Windows binaries will be in this folders:
~/bitcoin-0.16.2/depends/x86-64-w64-mingw32 (Windows 64 bit binaries)
~/bitcoin-0.16.2/depends/i686-w64-mingw32 (Windows 32 bit binaries)
[...]
Then, your error message:
to: /root/bitcoin/depends/x86_64-w64-mingw32
bash: ./configure: No such file or directory[/sup]
So, obviously my advice still holds:
Did you even try it out before replying ?