The safest way to flash factory images - This is a manual step-by-step procedure to flash Android 5.0 (LRX21T) factory images onto the Nexus 4 (aka mako).

secure_flashing_mako_lrx21t

# Create a new working directory and cd into it
~$ mkdir -p /path/n4update && cd /path/n4update
 
# Download all files you need
/path/n4update$ wget --no-check-certificates https://dl.google.com/dl/android/aosp/occam-lrx21t-factory-51cee750.tgz
# Download openrecovery-twrp-2.8.2.0-mako.img from http://techerrata.com/browse/twrp2/mako to the same path
# Download CF-Auto-Root-mako-occam-nexus4.zip from http://autoroot.chainfire.eu to the same path

# Extract downloaded file archives
/path/n4update$ mkdir -p ./images && tar zxvf occam-lrx21t-factory-51cee750.tgz -C ./images
/path/n4update$ unzip -jXVK ./images/occam-lrx21t/image-occam-lrx21t.zip -d ./images/occam-lrx21t
/path/n4update$ unzip -XVK CF-Auto-Root-mako-occam-nexus4.zip -d ./cf

# Remove unneeded archive files
/path/n4update$ rm CF-Auto-Root-mako-occam-nexus4.zip
/path/n4update$ rm occam-lrx21t-factory-51cee750.tgz
/path/n4update$ rm ./images/occam-lrx21t/image-occam-lrx21t.zip

# Update required flashing utility tools via SDK manager's command line options
/path/n4update$ android.[bat|sh] update sdk -u -t platform-tools,tools
/path/n4update$ android.[bat|sh] update adb

# Boot into bootloader mode
/path/n4update$ adb reboot bootloader

# In bootloader mode, make sure the device is recognized
/path/n4update$ fastboot devices

# Erase old boot, cache, system & userdata partitions
/path/n4update$ fastboot erase boot
/path/n4update$ fastboot erase cache
/path/n4update$ fastboot erase system
/path/n4update$ fastboot erase userdata

# IGNORE THIS COMMAND, IF YOU HAVE A CUSTOM RECOVERY INSTALLED AND WANT TO KEEP IT.
# IF YOU HAVE THE STOCK RECOVERY, DO NOT IGNORE THE NEXT LINE.
/path/n4update$ fastboot erase recovery

# Flash new bootloader & reboot into
/path/n4update$ fastboot flash bootloader ./images/occam-lrx21t/bootloader-mako-makoz30f.img
/path/n4update$ fastboot reboot-bootloader

# Flash new radio & reboot bootloader
/path/n4update$ fastboot flash radio ./images/occam-lrx21t/radio-mako-m9615a-cefwmazm-2.0.1701.04.img
/path/n4update$ fastboot reboot-bootloader

# Do wipe again.
/path/n4update$ fastboot -w

# Flash new boot, cache, system & userdata partitions
/path/n4update$ fastboot flash system ./images/occam-lrx21t/system.img
/path/n4update$ fastboot flash userdata ./images/occam-lrx21t/userdata.img
/path/n4update$ fastboot flash cache ./images/occam-lrx21t/cache.img
/path/n4update$ fastboot flash boot ./images/occam-lrx21t/boot.img

# ONLY REQUIRED, IF YOU ERASED THE RECOVERY PARTITION BEFORE.
# USE ONLY ONE OF THE FOLLOWING TWO LINES (1. Stock, 2. TWRP)!
/path/n4update$ fastboot flash recovery ./images/occam-lrx21t/recovery.img
/path/n4update$ fastboot flash recovery ./openrecovery-twrp-2.8.2.0-mako.img

# Reboot the system using the CF-Auto-Root boot image
/path/n4update$ fastboot boot ./cf/image/CF-Auto-Root-mako-occam-nexus4.img

# Device will reboot when CF-Auto-Root finished its job.
# Done.
# Bye