[phenixbb] geometry weight and rmsd bonds - angles

Lionel Costenaro lcocri at ibmb.csic.es
Thu Aug 12 03:18:15 PDT 2010


I'm using phenix.refine for the first time and have some problem to get it
reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8).
I set the bonds rmsd_max and angles rmsd_max to these values and try
different values for:
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.
I refine the structure with refmac so far, but need to refine the
occupancies (so phenix).
Am I doing something wrong? Should I just use phenix to refine only the
occupancy (I am actually doing it)?
Any help or comment are welcome.

Some information:
space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate
ligand covalently link to the protein (correct dictionary and link
parameters for refmac or phenix -add link to cif),
resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not used,
R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac)

phenix version 1.6 289 (gui)

Best regards,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100812/698c753c/attachment-0003.htm>

More information about the phenixbb mailing list