Hi Mohamed,
1. If I see a small drop in R/Rfree when I request solvent update (I over-rode the default cut-off of 2.8 A), should I keep those waters?
keep them if they makes chemical/physical sense and fit map, or delete otherwise.
2. Where can I find the values for favored phi/psi values for Ramachandran?
Hm.. I guess you get these values from Ramachandran plot, that's what it is for..
Using the FEM map, I can see some residues flagged as outliers but when they are fixed in Coot (real space refine tool) to a favored region, they actually come out of the density. This makes me suspect that those outliers are real. When I use Ramachandran restraints, obviously the outliers are 'fixed' but clashscore increases. In other cases, the tweak needed to fix them are quite small.
Well this is difficult to comment. You need to employ your scientific judgment to make sure the model of your crystal structure makes sense. Ideally, any outliers that cannot be justified by the experimental data should be fixed. Pavel