usefragsph not on There are 23 ligand heavy atoms Ligand center of coords (x y z): -3.88430434782609 5.19069565217391 14.7713043478261 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 706 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 488 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 486 Number of spheres polar: 80, nonpolar: 289, out of current total: 486 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -12.07255 6.01743 -4.75410 15.03689 4.80992 24.47363 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 174 Number of spheres after second pass removing spheres absolutely <0.8 from each other: 153 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 127 Spheres center of coords (x y z): -4.12011472440945 5.61987039370079 11.8492850393701 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: 4.52055339355334 Final number of output spheres is: 45 Number of polar spheres: 7 Number of nonpolar spheres: 26 Number of spheres that are near neither polar nor nonpolar receptor atoms: 12 Final number of spheres that are from crystallographic ligand: 23