usefragsph not on There are 22 ligand heavy atoms Ligand center of coords (x y z): 2.75272727272727 -3.27227272727273 5.77931818181818 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1711 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 761 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 761 Number of spheres polar: 154, nonpolar: 478, out of current total: 761 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -6.94593 12.73000 -13.24878 6.32859 -4.16565 15.54712 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 383 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 327 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 309 Spheres center of coords (x y z): 6.79719915857605 -6.45792064724919 4.11505944983819 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: 6.42812353801298 Final number of output spheres is: 60 Number of polar spheres: 18 Number of nonpolar spheres: 41 Number of spheres that are near neither polar nor nonpolar receptor atoms: 1 Final number of spheres that are from crystallographic ligand: 22