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ugly clunk sound

It is a floppy E string that is too loose and slapping either the top of the pickup or slapping the fret at the end of the fretboard. A bandaid is lowering your pickup if it is the string hitting it. raising you string height will work if it the fretboard.
You can also play around with the EQ right around the 400 hz range, should get rid of some of it.

But the real problem is your string tension is to low/ not tight enough. You are asking a string never designed for that frequency to go down to D. Only way to do that is to detune/ detension the string. Thus the flop and clack.

You can either buy a set of strings for a five string, detune the entire instrument to BEAD, and hope that your four string neck can handle the tension. Or you can go ahead and make the jump to five string, that you are already on the path to doing with you drop D tuning.

That is the route I would/ have already gone. You would then have your D on it's own string, plus a couple lower notes. Be a lot easier to play a low E at the 5th fret of the B string, and sound better than an open E.

Had similar problem many years ago, switched to 5/6/7 string basses, was still annoyed by the clack noise. I have a very heavy finger style, fast and hard. lol. But I eventually got rid of my fret noise completely, by getting rid of the frets. lol.

I have been playing heavy prog rock fretless for many years, nothing sounds better in my opinion.

Hope this helps you find your way to better sound.
 
You could also buy the heaviest gauge strings for a 4 string you can (I'd recommend Ernie Ball but that's just me) and that should help alleviate the problem, though you most likely will also need to adjust the setup on your bass (truss rod, action and then you'd need to adjust the intonation) to accommodate the differing tension and diameter of the strings. But seeing as you're relatively new to bass I wouldn't suggest doing anything to the setup without having a good understanding of what each process does first. Some music shops will make those changes for you along with putting the strings on for a nominal fee on top of the price of strings.
 
What Kevin said, the E string's hitting the pickup. If your bass is a Jazz style it's particularly easy for this to happen. I suggest raising the bridge under the E string, and lowering the neck pickup a bit, the E side only.
If this is not enough the next step is heavier strings, like 50-110 gauges. That's what I did with my Jazz and it worked great BUT I had to widen the slots in the nut in order for the fatter strings to fit.
 
I don't know if I'd alter the action if it's only hitting the pickup. Be better to lower the pickup a fraction so you have some playing consistency along the neck. This is what I did with my Stingray for my low B and it worked a charm. If you do lower the pickup and it makes the E string too quiet, you'd be best raising it again and getting a thicker gauge string (something like heavy bottom light tops or heavier gauge on all - you have a few options here).
 
A bit of a late response but my EMG35HZ pups made the same noise and I adjusted the strings, PUps, truss rod, went to flats even.
Even with my bass looking like a archers bow and being impossible to play, the clunking sound was still there.