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Dear All,
I am refining a structure of protein/DNA complex at 2.6Å with a space group
of C2. This structure solution was given by Molecular Replacement in CNS.
After cycles of refinement and model building, the Rfree now is 29.6%.
Since part of the complex is dynamics, even at this Rfree, the part has very
choppy density. So I was trying to add water using water_pick.inp in CNS
hoping I can get Rfree down a little bit. However, when I searched peak at
4, 3, 2 sigma and minimize the PDB files, all the Rfree jumped up. The
bindividul refiment didnt help. I do go back to check the hydrogen boding
environment in Fo-Fc map, they are fine. But the densities are not
necessarily round. I was told by people around that adding water always
helps them, whether big or small. So does anybody here have the same
experience as I do? Any suggestion would be appreciated. Thanks.
Cortney
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