Starting phenix.real_space_refine on Tue Aug 4 23:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u2b_26311/08_2026/7u2b_26311.cif" } resolution = 4.1 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= 0.003 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: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 34 5.16 5 C 4408 2.51 5 N 1316 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7316 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1111 Unexpected atoms: {' G%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 53} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 26} Link IDs: {'rna2p': 5, 'rna3p': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {' A%rna2p_pur:plan': 1, ' A%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2500 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3647 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 24 OP3 G C 1 .*. O " Time building chain proxies: 1.70, per 1000 atoms: 0.23 Number of scatterers: 7316 At special positions: 0 Unit cell: (70.15, 95.45, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 53 15.00 O 1505 8.00 N 1316 7.00 C 4408 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.