96 civic engine (D16Y7) knocking… Bearings and rods in good shape?

What can be causing the knockings? The knocking sounds like if the engine spun a bearing and if the rod was the one causing the knock although it's NOT as loud, BUT the bearings and rods are in good shape, bearings look new…, can the head or something else cause the knocking noise?

I've checked the head and it look good, no signs of valve piston contact or bent valves. I'll be takin the head apart to verify everything is good.

Edit, honda is automatic

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