To suggest that all the major world powers would have signed a deal that leaves space for Iran to develop nuclear weapons, and that the IAEA might have been happily certifying the compliance to the terms of the deal without bothering to make sure that Iran isn't actually developing nuclear weapons, would be supremely naive.

A more complete quote from the IAEA statement that you quoted is:

"The Agency’s overall assessment was that a range of activities relevant to the development of a nuclear explosive device were conducted in Iran prior to the end of 2003 as a coordinated effort, and some activities took place after 2003. The Agency also assessed that these activities did not advance beyond feasibility and scientific studies, and the acquisition of certain relevant technical competences and capabilities. The same report stated that the Agency had no credible indications of activities in Iran relevant to the development of a nuclear explosive device after 2009. Based on the Director General’s report, the Board of Governors declared that its consideration of this issue was closed."

In fact, what IAEA is diplomatically saying is "we don't give a damn what Netanyahu claims, we have reports and information that proves that the claims are not true and we don't have to discuss it any further".