The Layer Score filter ensures the proteins will fold up into desirable and realistic shapes. It will categorize each backbone residue as either 'core', 'surface', or 'boundary'. If you think of the protein as being suspended in a liquid, the 'surface' residues are those most exposed to the liquid. Subsequently, the 'core' residues are those that are most protected and the 'boundary' residues are the ones that lie between the 'core' and the 'surface'. Most residues are categorized as either 'core' or 'surface'.