Pci-e 16x has a bandwidth of 8GB/s and therefore your 4x slot has 2GB/s.
That's the same as good old AGP 3 which also sports 2GB/s bandwidth.
Your X1650 will come nowhere near needing the 2GB/s data transfer rate of Pci-e 4x.........so it isn't going to be slowed down by the restriction of operating at 4x rather than 16x.
What's the rest of your pc specification?
...cpu/memory/monitor etc....and what settings are you running the game at?