CONFIG_HAVE_AT91_USB_CLK is not available for thedefaultarchitecture x86.
Result is shown for architecture arm

CONFIG_HAVE_AT91_USB_CLK (not configurable)

modulename: clk-usb.ko

configname: CONFIG_HAVE_AT91_USB_CLK

Linux Kernel Configuration
└─>Atmel SoCs
└─>HAVE_AT91_USB_CLK
In linux kernel since version 3.10 (release Date: 2013-06-30)  
source code:
drivers/clk/at91/clk-usb.c