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Cyclone IV PLL power supply has VCCA (PLL analog power supply) and VCCD_PLL (PLL digital power supply), but GND has only GND [GNDA] of VCCA. Do you have a GND pin for VCCD_PLL?

Clock/PLL

VCCD_PLL is the digital power supply for the PLL and does not have a pin like GNDA. Shared with GND pin.

GNDA becomes a dedicated GND pin for VCCA only.

VCCA should be separated from other power supplies to improve jitter performance.
For details, please refer to the Device Pin Connection Guidelines and the pinout file at the URL link below.

Device Pin Connection Guidelines
  https://www.altera.com/en_US/pdfs/literature/dp/cyclone-iv/pcg-01008.pdf

pinout file
  https://www.altera.com/support/literature/lit-dp.html#Cyclone-IV

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