Starting phenix.real_space_refine
on Sat Oct 24 09:32:51 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wv5_32846/10_2026/7wv5_32846.map"
  }
  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=  -0.001 sd=   0.068
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: 5
    Type Number    sf(0)   Gaussians
     P      90      5.49       5
     S      34      5.16       5
     C    7898      2.51       5
     N    2144      2.21       5
     O    2792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12958
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 5284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 5284
          Classifications: {'peptide': 659}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 5284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 5284
          Classifications: {'peptide': 659}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 632}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 917
          Classifications: {'RNAv2': 46}
          Modifications used: {'rna3p_pyr': 46}
          Link IDs: {'rna3p': 45}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 1009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 1009
          Unusual residues: {'  I%rna3p': 46}
          Unexpected atoms: {'  I%rna3p,C1'': 46, '  I%rna3p,C2': 46, '  I%rna3p,C2'': 46, '  I%rna3p,C3'': 46, '  I%rna3p,C4': 46, '  I%rna3p,C4'': 46, '  I%rna3p,C5': 46, '  I%rna3p,C5'': 46, '  I%rna3p,C6': 46, '  I%rna3p,C8': 46, '  I%rna3p,N1': 46, '  I%rna3p,N3': 46, '  I%rna3p,N7': 46, '  I%rna3p,N9': 46, '  I%rna3p,O2'': 46, '  I%rna3p,O3'': 46, '  I%rna3p,O4'': 46, '  I%rna3p,O5'': 46, '  I%rna3p,O6': 46, '  I%rna3p,OP1': 45, '  I%rna3p,OP2': 45, '  I%rna3p,P': 45}
          Classifications: {'undetermined': 46}
          Modifications used: {'rna3p': 46}
          Link IDs: {'rna3p': 45}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "K"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "M"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "N"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen chiralities: 5
  Number of atoms with unknown nonbonded energy type symbols: 1009
    "ATOM  11486  C1'   I F   1 .*.     C  "
    "ATOM  11487  C2    I F   1 .*.     C  "
    "ATOM  11488  C2'   I F   1 .*.     C  "
    "ATOM  11489  C3'   I F   1 .*.     C  "
    "ATOM  11490  C4    I F   1 .*.     C  "
    "ATOM  11491  C4'   I F   1 .*.     C  "
    "ATOM  11492  C5    I F   1 .*.     C  "
    "ATOM  11493  C5'   I F   1 .*.     C  "
    "ATOM  11494  C6    I F   1 .*.     C  "
    "ATOM  11495  C8    I F   1 .*.     C  "
    ... (remaining 999 not shown)
  Time building chain proxies: 2.54, per 1000 atoms: 0.20
  Number of scatterers: 12958
  At special positions: 0
  Unit cell: (108.328, 168.601, 100.183, 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      34     16.00
     P      90     15.00
     O    2792      8.00
     N    2144      7.00
     C    7898      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: 1009
    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.