Hi Ralf,

Indeed some bond length or angle restraint outliers are from the ligand when refining with phenix.
However I don't think this is the problem, I give to refmac and phenix the same ligand dictionary (cif file from ProDRG with link definition added with JLigand). Refmac / phenix give me the following outliers >4 sigma : bond length 0 / 6, bond angle 0 / 23, dihedral 23 / 13, chiral 0 / 0, plan 3 /13. Clearly phenix is not doing a good job (R decrease, but not Rfree).
For refmac I'm using an x-ray weighting term (matrix) of 0.8, which is more or less expected for 1.3A resolution.
I don't really know how to fix the weights in phenix as I never used it before and did not find any hint in the manual or bb.

Lionel



2010/8/12 Ralf W. Grosse-Kunstleve <rwgk@cci.lbl.gov>
Hi Lionel,

> wxc_scale (from default 0.5 downto 0.015),  wxu_scale (from default 1 down
> to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu.
> Whatever the parameters, phenix never reached final rmsd better than 0.022
> and 2.2.

The first thing I'd check is the phenix.refine log with the list
of worst restraints. Look for "Sorted by residual". Without
having seen your structure, my first suspect would be problems
with the ligand restraints or the covalent link to the protein.

Ralf
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