Starting phenix.real_space_refine
on Wed Aug  5 11:19:25 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.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/8jl0_36385/08_2026/8jl0_36385.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl0_36385/08_2026/8jl0_36385.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=   0.002 sd=   0.033
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      46      5.49       5
     S      33      5.16       5
     C    5757      2.51       5
     N    1583      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9244
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4572
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549}
          Chain breaks: 1
          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: 3712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3712
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 28, 'TRANS': 440}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 450
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "C"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 466
          Unexpected atoms: {'  A%rna2p_pur,OP3': 1}
          Classifications: {'RNAv2': 22}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM   8757  OP3   A C   1 .*.     O  "
  Time building chain proxies: 1.95, per 1000 atoms: 0.21
  Number of scatterers: 9244
  At special positions: 0
  Unit cell: (84.84, 115.08, 112.56, 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      33     16.00
     P      46     15.00
     O    1825      8.00
     N    1583      7.00
     C    5757      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: 1
    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.