1) You say 3000 reflections - 400 parameters, but you arent including
the restraints as "observations" - refinement and rebuilding IS possible
at 3.2A..
2) B factors not unreasonable for the data.. You may want to use fixed
Bs with TLS or restrain Bs strictly..
3) How can your FreeR and r factor be so close - that MUST be wrong..
4) You can tighten the geometry with coot or with stricter restraints.
Maybe set the occs of the bad residues to 0.00 and see what they look
like after refining the other better determined parts? They could then
perhaps be rebuilt with more acceptable geometry.
Eleanor
If you are sure of On 01/06/2012 08:14 AM, 商元 wrote:
Dear All,
I have a set of 3.2A data containing only 3000 reflections. From the SAD
phasing and iterative modeling and density modification, I get a
preliminary structure with bad geometric conformations(~8/160 ramachandran
outliers in Coot). After Phenix MLHL refinement, the geometry is still bad
with (10% ramachandran outliers and 25% Rotamer outliers), and the
B-factors are all too high(all between 80 to 170, average ~120), and
R-factor/R-free have a value of 0.328/0.326.
The poor geometry of my model and the unusual B-factors indicates there
are still a lot improvement in my model. The question is, as I only have
~3000 reflections, and the atoms in the sequence is around 1000, and each
atom there are 4 parameters to be refined(X,Y,Z,B-factor,
assuming occupancy is 1), so how to refine my model to avoid
over-refinement? Should I trust the electron-density map of the refined mtz
data, or should I adjust the local geometries using Coot rotamers tools?
How to set a reasonable B-factor values in the refinement?
Best Regards,
Yuan
