Starting phenix.real_space_refine
on Sat Aug  8 14:23:58 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7nkc_12437/08_2026/7nkc_12437.cif"
  }
  resolution = 4.46
  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=   0.020 sd=   0.211
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      23      5.49       5
     S     106      5.16       5
     C    9319      2.51       5
     N    2598      2.21       5
     O    2874      1.98       5
     H   13868      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 28788
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 11524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 716, 11524
          Classifications: {'peptide': 716}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 31, 'TRANS': 684}
    Chain: "B"
      Number of atoms: 11704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 735, 11704
          Classifications: {'peptide': 735}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 702}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 4075
          Classifications: {'peptide': 249}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
    Chain: "D"
      Number of atoms: 491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 491
          Unexpected atoms: {'  C%rna2p_pyr,HO3'': 1}
          Classifications: {'RNAv2': 15}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 3, 'rna3p': 11}
    Chain: "E"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 255
          Classifications: {'RNAv2': 8}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 1, 'rna3p': 6}
    Chain: "F"
      Number of atoms: 739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 739
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Chain breaks: 3
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM  27787 HO3'   C D  15 .*.     H  "
  Time building chain proxies: 4.36, per 1000 atoms: 0.15
  Number of scatterers: 28788
  At special positions: 0
  Unit cell: (98, 130.2, 124.6, 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     106     16.00
     P      23     15.00
     O    2874      8.00
     N    2598      7.00
     C    9319      6.00
     H   13868      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.