INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoo_11326/12_2022/6zoo_11326.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6zoo_11326.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 Build ligand and use monomer library to name atoms : LMT Using monomer library entry LMT as template Build ligand and use monomer library to name atoms : SNK Using monomer library entry SNK as template Build ligand and use monomer library to name atoms : PQN Using monomer library entry PQN as template group index 1 change? False ChiralClass Atom H18(53) xyz:( 0.802, 0.342, -1.080) Atom C18(21) xyz:( 1.035, 0.750, -0.105) R Atom C17(20) xyz:(-0.204, 0.676, 0.788) Atom C19(22) xyz:( 1.469, 2.206, -0.253) Atom C20(23) xyz:( 2.167, -0.057, 0.527) not correct chiralisation group index 2 change? False ChiralClass Atom H23(63) xyz:( 4.510, -2.469, -1.415) Atom C23(26) xyz:( 5.117, -2.032, -0.631) R Atom C22(25) xyz:( 4.472, -0.735, -0.151) Atom C24(27) xyz:( 5.223, -3.010, 0.535) Atom C25(28) xyz:( 6.516, -1.735, -1.176) not correct chiralisation eLBOW is skipping CLA More than 20 percent of the atoms are missing for 3PH as compared to the Monomer Library More than 20 percent of the atoms are missing for 3PH as compared to the Chemical Components 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