Next, a more complicated scenario with the apo protein to demonstrate hierarchically related conformational heterogeneity, such as an alternative conformation within a loop. For example, in the 'loop out' conformation (state 1), there are multiple positions of a single leucine side chain (state 2) (Figure ). In the current mmCIF format, you could encode the three conformations as A (loop in), B (loop out, position 1), C (loop out, position 2), but this would have no descriptive or hierarchical relationship to each other. In our proposed mmCIF additions, we could encode the loop conformational heterogeneity in the conformational state 1 and the leucine conformational heterogeneity within the conformational state 2. We see this as another category of conformational heterogeneity state 2 within the atom_site loop and has the exact requirements as the other conformational heterogeneity layer. However, to have a conformational heterogeneity state 2 category, the atom must have a conformational heterogeneity state 1 category. For refinement, restraints would be linked to each level of conformation, such that all conformations in conformational heterogeneity state 1 (loop in and loop out) would have to equal 1, while the categories in conformational heterogeneity state 2 (conformations in loop out) would have to sum to occupancy of the conformational heterogeneity state 1 class it belongs in (loop in) (Figure ). Clashes could be evaluated in PDB deposition validation by all atoms with the same label at the same hierarchy level, extending the current validation scheme . A full example of PDB 6b90 represented in the historical PDB format, proposed mmCIF, and ensemble representation is available in the Supplementary Materials.