TABLE 1.
CMM validation parameters
| Parameters | Acceptable | Borderline | Dubious | ||
|---|---|---|---|---|---|
| Low | High | Low | High | ||
| Occupancy | [0.9, 1.0] | (0.1, 0.9) | [0.0, 0.1] | ||
| B‐factor ratio | [0.86,1.0] | [0.54, 0.86) | [0.0, 0.54) | ||
| Atomic contacts | Usual donor atoms# | Occasionally found donors# | Unusual# | ||
| Coordination geometry | Preferred coordination geometry# | Other coordination numbers# | Unusual# | ||
| Valence | |||||
| I | |||||
| Na, K, Cu | [0.7, 1.3] | [0.4, 0.7) | (1.3, 1.6] | [0, 0.4) | >1.6 |
| Mg, Ca | [1.7, 2.3] | [1.4, 1.7) | (2.3, 2.6] | [0, 1.4) | >2.6 |
| II | |||||
| Mn, Fe*, Co | [1.6, 2.4] | [1.2, 1.6) | (2.4, 2.8] | [0, 1.2) | >2.8 |
| Ni, Cu*, Zn | [1.7, 2.3] | [1.3, 1.7) | (2.3, 2.7] | [0, 1.3) | >2.7 |
| III | |||||
| Fe, Co*, Ni* | [2.7, 3.3] | [2.5, 2.7) | (3.3, 3.5] | [0, 2.5) | >3.5 |
| nVECSUM | [0, 0.10] | (0.10, 0.23] | (0.23, 1.0] | ||
| gRMSD | [0, 13.5] | (13.5, 21.5] | (21.5, 180] | ||
| Vacancy | [0, 10%] | (10%, 25%] | (25%, 100%] | ||
Note: The thresholds for the occupancy parameter are updated in the present CMM version. The parameters included in scoring metal ions for the approximated ranking are in bold. For the parameters with different thresholds for low‐resolution structures, both sets of thresholds are shown in the low and high columns. An asterisk (*) after a metal in the valence cell indicates insufficient data to set the threshold values for that metal. A hash symbol (#) indicates that these threshold values were taken or derived from previous studies (Harding et al., 2010; Kuppuraj et al., 2009). The square and round brackets indicate a closed and open interval.