Repository logo

Real-space refinement in PHENIX for cryo-EM and crystallography.

Accepted version

Change log


Sobolev, Oleg V 
Terwilliger, Thomas C 


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.



PHENIX, atomic-centered targets, cryo-EM, crystallography, map interpolation, real-space refinement, Animals, Computer Simulation, Cryoelectron Microscopy, Crystallography, Databases, Protein, Humans, Macromolecular Substances, Models, Molecular, Software, TRPV Cation Channels, Validation Studies as Topic

Journal Title

Acta Crystallogr D Struct Biol

Conference Name

Journal ISSN


Volume Title



International Union of Crystallography (IUCr)
Wellcome Trust (082961/Z/07/A)
National Institutes of Health (NIH) (via University of California) (6801943)
Wellcome Trust (082961/Z/07/Z)
National Institute of General Medical Sciences (P01GM063210)
Wellcome Trust (209407/Z/17/Z)
Is derived from: