[phenixbb] close contact and torsion angle

Hi, There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what? I added hydrogen for refinement since the resolution is 1.47 A. Should I remove all these added hydrogens and refine again? Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause? And should I re-refine to correct them? Or just go ahead to deposit it? Thanks! chuan