[phenixbb] Low resolution refinement - rotamers and Ramachandran

[mohamed noor]

Dear developers

I am refining a low resolution structure (3.8 A). After I fix most of the
outliers (red bars) in Coot, phenix.refine is causing my structure to be
worse than the start with 13 % Ramachandran outlier and 13 % rotamer
outlier.

Secondly, when I used phase_and_build to build my model, my R/Rfree is
around 30/35 with atoms from some residues missing. When I fill them in
with Coot, fix the outliers above and re-refine, R/Rfree jumps to 36/42 and
the rmsd angles are too high (2.9).

I have already used weight optimization and NCS. Am I doing something wrong?

Thanks.
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