You may see the following Quartus® II Fitter error if you make a PLL_TYPE ATX assignment to the top level of a Stratix® V GX Low Latency PHY configured with an "FPGA fabric transceiver interface width" of 40 or 66, using Quartus® II Software Versions 11.0SP1 and earlier.
Internal Error: Sub-system: CUT, File: /quartus/db/cut/cut_stratixv_lc_pll_group.cpp, Line: 132
altera_xcvr_low_latency_phy
For the configuration above, the Low Latency PHY will instantiate a Gearbox and fPLL. The ATX PLL_TYPE assignment will conflict with the fPLL insantiated inside the PHY and cause an error.
To work around this issue, you can either:
Assign the PLL_TYPE ATX assignment to the tx_pll only.
Or
Upgrade to Quartus II Software Version 11.1 which has a Tx PLL drop down option. In this case you must remove the PLL_TYPE ATX assignment.