To support the millions of fileformats out there, YASARA uses OpenBabel, a library available from http://openbabel.sourceforge.net . OpenBabel has mainly one weak spot, and that's residue names and numbers. Many of the supported file formats do not even know the concept of 'residues' because they come from quantum chemistry, where one usually works with just one molecule. So after loading a structure with OpenBabel, click on various residues and check that the names and numbers are correct. Otherwise try to export the structure in PDB format before loading it in YASARA.