INPUT Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f68_28877/12_2022/8f68_28877.pdb Reading option "hydrogens=False" from command line Writing effective parameters to 8f68_28877.eff Ligand restraint generation using eLBOW, phenix.elbow eLBOW is skipping HEM Attempting to download Chemical Components file for HEO Running eLBOW on HEO.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 FE ( 1) xyz:( 0.184, -3.116, -1.296) and Atom NB (17) xyz:(-2.107, 0.613, 1.686) should be unknown, not 5.30 Bond between Atom FE ( 1) xyz:( 0.184, -3.116, -1.296) and Atom NC (23) xyz:(-2.107, 2.778, -2.064) should be unknown, not 6.37 Bond between Atom CHA( 2) xyz:( 5.834, 2.399, 4.548) and Atom C1A( 7) xyz:(-2.401, -4.307, -2.065) should be unknown, not 12.51 Bond between Atom CHA( 2) xyz:( 5.834, 2.399, 4.548) and Atom HHA(60) xyz:(-5.395, -1.528, 0.928) should be unknown, not 12.43 Bond between Atom CHB( 3) xyz:( 1.181, 2.597, 3.671) and Atom C4A(10) xyz:(-2.404, -1.935, -2.071) should be unknown, not 8.15 Bond between Atom CHB( 3) xyz:( 1.181, 2.597, 3.671) and Atom HHB(61) xyz:(-0.600, -2.911, -2.577) should be unknown, not 8.52 Bond between Atom CHC( 4) xyz:( 0.693, 6.041, 6.257) and Atom HHC(62) xyz:( 0.975, 2.782, -2.641) should be unknown, not 9.48 Bond between Atom CHD( 5) xyz:( 5.100, 7.625, 5.137) and Atom HHD(63) xyz:(-3.933, 4.135, 0.752) should be unknown, not 10.63 Bond between Atom C1A( 7) xyz:(-2.401, -4.307, -2.065) and Atom C2A( 8) xyz:( 3.734, 1.333, 2.737) should be unknown, not 9.62 Bond between Atom C2A( 8) xyz:( 3.734, 1.333, 2.737) and Atom CAA(12) xyz:(-5.931, -3.047, -1.755) should be unknown, not 11.52 Bond between Atom C3A( 9) xyz:( 2.450, 1.865, 2.248) and Atom C4A(10) xyz:(-2.404, -1.935, -2.071) should be unknown, not 7.53 Bond between Atom C3A( 9) xyz:( 2.450, 1.865, 2.248) and Atom CMA(11) xyz:(-3.443, -3.766, -3.576) should be unknown, not 10.02 Bond between Atom NB (17) xyz:(-2.107, 0.613, 1.686) and Atom C1B(18) xyz:( 1.391, 2.670, 5.444) should be unknown, not 5.53 Bond between Atom NB (17) xyz:(-2.107, 0.613, 1.686) and Atom C4B(21) xyz:( 1.305, 4.468, 6.877) should be unknown, not 7.31 Bond between Atom C2B(19) xyz:(-0.019, 2.777, 5.890) and Atom C3B(20) xyz:( 4.013, 2.102, -1.666) should be unknown, not 8.59 Bond between Atom C2B(19) xyz:(-0.019, 2.777, 5.890) and Atom CMB(22) xyz:( 2.285, -2.289, -1.356) should be unknown, not 9.14 Bond between Atom C3B(20) xyz:( 4.013, 2.102, -1.666) and Atom C4B(21) xyz:( 1.305, 4.468, 6.877) should be unknown, not 9.27 Bond between Atom NC (23) xyz:(-2.107, 2.778, -2.064) and Atom C1C(24) xyz:( 1.500, 6.866, 4.747) should be unknown, not 8.72 Bond between Atom NC (23) xyz:(-2.107, 2.778, -2.064) and Atom C4C(27) xyz:( 3.536, 7.508, 4.117) should be unknown, not 9.61 Bond between Atom C2C(25) xyz:( 1.589, 8.249, 4.900) and Atom CMC(28) xyz:(-1.018, 4.913, -3.739) should be unknown, not 9.62 Bond between Atom C3C(26) xyz:( 2.839, 8.639, 4.516) and Atom CAC(29) xyz:(-3.663, 5.521, -2.090) should be unknown, not 9.78 Bond between Atom ND (31) xyz:(-2.107, -1.552, -2.064) and Atom C1D(32) xyz:( 5.839, 6.142, 5.885) should be unknown, not 13.62 Bond between Atom ND (31) xyz:(-2.107, -1.552, -2.064) and Atom C4D(35) xyz:( 6.137, 3.760, 5.686) should be unknown, not 12.50 Bond between Atom C2D(33) xyz:( 7.349, 5.876, 5.655) and Atom CMD(36) xyz:(-3.925, 2.853, 3.701) should be unknown, not 11.83 Bond between Atom C3D(34) xyz:( 7.530, 4.413, 5.541) and Atom CAD(37) xyz:(-4.729, -0.241, 3.795) should be unknown, not 13.23 HEO FE NA single 2.127 0.020 2.127 HEO FE NB single 5.296 0.020 5.296 2.126 Sorry: Bond length too long : 5.30