Starting phenix.real_space_refine on Fri Jul 3 06:39:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ysh_34075/07_2026/7ysh_34075.map" } resolution = 2.74 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= 0.003 sd= 0.170 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 68 5.16 5 C 7979 2.51 5 N 2132 2.21 5 O 2299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 12480 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: "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: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1679 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 196} Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1670 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 195} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {'IDS': 4, 'SGN': 5} Unexpected atoms: {'SGN,N2': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 13 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: "D" 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 44.956 47.129 41.364 1.00 40.63 S Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM12325 N2 SGN F 1 .*. N " "HETATM12361 N2 SGN F 3 .*. N " "HETATM12396 N2 SGN F 5 .*. N " "HETATM12431 N2 SGN F 7 .*. N " "HETATM12466 N2 SGN F 9 .*. N " Time building chain proxies: 2.86, per 1000 atoms: 0.23 Number of scatterers: 12480 At special positions: 0 Unit cell: (87.68, 129.328, 147.96, 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 68 16.00 O 2299 8.00 N 2132 7.00 C 7979 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.