Hi everyone,

I would like to have commnets from experts on the following issues.

I am refining DNA-protein complex at 3 A resolution and my current Rfree is 21.5 % (phenix.refine).

1. 

I am getting difference map peaks (in Coot) of magnitude less than -5 sigmas (0.24 e/A3) (~10 or more peaks) and equal number of positive peaks of same magnitudes.

The positive peaks hardly have 2fo-fc of more than 1.0 sigma level. I presumed this well could be due to bulk solvent or improper mask. Therefore I optimized the mask parameters (by giving option under "General refinement parameters" in phenix.refine GUI). I could get my R free lower as expected but I still got these peaks back. Although I am not absolutely sure, but positive peaks are more in  polar pocket of protein and negative peaks are more in non-polar and aromatic pockets. I have PEG, Na acetate in my crystal soup. What these negative peaks represent for?

2. 

During addition of atoms like Na+, Cl- in map, do one need to careful about of the its coordination valency in surrounding pocket. ?

I will be highly thankful to you for the same.

Ravi