How to connect GPIO16 and RST of ESP8266?
Most of the people face the problem while connecting them. The issue is that GPIO16 provides a strong HIGH during deepSleep and your external reset from Serial-TTL is fighting to make a reset, but loosing, the GPIO16 is the strongest.
To avoid such issue, simply replace the wire by a 470R or 1K between GPIO16 and RES, which will allow the Serial-TTL to win. (you can also use a schottky diode with the cathode on GPIO16 side)