Starting phenix.real_space_refine on Fri Jul 3 23:03:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eno_28275/07_2026/8eno_28275.map" } resolution = 2.71 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= 0.022 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 143 5.16 5 C 10496 2.51 5 N 2781 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 16485 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3756 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 451} Chain breaks: 1 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: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3235 Classifications: {'peptide': 407} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 387} Chain breaks: 3 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: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 111} Chain breaks: 1 Chain: "A" 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: "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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2055 SG CYS A 275 51.347 36.265 124.754 1.00103.82 S ATOM 1136 SG CYS A 154 31.675 46.958 125.825 1.00 53.84 S ATOM 4515 SG CYS B 95 32.936 49.940 121.621 1.00 53.26 S ATOM 431 SG CYS A 62 37.141 44.993 122.886 1.00 68.36 S ATOM 618 SG CYS A 88 31.225 44.987 119.875 1.00 68.56 S ATOM 618 SG CYS A 88 31.225 44.987 119.875 1.00 68.56 S ATOM 4968 SG CYS B 153 28.489 48.252 122.620 1.00 65.54 S ATOM 4335 SG CYS B 70 30.009 49.971 115.706 1.00 60.21 S ATOM 4515 SG CYS B 95 32.936 49.940 121.621 1.00 53.26 S ATOM 9658 SG CYS C 275 34.962 35.504 49.456 1.00107.63 S ATOM 8739 SG CYS C 154 52.761 49.070 48.692 1.00 61.30 S ATOM 11924 SG CYS D 95 50.995 51.748 52.925 1.00 51.87 S ATOM 8034 SG CYS C 62 47.671 46.131 51.495 1.00 52.85 S ATOM 8221 SG CYS C 88 53.314 47.033 54.648 1.00 63.52 S ATOM 8221 SG CYS C 88 53.314 47.033 54.648 1.00 63.52 S ATOM 12377 SG CYS D 153 55.679 50.738 51.891 1.00 72.65 S ATOM 11744 SG CYS D 70 53.909 52.222 58.800 1.00 64.33 S ATOM 11924 SG CYS D 95 50.995 51.748 52.925 1.00 51.87 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM16350 S1 CLF B 601 .*. S " "HETATM16428 S1 CLF D 602 .*. S " Time building chain proxies: 3.61, per 1000 atoms: 0.22 Number of scatterers: 16485 At special positions: 0 Unit cell: (85.15, 96.2, 150.8, 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 143 16.00 O 3031 8.00 N 2781 7.00 C 10496 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.