50,000 times 60 aa is pretty likely to swamp your memory. This is probably expected but not desired behavior – not a memory leak but not a good use of memory. If the old ++ version can handle that many poses then it’s probably optimized better.
I’m not aware of any reason why ++ clustering should fail against 3.0 structures. A PDB is a PDB is a PDB, so the old code should be able to read them in.