Starting phenix.real_space_refine
on Thu Aug  6 08:17:12 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6t0u_10359/08_2026/6t0u_10359.cif"
  }
  resolution = 3.12
  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=   0.006
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      23      5.49       5
     S      93      5.16       5
     C    8863      2.51       5
     N    2477      2.21       5
     O    2720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 14176
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5741
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 704, 5733
          Classifications: {'peptide': 704}
          Link IDs: {'PTRANS': 25, 'TRANS': 678}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 704, 5733
          Classifications: {'peptide': 704}
          Link IDs: {'PTRANS': 25, 'TRANS': 678}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5846
    Chain: "B"
      Number of atoms: 5923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 5923
          Classifications: {'peptide': 740}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2020
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 12, 'TRANS': 238}
    Chain: "V"
      Number of atoms: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 492
          Unexpected atoms: {'  A%rna3p_pur,OP3': 1}
          Classifications: {'RNAv2': 23}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 11, 'rna3p': 11}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 455 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 455 " occ=0.50
  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM  13707  OP3   A V   1 .*.     O  "
  Time building chain proxies: 3.53, per 1000 atoms: 0.25
  Number of scatterers: 14176
  At special positions: 0
  Unit cell: (96.39, 115.83, 117.45, 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      93     16.00
     P      23     15.00
     O    2720      8.00
     N    2477      7.00
     C    8863      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.