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There are two timesteps in EnergyPlus, the Zone timestep (which is the user input) and a System timestep (which is not). See the description here that states:

There is also second type of timestep inside EnergyPlus that is known as the System Timestep. This is a variable-length timestep that governs the driving timestep for HVAC and Plant system modeling. The user cannot directly control the system timestep (except by use of the ConvergenceLimits object). When the HVAC portion of the simulation begins its solution for the current zone timestep, it uses the zone timestep as its maximum length but then can reduce the timestep, as necessary, to improve the solution. The technical details of the approach are explained in the Engineering Documentation under “Integrated Solution Manager”. Users can see the system timestep used if they select the “detailed” frequency option on an HVAC output variable (e.g. Zone Air Temperature). To contrast, the “Zone” variables will only be reported on the zone timestep (e.g. Zone Mean Air Temperature).

And there is engineering documentation for the Variable (System) Timestep here.