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Preheat oven to 400°F with rack in lower third.
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Rinse turkey inside and out, then pat dry. Mix together 2 teaspoon salt and 1 teaspoon pepper and rub all over turkey inside and out. Put onion and thyme in large cavity. Pin neck skin to body with skewer. Center kitchen string under back of breast and bring ends over to pin wings, then crisscross string and tie ends of drumsticks together. Put turkey on a metal rack in roaster and brush with 4 tablespoons melted butter. Cover pan (if using a roasting pan, cover turkey with parchment paper, then foil) and roast 1 hour.
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Baste with pan juices and add water to pan. Continue to roast, covered, until an instant-read thermometer inserted into fleshy part of each thigh (test both; close to but not touching bone) registers 170°F, 30 minutes to 1 hour.
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Baste with remaining tablespoon melted butter and roast, uncovered, until skin is browned, about 15 minutes more (total roasting time: 1 3/4 to 2 1/4 hours). Carefully tilt turkey so juices from inside large cavity run into pan. Transfer turkey to a platter and let stand, loosely covered with foil, 30 minutes (temperature of thigh meat will rise to 175 to 180°F).