Starting phenix.real_space_refine
on Wed Aug  5 03:19:49 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7vg2_31963/08_2026/7vg2_31963.cif"
  }
  resolution = 3.1
  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=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P      71      5.49       5
     S      35      5.16       5
     C    4939      2.51       5
     N    1402      2.21       5
     O    1753      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 8203
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 845, 6695
          Classifications: {'peptide': 845}
          Link IDs: {'PTRANS': 38, 'TRANS': 806}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 743
          Unexpected atoms: {'  A%rna2p_pur,OP3': 1}
          Classifications: {'RNAv2': 35}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 2, 'rna3p': 32}
    Chain: "D"
      Number of atoms: 762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 762
          Classifications: {'RNAv2': 36}
          Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 19}
          Link IDs: {'rna3p': 35}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3250  SG  CYS A1091      80.111  40.909  60.628  1.00 37.81           S
  ATOM   3265  SG  CYS A1093      77.913  44.550  59.990  1.00 40.00           S
  ATOM   3469  SG  CYS A1119      77.965  41.631  57.831  1.00 29.71           S

  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM   6718  OP3   A C   1 .*.     O  "
  Time building chain proxies: 1.52, per 1000 atoms: 0.19
  Number of scatterers: 8203
  At special positions: 0
  Unit cell: (116.6, 107.8, 97.9, 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
     Ca      2     19.99
     S      35     16.00
     P      71     15.00
     O    1753      8.00
     N    1402      7.00
     C    4939      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.