Starting phenix.real_space_refine
on Fri Aug  7 12:38:54 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mqb_23941/08_2026/7mqb_23941.cif"
  }
  resolution = 3.25
  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=   0.002 sd=   0.012
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 11544 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: 5
    Type Number    sf(0)   Gaussians
     P      16      5.49       5
     S      48      5.16       5
     C    8064      2.51       5
     N    2328      2.21       5
     O    2304      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 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: 12760
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1548
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 199}
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 68
    Chain: "B"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 47
          Unexpected atoms: {'  G%rna3p_pur,OP3': 1}
          Classifications: {'RNAv2': 2}
          Modifications used: {'rna3p_pur': 2}
          Link IDs: {'rna3p': 1}
  Restraints were copied for chains:
    C, E, G, I, K, M, O, D, F, H, J, L, N, P
  Number of atoms with unknown nonbonded energy type symbols: 8
    "ATOM   1572  OP3   G B 603 .*.     O  "
    "ATOM   3167  OP3   G D 603 .*.     O  "
    "ATOM   4762  OP3   G F 603 .*.     O  "
    "ATOM   6357  OP3   G H 603 .*.     O  "
    "ATOM   7952  OP3   G J 603 .*.     O  "
    "ATOM   9547  OP3   G L 603 .*.     O  "
    "ATOM  11142  OP3   G N 603 .*.     O  "
    "ATOM  12737  OP3   G P 603 .*.     O  "
  Time building chain proxies: 1.57, per 1000 atoms: 0.12
  Number of scatterers: 12760
  At special positions: 0
  Unit cell: (105.4, 105.4, 88.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P      16     15.00
     O    2304      8.00
     N    2328      7.00
     C    8064      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: 8
    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.