He was doing 106 before he applied the brakes. He got down to 102 in the 3 seconds before the train crashed. Trains don’t instantly stop and he waited far too late to apply the brakes.
Apparently he had to switch the brake to manual mode before he could apply the brake
There was a guest on Fox at about 3 explaining how the system worked. A later question affirmed the engineer would usually Use what amounted to “auto pilot” Technology was sensitive enough to adjust speed of train to automatically adjust to terrain.