Starting phenix.real_space_refine on Sat Jul 4 12:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfc_27404/07_2026/8dfc_27404.map" } resolution = 2.48 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= 0.050 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: 10 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 36 7.16 5 Al 2 5.89 5 P 4 5.49 5 Mg 2 5.21 5 S 184 5.16 5 C 12770 2.51 5 N 3416 2.21 5 O 4289 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 20713 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "D" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Classifications: {'water': 152} Link IDs: {None: 151} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 59.960 34.612 26.567 1.00 44.32 S ATOM 1170 SG CYS A 154 46.340 52.145 21.510 1.00 34.77 S ATOM 4554 SG CYS B 95 43.803 51.476 26.303 1.00 44.22 S ATOM 465 SG CYS A 62 49.106 47.637 25.314 1.00 37.18 S ATOM 652 SG CYS A 88 48.588 54.021 27.092 1.00 39.97 S ATOM 652 SG CYS A 88 48.588 54.021 27.092 1.00 39.97 S ATOM 5007 SG CYS B 153 44.366 56.249 24.068 1.00 54.18 S ATOM 4374 SG CYS B 70 43.576 55.750 31.074 1.00 60.52 S ATOM 4554 SG CYS B 95 43.803 51.476 26.303 1.00 44.22 S ATOM 10054 SG CYS C 275 62.680 70.133 95.323 1.00 48.24 S ATOM 9135 SG CYS C 154 51.855 51.047 101.815 1.00 39.02 S ATOM 12519 SG CYS D 95 48.670 51.483 97.345 1.00 42.50 S ATOM 8430 SG CYS C 62 53.797 55.884 97.765 1.00 30.44 S ATOM 8617 SG CYS C 88 53.495 49.532 96.088 1.00 48.51 S ATOM 8617 SG CYS C 88 53.495 49.532 96.088 1.00 48.51 S ATOM 12972 SG CYS D 153 50.220 46.950 99.588 1.00 39.79 S ATOM 12339 SG CYS D 70 48.429 47.123 92.696 1.00 45.85 S ATOM 12519 SG CYS D 95 48.670 51.483 97.345 1.00 42.50 S ATOM 16886 SG CYS E 132 47.006 40.659 113.776 1.00 21.13 S ATOM 16615 SG CYS E 97 50.621 39.823 109.096 1.00 25.40 S ATOM 18951 SG CYS F 132 53.612 41.056 114.761 1.00 20.58 S ATOM 18680 SG CYS F 97 50.712 45.727 112.318 1.00 12.88 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM20093 S1 CLF B 600 .*. S " "HETATM20141 S1 CLF D 600 .*. S " Time building chain proxies: 4.62, per 1000 atoms: 0.22 Number of scatterers: 20713 At special positions: 0 Unit cell: (100.672, 99.008, 163.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Mo 2 41.97 Fe 36 26.01 S 184 16.00 P 4 15.00 Al 2 13.00 Mg 2 11.99 F 8 9.00 O 4289 8.00 N 3416 7.00 C 12770 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.