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As the original author of the Reference Buildings back in 2005-2007, I can say that the selection of HVAC types and zoning are based partly, maybe largely, on "engineering judgement", and partly on CBECS to confirm or substantiate the said "engineering judgement". Furthermore, there's a history behind the Reference Buildings dating back to work done for the Gas Research Institute in the early 90s, during which I went over with an engineer (the late Bruce Birdsall) the various building types and decided the most prevalent HVAC systems then being used. When DOE asked me to update the GRI work for the Reference Building, I analyzed the latest CBECS and apparently so did Dave Winiarski at PNNL and made changes where appropriate. I found some issues such as: (1) the prevalence of HVAC system or fuel mix may differ in different parts of the country, (2) for some building types and/or climates there were several (esp. two) HVAC systems or fuel mix of similar prevalence. Since I haven't been involved in this work since 2007, I don't know how these issues since have been resolved or treated. My main suggestion on interpreting the HVAC system configurations and zoning in these Reference Buildings is to regard them as the best shot effort by whoever was doing it to characterize with a single model a diverse building/HVAC population, and take it from there.