[phenixbb] hydrogens in low resolution structure refinement

Dear all! I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be? Thanks in advance! Stefanie