Hi Brennan,
using recent Phenix will fix the problem, let me know otherwise.
phenix.refine have caused B values to decrease each round of refinement to values of around 10 (I guess 20 is a more common value).
B~20A**2 is a more common value if data resolution is ~1.25...1.75A.
Otherwise a more common value can be very different from 20A**2. See
plot below.
Pavel