Statistical quality indicators for electron-density maps
Statistical quality indicators for electron-density maps
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DOI：
10.1107/s0907444911035918
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发表时间：
2012-04-01
期刊：
影响因子：
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通讯作者：
Tickle, Ian J.
中科院分区：
文献类型：
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作者：
Tickle, Ian J.
回顾了结构模型与观测到的电子密度的局部一致性的常用验证指标，即实空间 R (RSR) 和实空间相关系数 (RSCC)。有人认为，所有验证技术的主要目标是验证模型的准确性，因为精度是晶体和数据的固有属性。事实证明，上述两个指标的主要弱点是它们无法区分模型的准确性和精度。此外，这些指标在通常的实施中都没有表明结果的统计显着性。回顾了电子密度图的统计特性，并提出了一种改进的基于可能性的替代度量。这自然会导致使用真实空间差异密度 Z 得分 (RSZD) 对差异密度进行 chi(2) 显着性检验。这是纯粹的局部模型精度的度量，这是晶体学家在向 PDB 提交结构模型之前进行有效模型验证和结构优化所需的。还提出了一种新的实空间观测密度Z分数（RSZO）；这是纯粹的模型精度指标，作为其他精度指标（例如 B 因子）的替代品。
The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a chi(2) significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.