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. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data-restraints weight 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. Re-refinement of 385 cryo-EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps. Synopsis A description of the implementation of real-space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re-refinement of cryo-EM derived models