REFMAC5 for the refinement of macromolecular crystal structures.
REFMAC5 for the refinement of macromolecular crystal structures.
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DOI：
10.1107/s0907444911001314
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发表时间：
2011-04
期刊：
影响因子：
--
通讯作者：
Vagin AA
中科院分区：
文献类型：
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作者：
Murshudov GN;Skubák P;Lebedev AA;Pannu NS;Steiner RA;Nicholls RA;Winn MD;Long F;Vagin AA
介绍了大分子晶体结构精化程序REFMAC 5的基本原理。本文介绍了大分子晶体学精修程序REFMAC 5的各个组成部分，该程序是作为CCP 4套件的一部分分发的。REFMAC 5利用不同的似然函数，这取决于所采用的衍射数据（振幅或强度），孪生的存在和SAD/SIRAS实验衍射数据的可用性。为了确保精细模型的化学和结构完整性，REFMAC 5提供了几类约束和模型参数化的选择。可靠的模型，在分辨率至少低至4 μ m，可以实现由于低分辨率的细化工具，如二级结构的约束，约束已知的同源结构，自动的全球和本地NCS的约束，“身体”的约束和使用新的远程约束原子位移参数（ADP）的基础上的Kullback-Leibler分歧。 REFMAC 5还提供TLS参数化，并且当高分辨率数据可用时，可快速细化各向异性ADP。在双晶存在的情况下，以全自动的方式进行细化。REFMAC 5是一款灵活且高度优化的细化包，非常适合大分子晶体学中遇到的整个分辨率光谱的细化。
The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.