[phenixbb] Refinement Strategy vs. R gap
yuri.pompeu at ufl.edu
Wed Mar 16 11:10:28 PDT 2011
I am refining a liganded structure at 2.1 and I am pretty far into my
modeling. Rfree = .265 rwork= .20
My asu has 399 residues one prosthetic group (3178 atoms) and 236 HOH.
I just want to do one last refinement round before submission and I am
not sure about the strategy I should select as I am running into the
I- If I refine individuals sites and real space (XYZ) and individual
ADP with aniso/iso selection automatic my Rfree goes up slightly and
Rwork drops to about .196. I also select optimize x-ray/ADp weight I
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 !!
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.
Could someone point me in the right direction, there is probably
something I am overlooking.
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