Re: [phenixbb] geometry weight and rmsd bonds - angles

0.022A rmsd on bonds seems to be a reasonable value at 1.3A. On a different but related note, is there some way to print out the list of bond length deviations from ideal values for all the restrained bonds in the structure? If yes, could you do me a favor and forward me such list for you model? Off-list of course, but I promise to post the findings (assuming that they are interesting). Ed. On Thu, 2010-08-12 at 17:11 +0200, 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 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

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