Starting phenix.real_space_refine
on Fri Aug  7 17:07:18 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yym_14383/08_2026/7yym_14383.cif"
  }
  resolution = 4.19
  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=   0.001 sd=   0.026
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      55      5.49       5
     S      57      5.16       5
     C    7080      2.51       5
     N    1945      2.21       5
     O    2261      1.98       5
     H   10961      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: 22359
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 20618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1281, 20618
          Classifications: {'peptide': 1281}
          Link IDs: {'PTRANS': 76, 'TRANS': 1204}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 1741
          Unexpected atoms: {'  A%rna2p_pur,HO3'': 1}
          Classifications: {'RNAv2': 55}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 27, 'rna3p_pyr': 27}
          Link IDs: {'rna3p': 54}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'  U%rna3p_pyr:plan': 2}
          Unresolved non-hydrogen planarities: 16
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM  22352 HO3'   A B  59 .*.     H  "
  Time building chain proxies: 3.66, per 1000 atoms: 0.16
  Number of scatterers: 22359
  At special positions: 0
  Unit cell: (97.704, 105.156, 163.944, 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      57     16.00
     P      55     15.00
     O    2261      8.00
     N    1945      7.00
     C    7080      6.00
     H   10961      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.