Time domain finite element (FE) analysis is a powerful tool for the study of Soil-Structure-Interaction (SSI) phenomena, but it requires a rigorous calibration of all aspects of the numerical model. This study presents three-dimensional (3D) FE analyses that are calibrated and validated against real scale free and forced vibration experiments on the prototype structure of EUROPROTEAS which is founded on soft alluvial sediments. The proposed calibration procedure exploits data recorded during experiments on structures with different structural stiffness, that mobilised SSI effects at different intensities. Particular focus is placed on the modelling of the soil-foundation interface, where zero thickness elastoplastic interface elements are used to allow foundation separation from the soil. A novel approach to simulate contact imperfections (gaps) between the foundation and the adjacent soil is proposed. The results demonstrate the significant impact of the interface gaps and soil nonlinearity on the response of the examined SSI systems, highlighting the importance of a rigorous model calibration.