Starting phenix.real_space_refine
on Mon Jul  6 15:38:52 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ybp_10770/07_2026/6ybp_10770.map"
  }
  resolution = 3.48
  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=   0.008 sd=   0.059
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     157      5.16       5
     C   22970      2.51       5
     N    6423      2.21       5
     O    6842      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 189 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: 36410
  Number of models: 1
  Model: ""
    Number of chains: 24
    Chain: "A"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "B"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "C"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "D"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "E"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "F"
      Number of atoms: 3910
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3910
          Classifications: {'peptide': 506}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 484}
    Chain: "G"
      Number of atoms: 2135
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2135
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 18, 'TRANS': 264}
          Chain breaks: 5
    Chain: "H"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1565
          Classifications: {'peptide': 208}
          Link IDs: {'PTRANS': 11, 'TRANS': 196}
    Chain: "I"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2183
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 4
    Chain: "J"
      Number of atoms: 2305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2305
          Classifications: {'peptide': 303}
          Link IDs: {'PTRANS': 20, 'TRANS': 282}
          Chain breaks: 3
    Chain: "K"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2217
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 18, 'TRANS': 274}
          Chain breaks: 4
    Chain: "L"
      Number of atoms: 2208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2208
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 18, 'TRANS': 272}
          Chain breaks: 4
    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: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C3B': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C6A': 1, 'COA,C8A': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N6A': 1, 'COA,N7A': 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,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 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: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C3B': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C6A': 1, 'COA,C8A': 1, 'COA,CAP': 1, 'COA,CBP': 1, 'COA,CCP': 1, 'COA,CDP': 1, 'COA,CEP': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N6A': 1, 'COA,N7A': 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,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 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: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'COA': 1}
          Unexpected atoms: {'COA,C1B': 1, 'COA,C2A': 1, 'COA,C2B': 1, 'COA,C3B': 1, 'COA,C4A': 1, 'COA,C4B': 1, 'COA,C5A': 1, 'COA,C5B': 1, 'COA,C6A': 1, 'COA,C8A': 1, 'COA,N1A': 1, 'COA,N3A': 1, 'COA,N6A': 1, 'COA,N7A': 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,O6A': 1, 'COA,O7A': 1, 'COA,O8A': 1, 'COA,O9A': 1, 'COA,P1A': 1, 'COA,P2A': 1, 'COA,P3B': 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}
  Number of atoms with unknown nonbonded energy type symbols: 247
    "HETATM36074  C1B COA A 601 .*.     C  "
    "HETATM36075  C2A COA A 601 .*.     C  "
    "HETATM36076  C2B COA A 601 .*.     C  "
    "HETATM36077  C2P COA A 601 .*.     C  "
    "HETATM36078  C3B COA A 601 .*.     C  "
    "HETATM36079  C3P COA A 601 .*.     C  "
    "HETATM36080  C4A COA A 601 .*.     C  "
    "HETATM36081  C4B COA A 601 .*.     C  "
    "HETATM36082  C5A COA A 601 .*.     C  "
    "HETATM36083  C5B COA A 601 .*.     C  "
    ... (remaining 237 not shown)
  Time building chain proxies: 8.07, per 1000 atoms: 0.22
  Number of scatterers: 36410
  At special positions: 0
  Unit cell: (160.48, 160.48, 175.82, 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     157     16.00
     P      18     15.00
     O    6842      8.00
     N    6423      7.00
     C   22970      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: 247
    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.