Starting phenix.real_space_refine on Sun Oct 25 23:17:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bek_16006/10_2026/8bek_16006.cif" } resolution = 2.86 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= 0.002 sd= 0.022 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 51 5.49 5 Mg 2 5.21 5 S 127 5.16 5 C 11481 2.51 5 N 3240 2.21 5 O 3734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 18635 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 709, 5755 Classifications: {'peptide': 709} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 676} Chain breaks: 1 bond proxies already assigned to first conformer: 5865 Chain: "B" Number of atoms: 5854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 732, 5843 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 700} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 732, 5843 Classifications: {'peptide': 732} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 700} Chain breaks: 2 bond proxies already assigned to first conformer: 5944 Chain: "C" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5843 Classifications: {'peptide': 737} Link IDs: {'PTRANS': 29, 'TRANS': 707} Chain: "M" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pyr': 2} Link IDs: {'rna3p': 1} Chain: "R" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 355 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "V" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 307 Unexpected atoms: {' A%rna3p_pur,OP3': 1} Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" 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 AARG A 508 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 508 " occ=0.50 residue: pdb=" N AARG B 249 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 249 " occ=0.50 Number of atoms with unknown nonbonded energy type symbols: 1 "ATOM 18196 OP3 A V 1 .*. O " Time building chain proxies: 5.43, per 1000 atoms: 0.29 Number of scatterers: 18635 At special positions: 0 Unit cell: (118.371, 127.541, 120.872, 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 127 16.00 P 51 15.00 Mg 2 11.99 O 3734 8.00 N 3240 7.00 C 11481 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.