[phenixbb] phenix refinement question

Katarina Moravcevic katarinm at mail.med.upenn.edu
Mon Nov 15 13:09:35 PST 2010

Hi all,
I have only started using PHENIX and have made an interesting observation.
If I run my model through PHENIX refine (individual sites, individual ADPs,
occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP
weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry
values (data is to 1.7A). However, if I now take this refined model and run
it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21.
Can anyone explain why is there such a big difference? Will this be an issue
during PDB submission?
Any and all comments are appreciated.
Thank you all in advance
Katarina M.
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