This command checks the alignment of the template structures (all but the last entry in the alignment): For each pairwise superposition of the templates, it reports those equivalent pairs of Cα atoms that are more than eqvdst Å away from each other. Such pairs are almost certainly misaligned. The pairwise superpositions are done using the Cα atoms and the given alignment. The number of such pairs is returned.
Note that the target structures are actually changed by the superpositions carried out by this command. If you want to use these superpositions as a crude initial model for automodel model building (rather than setting automodel.initial_malign3d) please bear in mind that the later templates in your alignment are always fitted on the earlier templates. Thus, a more reliable initial model will be obtained if you list the higher coverage templates earlier in the knowns variable in your automodel script (e.g., always list multimeric templates before monomers).
If you want to use the original non-superposed structures, either avoid calling this command, or delete and recreate the alignment object afterwards to force it to reread the structure files.