CONFIG_SOC_SAMA5D3 is not available for thedefaultarchitecture x86.
Result is shown for architecture arm

SAMA5D3 family

modulename: sama5d3.ko

configname: CONFIG_SOC_SAMA5D3

Linux Kernel Configuration
└─>AT91/Microchip SoCs
└─>SAMA5D3 family
In linux kernel since version 3.1 (release Date: 2011-10-24)  
Select this if you are using one of Microchip's SAMA5D3 family SoC.
This support covers SAMA5D31, SAMA5D33, SAMA5D34, SAMA5D35, SAMA5D36.

source code:
drivers/clk/at91/