[phenixbb] Refinement Strategy vs. R gap

Yuri yuri.pompeu at ufl.edu
Wed Mar 16 11:10:28 PDT 2011

Hello phenixers,
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 
should say.
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.
Thank you
Yuri Pompeu

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