CheckCIF-DIFMX01

PROC-NAME: DIFMX01 Type_2

PURPOSE: To check that _refine_diff_density_max is within expected limits.

PROCEDURE:

DMAX = _refine_diff_density_max

DTEST = 0.1 * ZMAX

TEST

IF DMAX > DTEST*2 issue ALERT A

         "Alert A The maximum difference density is > 0.1*ZMAX*2.00"

> DTEST issue ALERT B

         "Alert B The maximum difference density is > 0.1*ZMAX*1.00"

> DTEST*.75 issue ALERT C

         "Alert C The maximum difference density is > 0.1*ZMAX*0.75"

        The maximum residual electron density is larger than normally expected, even after making an allowance for the heaviest element in the structure. This is often an indication that (a) the absorption corrections are inadequate; (b) the overall quality of the data may be poor, leading to spurious peaks and holes of residual electron density; (c) there is twinning which has not been allowed for where overlap from the second twin domain (which may have been ignored in the data collection) causes errors in the intensities of some reflections; (d) the model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms.

        If you believe you have eliminated all potential causes of this alert, but the maximum residual electron density still remains larger than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum.

IF DMAX < 0.0 issue ALERT A

         "Alert A The maximum difference density is < 0.0"

        The maximum residual electron density should have a positive value. Have you reversed the minimum and maximum entries?

(http://journals.iucr.org/services/cif/checking/DIFMX_01.html)

目的：检查_refine_diff_density_max是否在预期范围内。

过程：

DMAX = _refine_diff_density_max

DTEST = 0.1 * ZMAX

检查

若DMAX大于DTEST*2，则发布A级警告

         "Alert A The maximum difference density is > 0.1*ZMAX*2.00"

若DMAX大于DTEST，则发布B级警告

         "Alert B The maximum difference density is > 0.1*ZMAX*1.00"

若DMAX大于DTEST*.75，则发布C级警告

         "Alert C The maximum difference density is > 0.1*ZMAX*0.75"

        即使考虑到结构中最重的元素，最小残余电子密度峰也比正常预期值更负。这通常表明：(a)吸收校正不充分；(b)数据的整体质量可能较差，导致出现虚假的残余电子密度峰(鬼峰)和残余电子密度空穴；(c)由于第二孪晶组分(在数据收集中可能已被忽略)的重叠引起某些衍射点的强度出现错误而导致不被允许的孪晶；(d)由于元素指认错误、原子缺失或未建模或无序处理不充分或溶剂原子导致的模型不正确或不完整。

        若你认为你已经消除了导致此警告的所有潜在原因，但最小残余电子密度峰仍然比预期值更负，则必须给出最接近此最小残余电子密度峰的原子的名称及它们之间的距离。

若DMAX小于0.0，则发布A级警告

         "Alert A The maximum difference density is < 0.0"

        最小残余电子密度应为负值。检查是否忘记负号或将最小和最大值填反了。

例：DIFMX01_ALERT_2_B The maximum difference density is > 0.1*ZMAX*1.00

_refine_diff_density_max given = 0.982

Test value = 0.700

警告原因：最小残余电子密度值超出预期范围。

解决策略：可能的解决办法：吸收矫正；数据不好，重新收集数据；模型错误，包括归属错误、原子丢失、无序或溶剂处理有误。若无法更正，则指定最接近此最小残余电子密度峰的原子名称及它们之间的距离。

关于该警告的一个具体解释例子参考下面链接中的公众号文章： https://mp.weixin.qq.com/s/irYbkyXuk1kRluJryBZYeg