A system for generating and using a predictive model to control building equipment includes building equipment operable to affect one or more variables in a building and an operating data aggregator that collects a set of operating data for the building equipment. The system includes an autocorrelation corrector that removes an autocorrelated model error from the set of operating data by determining a residual error representing a difference between an actual output of the building equipment and an output predicted by the predictive model, using the residual error to calculate an autocorrelation for the model error, and transforming the set of operating data using the autocorrelation. The system includes a model generator module that generates a set of model coefficients for the predictive model using the transformed set of operating data and a controller that controls the building equipment by executing a model-based control strategy that uses the predictive model.