As per the eligibility to apply for NATA Entrance Exam you must have minimum 50% aggregate score Physics, Chemistry & Mathematics. You can check the further eligibility with the given below link.

https://engineering.careers360.com/articles/nata

Good Luck!

Hey.

The eligibility criteria for NATA states that you  must have scored minimum 50% marks in aggregate in physic, chemistry and mathematics. Further, you also need to score minimum 50% aggregate marks in the qualifying exam. As you've scored more than 50% in qualifying exam but scored less than 50% in PCM you don't seem to be eligible. 

You can use the link below for any other details regarding it.

https://www.google.co.in/amp/s/engineering.careers360.com/articles/nata/amp

Best of luck