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

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30.


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.

Keywords: PHENIX; atomic-centered targets; cryo-EM; crystallography; map interpolation; real-space refinement.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Computer Simulation
  • Cryoelectron Microscopy / methods*
  • Crystallography / methods
  • Databases, Protein / standards
  • Humans
  • Macromolecular Substances / chemistry
  • Models, Molecular
  • Software*
  • TRPV Cation Channels / chemistry
  • Validation Studies as Topic


  • Macromolecular Substances
  • TRPV Cation Channels