usefragsph not on There are 13 ligand heavy atoms Ligand center of coords (x y z): 13.9171538461538 67.1539230769231 10.5534615384615 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 778 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 427 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 425 Number of spheres polar: 229, nonpolar: 128, out of current total: 425 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: 4.00615 23.69695 57.18533 77.13942 0.72790 20.53853 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 150 WARNING: spheres 3 and 4 are both crystallographic and are <0.8 to each other (not removing either of them) WARNING: spheres 4 and 3 are both crystallographic and are <0.8 to each other (not removing either of them) Number of spheres after second pass removing spheres absolutely <0.8 from each other: 107 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 52 Spheres center of coords (x y z): 14.8435236538462 65.2592225 14.8582744230769 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: 5.31110746254093 Final number of output spheres is: 45 Number of polar spheres: 25 Number of nonpolar spheres: 9 Number of spheres that are near neither polar nor nonpolar receptor atoms: 11 Final number of spheres that are from crystallographic ligand: 13