We are generating pdb files with chemdraw3D, which turn out to not be "real" pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers blank, such as Oxygen #2, and Carbon #18: HETATM 17 C16 LIG 1 -83.510 -0.856 0.582 1.00 20.00 C HETATM 18 O01 LIG 1 -86.640 -2.401 -0.357 1.00 20.00 O HETATM 19 O LIG 1 -75.199 2.925 2.145 1.00 20.00 O HETATM 20 C17 LIG 1 -83.058 -0.188 1.872 1.00 20.00 C HETATM 21 C LIG 1 -76.676 0.780 -1.835 1.00 20.00 C After editing it to add in the missing numbers, I re-ran elbow, and found that the resulting optimized ligand had imploded, producing altered atom connectivity. If I ran it with --final_geometry it came out OK. If you would like files to reproduce the error, I am happy to send them. Best, Kendall Nettles