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bioRxiv · 10.1101/249607

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

Afonine, P. V.·Poon, B. K.·Read, R. J.·Sobolev, O. V.·Terwilliger, T. C.·Urzhumtsev, A.·Adams, P. D.
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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. 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 [A] or better shows significant improvement of models and the fit of these models to the target maps.\n\nSynopsisA 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.

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Afonine, P. V., Poon, B. K., Read, R. J., Sobolev, O. V., Terwilliger, T. C., Urzhumtsev, A., Adams, P. D.. 2018-01-17. Real-space refinement in Phenix for cryo-EM and crystallography. https://doi.org/10.1101/249607

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