As Dave said, check the motors are all aligned properly.
Pre-flight calibration is performed automatically anyway and shouldnt have any effect by running it manually unless temperature has radically changed before takeoff.
You have many defaults and there needs to be more tuning.
Connect to MissionPlanner and do the Initial Parameters settings.
Then check through the tuning guide
and set up the Harmonic Notch Filter
then run Autotune
These some parameters you can use as a starting point (in addition to the Initial Params) although an F450 frame can be very hard to tune due to the flexibility
INS_HNTCH_ENABLE,1 ← set this then refresh params to see the rest
These PIDs can depend very much on your motors, props and ESCs so just be cautious at first and try to take off and hover for a while, maybe only gentle movements if any at all.
Let’s see the .bin log file from that and we can set the Harmonic Notch filter better before moving on.