This may be true for older software which restraints B-factors only to bonded atoms, but it is not the case in Phenix*, which takes into account all nearby atoms, not just bonded ones. The result is that individual B-factor refinement is very stable at low resolution - we don't know what the limit is, but it routinely works very well at 4A.
B-factor refinement being stable is one thing; quieting my paranoia regarding over-fitting at low resolutions is another.
Thanks for pointing this out to me - I'll have to check out the details of how phenix handles it, and give it a try.
Pete
