Starting phenix.real_space_refine
on Mon Jul  6 11:16:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8pn7_17777/07_2026/8pn7_17777.cif"
  }
  resolution = 2.03
  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=   0.029
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      18      5.49       5
     S     150      5.16       5
     C   21030      2.51       5
     N    5934      2.21       5
     O    7740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 34872
  Number of models: 1
  Model: ""
    Number of chains: 36
    Chain: "A"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "B"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "C"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "D"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "E"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "F"
      Number of atoms: 3909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3909
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "G"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "H"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "I"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "J"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "K"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "L"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1594
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 13, 'TRANS': 198}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "F"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C2P': 1, 'COA,C3B': 1, 'COA,C3P': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C5P': 1, 'COA,C6A': 1, 'COA,C6P': 1, 'COA,C7P': 1, 'COA,C8A': 1, 'COA,C9P': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N4P': 1, 'COA,N6A': 1, 'COA,N7A': 1, 'COA,N8P': 1, 'COA,N9A': 1, 'COA,O1A': 1, 'COA,O2A': 1, 'COA,O2B': 1, 'COA,O3A': 1, 'COA,O3B': 1, 'COA,O4A': 1, 'COA,O4B': 1, 'COA,O5A': 1, 'COA,O5B': 1, 'COA,O5P': 1, 'COA,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,O9P': 1, 'COA,OAP': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 1, 'COA,S1P': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'COA:plan-1': 1, 'COA:plan-2': 1, 'COA:plan-3': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "G"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "J"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "L"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'BTI': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 216
          Classifications: {'water': 216}
          Link IDs: {None: 215}
    Chain: "B"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 225
          Classifications: {'water': 225}
          Link IDs: {None: 224}
    Chain: "C"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 231
          Classifications: {'water': 231}
          Link IDs: {None: 230}
    Chain: "D"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 226
          Classifications: {'water': 226}
          Link IDs: {None: 225}
    Chain: "E"
      Number of atoms: 223
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 223
          Classifications: {'water': 223}
          Link IDs: {None: 222}
    Chain: "F"
      Number of atoms: 213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 213
          Classifications: {'water': 213}
          Link IDs: {None: 212}
    Chain: "G"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "H"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "I"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 27
          Classifications: {'water': 27}
          Link IDs: {None: 26}
    Chain: "J"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 25
          Classifications: {'water': 25}
          Link IDs: {None: 24}
    Chain: "K"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "L"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 24
          Classifications: {'water': 24}
          Link IDs: {None: 23}
  Number of atoms with unknown nonbonded energy type symbols: 288
    "HETATM33019  C1B COA A 601 .*.     C  "
    "HETATM33020  C2A COA A 601 .*.     C  "
    "HETATM33021  C2B COA A 601 .*.     C  "
    "HETATM33022  C2P COA A 601 .*.     C  "
    "HETATM33023  C3B COA A 601 .*.     C  "
    "HETATM33024  C3P COA A 601 .*.     C  "
    "HETATM33025  C4A COA A 601 .*.     C  "
    "HETATM33026  C4B COA A 601 .*.     C  "
    "HETATM33027  C5A COA A 601 .*.     C  "
    "HETATM33028  C5B COA A 601 .*.     C  "
    ... (remaining 278 not shown)
  Time building chain proxies: 7.88, per 1000 atoms: 0.23
  Number of scatterers: 34872
  At special positions: 0
  Unit cell: (149.823, 154.008, 138.942, 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     150     16.00
     P      18     15.00
     O    7740      8.00
     N    5934      7.00
     C   21030      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: 288
    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.