Starting phenix.real_space_refine on Fri Jul 3 23:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.map" model { file = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dby_27317/07_2026/8dby_27317.cif" } resolution = 2.26 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= 0.033 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 138 5.16 5 C 10168 2.51 5 N 2702 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 16794 Number of models: 1 Model: "" Number of chains: 12 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: 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: 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: 17 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 17 Unusual residues: {' FE': 2, '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: 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: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Unexpected atoms: {'CLF,S1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 249 Classifications: {'water': 249} Link IDs: {None: 248} Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Classifications: {'water': 256} Link IDs: {None: 255} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 24.390 52.573 58.418 1.00 35.40 S ATOM 1170 SG CYS A 154 22.651 33.615 46.326 1.00 25.15 S ATOM 4549 SG CYS B 95 26.918 35.091 43.479 1.00 38.94 S ATOM 465 SG CYS A 62 25.806 38.893 48.750 1.00 22.00 S ATOM 652 SG CYS A 88 28.585 32.914 48.465 1.00 33.57 S ATOM 652 SG CYS A 88 28.585 32.914 48.465 1.00 33.57 S ATOM 5002 SG CYS B 153 25.800 30.059 44.880 1.00 36.56 S ATOM 4369 SG CYS B 70 32.605 31.514 43.370 1.00 32.38 S ATOM 4549 SG CYS B 95 26.918 35.091 43.479 1.00 38.94 S ATOM 10053 SG CYS C 275 99.106 31.918 58.411 1.00 35.78 S ATOM 9134 SG CYS C 154 100.854 50.890 46.325 1.00 25.77 S ATOM 12513 SG CYS D 95 96.494 49.486 43.498 1.00 38.34 S ATOM 8429 SG CYS C 62 97.708 45.674 48.642 1.00 21.26 S ATOM 8616 SG CYS C 88 94.900 51.619 48.455 1.00 33.41 S ATOM 8616 SG CYS C 88 94.900 51.619 48.455 1.00 33.41 S ATOM 12966 SG CYS D 153 97.672 54.524 44.872 1.00 32.04 S ATOM 12333 SG CYS D 70 90.851 52.973 43.337 1.00 33.74 S ATOM 12513 SG CYS D 95 96.494 49.486 43.498 1.00 38.34 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM15962 S1 BCLF B 602 .*. S " "HETATM16010 S1 BCLF D 601 .*. S " Time building chain proxies: 4.18, per 1000 atoms: 0.25 Number of scatterers: 16794 At special positions: 0 Unit cell: (124.15, 85.15, 94.9, 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 138 16.00 O 3752 8.00 N 2702 7.00 C 10168 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.