usefragsph not on There are 13 ligand heavy atoms Ligand center of coords (x y z): -4.90769230769231 3.54938461538462 14.6925384615385 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 602 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 415 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 405 Number of spheres polar: 93, nonpolar: 220, out of current total: 405 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -13.04667 4.39397 -6.01203 13.43485 5.72685 24.14248 Number of spheres after removing spheres too close to each other (approximately <1.5 angstroms): 139 Number of spheres after second pass removing spheres absolutely <0.8 from each other: 119 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 110 Spheres center of coords (x y z): -4.29785163636364 5.60743845454546 11.6124747272727 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: 5.41047900693266 Final number of output spheres is: 45 Number of polar spheres: 10 Number of nonpolar spheres: 24 Number of spheres that are near neither polar nor nonpolar receptor atoms: 11 Final number of spheres that are from crystallographic ligand: 13