Hi Gino, just a few comments:
I am aware of all approximation made in defining the Wilson B-factor and how one should not take the Wilson B-factor too literally (etc.. etc...). But, as a matter of fact, Phenix kept over-refining my B-factor to crazy values.
I would say refining and not over-refining, because nobody knows where "over" starts.
1. Was your diffraction anisotropic? If so, try the Diffraction Anisotropy Server. The server applies a negative isotropic B-factor correction to your data. In my case, corrected structure factor amplitudes resulted in a 2.5% drop in the Rfree
That server removes reflections by sigma value and in selected directions. In some cases it can easily be a few thousands of Fobs. So, it it not surprising that the R-factors dropped. You can't compare the R-factors for the datasets containing different amount of reflections.
and the average B-factor of my structure
and it is not surprising that the B-factor dropped: instead of keeping it in ATOM records you gave it away to uncle Sam, by applying negative-B correction. Just a trade, matter of where you keep these extra B-factor value.
SECOND How many macrocycles of refinement are you using? In my case Phenix kept bumping up the average B-factor of my structure by ~10A2 macrocycle. A 10 macrocycles refinement would bring the averaged B-factor to ~200A2. So don't over-refine. Stick to 2-3 cycles (provided your geometry is good, of course).
Interesting. I've never seen it before. Did you try to change the target weights for ADP refinement: manually or automatically? If you did and none helped (although I'm still not sure if help is needed) I would be interested to see the data and model.
THIRD Do you have NCS and are you using TLS? If so, try to first use NCS to refine atom positions, then do TLS refinement without imposing NCS. If you think about, it doesn't make too much sense to use ncs-restraints when splitting a structure in TLS groups.
Regarding NCS: in ADP refinement it is applied only to local ADPs, and not total ones. See recent publication regarding this in PHENIX newsletter: http://www.phenix-online.org/newsletter/CCN_2010_07.pdf see page 28. So you can safely refine everything in one go (I guess). All the best! Pavel.