A building control system uses an empirical technique to determine the uncertainty in parameters of an energy use model. The energy use model is used to predict energy consumption of a building site as a function of the model parameters and one or more predictor variables. The empirical technique includes obtaining a set of data points, each of the data points including a value for the one or more predictor variables and an associated energy consumption value for the building site. Multiple samples are generated from the set of data points, each of the multiple samples including a plurality of data points selected from the set of data points. For each of the multiple samples, the model parameters are estimated using the plurality of data points included in the sample. The uncertainty in the model parameters is determined using the multiple estimates of the model parameters.