Rosetta has two common modes for representing a protein: centroid mode and fullatom mode. Centroid mode has a complete backbone but replaces the sidechain with a single large “centroid” atom of variable radius; fullatom mode includes all atoms.
The CEN atoms are the sidechain replacements for centroid mode.
Centroid mode is used in the early stages of abinitio, docking, and some other protocols. Some of these protocols require an out::file::fullatom flag so that they will run the fullatom stage and report all sidechains rather than centroids.
Most protocols expect to take a fullatom PDB, although they should be able to take a centroid PDB and replace it with fullatom as necessary.