usefragsph not on There are 42 ligand heavy atoms Ligand center of coords (x y z): -10.2980952380952 -4.49657142857143 34.4243333333333 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 2603 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 1215 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 1213 Number of spheres polar: 224, nonpolar: 823, out of current total: 1213 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -20.27806 -1.92982 -14.48074 5.48187 24.47957 44.36733 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 645 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 559 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 535 Spheres center of coords (x y z): -12.3760285794393 -3.25652753271028 34.0287407476636 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: 5.34578085873308 Final number of output spheres is: 60 Number of polar spheres: 8 Number of nonpolar spheres: 51 Number of spheres that are near neither polar nor nonpolar receptor atoms: 1 Final number of spheres that are from crystallographic ligand: 42