Starting phenix.real_space_refine on Fri Jul 3 23:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.cif" model { file = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8enn_28274/07_2026/8enn_28274.map" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10093 2.51 5 N 2672 2.21 5 O 3811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16749 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3586 Classifications: {'peptide': 453} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 432} Chain breaks: 4 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' FE': 1, '1N7': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "B" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 273 Classifications: {'water': 273} Link IDs: {None: 272} Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1978 SG CYS A 275 49.873 36.397 101.670 1.00 85.80 S ATOM 1059 SG CYS A 154 31.614 49.269 102.823 1.00 41.77 S ATOM 4345 SG CYS B 95 33.250 52.000 98.577 1.00 38.28 S ATOM 354 SG CYS A 62 36.804 46.716 100.018 1.00 33.83 S ATOM 541 SG CYS A 88 30.845 47.419 96.860 1.00 50.41 S ATOM 541 SG CYS A 88 30.845 47.419 96.860 1.00 50.41 S ATOM 4798 SG CYS B 153 28.473 50.872 99.635 1.00 48.92 S ATOM 4165 SG CYS B 70 30.115 52.565 92.825 1.00 55.47 S ATOM 4345 SG CYS B 95 33.250 52.000 98.577 1.00 38.28 S ATOM 9849 SG CYS C 275 32.957 37.671 26.402 1.00 41.73 S ATOM 8930 SG CYS C 154 52.364 48.841 25.418 1.00 34.19 S ATOM 12309 SG CYS D 95 50.919 51.714 29.671 1.00 48.70 S ATOM 8225 SG CYS C 62 46.929 46.663 28.126 1.00 25.03 S ATOM 8412 SG CYS C 88 52.777 46.760 31.392 1.00 42.60 S ATOM 8412 SG CYS C 88 52.777 46.760 31.392 1.00 42.60 S ATOM 12762 SG CYS D 153 55.582 50.106 28.613 1.00 60.25 S ATOM 12129 SG CYS D 70 53.989 51.737 35.515 1.00 54.91 S ATOM 12309 SG CYS D 95 50.919 51.714 29.671 1.00 48.70 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM15743 S1 CLF B 601 .*. S " "HETATM15834 S1 CLF D 602 .*. S " Time building chain proxies: 3.74, per 1000 atoms: 0.22 Number of scatterers: 16749 At special positions: 0 Unit cell: (85.15, 98.15, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 3811 8.00 N 2672 7.00 C 10093 6.00 sf(0) = scattering factor at diffraction angle 0. Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 2 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary.