What can be the problem of DTC P0016 crank or cam misalignment or out of synchronize after water pump replacement and timing marks are perfectly aligned?

Answer 1

engines equipped with VVTI systems may also show that code (P0016) at certain engine speed,usually high speed,due to dirty engine oil.so replace oil and oil filter with proper viscousity engine oil and the code will will not appear again.

Answer 2

P0016 - Crankshaft Position - Camshaft Position Correlation (Bank 1 Sensor A)

symptoms
The engine may turn over but not start up
The engine may rattle near the harmonic balancer which means that the tone ring is damaged
The engine may start up and run, but run rough

cause
Timing chain is stretched, or timing belt skipped a tooth because its worn
Timing belt/chain not aligned
Tone ring on the crankshaft slipped or broken
Tone ring on the camshaft slipped or broken
Faulty crank sensor
Faulty cam sensor
Bad wiring to crank or cam sensor
Timing belt or chain tensioner faulty

The fix
Check the cam and crank sensors and their wiring for damage. If you see broken/frayed wires, repair.
If you have a scope, check the cam and crank patterns. If a pattern is missing, suspect a bad sensor or a slipping tone ring.
Remove the cam gear and crankshaft balancer and tone rings for proper alignment, make sure they're not loose or broken and they haven't sheared the alignment key. If they are correctly installed, replace the sensor. If the signal looks normal, then check the timing chain/belt for proper alignment. If it's not aligned, check for a damaged tensioner.
Also check that the belt or chain isn't stretched. replace and recheck.