producing at the rate of process time, not getting proper throughput

I am new to VC and i have built one small production line, but when i am giving process time to certain machines as 35 JPH, in return machine is producing less i.e. around 24-27 JPH, this is because of time loss in door opening door closing, the servo motors of the tools of machine coming down towards product and after operation again going up. I checked it for different machine, time for each machine is different for these operations, then how can i achieve my throughput in such case, my results from layout in VC are not matching with theoretical results at all. Can someone please tell me what approach we generally follow for such problems and to build such layout.