INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxr_10995/12_2022/6yxr_10995.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6yxr_10995.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 Attempting to download Chemical Components file for LUT Running eLBOW on LUT.cif MoleculeClass : C:40 O: 2 (CHEMICAL COMPONENTS format) 98 atoms 99 bonds 176 angles 242 dihedrals 2 rings (groups, rings, atoms) 2 12 3 chirals : S R S Build ligand and use user provided restraints : LUT Build ligand and use monomer library to name atoms : DGD Using monomer library entry DGD as template Build ligand and use monomer library to name atoms : XAT Using monomer library entry XAT as template Build ligand and use chemical components : SF4 MoleculeClass : S: 4 Fe: 4 (CHEMICAL COMPONENTS format) 8 atoms 12 bonds 0 angles 0 dihedrals 0 rings 0 chirals Mapped the ligand (SF4) to the monomer library restraints Attempting to download Chemical Components file for CHL Running eLBOW on CHL.cif Residue has metal at the centre of a coordination sphere. Using input geometry to generate restraints. Hydrogens may not be added. Difficulties in the ring structures may lead to problems later Suspicious bonds Bond between Atom MG ( 1) xyz:( 6.580, 0.302, 0.016) and Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) should be unknown, not 6.93 Bond between Atom MG ( 1) xyz:( 6.580, 0.302, 0.016) and Atom NB (17) xyz:( 3.718, 5.302, 6.287) should be unknown, not 8.52 Bond between Atom MG ( 1) xyz:( 6.580, 0.302, 0.016) and Atom NC (25) xyz:( 5.585, 5.122, 3.818) should be unknown, not 6.22 Bond between Atom CHB( 3) xyz:( 1.365, 6.319, 5.310) and Atom C4A(10) xyz:( 0.233, 3.070, -0.381) should be unknown, not 6.65 Bond between Atom CHD( 5) xyz:( 6.684, 2.819, 5.019) and Atom C1D(35) xyz:( 4.222, -0.945, -0.638) should be unknown, not 7.23 Bond between Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) and Atom C1A( 7) xyz:( 3.071, 1.247, -1.653) should be unknown, not 6.34 Bond between Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) and Atom C4A(10) xyz:( 0.233, 3.070, -0.381) should be unknown, not 5.04 Bond between Atom C2A( 8) xyz:( 2.282, 4.296, -1.116) and Atom CAA(12) xyz:( 3.062, 0.020, 0.523) should be unknown, not 4.65 Bond between Atom C2B(19) xyz:( 2.553, 6.987, 7.317) and Atom CMB(22) xyz:( 5.949, 5.239, 2.016) should be unknown, not 6.53 Bond between Atom C3B(20) xyz:( 3.884, 7.271, 7.456) and Atom CAB(23) xyz:( 9.072, 4.708, 1.805) should be unknown, not 8.09 Bond between Atom C2C(27) xyz:( 7.661, 6.298, 4.566) and Atom CMC(30) xyz:(10.978, 0.896, -2.977) should be unknown, not 9.85 Bond between Atom C3C(28) xyz:( 8.016, 4.879, 4.389) and Atom CAC(32) xyz:(10.522, -2.263, -2.558) should be unknown, not 10.27 Bond between Atom C1D(35) xyz:( 4.222, -0.945, -0.638) and Atom C2D(36) xyz:( 5.878, 1.199, 4.603) should be unknown, not 5.90 Bond between Atom C2D(36) xyz:( 5.878, 1.199, 4.603) and Atom CMD(39) xyz:( 7.554, -4.469, 2.395) should be unknown, not 6.31 Bond between Atom CGD(43) xyz:( 2.396, -0.649, 4.486) and Atom O1D(44) xyz:( 2.723, -3.165, -1.103) should be unknown, not 6.14 Bond between Atom CGD(43) xyz:( 2.396, -0.649, 4.486) and Atom O2D(45) xyz:( 1.675, -4.452, 0.355) should be unknown, not 5.66 Bond between Atom C10(56) xyz:(-10.333, 1.507, 3.163) and Atom C11(57) xyz:(-12.863, 0.323, -0.002) should be unknown, not 4.22 Bond between Atom C15(61) xyz:(-15.196, 0.890, 2.895) and Atom C16(62) xyz:(-17.830, -0.157, -0.071) should be unknown, not 4.10 Bond between Atom CHB( 3) xyz:( 1.365, 6.319, 5.310) and Atom H1 (67) xyz:( 4.037, 3.665, 0.123) should be unknown, not 6.41 Bond between Atom CHC( 4) xyz:( 5.858, 7.026, 5.816) and Atom H2 (68) xyz:(10.036, 2.726, -0.547) should be unknown, not 8.74 Bond between Atom CHD( 5) xyz:( 6.684, 2.819, 5.019) and Atom H3 (69) xyz:( 9.272, -3.013, 0.154) should be unknown, not 8.02 Bond between Atom CMA(11) xyz:( 2.272, 3.070, 1.060) and Atom H4 (70) xyz:( 2.181, 1.396, -3.291) should be unknown, not 4.66 Bond between Atom CMA(11) xyz:( 2.272, 3.070, 1.060) and Atom H5 (71) xyz:( 3.327, 2.721, -2.973) should be unknown, not 4.18 Bond between Atom CMA(11) xyz:( 2.272, 3.070, 1.060) and Atom H6 (72) xyz:( 3.915, 1.046, -3.100) should be unknown, not 4.91 Bond between Atom C9 (55) xyz:(-12.372, 1.507, 1.722) and Atom H44(110) xyz:(-10.016, -0.734, -1.485) should be unknown, not 4.57 Bond between Atom C9 (55) xyz:(-12.372, 1.507, 1.722) and Atom H45(111) xyz:(-9.192, -1.152, 0.036) should be unknown, not 4.47 Bond between Atom C10(56) xyz:(-10.333, 1.507, 3.163) and Atom H47(113) xyz:(-11.617, 1.126, -1.566) should be unknown, not 4.92 Bond between Atom C14(60) xyz:(-17.235, 0.890, 1.454) and Atom H53(119) xyz:(-14.261, -1.848, -0.316) should be unknown, not 4.41 Bond between Atom C14(60) xyz:(-17.235, 0.890, 1.454) and Atom H55(121) xyz:(-15.180, -1.389, -1.770) should be unknown, not 4.45 Bond between Atom C2A( 8) xyz:( 2.282, 4.296, -1.116) and Atom H67(133) xyz:( 2.907, -0.886, -1.422) should be unknown, not 5.23 Bond between Atom C15(61) xyz:(-15.196, 0.890, 2.895) and Atom H69(135) xyz:(-16.670, 0.563, -1.738) should be unknown, not 4.87 CHL MG NA single 6.927 0.020 6.927 1.895092 Sorry: Bond length too long : 6.93