Hi Ravi,
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?
Compute 2mFo-DFc and mFo-DFc Average Kick maps and see if these peaks are still there. If they disappear - lucky you, if not, then will think more. If you do not know what an Average Kick map is, check slide #20 here: http://cci.lbl.gov/~afonine/rsr/afonine_05OCT2009_.pdf
2. During addition of atoms like Na+, Cl- in map, do one need to careful about of the its coordination valency in surrounding pocket. ?
Not 100% sure, but at 3A resolution yes... Hope some one else comments on this. Pavel.