Few sites in Israel are better preserved than its main nuclear research facility and reactor, 8 miles from the city of Dimona in the southern Negev desert.So when two Iranian ballistic missiles dodged the country’s reputable air defenses and crashed into residential areas of Dimona and another nearby city of Arad on Saturday night, even war-ready Israelis were horrified by the scenes of destruction.Perhaps, as worrying as the damage was the damage, was the Army’s admission that it had tried to stop the missiles, which fell at an interval of about three hours. The failures raised questions about Israel’s multilayered missile defense system and its ability to protect its citizens.And concerns rose again that the military might hold back on firing its most expensive and sophisticated missiles after reports that its stockpile may have been depleted in last year’s 12-day war with Iran. Israeli military officials say they are investigating what went wrong, but have remained tight-lipped about details.During a tour of the affected sites on Sunday, Prime Minister Benjamin Netanyahu said it was a “miracle” that no one was killed. He urged Israelis to use the time provided by the incoming missile alert to move to bomb shelters. “Don’t be complacent,” he warned. He offered no explanation for the failed interception, nor did he mention the air defense system in which Israel and the US have invested heavily for decades. While the military reports an interception rate of Iran’s ballistic missiles at more than 90%, officials and experts stress that defenses can never be 100% streamlined. Ran Kochaev, a brigadier general in the reserves, said, “Dimona is protected by multilayered defense systems – Israeli and American – but nothing is perfect. There was an operational failure.” Brigadier General Effie Defrin, the army’s chief spokesperson, said on Sunday. NYT