INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tu4_10587/12_2022/6tu4_10587.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6tu4_10587.eff Ligand restraint generation using eLBOW, phenix.elbow Attempting to download Chemical Components file for 9UE Running eLBOW on 9UE.cif Processing a loop 9UE O2 C7 double 1.333 0.020 1.333 9UE C5 C6 single 1.331 0.020 1.331 9UE C5 C4 single 2.332 0.020 2.332 9UE C C1 single 1.488 0.020 1.488 9UE C19 N1 single 1.821 0.020 1.821 9UE C6 C29 single 1.261 0.020 1.261 9UE C6 N single 1.909 0.020 1.909 9UE O1 C4 double 1.047 0.020 1.047 9UE C4 O single 1.112 0.020 1.112 9UE C34 C29 aromatic 1.542 0.020 1.542 9UE C34 C33 aromatic 1.227 0.020 1.227 9UE C7 N single 2.531 0.020 2.531 9UE C7 C8 single 0.817 0.020 0.817 9UE BR C28 single 1.886 0.020 1.886 9UE C1 C2 single 2.001 0.020 2.001 9UE C1 C15 single 1.097 0.020 1.097 9UE C29 C30 aromatic 1.267 0.020 1.267 9UE C20 C8 single 1.936 0.020 1.936 9UE C20 C21 single 0.947 0.020 0.947 9UE O C3 single 0.969 0.020 0.969 9UE C33 C32 aromatic 1.455 0.020 1.455 9UE C3 C2 single 1.915 0.020 1.915 9UE C3 C35 single 1.561 0.020 1.561 9UE N1 C8 single 1.905 0.020 1.905 9UE N1 C9 single 1.557 0.020 1.557 9UE C10 C18 single 1.719 0.020 1.719 9UE C10 C9 single 1.548 0.020 1.548 9UE C10 N2 single 0.000 0.020 0.000 9UE C17 C12 single 1.420 0.020 1.420 9UE C15 C14 double 2.104 0.020 2.104 9UE C9 O3 double 1.620 0.020 1.620 9UE C30 C31 aromatic 1.400 0.020 1.400 9UE C32 C31 aromatic 1.368 0.020 1.368 9UE C32 O5 single 1.448 0.020 1.448 9UE C28 C21 aromatic 1.154 0.020 1.154 9UE C28 N3 aromatic 1.604 0.020 1.604 9UE C21 C22 aromatic 1.717 0.020 1.717 9UE N2 C11 single 2.645 0.020 2.645 9UE C11 O4 double 0.802 0.020 0.802 9UE C11 C12 single 3.171 0.020 3.171 1.527126 Sorry: Bond length too long : 3.17