This article presents the development and calibration of a numerical model simulating the response of large structure to a localized dynamic loading. A novel rockfall protection structure composed of piled up concrete blocks interconnected via metallic components is studied, where the underlying intricacies are revealed by real-scale impact experiments. The numerical model is developed using the SICONOS software based on the Non-Smooth Contact Dynamics (NSCD) method to further investigate the efficiency and performance of this new structure type. All geometrical features and mechanical properties of the real structure components are incorporated via specific developments pertinent to the modeling requirements in SICONOS. Some parameters peculiar to the numerical model are calibrated against the spatial-temporal measurements from two full-scale impact experiments. The Bayesian interface statistical learning method aided by the polynomial chaos expansion based meta-model of the NSCD model is deployed for the calibration. The additional understanding of the model dynamics through the byproducts of meta-model are highlighted. In the end, the NSCD model is successfully calibrated against the spatial-temporal response of the experimental structure for impact energies up to 1 MJ.