usefragsph not on There are 54 ligand heavy atoms Ligand center of coords (x y z): -9.18683333333333 15.9270555555556 27.8862777777778 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1297 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 698 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 698 Number of spheres polar: 108, nonpolar: 404, out of current total: 698 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -18.87993 0.78396 5.93857 25.88731 17.62300 37.97300 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 245 Number of spheres after second pass removing spheres absolutely <0.8 from each other: 212 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): -9.18683333333333 15.9270555555556 27.8862777777778 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: 1.37673245385649 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: 11 Number of nonpolar spheres: 31 Number of spheres that are near neither polar nor nonpolar receptor atoms: 3 Final number of spheres that are from crystallographic ligand: 45