Huge file dumps like these are impossible to work with. We’re not familiar with your system, naming conventions, etc. and when I spent time (above) trying to figure out what was going on, I chased down an irrelevant file and it ended up as a waste of time.
I provided a pretty bulletproof protocol above. If you have a docked complex with the ligand positioned appropriately, there’s nothing else to do besides what I’ve suggested. Check your output after everything you do.