Slow initialization of large array of small objects

I've stumbled upon this case today and I'm wondering what is the reason behind this huge difference in time.

The first version initializes an 5k x 5k array of raw ints:

public void initializeRaw() {
  int size = 5000;
  int[][] a = new int[size][size];
  for (int i = 0; i < size; i++)
    for (int j = 0; j < size; j++)
      a[i][j] = -1;
}

and it takes roughly 300ms on my machine. On the other hand, initializing the same array with simple 2-int structs:

public class Struct { public int x; public int y; }

public void initializeStruct() {
  int size = 5000;
  Struct[][] a = new Struct[size][size];
  for (int i = 0; i < size; i++)
    for (int j = 0; j < size; j++)
      a[i][j] = new Struct();
}

takes over 15000ms.

I would expect it to be a bit slower, after all there is more memory to allocate (10 bytes instead of 4 if I'm not mistaken), but I cannot understand why could it take 50 times longer.

Could anyone explain this? Maybe there is just a better way to to this kind of initialization in Java?

EDIT: For some comparison - the same code that uses Integer instead of int/Struct works 700ms - only two times slower.