Starting phenix.real_space_refine on Fri Aug 7 07:33:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpl_14857/08_2026/7zpl_14857.cif" } resolution = 3.12 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= 0.013 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 24 5.49 5 Mg 1 5.21 5 S 148 5.16 5 C 12498 2.51 5 N 3440 2.21 5 O 3808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s 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: 19919 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "B" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4914 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 650 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "V" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "E" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4914 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 589} Chain breaks: 2 Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 650 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "U" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 262 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 2 "ATOM 9720 OP3 A V 1 .*. O " "ATOM 19679 OP3 A U 1 .*. O " Time building chain proxies: 4.79, per 1000 atoms: 0.24 Number of scatterers: 19919 At special positions: 0 Unit cell: (177.24, 131.04, 97.44, 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 148 16.00 P 24 15.00 Mg 1 11.99 O 3808 8.00 N 3440 7.00 C 12498 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.