Do you have alarms or anything of sort? (it might matter)
Disable all syncs, try to off (most) of those chat apps like wechat and line etc(go to settings>apps force stop), wechat in particular drains quite a lot.
I don't use stock but mine is close to it but I deleted lots of bloats from TB.
I only leave whatsapp on.
Infact, try out using Airplane, if even in airplane the battery still sucks, try reflashing everything using bootloader.
Device Name: Nexus 5 HammerHead
Kernel & Tweaks: Franco/Trinity
Devices I meddled with:
Google Nexus 5(my new lady), Google Nexus 4(Sold), Samsung Nexus S(present), LG Optimus 4X HD P880(sold), HTC Sensation XE Pyramid(sold), Samsung Galaxy Wonder i8150(spare)