Starting phenix.real_space_refine
on Thu Aug  6 06:29:54 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dmb_27533/08_2026/8dmb_27533.cif"
  }
  resolution = 3.1
  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=   0.006
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: 7
    Type Number    sf(0)   Gaussians
     P     274      5.49       5
     Mg      2      5.21       5
     S       9      5.16       5
     C    4303      2.51       5
     N    1586      2.21       5
     O    2323      1.98       5
     H    5728      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  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: 14225
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "P"
      Number of atoms: 5376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 5376
          Classifications: {'peptide': 328}
          Link IDs: {'PTRANS': 20, 'TRANS': 307}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "W"
      Number of atoms: 7634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 7634
          Unexpected atoms: {'  C%rna3p_pyr,HO3'': 1}
          Classifications: {'RNAv2': 237}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103}
          Link IDs: {'rna2p': 25, 'rna3p': 211}
          Chain breaks: 4
    Chain: "X"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 893
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "Y"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 320
          Classifications: {'DNA': 10}
          Modifications used: {'3*END': 1, '5*END': 1}
          Link IDs: {'rna3p': 9}
    Chain: "W"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM  13003 HO3'   C W 282 .*.     H  "
  Time building chain proxies: 2.63, per 1000 atoms: 0.18
  Number of scatterers: 14225
  At special positions: 0
  Unit cell: (108.68, 128.128, 102.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       9     16.00
     P     274     15.00
     Mg      2     11.99
     O    2323      8.00
     N    1586      7.00
     C    4303      6.00
     H    5728      1.00
    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.