usefragsph not on There are 44 ligand heavy atoms Ligand center of coords (x y z): -1.48511363636364 0.364454545454545 19.0272045454545 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 2490 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 1020 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 1020 Number of spheres polar: 316, nonpolar: 612, out of current total: 1020 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -11.45480 8.44734 -9.63213 10.36065 9.05537 29.02563 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 528 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 425 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 339 Spheres center of coords (x y z): -0.582409380530974 3.12970480825959 17.9232440117994 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: 4.95081989480217 Final number of output spheres is: 60 Number of polar spheres: 23 Number of nonpolar spheres: 34 Number of spheres that are near neither polar nor nonpolar receptor atoms: 3 Final number of spheres that are from crystallographic ligand: 44