usefragsph not on There are 35 ligand heavy atoms Ligand center of coords (x y z): 20.6163142857143 69.5367142857143 40.3416285714286 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1476 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 785 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 781 Number of spheres polar: 199, nonpolar: 384, out of current total: 781 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: 10.64293 30.35111 59.70503 79.42764 30.34591 50.30862 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 265 Number of spheres after second pass removing spheres absolutely <0.8 from each other: 216 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 200 Spheres center of coords (x y z): 21.49149825 69.6601857 38.2166288 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: 5.34465335573538 Final number of output spheres is: 45 Number of polar spheres: 18 Number of nonpolar spheres: 24 Number of spheres that are near neither polar nor nonpolar receptor atoms: 3 Final number of spheres that are from crystallographic ligand: 35