I am trying to use DEN refinement as implemented in the Phenix-1.9 release to refine a structure at 3.6 Angstrom resolution. The asu consists of 8 copies of hetero-dimers (of roughly 40 KDa sunbunits each). The structure of one of the subunits has already been solved at about 2 Angstrom, whereas for the other no homologous model is available. After automatic + manual building, I have now a model with Rfree = 28 / R = 23, with some protomers better built than others. I have used this pdb model as input for DEN refinement, adding the known higher-resolution structure as a (partial) reference model, and ncs restraints previously found (and run a DEN parameters optimisation). The final DEN Rfee got significantly worse.

I would appreciate any advise for a better DEN strategy to be adopted in this case, if possible. In particular I was wondering whether it can be worth building a model for the missing subunit (or part of it) based on structural similarity of the current unrefined 3D structure.

I thank you in advance for the suggestions.

With kind regards,

Marina