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

“Real-space refinement in PHENIX for cryo-EM and crystallography” (2018), by Pavel V. Afonine et al. Materials Science research paper. Original abstract below, unchanged. A free PDF is available.

- Authors: Pavel V. Afonine, Billy K. Poon, Randy J. Read, Oleg V. Sobolev, Thomas C. Terwilliger, Alexandre Urzhumtsev, Paul D. Adams
- Published: May 30, 2018
- Field: Materials Science
- DOI: https://doi.org/10.1107/s2059798318006551
- Free PDF: https://www.biorxiv.org/content/biorxiv/early/2018/01/17/249607.full.pdf

## Abstract

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.

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