Starting phenix.real_space_refine
on Tue Aug  4 22:15:22 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.map

Processing PHIL parameters:
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  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yfy_33801/08_2026/7yfy_33801.map"
  }
  resolution = 3.4
  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=   0.007 sd=   0.124
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      41      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    4172      2.51       5
     N    1172      2.21       5
     O    1339      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 6770
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 734, 5898
          Classifications: {'peptide': 734}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 36, 'TRANS': 697}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 320
          Classifications: {'RNAv2': 15}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 14}
    Chain: "B"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 550
          Unexpected atoms: {'  U%rna2p_pyr,OP3': 1}
          Classifications: {'RNA': 1, 'RNAv2': 25}
          Modifications used: {'rna2p': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 7, 'rna3p': 18}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    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   6239  OP3   U B   1 .*.     O  "
  Time building chain proxies: 1.80, per 1000 atoms: 0.27
  Number of scatterers: 6770
  At special positions: 0
  Unit cell: (73.916, 85.873, 114.135, 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      44     16.00
     P      41     15.00
     Mg      2     11.99
     O    1339      8.00
     N    1172      7.00
     C    4172      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.