Hello, I am refining a structure at 2.1Å, using Refmac and manual constructions in coot. I have few Ca, Cl and Mg in my structure and some of them have a clearly anisotropic distribution, then I decided to use ANISOU line in pdb file only for these atoms. In refinement parameters of Refmac I set "mixed (isotropic/anisotropic) temperature factors". And I have a problem with some of them which are obviously badly refined (see attached picture).
What could be the reason of that? What should I badly set? Thank you for your help.