Magic Resistance and it usage against ap damge champions

In a recent game of Poro King I loss. But that is not my problem I was the tank on my team and no matter what I died more times than I could count due to damage but odd thing was my magic resist was over 100 and i had over 100 armor as well. So my question is what was i doing wrong to be so weak because I got chunk down more and more. For more infomation I was playing Nautilus runes where hypid pen mark, armor seal, ap quints and mr/lvl and flat mr glyphs with a 0/21/9 mast. The blue team had only two champions runing magic pen but still i got destroyed in both early and late game. Please help me understand what is did wrong.

After looking over the game I see that magic pen is very strong and in some cases out scales mr. But I'm not sure why. Also after doing some research on this subject on the lol wiki it stated that the order of application of magic pen was done not once but in order of four which is odd here look at this.

When attacking, armor penetration and armor reduction are considered in the following order

1. Armor reduction, flat
2. Armor reduction, percentage
3. Armor penetration, percentage
4. Armor penetration, flat

Magic penetration and magic reduction are considered on the target champion in the following order

1. Percentage magic reduction
2. Flat magic reduction
3. Flat magic penetration
4. Percentage magic penetration

By looking at this it look like the system favors attackers and makes it useless do go defensive.