Finite element (FE) method has been successfully applied to analysis of equilibrium protein dynamics because of its high accuracy and computational efficiency compared with the methods based on the full atomistic force field. However, even using the FE method, analysis of macromolecular protein assemblies is still challenging due to its huge number of DOFs. In order to handle this problem, we here apply the enhanced Craig-Bampton (CB) method that was a recently developed, robust FE model reduction technique. To illustrate, its performance is investigated by analyzing the molecular structure of the Middle East Respiratory Syndrome coronavirus (MERS-CoV) 3C-like protease.