ABSTRACT Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount of instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.

中文翻译：

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细化大分子模型——与X射线衍射实验数据达到最佳一致性

摘要 大分子 X 射线晶体结构的细化涉及使用具有数百种不同设置的复杂软件。基础概念的复杂性和大量的指令可能使经验不足的晶体学家难以在他们的改进中获得最佳结果。本教程回顾提供了为大分子模型的倒易空间细化选择最佳设置的指南，并提供了手动模型校正的实用技巧。为了帮助有抱负的晶体学家驾驭这个过程，本文描述了蛋白质结构精修的一些最实用的重要概念。涵盖的主题包括无 R 的使用和目的、几何约束、对原子位移参数 (ADP) 的约束、细化权重、ADP 的各种参数化（完全各向异性细化和 TLS），并省略了映射。我们还为 Coot 中的手动模型校正、密度差或缺失的侧链建模以及配体识别、拟合和改进提供了实用技巧。