Starting phenix.real_space_refine
on Thu Aug  6 23:24:41 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ori_13038/08_2026/7ori_13038.cif"
  }
  resolution = 3.9
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      46      5.49       5
     Mg      1      5.21       5
     S     108      5.16       5
     C   10917      2.51       5
     N    2879      2.21       5
     O    3374      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  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: 17326
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 237
          Unexpected atoms: {'  A%rna3p_pur,OP3': 1}
          Classifications: {'RNAv2': 11}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 8}
    Chain: "T"
      Number of atoms: 439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 439
          Classifications: {'RNAv2': 21}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 4, 'rna3p': 16}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 256
          Classifications: {'RNAv2': 12}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 1, 'rna3p': 10}
    Chain: "A"
      Number of atoms: 16383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2007, 16383
          Classifications: {'peptide': 2007}
          Link IDs: {'PTRANS': 67, 'TRANS': 1939}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 11
          Unusual residues: {' MG': 1, ' ZN': 1, 'POP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  15963  SG  CYS A2064      66.994  30.063  27.886  1.00143.63           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   POP A2303 " occ=0.74
      ... (7 atoms not shown)
      pdb=" P2  POP A2303 " occ=0.74
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM     23  OP3   A H   1 .*.     O  "
  Time building chain proxies: 3.61, per 1000 atoms: 0.21
  Number of scatterers: 17326
  At special positions: 0
  Unit cell: (111.065, 132.82, 136.255, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S     108     16.00
     P      46     15.00
     Mg      1     11.99
     O    3374      8.00
     N    2879      7.00
     C   10917      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.