered structure at 1.45 A and find that after doing just about everything including optimization of weights, etc that there are still areas of positive density residing over S atoms of Met, backbone atoms, etc. I have added hydrogens and used them during refinement as well. The maps are of a high quality and Free R factors are quite good, ~ 17%. Is there anything that can be played with more such as values used in the ADP restraints window to try and achieve a difference map with far fewer areas of significant positive density (all greater then or equal to 4 sigma)?
I am not sure exactly what effect the values of distance power, average power, etc will have on refinement. The other option I was thinking of was the scattering table options. I have other structures of this protein that extend to about 1.2.