Could there be a reason for painful urination other than std, uti and crystals in the urine. i have been checked and dont have any of those conditions. could this symptom be related to some other issue with kidney and bladder?

If you have been tested/you are negative for STD, UTI and crystals in the urine, but you are still experiencing painful urination, you could have painful bladder syndrome (Interstitial Cystitis). In this condition, the protective lining of the bladder is broken down which allows the urine to irritate the bladder cell layers. Cause is not known, but may be related to autoimmune disease or allergy