CONFIG_AT91_PROGRAMMABLE_CLOCKS is not available for thedefaultarchitecture x86.
Result is shown for architecture arm

Programmable Clocks

configname: CONFIG_AT91_PROGRAMMABLE_CLOCKS

Linux Kernel Configuration
└─>Atmel AT91 System-on-Chip
└─>Programmable Clocks
In linux kernel since version 2.6.16 (release Date: 2006-03-19)  
Select this if you need to program one or more of the PCK0..PCK3
programmable clock outputs.