From Eterna Wiki
A misfold occurs when one part of the RNA structure does not fold in the right place. In EteRNA, this is denoted by a red highlighting in the target structure (see picture below). It is often helpful to check if you have a misfold by toggling between natural view and target view. Misfolds are usually what stop players from solving puzzles. If fixing all misfolds does not solve the puzzle, try adjusting the constraints.
<img title="aa" src="/wiki/images/1397795033.png" border="0" alt="aa" />