Starting phenix.real_space_refine
on Sun Aug  9 13:26:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.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/6y0c_10667/08_2026/6y0c_10667.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y0c_10667/08_2026/6y0c_10667.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=   0.000 sd=   0.002
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      19      5.49       5
     S     132      5.16       5
     C   11063      2.51       5
     N    3001      2.21       5
     O    3322      1.98       5
     H   17430      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 121 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: 34967
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 11153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 688, 11153
          Classifications: {'peptide': 688}
          Link IDs: {'PTRANS': 31, 'TRANS': 656}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 10982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 686, 10982
          Classifications: {'peptide': 686}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 660}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 12190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 761, 12190
          Classifications: {'peptide': 761}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 732}
          Chain breaks: 1
    Chain: "IN1"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 642
          Unexpected atoms: {'  A%rna3p_pur,HO5'': 1, '  G%rna3p_pur,HO3'': 1, '  U%rna3p_pyr,HO3'': 1}
          Classifications: {'RNAv2': 20}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 6}
          Link IDs: {'rna2p': 5, 'rna3p': 14}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Number of atoms with unknown nonbonded energy type symbols: 3
    "ATOM  34356 HO5'   AIN1   1 .*.     H  "
    "ATOM  34779 HO3'   GIN1  14 .*.     H  "
    "ATOM  34961 HO3'   UIN1  44 .*.     H  "
  Time building chain proxies: 4.21, per 1000 atoms: 0.12
  Number of scatterers: 34967
  At special positions: 0
  Unit cell: (124.775, 133.455, 109.585, 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     132     16.00
     P      19     15.00
     O    3322      8.00
     N    3001      7.00
     C   11063      6.00
     H   17430      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: 3
    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.