Starting phenix.real_space_refine on Sat Oct 24 14:59:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.map" model { file = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8qfs_18383/10_2026/8qfs_18383.cif" } resolution = 2.7 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= 0.006 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 P 64 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 8204 2.51 5 N 2265 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13294 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2937 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 372} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1309 Unexpected atoms: {' G%rna3p_pur,OP3': 1} Classifications: {'RNA': 5, 'RNAv2': 56} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p': 6, 'rna3p_pur': 21, 'rna3p_pyr': 20} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 9015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9015 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 42, 'TRANS': 1140} Chain breaks: 14 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 32, 'ASP:plan': 13, 'PHE:plan': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'GLN:plan1': 10, 'ARG:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 2961 OP3 G B 1 .*. O " Time building chain proxies: 2.17, per 1000 atoms: 0.16 Number of scatterers: 13294 At special positions: 0 Unit cell: (109.714, 122.718, 142.222, 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) S 37 16.00 P 64 15.00 Mg 1 11.99 O 2723 8.00 N 2265 7.00 C 8204 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: 1 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.