Reproduce the problem with:
Structure pdb = StructureIO.getStructure("BIO:5TLS:1");

Fails with exception "Comparison method violates its general contract!". The problem is in the code below, which returns 0 ("equal") if transformation IDs are not equal, which leads in this particular case to
...
JA=HA
HA=GA
JA > GA
(and probably other contradictions, but here it breaks). Comparators in Java must establish total order.