INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jeo_9807/12_2022/6jeo_9807.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 6jeo_9807.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 : 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 eLBOW is skipping CLA 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 Attempting to download Chemical Components file for CL0 Running eLBOW on CL0.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:( 6.674, 0.339, 0.037) and Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) should be unknown, not 6.94 Bond between Atom MG ( 1) xyz:( 6.674, 0.339, 0.037) and Atom NB (17) xyz:( 3.718, 5.302, 6.287) should be unknown, not 8.51 Bond between Atom MG ( 1) xyz:( 6.674, 0.339, 0.037) and Atom NC (25) xyz:( 5.585, 5.122, 3.818) should be unknown, not 6.19 Bond between Atom CHA( 2) xyz:( 3.769, 0.037, -2.930) and Atom C4D(37) xyz:( 4.314, 0.273, 1.441) should be unknown, not 4.41 Bond between Atom CHB( 3) xyz:( 1.365, 6.319, 5.310) and Atom C4A(10) xyz:( 0.859, 3.154, -0.322) should be unknown, not 6.48 Bond between Atom CHD( 5) xyz:( 6.684, 2.819, 5.019) and Atom C1D(34) xyz:( 4.316, -0.908, -0.617) should be unknown, not 7.16 Bond between Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) and Atom C1A( 7) xyz:( 3.417, 1.461, -2.400) should be unknown, not 6.85 Bond between Atom NA ( 6) xyz:( 2.915, 5.141, 3.353) and Atom C4A(10) xyz:( 0.859, 3.154, -0.322) should be unknown, not 4.66 Bond between Atom C2A( 8) xyz:( 2.908, 4.380, -1.057) and Atom CAA(12) xyz:( 3.408, 0.234, -0.224) should be unknown, not 4.26 Bond between Atom C2B(19) xyz:( 2.553, 6.987, 7.317) and Atom CMB(22) xyz:( 8.292, 4.247, -3.254) should be unknown, not 12.34 Bond between Atom C3B(20) xyz:( 3.884, 7.271, 7.456) and Atom CAB(23) xyz:(10.505, 3.897, -1.011) should be unknown, not 11.27 Bond between Atom C2C(27) xyz:( 7.661, 6.298, 4.566) and Atom CMC(30) xyz:( 8.435, 2.192, 4.725) should be unknown, not 4.18 Bond between Atom C3C(28) xyz:( 8.016, 4.879, 4.389) and Atom CAC(31) xyz:( 7.753, -0.897, 5.124) should be unknown, not 5.83 Bond between Atom C1D(34) xyz:( 4.316, -0.908, -0.617) and Atom C2D(35) xyz:( 5.878, 1.199, 4.603) should be unknown, not 5.84 Bond between Atom C2D(35) xyz:( 5.878, 1.199, 4.603) and Atom CMD(38) xyz:( 7.957, -4.917, 0.345) should be unknown, not 7.74 Bond between Atom C3D(36) xyz:( 5.105, 1.143, 3.269) and Atom CAD(39) xyz:( 3.955, -1.279, -2.173) should be unknown, not 6.07 Bond between Atom CAD(39) xyz:( 3.955, -1.279, -2.173) and Atom OBD(40) xyz:( 5.122, -5.176, -2.258) should be unknown, not 4.07 Bond between Atom C10(55) xyz:(-9.843, 1.179, 3.221) and Atom C11(56) xyz:(-12.439, 0.295, 0.160) should be unknown, not 4.11 Bond between Atom CHB( 3) xyz:( 1.365, 6.319, 5.310) and Atom H1 (66) xyz:( 5.353, 3.347, -2.605) should be unknown, not 9.35 Bond between Atom CHC( 4) xyz:( 5.858, 7.026, 5.816) and Atom H2 (67) xyz:( 9.527, 2.932, 1.841) should be unknown, not 6.78 Bond between Atom CHD( 5) xyz:( 6.684, 2.819, 5.019) and Atom H3 (68) xyz:( 8.279, -2.694, 2.591) should be unknown, not 6.23 Bond between Atom CMA(11) xyz:( 2.898, 3.154, 1.119) and Atom H4 (69) xyz:( 1.799, 2.279, -3.167) should be unknown, not 4.51 Bond between Atom CMA(11) xyz:( 2.898, 3.154, 1.119) and Atom H5 (70) xyz:( 3.114, 3.459, -2.954) should be unknown, not 4.09 Bond between Atom CMA(11) xyz:( 2.898, 3.154, 1.119) and Atom H6 (71) xyz:( 3.425, 1.921, -3.794) should be unknown, not 5.09 Bond between Atom C9 (54) xyz:(-11.882, 1.179, 1.780) and Atom H45(110) xyz:(-9.691, -0.377, -1.690) should be unknown, not 4.39 Bond between Atom C9 (54) xyz:(-11.882, 1.179, 1.780) and Atom H46(111) xyz:(-8.792, -1.146, -0.361) should be unknown, not 4.42 Bond between Atom C10(55) xyz:(-9.843, 1.179, 3.221) and Atom H49(114) xyz:(-11.270, 1.449, -1.234) should be unknown, not 4.69 Bond between Atom C14(59) xyz:(-16.760, 0.644, 1.646) and Atom H55(120) xyz:(-13.881, -1.739, -0.584) should be unknown, not 4.35 Bond between Atom C14(59) xyz:(-16.760, 0.644, 1.646) and Atom H57(122) xyz:(-14.871, -0.945, -1.832) should be unknown, not 4.26 Bond between Atom C15(60) xyz:(-14.721, 0.644, 3.087) and Atom H59(124) xyz:(-16.332, 0.942, -1.252) should be unknown, not 4.64 Bond between Atom C2A( 8) xyz:( 2.908, 4.380, -1.057) and Atom H71(136) xyz:( 3.253, -0.672, -2.169) should be unknown, not 5.18 CL0 MG NA single 6.942 0.020 6.942 1.895092 Sorry: Bond length too long : 6.94