Starting phenix.real_space_refine on Fri Jul 3 06:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ysu_34082/07_2026/7ysu_34082.cif" } resolution = 3.2 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= 0.009 sd= 0.113 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 Zn 1 6.06 5 Cu 1 5.60 5 S 63 5.16 5 C 7923 2.51 5 N 2144 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 12430 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7527 Classifications: {'peptide': 921} Link IDs: {'PTRANS': 51, 'TRANS': 869} Chain breaks: 1 Chain: "C" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 196} Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 196} Chain: "B" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 176 Unusual residues: {'IDS': 5, 'SGN': 5} Unexpected atoms: {'SGN,N2': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5570 SG CYS A 739 44.317 45.769 99.144 1.00115.03 S Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM12276 N2 SGN F 2 .*. N " "HETATM12311 N2 SGN F 4 .*. N " "HETATM12346 N2 SGN F 6 .*. N " "HETATM12381 N2 SGN F 8 .*. N " "HETATM12416 N2 SGN F 10 .*. N " Time building chain proxies: 2.31, per 1000 atoms: 0.19 Number of scatterers: 12430 At special positions: 0 Unit cell: (85.936, 121.568, 142.528, 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) Zn 1 29.99 Cu 1 28.99 S 63 16.00 O 2298 8.00 N 2144 7.00 C 7923 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: 5 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.