This article presents the development and calibration of a numerical model simulating the response of a novel rockfall protection structure subjected to localised dynamic loading. This structure is made of piled-up concrete blocks interconnected via metallic components whose dynamics response under projectile impact is examined via real-scale experiments. The corresponding numerical model is developed in a python based open source software SICONOS which implements the Non-Smooth Contact Dynamics (NSCD) method. The geometrical features and mechanical properties are incorporated in the model via specific developments pertinent to the modelling 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 the meta-model is highlighted. In the end, the NSCD model is successfully calibrated against the spatial-temporal response of the experimental structure with more than 90% accuracy for impact energies up to 1 MJ.