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As said earlier the grass physics in the Welcome to the Jungle level is particularly taxing on the CPU. I remember a DF video showing ~10fps gains on that level just from having HT though that i5 at 4.6 should be pretty snappy. GPU Usage for you look okay ?
Which benchmarks are you referring to ?
****Update*****
After upgrading my machine, using a new motherboard (Z97-A), new CPU (4690K @4.6Ghz), sticking it on a new SSD drive and still using the 980TI of course, I can still not run Crysis on very high at 1080p. I get below 60fps as soon as I enter a grassy area, which is odd because benchmarks I see in this game achieve upto and even surpasses 100fps when at 1080p resolution.
When I get 40-50fps it drops to around 60%. When I am getting 100+ Fps (looking at a wall for instance in doors) it goes to nearly 100% which is strange. CPU around 85%
Simplistic answer: when you look at floors walls ceilings etc the cpu isnt under load (no scene/object rendering to be done) hence fps shoots up as the gpu can work at full speed as it doesn't have to wait for the cpu.
all you can do is tweak some of the settings to reduce cpu load or OC your cpu a bit more
Should've got the i7?
If i can be bothered I'll try it on mine with 4cores/HT off in the grassy area =]
I hope you didn't upgrade just for Crysis 3!
It's a very average game anyway. Crysis 2 is actually more fun and even that isn't amazing.