Starting phenix.real_space_refine
on Thu Jul  2 01:48:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e50_27899/07_2026/8e50_27899.map"
  }
  resolution = 3.67
  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=   0.002
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       4      5.49       5
     S      24      5.16       5
     C    3394      2.51       5
     N     905      2.21       5
     O     950      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  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: 5277
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 651, 5202
          Classifications: {'peptide': 651}
          Link IDs: {'PTRANS': 21, 'TRANS': 629}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'COA': 1, 'NKO': 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': 2}
          Link IDs: {None: 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
  Number of atoms with unknown nonbonded energy type symbols: 48
    "HETATM 5203  C1B COA A 901 .*.     C  "
    "HETATM 5204  C2A COA A 901 .*.     C  "
    "HETATM 5205  C2B COA A 901 .*.     C  "
    "HETATM 5206  C2P COA A 901 .*.     C  "
    "HETATM 5207  C3B COA A 901 .*.     C  "
    "HETATM 5208  C3P COA A 901 .*.     C  "
    "HETATM 5209  C4A COA A 901 .*.     C  "
    "HETATM 5210  C4B COA A 901 .*.     C  "
    "HETATM 5211  C5A COA A 901 .*.     C  "
    "HETATM 5212  C5B COA A 901 .*.     C  "
    ... (remaining 38 not shown)
  Time building chain proxies: 1.07, per 1000 atoms: 0.20
  Number of scatterers: 5277
  At special positions: 0
  Unit cell: (69.72, 93.24, 99.96, 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      24     16.00
     P       4     15.00
     O     950      8.00
     N     905      7.00
     C    3394      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: 48
    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.