The pixhawk flight computer is mounted on damping foams that comes with it, and no cables or other hardware are interfering it.
There are no loose or shaking parts on the drone, everything is tight and rigid.
I have lowered imu_gyro_cutoff parameter to 40hz down from 60hz (Default value for S500) and it helped to the vibration problem.
I spent quite a lot of time on analyzing logs, but I cant figure out the cause of the vibrations, perhaps someone with more experience could throw a bone.
I’m dealing with this issue on a different custom frame. Actually I offer you three steps.
1- You can increase IMU_DGYRO_ CUTOFF value little bit. There is an issue in this regard. Gurus can comment on the topic in more detail.
2- If it is possible [for Self-Tightened Probs, it can be a little difficult ]. Check propeller balance
3- if you can obtain, use an extra vibration damper isolator plate like in the image witn 3M Foam [Included with the Pixhawk4 Set]
@mehmetydz87 thank you for your advise! I will try to increase the IMU_DGYRO_CUTOFF in my next flight and see how this affects the vibrations.
Regarding the props and the damping plate, will try this too.
I will update here.