Real‐space refinement in PHENIX for cryo‐EM and crystallography

This article describes the implementation of real‐space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data‐restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low‐resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary‐structure and rotamer‐specific restraints, as well as restraints or constraints on internal molecular symmetry. The re‐refinement of 385 cryo‐EM‐derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. A description is provided of the implementation of real‐space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re‐refinement of cryo‐EM‐derived models.