This puzzle will have two filters enabled, the Residue IE and the Layer Score filter. If you look under your score, there will be a message similar to "No bonuses, 1 penalty acquired, all conditions met". If you click on the > arrow you will get more information about these filters.
The Layer Score filter is a new filter designed to ensure proteins fold up into desirable 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'.
In this puzzle, the filter requires 30% of your protein residues to be in the 'core'. If you do not meet this criteria, you will lose points. If you are losing points, you can click the 'Show' button in the filters dropdown below the score and it will highlight all of the residues that are on the surface and how many you still need to move into the 'core'.
You will need the updated client (released 01/16) to play this puzzle.
There is a bug where using 'Show expected residue burial' will cause instability with this puzzle.