[phenixbb] Hi Res Model. Maybe its time to Include Hydrogens?

Dear users, I am refining a 400 aa protein with data out to 1.16 A (real data). I am almost finished with refinement. I have good geometry, complete model and ligands Rw 0.11 Rf 0.13. Difference maps seem to be asking for more. See attached screen shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma. How should I handle this? I have used hydrogens all along (riding). Thanks for your time -- Yuri Pompeu