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Thermostats do not affect the reports for conditioned area. Zones with any kind of zone equipment or air loops will be considered conditioned in OpenStudio and EnergyPlus. This includes equipment like unit heaters and exhaust fans. The floor area of these zones will be counted as conditioned in the OpenStudio report under Zone Overview and will also affect the Gross Window-Wall Ratio (Conditioned) in the Envelope tab, and the Energy Per Conditioned Building Area column of the Site and Source Energy Summary. You may be able to work around this by adding the exhaust fan as loads at the space level to account for their energy use and not using any thermal zone equipment or air loops for the garage zones.