Starting phenix.real_space_refine
on Sat Jul  4 16:14:26 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ttb_41604/07_2026/8ttb_41604.cif"
  }
  resolution = 2.77
  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=   0.001
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: 8
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     Zn      1      6.06       5
     P       1      5.49       5
     S      63      5.16       5
     C    6954      2.51       5
     N    1889      2.21       5
     O    2093      1.98       5
     H   10922      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 21924
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 9162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 581, 9162
          Classifications: {'peptide': 581}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 6893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 6893
          Classifications: {'peptide': 426}
          Link IDs: {'PTRANS': 14, 'TRANS': 411}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 4897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 4897
          Classifications: {'peptide': 308}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 294}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Planarities with less than four sites: {'MLL%COO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 970
          Unexpected atoms: {'2RX,HA': 1}
          Classifications: {'peptide': 61}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 55}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'2RX:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' FE': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Number of atoms with unknown nonbonded energy type symbols: 1
    "HETATM21303  HA  2RX D  62 .*.     H  "
  Time building chain proxies: 3.09, per 1000 atoms: 0.14
  Number of scatterers: 21924
  At special positions: 0
  Unit cell: (106.683, 129.839, 114.953, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     Fe      1     26.01
     S      63     16.00
     P       1     15.00
     O    2093      8.00
     N    1889      7.00
     C    6954      6.00
     H   10922      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.