Starting phenix.real_space_refine
on Thu Jul  2 20:12:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7mo8_23920/07_2026/7mo8_23920.cif"
  }
  resolution = 4.5
  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: 4
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C    6207      2.51       5
     N    1711      2.21       5
     O    1863      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 9877
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 637, 4937
          Classifications: {'peptide': 637}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 595}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 180
          Unresolved non-hydrogen angles: 215
          Unresolved non-hydrogen dihedrals: 154
          Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 4, 'GLU:plan': 11, 'HIS:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 130
    Chain: "B"
      Number of atoms: 4843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 613, 4843
          Classifications: {'peptide': 613}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 583}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "D"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 97
          Unusual residues: {'IDS': 3, 'SGN': 3}
          Unexpected atoms: {'SGN,N2': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 11
  Number of atoms with unknown nonbonded energy type symbols: 3
    "HETATM 9787  N2  SGN D   1 .*.     N  "
    "HETATM 9821  N2  SGN D   3 .*.     N  "
    "HETATM 9855  N2  SGN D   5 .*.     N  "
  Time building chain proxies: 2.23, per 1000 atoms: 0.23
  Number of scatterers: 9877
  At special positions: 0
  Unit cell: (114.48, 122.04, 120.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      96     16.00
     O    1863      8.00
     N    1711      7.00
     C    6207      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: 3
    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.