usefragsph not on There are 54 ligand heavy atoms Ligand center of coords (x y z): -9.12677777777778 15.8818518518519 27.9344814814815 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1265 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 794 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 794 Number of spheres polar: 133, nonpolar: 489, out of current total: 794 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -19.12557 0.72294 5.97763 25.80006 17.68900 37.96500 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 271 Number of spheres after second pass removing spheres absolutely <0.8 from each other: 227 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 54 Spheres center of coords (x y z): -9.12677777777778 15.8818518518519 27.9344814814815 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: 1.37525466426512 WARNING: removing a crystallographic sphere since 54>45 max spheres are present WARNING: removing a crystallographic sphere since 53>45 max spheres are present WARNING: removing a crystallographic sphere since 52>45 max spheres are present WARNING: removing a crystallographic sphere since 51>45 max spheres are present WARNING: removing a crystallographic sphere since 50>45 max spheres are present WARNING: removing a crystallographic sphere since 49>45 max spheres are present WARNING: removing a crystallographic sphere since 48>45 max spheres are present WARNING: removing a crystallographic sphere since 47>45 max spheres are present WARNING: removing a crystallographic sphere since 46>45 max spheres are present Final number of output spheres is: 45 Number of polar spheres: 9 Number of nonpolar spheres: 33 Number of spheres that are near neither polar nor nonpolar receptor atoms: 3 Final number of spheres that are from crystallographic ligand: 45