In the bowl mix the water, yeast, honey, butter, and salt with a rubber spatula. Mix in the rye flour, wheat germ, and 1 cup each of the whole-wheat and all-purpose flours.
Add the remaining whole-wheat and all-purpose flours, knead until the dough is smooth and elasti. Transfer the dough to a lightly floured work surface. Knead so that the dough is soft and smooth.
Place the dough in a very lightly oiled large bowl; cover with plastic wrap. Let rise for about 1 hour.
Heat the oven to 375 degrees. Divide the dough into two equal pieces. roll the dough firmly into a cylinder, pressing down to make sure that the dough sticks to itself. Place each cylinder of dough in a greased 9 by 5-inch loaf pan.
Bake for 45 minutes. Transfer the bread immediately from the baking pans to wire racks; cool to room temperature.