Hi Lionel,

something I forgot to mention/ask: if you are using a CIF file for your ligand that was created by ProDRG then I would strongly recommend using phenix.ready_set or eLBOW to get a new CIF file and use it from now on with phenix.refine. We had a lot of problems with nonsensical ProDRG created CIF files in the past and still runinng into them from time to time.

The command

phenix.ready_set model.pdb

will create a CIF file for use in refinement.

Pavel.

On 8/12/10 8:11 AM, Lionel Costenaro wrote:

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 <[email protected]>

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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