Which CPU are you using? Ivy Bridge-E processors should give you PCI Express Revision 3.0 on the PCIe x16 slot. Sandy Bridge-E processors will give you PCI Express Revision 2.0 on the PCIe x16 slot.
The PCIe x1 slots are all connected to the X79 chipset so those will always be PCI Express Revision 2.0.
Which CPU are you using? Ivy Bridge-E processors should give you PCI Express Revision 3.0 on the PCIe x16 slot. Sandy Bridge-E processors will give you PCI Express Revision 2.0 on the PCIe x16 slot.
The PCIe x1 slots are all connected to the X79 chipset so those will always be PCI Express Revision 2.0.
Thanks,
GPUZ reported PCIE x16 3.0, and 2x PCIE 1x 4x 2.0.
It runs with an Intel Xeon E5 2690 V2 (or something with 10 cores, 20 threads).
If you look at the PCI Express Revision spec for the Intel Xeon Processor E5-2690 v2 you'll see that it is 3.0 so the PCIe x16 slot will operate in Revision 3.0 mode.