Starting phenix.real_space_refine
on Tue Aug  4 22:03:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swf_25472/08_2026/7swf_25472.map"
  }
  resolution = 3.79
  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=   0.003
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      34      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    4227      2.51       5
     N    1214      2.21       5
     O    1361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  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: 6873
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 778, 6167
          Classifications: {'peptide': 778}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 43, 'TRANS': 734}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 370
          Unexpected atoms: {'  U%rna2p_pyr,OP3': 1}
          Classifications: {'RNAv2': 17}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 14}
    Chain: "D"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 335
          Classifications: {'DNA': 1, 'RNAv2': 16}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 15}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM   6188  OP3   U B   1 .*.     O  "
  Time building chain proxies: 1.10, per 1000 atoms: 0.16
  Number of scatterers: 6873
  At special positions: 0
  Unit cell: (80.99, 101.92, 114.66, 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      36     16.00
     P      34     15.00
     Mg      1     11.99
     O    1361      8.00
     N    1214      7.00
     C    4227      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.