INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jlu_9839/12_2022/6jlu_9839.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6jlu_9839.eff Ligand restraint generation using eLBOW, phenix.elbow Build ligand and use monomer library to name atoms : LHG Using monomer library entry LHG as template Build ligand and use chemical components : OEX MoleculeClass : O: 5 Ca: 1 Mn: 4 (CHEMICAL COMPONENTS format) 10 atoms 15 bonds 0 angles 0 dihedrals 0 rings 0 chirals Mapped the ligand (OEX) to the monomer library restraints Build ligand and use monomer library to name atoms : PHO Using monomer library entry PHO as template Processing a loop Build ligand and use monomer library to name atoms : DGD Using monomer library entry DGD as template eLBOW is skipping CLA Build ligand and use monomer library to name atoms : PL9 Using monomer library entry PL9 as template Attempting to download Chemical Components file for DD6 Running eLBOW on DD6.cif group index 4 change? False ChiralClass Atom H35(77) xyz:(-4.333, -0.505, -12.401) Atom C34(29) xyz:(-3.831, 0.105, -11.648) R ring index: 1 Atom O4 (43) xyz:(-3.551, 1.381, -12.195) Atom C33(28) xyz:(-2.660, -0.492, -11.312) ring index: 1 Atom C35(30) xyz:(-4.886, 0.300, -10.296) ring index: 1 not correct chiralisation MoleculeClass : C:40 O: 3 (CHEMICAL COMPONENTS format) 97 atoms 99 bonds 179 angles 252 dihedrals 2 rings (groups, rings, atoms) 3 15 2 chirals : S R Build ligand and use user provided restraints : DD6 Attempting to download Chemical Components file for KC1 Running eLBOW on KC1.cif Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. Suspicious bonds Bond between Atom C1A( 3) xyz:( 2.778, 4.186, 6.507) and Atom CHA(30) xyz:(-2.207, 2.014, 0.929) should be unknown, not 7.79 Bond between Atom C2A( 7) xyz:( 1.604, 4.898, 7.100) and Atom CAA(19) xyz:(-4.291, -1.002, -0.847) should be unknown, not 11.52 Bond between Atom C2B( 8) xyz:( 3.984, 8.026, 1.943) and Atom CMB(35) xyz:( 1.849, -5.510, 0.507) should be unknown, not 13.78 Bond between Atom C2C( 9) xyz:( 8.390, 3.670, 4.084) and Atom CMC(36) xyz:( 6.956, 0.476, -1.029) should be unknown, not 6.20 Bond between Atom C2D(10) xyz:( 3.442, 1.103, 3.106) and Atom CMD(37) xyz:( 0.801, 5.081, 0.370) should be unknown, not 5.50 Bond between Atom C3A(11) xyz:( 1.809, 6.328, 6.835) and Atom CMA(34) xyz:(-3.145, -3.919, -0.289) should be unknown, not 13.43 Bond between Atom C3B(12) xyz:( 5.250, 7.503, 1.403) and Atom CAB(20) xyz:( 4.681, -4.261, -0.022) should be unknown, not 11.86 Bond between Atom C3C(13) xyz:( 7.803, 2.404, 4.529) and Atom CAC(21) xyz:( 5.980, 3.399, -0.294) should be unknown, not 5.25 Bond between Atom C3D(14) xyz:( 2.226, 1.505, 3.628) and Atom CAD(22) xyz:(-2.198, 3.241, -1.247) should be unknown, not 6.81 Bond between Atom C4D(18) xyz:( 2.302, 2.915, 3.831) and Atom CHA(30) xyz:(-2.207, 2.014, 0.929) should be unknown, not 5.44 Bond between Atom CHB(31) xyz:( 2.773, 7.423, 4.780) and Atom H15(60) xyz:(-0.282, -4.393, 0.617) should be unknown, not 12.89 Bond between Atom CHC(32) xyz:( 7.267, 5.599, 2.877) and Atom H16(61) xyz:( 5.160, -2.006, -0.762) should be unknown, not 8.69 Bond between Atom CHD(33) xyz:( 5.654, 1.673, 3.934) and Atom H17(62) xyz:( 3.092, 4.001, 0.655) should be unknown, not 4.77 KC1 NB C1B single 1.440 0.020 1.440 KC1 NB C4B single 1.437 0.020 1.437 KC1 NB MG single 1.871 0.020 1.871 KC1 ND C1D aromatic 1.415 0.020 1.415 KC1 ND C4D aromatic 1.464 0.020 1.464 KC1 ND MG single 1.834 0.020 1.834 KC1 C1A C2A single 1.496 0.020 1.496 KC1 C1A CHA double 7.790 0.020 7.790 1.527126 Sorry: Bond length too long : 7.79