First, your z homing feedrate is higher than z max.
#define HOMING_FEEDRATE {50*60, 50*60, 4*60, 0} // set the homing speeds (mm/min)
#define DEFAULT_MAX_FEEDRATE {500, 500, 3, 25} // (mm/sec)
But also, the effective Z speed can be lower than max, if the sender program (pronterface) has a setting like Z speed 120mm/min, then manual moves will be at that speed. You need to test and find good values for Z speed.