On Stratix® IV GX devices, VCCA_L/R must be 3.0V when using the ATX PLL. The 2.5V option for VCCA_L/R is not available when using the ATX PLL.
Trying to use 2.5V for VCCA_L/R will result in the following error.
Error: GXB Central Control Unit (CCU) "<path>|atx_pll_cent_unit" cannot be placed to location "<location>" because its side analog VCCEH setting 3.0V conflicts with the side wise power constraint "2.5V" applied to the following atoms
Info: Atom "<path>|cent_unit0" of type "GXB Central control unit" is at location <location>