Problems building an Arduino Micro with through-hole components

Question

So I'm trying to build an Arduino Micro using a bread-board and through-hole components. I'm leaving out the voltage regulator and voltage selector (see schematic at the bottom for reference). I'm powering off of USB, so the +5V line is connected to VUSB.

I checked over the circuit many times, so I think it's okay. Below is a picture of me trying to use an Arduino Micro to load the bootloader on to the Atmega32U4:

Arduino Micro circuit

I looked here and here as references for trying to load the bootloader, but every time I try it gives me an error. It seems like the MCU is not being recognized. Has anyone tried this before, and successfully done it? I'd like some pointers as to how to achieve this.

EDIT: I've moved the crystal (and 22 pF cap's) closer to pins 16 and 17. The steps I take are:

1. Upload "ArduinoISP" sketch to Arduino Micro (the "programmer").
2. Select "Arduino Micro" as the board to be programmed.
3. Select "Arduino as ISP (Atmega32U4)" as the programmer.
4. Burn bootloader.

Here is the verbose output (compilation and upload):

Arduino: 1.6.12 (Windows 7), Board: "Arduino/Genuino Micro"
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega32u4 -carduino -PCOM5 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m 
avrdude: Version 6.3, compiled on Sep 12 2016 at 17:24:16
 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
 Copyright (c) 2007-2014 Joerg Wunsch
 System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"
 Using Port : COM5
 Using Programmer : arduino
 Overriding Baud Rate : 19200
 AVR Part : ATmega32U4
 Chip Erase delay : 9000 us
 PAGEL : PD7
 BS2 : PA0
 RESET disposition : dedicated
 RETRY pulse : SCK
 serial program mode : yes
 parallel program mode : yes
 Timeout : 200
 StabDelay : 100
 CmdexeDelay : 25
 SyncLoops : 32
 ByteDelay : 0
 PollIndex : 3
 PollValue : 0x53
 Memory Detail :
 Block Poll Page Polled
 Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack
 ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
 eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
 flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
 lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
 calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
 signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00
 Programmer Type : Arduino
 Description : Arduino
 Hardware Version: 2
 Firmware Version: 1.18
 Topcard : Unknown
 Vtarget : 0.0 V
 Varef : 0.0 V
 Oscillator : Off
 SCK period : 0.1 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0xffffff (probably .reduced_core_tiny) (retrying)
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0xffffff (probably .reduced_core_tiny) (retrying)
Error while burning bootloader.
Reading | ################################################## | 100% 0.00s
avrdude: Device signature = 0xffffff (probably .reduced_core_tiny)
avrdude: Yikes! Invalid device signature.
 Double check connections and try again, or use -F to override
 this check.
avrdude done. Thank you.

Arduino Micro schematic

• Ignacio Vazquez-Abrams: Are you sure you aren't trying to build a radio receiver?
• Nick Gammon: My page about uploading bootloaders may help you.
• James Waldby - jwpat7: 1. Where is "here and here" ? 2. Edit question and show what commands or sequence you used for bootloader transfer. 3. What do you get when you try to read the fuses?
• Max Jacob: Loading the "ArduinoISP" program on to the programmer (the Arduino Micro on the left side of my picture) works without errors. I then unplug it from my computer and hook it up as shown in the second link. I select "Arduino/Genuino Micro" as the Board. I select the port that the programmer (Arduino Micro) is connected to. I select "ArduinoISP" as the programmer. I press "Burn Bootloader". I get the following: avrdude: Error: Could not find USBtiny device (0x2341/0x49) Error while burning bootaloader.
• Chris Stratton: Regardless if related to your present problem or not, you should put the crystal and its capacitors right at the relevant pins. The same goes for anything intended as a bypass capacitor.

Answer 1

I select "ArduinoISP" as the programmer. I press "Burn Bootloader". I get the following: avrdude: Error: Could not find USBtiny device (0x2341/0x49) Error while burning bootaloader.

You need to select Arduino as ISP from the Tools> Programmer menu. ArduinoISP is a dedicated in system programmer made by Arduino, confusing because the name of the sketch used with Arduino as ISP is ArduinoISP.

If you're using Windows you'll also likely encounter the issue that ATmega32U4 based boards can't be used for Arduino as ISP. The cause of this is explained at https://petervanhoyweghen.wordpress.com/2012/09/16/arduinoisp-on-the-leonardo as well as a solution. Unfortunately the solution described in that blog post no longer works as-is with recent versions of the Arduino IDE. I have updated the solution to work with recent Arduino IDE versions and added support for installation via Boards Manager here: https://github.com/per1234/ATmega32U4asISP

• Max Jacob: I got the following message when trying the steps on the github page: Arduino: 1.6.12 (Windows 7), Board: "Arduino/Genuino Micro" avrdude: Yikes! Invalid device signature. Double check connections and try again, or use -F to override this check. Error while burning bootloader. This report would have more information with "Show verbose output during compilation" option enabled in File -> Preferences.
• James Waldby - jwpat7: @MaxJacob, I'm imagining the Arduino Micro auto-resets when you start a download to it. If that is the case you need to disable the auto-reset after you download ArduinoISP to the Micro. The Micro should remain connected to your host computer (that runs Arduino IDE) when you click Tools, Burn Bootloader to copy the bootloader to your target system. The IDE will send the Bootloader to the Micro, and the Micro will send it on to your target system. Note, if you have other working Arduinos, use one to practice download/bootload process, in case your target system is just not working.
• Max Jacob: @jwpat7 I disabled auto-reset (placed 120 Ohm resistor between 5V and Reset) after uploading the Sketch, but I still get the same error when try to burn the bootloader. Sadly, I do not have any extra Arduinos around.
• Max Jacob: I want to zone in on why I'm having these issues. What is the simplest circuit necessary to burn the bootloader to the ATmega32U4 using an Arduino Micro (using "Arduino as ISP") as the programmer?
• per1234: If you have the correct board selected then usually the "invalid device signature" error indicates a wiring problem. If you have verbose output during upload enabled in File > Preferences you can see the actual signature that was read. What was it? It's probably helpful if you would edit your question to add the steps you used to do the Burn Bootloader and full verbose output from the console to your question so that all the information is located in one place instead of spread out over multiple comment threads. I agree with Chris Stratton about the crystal being too far away.