usefragsph not on There are 15 ligand heavy atoms Ligand center of coords (x y z): -0.7886 -32.8436666666667 -10.9480666666667 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 635 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 419 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 413 Number of spheres polar: 164, nonpolar: 126, out of current total: 413 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -9.99393 9.18075 -42.67245 -22.84761 -20.90933 -1.68348 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 247 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 207 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 179 Spheres center of coords (x y z): -0.435717765363128 -32.6354745810056 -13.5896339106145 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: 6.29086460860199 Final number of output spheres is: 60 Number of polar spheres: 24 Number of nonpolar spheres: 24 Number of spheres that are near neither polar nor nonpolar receptor atoms: 12 Final number of spheres that are from crystallographic ligand: 15