usefragsph not on
There are 13 ligand heavy atoms
Ligand center of coords (x y z): 39.9958461538461 28.6872307692308 40.959
Using crystallographic ligand as spheres for output
Starting number of spheres from sph/sph cluster 0: 650
FINISHED READING IN FILE sph/sph CLUSTER 0 
Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 414
Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 414
Number of spheres polar: 169, nonpolar: 159, out of current total: 414
Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: 31.02346 49.85949 18.98408 38.16855 31.22200 50.88624
Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 157
WARNING: spheres 3 and 4 are both crystallographic and are <0.8 to each other (not removing either of them)
WARNING: spheres 4 and 3 are both crystallographic and are <0.8 to each other (not removing either of them)
Number of spheres after second pass removing spheres absolutely <0.8 from each other: 126
Crystallographic spheres are present, so doing continuity based on crystallographic spheres
After continuity checking, number of spheres is: 71
Spheres center of coords (x y z): 43.5386494366197 28.4744345070423 44.7259070422535
Crystallographic ligand, so keeping spheres closest to ANY ligand atom, center of ligand (1/8), and center of spheres (1/8)
Average weighted-distance for final elimination is: 6.07424957149834
Final number of output spheres is: 45
Number of polar spheres: 27
Number of nonpolar spheres: 9
Number of spheres that are near neither polar nor nonpolar receptor atoms: 9
Final number of spheres that are from crystallographic ligand: 13