INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oy8_13110/04_2022/7oy8_13110.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 7oy8_13110.eff Preparation for phenix.refine Ligand restraint generation using eLBOW, phenix.elbow Attempting to download Chemical Components file for RQ0 Running eLBOW on RQ0.cif MoleculeClass : C:58 N: 1 O: 3 (CHEMICAL COMPONENTS format) 147 atoms 147 bonds 262 angles 328 dihedrals 1 rings (groups, rings, atoms) 1 6 0 chirals Build ligand and use user provided restraints : RQ0 Build ligand and use monomer library to name atoms : CRT Using monomer library entry CRT as template Build ligand and use monomer library to name atoms : BPH Using monomer library entry BPH as template Processing a loop group index 6 change? False ChiralClass Atom H8 (115) xyz:(-3.236, -5.062, -5.456) Atom C8 (53) xyz:(-4.225, -5.025, -5.017) R Atom C7 (52) xyz:(-4.453, -3.638, -4.380) Atom C9 (54) xyz:(-4.343, -6.088, -3.961) Atom C10(55) xyz:(-5.286, -5.268, -6.117) not correct chiralisation group index 7 change? False ChiralClass Atom H13(125) xyz:(-4.765, -7.767, -9.120) Atom C13(58) xyz:(-5.746, -8.053, -8.766) R Atom C12(57) xyz:(-6.140, -7.163, -7.556) Atom C14(59) xyz:(-6.753, -7.870, -9.873) Atom C15(60) xyz:(-5.724, -9.525, -8.333) not correct chiralisation Build ligand and use monomer library to name atoms : LMT Using monomer library entry LMT as template Attempting to download Chemical Components file for CD4 Running eLBOW on CD4.cif skipping pickle dump skipping pickle dump skipping pickle dump MoleculeClass : C:65 O:17 P: 2 (CHEMICAL COMPONENTS format) 208 atoms 207 bonds 399 angles 557 dihedrals 0 rings (groups, rings, atoms) 0 0 2 chirals : R R Build ligand and use user provided restraints : CD4 Build ligand and use monomer library to name atoms : PGW Using monomer library entry PGW as template Attempting to download Chemical Components file for 07D Running eLBOW on 07D.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 NB (21) xyz:( 4.698, 6.406, 4.056) and Atom MG (66) xyz:(184.942, 125.750, 128.747) should be unknown, not 249.56 Bond between Atom ND (22) xyz:( 3.220, 4.217, 3.289) and Atom MG (66) xyz:(184.942, 125.750, 128.747) should be unknown, not 252.06 Bond between Atom C1A(23) xyz:(182.505, 126.669, 127.876) and Atom C2A(27) xyz:( 2.049, 3.175, 7.102) should be unknown, not 249.80 Bond between Atom C1A(23) xyz:(182.505, 126.669, 127.876) and Atom CHA(50) xyz:(186.613, 130.276, 131.772) should be unknown, not 6.71 Bond between Atom C2A(27) xyz:( 2.049, 3.175, 7.102) and Atom CAA(39) xyz:(187.300, 129.820, 126.964) should be unknown, not 254.41 Bond between Atom C2B(28) xyz:( 4.530, 8.772, 4.714) and Atom CMB(55) xyz:(183.626, 124.753, 123.386) should be unknown, not 244.15 Bond between Atom C2C(29) xyz:( 8.216, 3.887, 3.435) and Atom CMC(56) xyz:(181.986, 121.447, 130.458) should be unknown, not 245.26 Bond between Atom C2D(30) xyz:( 2.794, 2.372, 1.623) and Atom CMD(57) xyz:(185.199, 127.379, 134.211) should be unknown, not 257.83 Bond between Atom C3A(31) xyz:( 1.653, 4.598, 7.127) and Atom C4A(35) xyz:(182.624, 124.341, 128.318) should be unknown, not 248.55 Bond between Atom C3A(31) xyz:( 1.653, 4.598, 7.127) and Atom CMA(54) xyz:(183.680, 129.886, 125.719) should be unknown, not 250.79 Bond between Atom C3B(32) xyz:( 5.902, 8.544, 4.214) and Atom CAB(40) xyz:(182.860, 121.998, 125.163) should be unknown, not 242.52 Bond between Atom C3C(33) xyz:( 7.559, 2.914, 2.734) and Atom CAC(41) xyz:(184.768, 121.942, 132.677) should be unknown, not 249.91 Bond between Atom C3D(34) xyz:( 1.864, 2.116, 2.771) and Atom CAD(42) xyz:(186.622, 131.503, 129.596) should be unknown, not 258.77 Bond between Atom C4A(35) xyz:(182.624, 124.341, 128.318) and Atom CHB(51) xyz:( 2.681, 6.925, 5.847) should be unknown, not 247.32 Bond between Atom C4D(38) xyz:( 2.168, 3.185, 3.811) and Atom CHA(50) xyz:(186.613, 130.276, 131.772) should be unknown, not 257.97 Bond between Atom NC (59) xyz:( 6.107, 3.715, 4.331) and Atom MG (66) xyz:(184.942, 125.750, 128.747) should be unknown, not 249.71 Bond between Atom CHB(51) xyz:( 2.681, 6.925, 5.847) and Atom H50(116) xyz:(184.434, 127.010, 124.492) should be unknown, not 248.05 Bond between Atom CHC(52) xyz:( 7.435, 6.094, 3.981) and Atom H51(117) xyz:(183.135, 121.779, 127.843) should be unknown, not 244.12 Bond between Atom CHD(53) xyz:( 5.114, 2.735, 1.904) and Atom H52(118) xyz:(185.009, 124.691, 133.158) should be unknown, not 253.90 07D C4 C3 single 1.525 0.020 1.525 07D C5 C6 single 1.511 0.020 1.511 07D C5 C3 single 1.520 0.020 1.520 07D C6 C7 single 1.519 0.020 1.519 07D C7 C8 double 1.303 0.020 1.303 07D C8 C10 single 1.524 0.020 1.524 07D C8 C9 single 1.537 0.020 1.537 07D C10 C11 single 1.503 0.020 1.503 07D C13 C15 single 1.520 0.020 1.520 07D C13 C12 double 1.299 0.020 1.299 07D C13 C14 single 1.511 0.020 1.511 07D C15 C16 single 1.503 0.020 1.503 07D C17 C16 single 1.528 0.020 1.528 07D C17 C18 double 1.293 0.020 1.293 07D C20 C18 single 1.533 0.020 1.533 07D C1 C2 single 1.505 0.020 1.505 07D C1 O2A single 1.451 0.020 1.451 07D C11 C12 single 1.521 0.020 1.521 07D C18 C19 single 1.540 0.020 1.540 07D C2 C3 double 1.289 0.020 1.289 07D NB C1B double 1.493 0.020 1.493 07D NB C4B single 1.481 0.020 1.481 07D NB MG single 249.557 0.020 249.557 1.895092 Sorry: Bond length too long : 249.56