Hi, In upcoming version of PHENIX there will be more detailed manual for phenix.refine. Until recently phenix.refine was not using H atoms by default. We changed this behavior very recently. In newer version, if you have an input PDB file with H atoms (generated for example, with phenix.reduce), then phenix.refine will use these hydrogens by default. You don't need to do anything special for this.
I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac.
This is partially because Refmac uses "2nd derivatives' minimizer". Saying differently, given a pretty refined model out of phenix.refine Refmac can possibly refine it some more to deeper minimum. The downside of this is sometime higher Rfree factors. However, if you have a pretty bad starting model, phenix.refine is more powerful than Refmac to bring this model to a reasonably refined state.
B-factors on the other hand seem to be less restrained in phenix.
Here is how B-factors are restrained in phenix.refine (if TLS is not used): http://www.ccp4.ac.uk/newsletters/newsletter42/content.html look for "* The Phenix refinement framework *" by Afonine P.V., Grosse-Kunstleve R.W, Adams P.D. It is pretty old text, but reflects some general things. Note that "k" and (Bi+Bj) in the ADP restraints target formula have now different empirically found values. And yes, playing with wxc_scale is definitely good thing to do if you're not happy with either Rfree-Rwork gap or stereochemistry. Analogously to wxc_scale in coordinates refinement, to play with B-factors restraints use wxu_scale.
If I take the phenix refined coordinates, keep the aniso records from TLS and run some refmac cycles, my structure is better than average with regards to the clash scores (69 %). I do not know how valid refinement strategy this is. (Rfree-R = 5.4 %)
Please look another post on phenixbb (Subject: "Re: [phenixbb] R-factor problem !!!") regarding how tricky and error prone could be to jump between different programs. Pavel.