usefragsph not on There are 14 ligand heavy atoms Ligand center of coords (x y z): -3.96028571428571 -12.1099285714286 -17.9162857142857 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 387 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 268 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 268 Number of spheres polar: 78, nonpolar: 138, out of current total: 268 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -12.19503 5.90726 -21.99475 -2.20614 -25.30928 -9.00541 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 141 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 127 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 96 Spheres center of coords (x y z): -3.20966895833333 -12.0034960416667 -20.3324679166667 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: 3.92888350733895 Final number of output spheres is: 60 Number of polar spheres: 8 Number of nonpolar spheres: 41 Number of spheres that are near neither polar nor nonpolar receptor atoms: 11 Final number of spheres that are from crystallographic ligand: 14