Detection of protein complexes and their structures is crucial for understanding their role in the basic biology of organisms. Computational docking methods can provide researchers with a good starting point for the analysis of protein complexes. However, these methods are often not accurate and their results need to be further refined to improve interface packing. In this paper, we introduce a refinement method that incorporates evolutionary information into a novel scoring function by employing Evolutionary Trace (ET)-based scores. Our method also takes Van der Waals interactions into account to avoid atomic clashes in refined structures. We tested our method on docked candidates of eight protein complexes and the results suggest that the proposed scoring function helps bias the search toward complexes with native interactions. We show a strong correlation between evolutionary-conserved residues and correct interface packing. Our refinement method is able to produce structures with better lRMSD (least RMSD) with respect to the known complexes and lower energies than initial docked structures. It also helps to filter out false-positive complexes generated by docking methods, by detecting little or no conserved residues on false interfaces. We believe this method is a step toward better ranking and prediction of protein complexes.