Comprehend
Definition 1 of 3
Pro Tip 1/3
Emotive Confusion
Note that 'comprehend' conveys a rational understanding, not an emotional one. He understood her words, but he couldn't comprehend her pain.
Pro Tip 2/3
Full Clarity
'Comprehend' implies you are fully clear about the topic, with no confusion. After the lecture, I could comprehend the complex theory.
Pro Tip 3/3
Sudden Realization
'Comprehend' is sometimes used when someone suddenly understands an idea. She read the clue again and finally comprehended the puzzle.