In cases like 1m4x the assembly operators are given as cartesian products where 2 (or more) operators have to be applied in turn. E.g. is 1m4x:

loop_
_pdbx_struct_assembly_gen.assembly_id 
_pdbx_struct_assembly_gen.oper_expression 
_pdbx_struct_assembly_gen.asym_id_list 
1 '(1-60)(61-88)'           A,B,C 
2 '(61-88)'                 A,B,C 
3 '(1-5)(61-88)'            A,B,C 
4 '(1,2,6,10,23,24)(61-88)' A,B,C 
5 '(1-5)(63-68)'            A,B,C 
6 '(1,10,23)(61,62,69-88)'  A,B,C 
7 '(P)(61-88)'              A,B,C 

BioJava deals correctly with this but assigning sequential operator ids instead of the original ones in _pdbx_struct_oper_list.id. It'd be better to use the original operators so that the resulting identifiers can be recognised by other tools (e.g. when outputting assemblies to mmcif files).