Dear All,
I have a protein structure I am trying to refine using Refmac. There are
~158,000 atoms modeled (no waters) in the asymetric unit with ~495,000
reflections. There is data to 3.0A resolution with the 2 sigma cutoff at 3.5A.
I have four NCS copies in my asymetric unit and when I specify NCS restraints,
my Rfree gets slightly worst (from 28% to 31%). Varying the weighting term
has not made a difference and the Rfree is generally constant between
refinement cycles. My questions are:
1) For an all-atom refinement my observation to parameter is ~1.3. What is the
most suitable refinement method for this scenario? Is there a way to find out
roughly my observation:parameter ratio based on the type of refinement I
choose? How much are the restraints adding to my observations in the ratio?
2) It makes sense that NCS restraints should help the refinement, but it is not
as judged by the Rfree, or is the 28-31% difference acceptable at this
resolution?
3) I have the same sort of problem when including phases in the refinement.
Thank you,
Kianoush
*********************
Kianoush Sadre-Bazzaz
Graduate Student, Chris Hill Lab
University of Utah Biochemistry Department
15 N Medical Drive East RM 4100
Salt Lake City UT 84112-5650 USA
(801)585-7068
[EMAIL PROTECTED]
---------------------------------
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
