Starting phenix.real_space_refine
on Thu Aug  6 00:09:26 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kx9_23063/08_2026/7kx9_23063.map"
  }
  resolution = 3.5
  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=   0.003 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 25 atoms to isotropic.
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      40      5.49       5
     Mg      2      5.21       5
     S      33      5.16       5
     C    4015      2.51       5
     N    1170      2.21       5
     O    1318      1.98       5
     H    5846      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 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: 12424
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 11133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 734, 11133
          Classifications: {'peptide': 734}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 38, 'TRANS': 695}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 254
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 104
    Chain: "B"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 774
          Unexpected atoms: {'  U%rna2p_pyr,OP3': 1}
          Classifications: {'RNA': 1, 'RNAv2': 23}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 7, 'rna3p': 16}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "C"
      Number of atoms: 515
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 515
          Unexpected atoms: {'  A%rna3p_pur,HO3'': 1}
          Classifications: {'RNAv2': 16}
          Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      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: 2
    "ATOM  11154  OP3   U B   1 .*.     O  "
    "ATOM  12415 HO3'   A C  23 .*.     H  "
  Time building chain proxies: 1.99, per 1000 atoms: 0.16
  Number of scatterers: 12424
  At special positions: 0
  Unit cell: (79.35, 109.25, 75.9, 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      33     16.00
     P      40     15.00
     Mg      2     11.99
     O    1318      8.00
     N    1170      7.00
     C    4015      6.00
     H    5846      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: 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.