Starting phenix.real_space_refine
on Thu Oct 22 22:03:17 2026 by dcliebschner
===============================================================================

Processing files:
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  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yg6_33809/10_2026/7yg6_33809.map"
  }
  resolution = 3.2
  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=   0.175
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       9      5.49       5
     Mg      2      5.21       5
     S      35      5.16       5
     C    3805      2.51       5
     N    1059      2.21       5
     O    1115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  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: 6025
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Unexpected atoms: {'  U%rna2p_pyr,OP3': 1}
          Classifications: {'RNA': 1, 'RNAv2': 8}
          Modifications used: {'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 1, 'rna3p': 7}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 5834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 727, 5834
          Classifications: {'peptide': 727}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 38, 'TRANS': 688}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    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: 1
    "ATOM     21  OP3   U B   1 .*.     O  "
  Time building chain proxies: 1.32, per 1000 atoms: 0.22
  Number of scatterers: 6025
  At special positions: 0
  Unit cell: (73.916, 80.438, 110.874, 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      35     16.00
     P       9     15.00
     Mg      2     11.99
     O    1115      8.00
     N    1059      7.00
     C    3805      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.