System Set Permissions Accidentally, and is Corrupt
The problem is solved quickly after digging on TWRP, and found out that there is a restore option.

Luckily, I have a backup of the System Partition.

The ROM installed on my device was CM 12.1, which is running Android 5.1 Lollipop.

The backup system (pre - installed ROM) was the stock ROM, which is running Android 4.4 Kitkat.

Guess I should just install that CM ROM.

By the way, I could get into the Operating System now, but I have another problem, which I will post in an another question.