On Wed, Mar 16, 2011 at 11:10 AM, Yuri
I am refining a liganded structure at 2.1 and I am pretty far into my modeling. Rfree = .265 rwork= .20
Not great, but not awful.
II- When I choose no XYZ refinement with anisotropic ADP for protein chain only with weight optimization Rwork plummets to 0.15 and Rfree also drops to 0.25. But my gap is now .10 !!
You shouldn't be refining any individual ADPs as anisotropic at this resolution - except perhaps metal ions. Use TLS groups instead; this often has the effect of reducing the R-free/R-work gap. (Note that phenix.refine will still output ANISOU records for all atoms in TLS groups, but they won't be individually refined.)
I checked my log file and it looks like in default automatic individual ADP phenix.refine is picking all the residues to be anisotropic even though I would not try that at 2.1 A.
That seems unlikely - can you send the logfile to [email protected] (*not* the list)? -Nat