Starting phenix.real_space_refine on Sat Jul 4 11:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.map" model { file = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ut9_26763/07_2026/7ut9_26763.cif" } resolution = 2.44 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= 0.001 sd= 0.023 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: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 36 7.16 5 P 5 5.49 5 Mg 2 5.21 5 S 181 5.16 5 C 12745 2.51 5 N 3410 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s 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: 20243 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" 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: "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: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3776 Classifications: {'peptide': 475} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 453} 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: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "F" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2053 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'ATP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 34.262 57.217 64.970 1.00 3.39 S ATOM 1170 SG CYS A 154 54.877 56.074 54.775 1.00 19.77 S ATOM 4549 SG CYS B 95 52.780 59.611 50.941 1.00 25.54 S ATOM 465 SG CYS A 62 48.929 58.465 56.120 1.00 17.76 S ATOM 652 SG CYS A 88 54.054 62.355 56.378 1.00 7.61 S ATOM 652 SG CYS A 88 54.054 62.355 56.378 1.00 7.61 S ATOM 5002 SG CYS B 153 58.100 59.286 52.807 1.00 21.02 S ATOM 4369 SG CYS B 70 55.979 65.708 50.649 1.00 20.59 S ATOM 4549 SG CYS B 95 52.780 59.611 50.941 1.00 25.54 S ATOM 10039 SG CYS C 275 48.830 133.419 59.051 1.00 26.79 S ATOM 9120 SG CYS C 154 30.583 132.368 44.804 1.00 30.68 S ATOM 12499 SG CYS D 95 33.084 128.059 42.439 1.00 15.17 S ATOM 8415 SG CYS C 62 36.117 130.108 48.002 1.00 30.20 S ATOM 8602 SG CYS C 88 30.718 126.526 48.089 1.00 0.00 S ATOM 8602 SG CYS C 88 30.718 126.526 48.089 1.00 0.00 S ATOM 12952 SG CYS D 153 27.789 128.704 43.261 1.00 26.21 S ATOM 12319 SG CYS D 70 29.847 122.054 42.546 1.00 19.19 S ATOM 12499 SG CYS D 95 33.084 128.059 42.439 1.00 15.17 S ATOM 16598 SG CYS E 97 63.147 47.099 53.984 1.00 9.13 S ATOM 16869 SG CYS E 132 68.504 46.279 56.879 1.00 31.04 S ATOM 18655 SG CYS F 97 67.834 51.892 53.755 1.00 22.17 S ATOM 18926 SG CYS F 132 68.611 46.982 50.334 1.00 43.71 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM20052 S1 CLF B 601 .*. S " "HETATM20101 S1 CLF D 602 .*. S " Time building chain proxies: 4.72, per 1000 atoms: 0.23 Number of scatterers: 20243 At special positions: 0 Unit cell: (115.23, 160.32, 102.705, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Fe 36 26.01 S 181 16.00 P 5 15.00 Mg 2 11.99 O 3862 8.00 N 3410 7.00 C 12745 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.