In most case, COOR CONVERT is not needed, unless you are working with crystallographic coordinates.
COOR ORIENT NOROT will translate the box w/o rotation to center it at the origin. The Cartesian origin (0,0,0) is generally recommended for image centering.
The protein is free to move, and is also not subject to image centering; you have also not included the NO molecules or any ions in the image centering, either. This will not go well.
BTW, this post has nothing to do with anything in the Script Archive forum; please choose a more appropriate forum for future posts.