Atmega2560 PWM bits disable

#include <avr/io.h>
#include <avr/interrupt.h>
#include <Arduino.h>

void initPWM()
{
  DDRB |= (1 << 5);  // PORTB5 pin as output for LED 1
  TCCR1A = _BV(COM1A1) | _BV(WGM10); // non-inverting mode, fast pwm with top as 0xFF
  TCCR1B = _BV(CS11); // prescaler set to clk/8

  DDRE |= (1 << 3); // PORTE3 pin as output for motor driver IN1
  TCCR3A = _BV(COM3A1) | _BV(WGM30);   // non-inverting mode, fast pwm with top as 0xFF
  TCCR3B = _BV(CS31);// prescaler set to clk/8

  DDRH |= (1 << 3); // PORTH3 pin as output for motor driver IN2
  TCCR4A = _BV(COM4A1) | _BV(COM4A0) | _BV(WGM40); // inverting mode, fast pwm with top as 0xFF
  TCCR4B = _BV(CS41);   // prescaler set to clk/8

  DDRL |= (1 << 3); // PORTL3 pin as output for LED2
  TCCR5A = _BV(COM5A1) | _BV(COM5A0) | _BV(WGM50); // inverting mode, fast pwm with top as 0xFF
  TCCR5B = _BV(CS51);   // prescaler set to clk/8
}

//Set motor speed and direction with count registers using information obtained by ADC
void changeDutyCycle(int dutycycle) {
  OCR1A = dutycycle;  // set PWM duty cycle for LED 1
  OCR3A = dutycycle;  // set PWM duty cycle for motor driver IN1
  OCR4A = dutycycle;  // set PWM duty cycle for motor driver IN2
  OCR5A = dutycycle;  // set PWM duty cycle for LED 2

}

int main()
{

  initPWM();// initialize PWM
  sei();// initialize Interrupts

  while (1)
  {
    if (flag == 1) {
      changeDutyCycle(128); // read ADC value is 1024/4 = 256 and set motor speed accordingly
    } else {
      changeDutyCycle(0);   // Stop PWM signals    
    }
  }


  return 0;
}
// Establish ISR using external interput on PORTD
ISR (INT0_vect) {
  flag =! flag; // flag with invert command
}

void initSwitchPD0()
{
  DDRD &= ~(1 << DDD2);     // Clear the PD0 pin
  // PD0 (INT0 pin) is now an input

  PORTD |= (1 << PORTD0);    // turn On the Pull-up
  // PD0 is now an input with pull-up enabled
  EICRA |= (1 << ISC01);    // set INT0 to trigger on ANY logic change
  EIMSK |= (1 << INT0);     // Turns on INT0

}

// Establish ISR using external interput on PORTD
ISR (INT0_vect) {
  flag =! flag; // flag with invert command
}