You can assign transceivers' REFCLK pin as an input clock to a general purpose PLL in Stratix® II GX and Stratix IV GX/GT devices, only if you have instantiated at least one transceiver channel within the block associated with that REFCLK pin. You can instantiate a dummy transceiver channel to use this REFCLK pin and keep the dummy transceiver channel in reset state during normal operation.
This information also applies to other GX/GT/GZ device families with dedicated high speed transceivers/REFCLK pins.