Prepare the leaven: Place the refreshed starter and water in a large glass bowl or Cambro tub. Stir to break up the starter. Add the whole wheat flour and mix with a spoon until no dry lumps remain. Cover with plastic wrap, and allow to ferment at room temperature for 8 to 12 hours.

Mix the dough: When bubbles break the surface of the leaven, it smells a bit sour, and it has swelled considerably in size, add the water and stir to combine. Add the AP flour and additional whole wheat flour to the bowl. Use your hands to mix, pinch and squeeze the dough in a circular motion until no dry lumps remain. Cover the bowl and let the dough rest for 15 minutes. This allows the flour to fully hydrate before adding the salt. Sprinkle the salt evenly over the surface of the dough and mix well to combine. The dough should feel somewhat sticky at this point.

Bulk fermentation: Set the bowl aside in a warm place (about 75°F) to bulk ferment for about 3 1/2 to 4 hours, depending on the temperature of the room. This could be 30 minutes shorter in the summer, or 30 minutes longer in the winter. Now you stretch andfold the dough in the bowl, in order to help develop the gluten and strengthen the dough to trap the fermented gases, creating beautiful air pockets in your loaf. Dampen your hands with water to prevent the dough from sticking and gently lift up one corner of the dough, and fold it to the center. You shouldn't be stretching so high that the dough tears. Rotate the bowl and repeat 3 to 4 more times until you have worked your way around the dough. Repeat this process every 35 minutes for 3.5 to 4 hours. Be extra gentle towards the end , so you don't deflate the dough.

Shape the dough: The dough should be puffy, bubbly, and have increased by at least 1/3 after 3.5 to 4 hours. There are 2 stages to shape the dough: pre-shape with a short resting period, and a tighter final shaping. Using a bowl scraper, gently remove the dough from the bowl and place on a lightly floured surface. Using your hands, bring the top of the dough to the center, then bring the bottom to the center, and then the two sides in. Tuck the resulting four corners to the middle as well, resulting in a slightly rounded form. Using your bench scraper, release the dough from the surface and flip it over seam side down. Cover the dough ball with plastic and allow to rest on your work surface for 15 minutes until it relaxes.

Final shape: use your bench scraper to flip the dough over onto a lightly floured surface, seam side up. Starting from the top, tuck the right side to the center, holding it in place while you bring the left side to the center overlapping with the first. Repeat this side-to-side stitching until you reach the bottom of the dough. Roll the bottom toward the center, tucking as you go to create tension, until the seam side is down. Flour the top of the loaf generously. Use your bench scraper to pick up the dough and flip it over, seam side up. Gently place it into your proofing basket. Cover the dough loosely with a cloth, then place the whole basket in a plastic bag, sealed with a clip. Place in the refrigerator to proof for 8 hours to 12 hours before baking.

Place a large Dutch oven on the center rack of your oven, then preheat your oven to 450 degrees F.

Remove your loaf from the refrigerator. Cut a piece of parchment paper to fit the Dutch oven and carefully flip your loaf onto the parchment seam side down. Score the top of the loaf with a razor blade about 1/4-inch deep to allow steam to release and the loaf to fully expand while baking. Use oven mitts to carefully remove the Dutch oven from the oven. Place the scored loaf, along with the parchment paper into the pot. Cover, and bake with the lid on for 20 minutes. Remove the loaf from the pot, and place back in the oven, on the center rack. This prevents the bottom crust from burning. Bake for another 15 to 20 minutes until the crust is a deep, mahogany color. Cool completely on a rack before slicing.