Your problem is that your board doesn't have the bootloader loaded into the chip.
You have success with the ATMEL-ICE ISP becaisebecause it is a ISPan in-system programmer (ISP) and you are downloading the code directly into the chip.
When you use the USB, I see from your output that the programmer is "butterfly" and the description indicates AVR109. These both indicate that the program is trying to be loaded through a bootloader.
A bootloader is a bit of code that resides in the codespace section of flash. It allows you to send the program through the UART. The bootloader then saves it to the codespace section of flash such that both the bootloader and your program co-exist.
To fix this, use the Arduino IDE along with your ATMEL-ICE ISP to load the bootloader into the microcontroller. This can be done by going into Tools and then Burn Bootloader (of course with the correct programmer selected).
This will then allow you to download your code through the Arduino IDE.
PS. You can program your sketch straight to your Arduino using your ATMEL-ICE ISP without downloading the bootloader. Do this by selecting the Upload Using Programmer option in the menus.