Real-space refinement in PHENIX for cryo-EM and crystallography.
Real-space refinement in PHENIX for cryo-EM and crystallography.
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DOI：
10.1107/s2059798318006551
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发表时间：
2018-06-01
期刊：
影响因子：
--
通讯作者：
Adams PD
中科院分区：
文献类型：
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作者：
Afonine PV;Poon BK;Read RJ;Sobolev OV;Terwilliger TC;Urzhumtsev A;Adams PD
本文介绍了PHENIX套件中的phenix.真实的_space_refined程序中实空间精化的实现及其在冷冻EM模型再精化中的应用。本文描述了PHENIX套件中phenix.真实的_space_refine程序中实空间精化的实现。使用简化的细化目标函数可以实现非常快速的计算，这反过来又使得有可能以很小的运行时成本来识别最佳数据约束权重作为例程细化的一部分。针对低分辨率数据的原子模型的细化受益于尽可能多的附加信息。除了共价几何的标准限制外，phenix.真实的_space_refine还利用了额外的信息，如二级结构和旋转异构体特定的限制，以及内部分子对称性的限制或约束。蛋白质数据库中385个cryo-EM衍生模型的重新改进，分辨率为6 μ m或更高，显示出模型的显著改进以及这些模型与靶图谱的拟合。
A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models. 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.