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

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Afonine, Pavel V., Poon, Billy K., Read, Randy J., Sobolev, Oleg V., Terwilliger, Thomas C., Urzhumtsev, Alexandre, Adams, Paul D.·2018·Acta Crystallographica Section D Structural Biology
DOI 10.1107/s2059798318006551

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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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Metadata

Authors
Afonine, P. V., Poon, B. K., Read, R. J., Sobolev, O. V., Terwilliger, T. C., Urzhumtsev, A., & Adams, P. D.
Venue
Acta Crystallographica Section D Structural Biology
Publisher
International Union of Crystallography (IUCr)
Published
2018-05-30
Volume
74
Issue
6
Pages
531-544
ISSN
2059-7983 (ISSN-L)
DOI
10.1107/s2059798318006551
OpenAlex
W2786390877
Cited by
3,281
References
5
FWCI
68.86
Type
journal article
Language
en
Open access
hybrid
Licence
Funders
  • National Institutes of Health (GM063210)
  • PHENIX Industrial Consortium
  • U.S. Department of Energy (DE-AC02-05CH11231)
  • French Infrastructure for Integrated Structural Biology (ANR-10-INBS-05)
  • Wellcome Trust (082961/ Z/07/Z)

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CoChat. (2026). Citation check: Real-space refinement in PHENIX for cryo-EM and crystallography. https://app.cochat.ai/papers/10.1107/s2059798318006551
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Afonine, P. V., Poon, B. K., Read, R. J., Sobolev, O. V., Terwilliger, T. C., Urzhumtsev, A., & Adams, P. D. (2018). Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallographica Section D Structural Biology. https://doi.org/10.1107/s2059798318006551

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