Starting phenix.real_space_refine on Tue Aug 4 20:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvv_17973/08_2026/8pvv_17973.cif" } resolution = 2.81 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= 1.000 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 50 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3979 2.51 5 N 1079 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 6477 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "C" Number of atoms: 1913 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Conformer: "B" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} bond proxies already assigned to first conformer: 1916 Chain: "R" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 549 Unexpected atoms: {' A%rna2p_pur,OP3': 1} Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 18, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain: "S" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS C 52 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 52 " occ=0.50 residue: pdb=" N AHIS C 137 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 137 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 5414 OP3 A R 1 .*. O " Time building chain proxies: 1.90, per 1000 atoms: 0.29 Number of scatterers: 6477 At special positions: 0 Unit cell: (75.9, 83.6, 99, 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 13 16.00 P 50 15.00 Mg 1 11.99 O 1355 8.00 N 1079 7.00 C 3979 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.