CheckCIF-DIFMN02

PROC-NAME: DIFMN02 Type_2

PURPOSE: To check that _refine_diff_density_min is within expected limits.

PROCEDURE:

DMIN = _refine_diff_density_min

DTEST = 0.1 * ZMAX

TEST

IF DMIN < -DTEST*2 issue ALERT A

         "Alert A The minimum difference density is < -0.1*ZMAX*2.00"

< -DTEST issue ALERT B

         "Alert B The minimum difference density is < -0.1*ZMAX*1.00"

< -DTEST*.75 issue ALERT C

         "Alert C The minimum difference density is < -0.1*ZMAX*0.75"

        The minimum residual electron density is more negative 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 minimum residual electron density still remains more negative than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum.

IF DMIN > 0.0 issue ALERT A

         "Alert A The minimum difference density is > 0.0"

        The minimum residual electron density should have a negative value. Have you forgotten the sign or reversed the minimum and maximum entries?

(http://journals.iucr.org/services/cif/checking/DIFMN_02.html)

目的：PURPOSE: 检查_refine_diff_density_min是否在预期范围内。

过程：

DMIN = _refine_diff_density_min

DTEST = 0.1 * ZMAX

检查

若DMIN小于-DTEST*2，则发布A级警告

         "Alert A The minimum difference density is < -0.1*ZMAX*2.00"

若DMIN小于-DTEST，则发布B级警告

         "Alert B The minimum difference density is < -0.1*ZMAX*1.00"

若DMIN小于-DTEST*.75，则发布C级警告

         "Alert C The minimum 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DMIN大于0.0则发布A级警告

         "Alert A The minimum 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：DIFMN02_ALERT_2_B The minimum difference density is < -0.1*ZMAX*1.00

_refine_diff_density_min given = -6.968

Test value = -5.300

警告原因：最小残余电子密度值超出预期范围。

解决策略：按上述蓝色中文内容检查数据和结构，进行相应改正即可。

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