When analyzing the resulting class reconstructions, it is extremely useful to also look at them in slices, not only as a thresholded map in for example UCSF Chimera. In the slices view you will get a much better impression of unresolved heterogeneity, which will show up as fuzzy or streaked regions in the slices. Slices also give a good impression of the atness of the solvent region.
When looking at your rendered maps in 3D, e.g. using UCSF Chimera, it is often a good idea to them all into the best one, as maps may rotate slightly during refinement.