usefragsph not on There are 23 ligand heavy atoms Ligand center of coords (x y z): 26.7087391304348 2.81686956521739 4.08356521739131 Using crystallographic ligand as spheres for output Starting number of spheres from sph/sph cluster 0: 914 FINISHED READING IN FILE sph/sph CLUSTER 0 Number of sphere points after cutting off spheres too far from center of ligand (10 angstroms): 328 Number of spheres after removing too far (>7 angstroms) and too close to receptor (<1.2 angstroms): 328 Number of spheres polar: 91, nonpolar: 198, out of current total: 328 Extents of grid to search are X1 X2 Y1 Y2 Z1 Z2: 19.96459 36.70676 -3.58764 12.81285 -4.82959 14.03678 Number of spheres after removing spheres too close to each other (approximately <1.0 angstroms): 147 Number of spheres after second pass removing spheres absolutely <0.5 from each other: 126 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): 25.8091384545455 5.04594872727273 5.27958763636363 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: 3.37542958153039 Final number of output spheres is: 60 Number of polar spheres: 12 Number of nonpolar spheres: 45 Number of spheres that are near neither polar nor nonpolar receptor atoms: 3 Final number of spheres that are from crystallographic ligand: 23