Content of XMEGA conf_clock.h: 
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_RCOSC
#define CONFIG_OSC_RC32_CAL         48000000UL
#define CONFIG_OSC_AUTOCAL_RC32MHZ_REF_OSC  OSC_ID_USBSOF
#define CONFIG_SYSCLK_SOURCE     SYSCLK_SRC_RC32MHZ
#define CONFIG_SYSCLK_PSADIV     SYSCLK_PSADIV_2
#define CONFIG_SYSCLK_PSBCDIV    SYSCLK_PSBCDIV_1_1
Content of conf_clock.h for AT32UC3A0, AT32UC3A1, AT32UC3B devices (USBB): 
#define CONFIG_PLL1_SOURCE          PLL_SRC_OSC0
#define CONFIG_PLL1_MUL             8
#define CONFIG_PLL1_DIV             2
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_PLL1
#define CONFIG_USBCLK_DIV           1 // Fusb = Fsys/(2 ^ USB_div)
Content of conf_clock.h for AT32UC3A3, AT32UC3A4 devices (USBB with high speed support): 
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_OSC0
#define CONFIG_USBCLK_DIV           1 // Fusb = Fsys/(2 ^ USB_div)
Content of conf_clock.h for AT32UC3C, ATUCXXD, ATUCXXL3U, ATUCXXL4U devices (USBC): 
#define CONFIG_PLL1_SOURCE          PLL_SRC_OSC0
#define CONFIG_PLL1_MUL             8
#define CONFIG_PLL1_DIV             2
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_PLL1
#define CONFIG_USBCLK_DIV           1 // Fusb = Fsys/(2 ^ USB_div)
#define CONFIG_SYSCLK_SOURCE        SYSCLK_SRC_PLL1
Content of conf_clock.h for SAM3S, SAM3SD, SAM4S devices (UPD: USB Peripheral Device): 
#define CONFIG_PLL1_SOURCE          PLL_SRC_MAINCK_XTAL
#define CONFIG_PLL1_MUL             16
#define CONFIG_PLL1_DIV             2
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_PLL1
#define CONFIG_USBCLK_DIV           2
Content of conf_clock.h for SAM3U device (UPDHS: USB Peripheral Device High Speed): 
Content of conf_clock.h for SAM3X, SAM3A devices (UOTGHS: USB OTG High Speed): 
#define CONFIG_USBCLK_SOURCE        USBCLK_SRC_UPLL
#define CONFIG_USBCLK_DIV           1
Content of conf_clocks.h for SAMD devices (USB): 
#  define CONF_CLOCK_FLASH_WAIT_STATES            2
#  define CONF_CLOCK_DFLL_ENABLE                  true
#  define CONF_CLOCK_DFLL_LOOP_MODE               SYSTEM_CLOCK_DFLL_LOOP_MODE_USB_RECOVERY
#  define CONF_CLOCK_DFLL_ON_DEMAND               true
#  define CONF_CLOCK_CONFIGURE_GCLK               true
#  define CONF_CLOCK_GCLK_0_ENABLE                true
#  define CONF_CLOCK_GCLK_0_RUN_IN_STANDBY        true
#  define CONF_CLOCK_GCLK_0_CLOCK_SOURCE          SYSTEM_CLOCK_SOURCE_DFLL
#  define CONF_CLOCK_GCLK_0_PRESCALER             1
#  define CONF_CLOCK_GCLK_0_OUTPUT_ENABLE         false