After reading few examples in php.net I fond a very good demonstration:
The NOT or complement operator ( ~ ) and negative binary numbers can be confusing.
~2 = -3  because you use the formula  ~x = -x - 1  The bitwise
  complement of a decimal number is the negation of the number minus 1.
NOTE: just using 4 bits here for the examples below but in reality PHP
  uses 32 bits.
Converting a negative decimal number (ie: -3) into binary takes 3
  steps: 1) convert the positive version of the decimal number into
  binary (ie: 3 = 0011) 2) flips the bits (ie: 0011 becomes 1100) 3) add
  1 (ie: 1100  + 0001 = 1101)
You might be wondering how does 1101 = -3. Well PHP uses the method
  "2's complement" to render negative binary numbers. If the left most
  bit is a 1 then the binary number is negative and you flip the bits
  and add 1. If it is 0 then it is positive and you don't have to do
  anything. So 0010 would be a positive 2. If it is 1101, it is negative
  and you flip the bits to get 0010. Add 1 and you get 0011 which equals
  -3.
source from php.net