Abstract-The inter-temporal consumption flexibility of commercial buildings can be harnessed to improve the energy efficiency of buildings, or to provide ancillary service to the power grid. To do so, a predictive model of the building's thermal dynamics is required. In this paper, we identify a physics-based model of a multi-purpose commercial building including its heating, ventilation and air conditioning system during regular operation. We present our empirical results and show that large uncertainties in internal heat gains, due to occupancy and equipment, present several challenges in utilizing the building model for long-term prediction. In addition, we show that by learning these uncertain loads online and dynamically updating the building model, prediction accuracy is improved significantly.