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
If your B-values still come out lowish,
try growing crystals that do not
diffract very well, that usually does the
trick.
HTH
Peter
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