usefragsph not on There are 39 ligand heavy atoms Ligand center of coords (x y z): -37.5807179487179 6.33728205128205 39.0086923076923 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 2261 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 1015 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 1013 Number of spheres polar: 164, nonpolar: 672, out of current total: 1013 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -47.56941 -27.58801 -3.31833 16.32933 29.20500 49.00801 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 532 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 459 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 416 Spheres center of coords (x y z): -34.4901703365384 4.45342081730769 39.2091012740384 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: 5.08791712487584 Final number of output spheres is: 60 Number of polar spheres: 9 Number of nonpolar spheres: 49 Number of spheres that are near neither polar nor nonpolar receptor atoms: 2 Final number of spheres that are from crystallographic ligand: 39