usefragsph not on There are 15 ligand heavy atoms Ligand center of coords (x y z): -10.0593333333333 10.5613333333333 7.04826666666667 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1407 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 1041 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 1040 Number of spheres polar: 316, nonpolar: 507, out of current total: 1040 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -19.96848 -0.08700 1.85160 20.56017 -2.94058 16.65948 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 489 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 431 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 431 Spheres center of coords (x y z): -10.9530679350348 13.7655032482598 5.37587721577726 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: 8.23990091259829 Final number of output spheres is: 60 Number of polar spheres: 29 Number of nonpolar spheres: 26 Number of spheres that are near neither polar nor nonpolar receptor atoms: 5 Final number of spheres that are from crystallographic ligand: 15