usefragsph not on There are 35 ligand heavy atoms Ligand center of coords (x y z): -1.37537142857143 10.0508 -41.5815428571429 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 1768 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 899 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 898 Number of spheres polar: 287, nonpolar: 429, out of current total: 898 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: -10.71254 8.61298 0.13285 19.86017 -51.53895 -31.62612 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 466 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 413 Crystallographic spheres are present, so doing continuity based on crystallographic spheres After continuity checking, number of spheres is: 383 Spheres center of coords (x y z): -1.26148352480418 10.2595378067885 -40.7853521409921 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: 4.9665161825776 Final number of output spheres is: 60 Number of polar spheres: 17 Number of nonpolar spheres: 31 Number of spheres that are near neither polar nor nonpolar receptor atoms: 12 Final number of spheres that are from crystallographic ligand: 35