4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong?
What is the resolution of your data? Backbone B-s usually are lower than the main chain. What is the Wilson B value reported by phenix.refine? You could re-refine and randomize all B-values and see what happens (I have to get back to you to to get the exact command for this). Maybe it is useful to obtain a copy of the latest verison of phenix.refine by downloading cci_apps from our server http://www.phenix-online.org. If your B-values still come out lowish, try growing crystals that do not diffract very well, that usually does the trick. HTH Peter