Starting phenix.real_space_refine
on Thu Aug  6 02:24:26 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.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/7uml_26603/08_2026/7uml_26603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uml_26603/08_2026/7uml_26603.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=   0.053 sd=   1.358
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      13      5.49       5
     S      37      5.16       5
     C    4272      2.51       5
     N    1126      2.21       5
     O    1302      1.98       5
     H    6477      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 13227
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 5980
          Classifications: {'peptide': 379}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 361}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 2741
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
    Chain: "C"
      Number of atoms: 2770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2770
          Classifications: {'peptide': 172}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 161}
    Chain: "D"
      Number of atoms: 551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 551
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 4, 'TRANS': 29}
    Chain: "E"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 531
          Classifications: {'peptide': 39}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 34}
    Chain: "F"
      Number of atoms: 263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 263
          Classifications: {'peptide': 17}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
    Chain: "R"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 391
          Unexpected atoms: {'  U%rna3p_pyr,HO3'': 1}
          Classifications: {'RNAv2': 13}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 11}
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM  13221 HO3'   U R  38 .*.     H  "
  Time building chain proxies: 2.39, per 1000 atoms: 0.18
  Number of scatterers: 13227
  At special positions: 0
  Unit cell: (143.65, 100.3, 114.75, 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      37     16.00
     P      13     15.00
     O    1302      8.00
     N    1126      7.00
     C    4272      6.00
     H    6477      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.