When connected to a computer, the USB connection provides a 5 V power supply. If an external power supply is present, the unit will run off of the external supply and not draw any power from USB. If only the USB power is present, then by default the auxiliary processor will be powered from USB, but the AVR and the VCC power pins on the board will not be powered.
An option is available for powering the entire board from USB. To power the board from USB, install a jumper to connect VUSB to VCC. When the board is powered this way, the voltage regulator will conduct current backwards, resulting in a VBAT around 4.6 – 5.0 V and a VCC around 4.3 – 4.6 V. In some cases, VCC will be low enough to trigger brown-out detection on the AVR. Therefore, if you are having trouble powering your AVR from USB, try changing your brown-out detection fuses to be tolerant of lower voltages.
Using the VCC-VUSB jumper can also cause other problems because the Orangutan is not being USB-compliant whenever it draws more than 100 mA from the USB. If the Orangutan draws too much power from USB, the host may respond by disconnecting the power supply to that port. Therefore, if you are having trouble powering your AVR from USB, you may be drawing too much power.