Not quite sure why you're attempting to use cell arrays here; the calling structure for fprintf expects the file id, a format string, and then all the variables to be substituted into the format string. The nice thing about fprintf is it does the string formatting for you; you don't need to convert all your data to strings like you're attempting to do.
Wasn't quite clear on your data format, but here's an example:
% Sample data
crd = rand(5,3);
r = 1;
orn = randi(10, [5 9]);
% Print
for ii = 1:length(crd)
fprintf(fid, 'region 1 sphere %f %d units box\r\n', crd(ii,1), r);
fprintf(fid, 'delete_atoms region 1\r\n');
fprintf(fid, 'lattice fcc 3.52 orient x %d %d %d %d %d %d %d %d %d\r\n', orn(ii,:));
end