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
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb