Starting phenix.real_space_refine (version: dev)
on Sun Dec 18 12:22:32 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.map

Processing PHIL parameters:
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  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a7u_3079/12_2022/5a7u_3079.pdb"
  }
  resolution = 4.8
  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
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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=   0.000
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 455
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 454
          Unusual residues: {' ZN': 1}
          Duplicate atoms: {'CYS,HB1': 1}
          Classifications: {'peptide': 27, 'undetermined': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 24, None: 1}
            Not linked:
              pdbres="SER A  27 "
              pdbres=" ZN A 162 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    114  SG  CYS A   8      12.679  11.581  19.010  1.00  0.00           S

  Number of atoms with unknown nonbonded energy type symbols: 1
    "ATOM    165  HB2 CYS A  11 .*.     H  "
  Time building chain proxies: 0.72, per 1000 atoms: 1.58
  Number of scatterers: 455
  At special positions: 0
  Unit cell: (38.36, 35.62, 36.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S       2     16.00
     O      34      8.00
     N      47      7.00
     C     140      6.00
     H     231      1.00
    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.