Starting phenix.real_space_refine on Sat Jul 4 11:02:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut8_26760/07_2026/7ut8_26760.map" } resolution = 2.43 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 6 5.49 5 Mg 2 5.21 5 S 180 5.16 5 C 12748 2.51 5 N 3411 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 20221 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3782 Classifications: {'peptide': 476} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 454} Chain: "B" Number of atoms: 4180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Conformer: "B" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} bond proxies already assigned to first conformer: 4273 Chain: "C" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3782 Classifications: {'peptide': 476} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 454} 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: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2053 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: 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: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2081 SG CYS A 275 33.388 60.631 65.167 1.00 19.66 S ATOM 1162 SG CYS A 154 53.648 59.586 54.829 1.00 10.26 S ATOM 4547 SG CYS B 95 51.765 63.160 51.069 1.00 8.81 S ATOM 457 SG CYS A 62 47.820 61.848 56.257 1.00 20.03 S ATOM 644 SG CYS A 88 53.457 65.754 56.495 1.00 20.47 S ATOM 644 SG CYS A 88 53.457 65.754 56.495 1.00 20.47 S ATOM 5000 SG CYS B 153 57.019 62.664 52.916 1.00 19.89 S ATOM 4367 SG CYS B 70 55.011 69.039 50.844 1.00 16.40 S ATOM 4547 SG CYS B 95 51.765 63.160 51.069 1.00 8.81 S ATOM 10043 SG CYS C 275 47.661 136.996 58.795 1.00 20.63 S ATOM 9124 SG CYS C 154 29.413 135.702 45.210 1.00 30.58 S ATOM 12503 SG CYS D 95 31.839 131.376 42.643 1.00 11.82 S ATOM 8419 SG CYS C 62 34.883 133.640 48.263 1.00 15.18 S ATOM 8606 SG CYS C 88 29.401 129.685 47.992 1.00 23.03 S ATOM 8606 SG CYS C 88 29.401 129.685 47.992 1.00 23.03 S ATOM 12956 SG CYS D 153 26.172 132.102 43.449 1.00 29.98 S ATOM 12323 SG CYS D 70 28.439 125.560 42.955 1.00 8.08 S ATOM 12503 SG CYS D 95 31.839 131.376 42.643 1.00 11.82 S ATOM 16607 SG CYS E 97 61.860 50.927 53.799 1.00 21.46 S ATOM 16878 SG CYS E 132 67.052 49.986 57.077 1.00 21.41 S ATOM 18660 SG CYS F 97 66.776 55.571 53.876 1.00 19.39 S ATOM 18931 SG CYS F 132 67.533 50.600 50.428 1.00 35.26 S Number of atoms with unknown nonbonded energy type symbols: 2 "HETATM20057 S1 CLF B 601 .*. S " "HETATM20106 S1 CLF D 602 .*. S " Time building chain proxies: 5.40, per 1000 atoms: 0.27 Number of scatterers: 20221 At special positions: 0 Unit cell: (116.065, 163.66, 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 180 16.00 P 6 15.00 Mg 2 11.99 O 3836 8.00 N 3411 7.00 C 12748 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.