Starting phenix.real_space_refine
on Sat May  2 05:27:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9neq_49330/05_2026/9neq_49330.map"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
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=   0.048 sd=   0.440
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: 3
    Type Number    sf(0)   Gaussians
     C     864      2.51       5
     N     224      2.21       5
     O     224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1312
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 A   1 "
              pdbres="LEU A   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 B   1 "
              pdbres="LEU B   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 C   1 "
              pdbres="LEU C   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 D   1 "
              pdbres="LEU D   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 E   1 "
              pdbres="LEU E   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 F   1 "
              pdbres="LEU F   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "G"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 G   1 "
              pdbres="LEU G   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 H   1 "
              pdbres="LEU H   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "I"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 I   1 "
              pdbres="LEU I   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "J"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 J   1 "
              pdbres="LEU J   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "K"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 K   1 "
              pdbres="LEU K   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 L   1 "
              pdbres="LEU L   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "K"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "M"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 M   1 "
              pdbres="LEU M   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 N   1 "
              pdbres="LEU N   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "O"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 O   1 "
              pdbres="LEU O   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "P"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 P   1 "
              pdbres="LEU P   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "Q"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 Q   1 "
              pdbres="LEU Q   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 R   1 "
              pdbres="LEU R   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "Q"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "S"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 S   1 "
              pdbres="LEU S   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "T"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 T   1 "
              pdbres="LEU T   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "U"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 U   1 "
              pdbres="LEU U   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "T"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "V"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 V   1 "
              pdbres="LEU V   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "W"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 W   1 "
              pdbres="LEU W   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "X"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 49
          Unusual residues: {'UQ4': 1}
          Classifications: {'peptide': 4, 'undetermined': 1}
          Link IDs: {'TRANS': 3, None: 1}
            Not linked:
              pdbres="UQ4 X   1 "
              pdbres="LEU X   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "W"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'UQ4': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'UQ4:plan-4': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 0.17, per 1000 atoms: 0.13
  Number of scatterers: 1312
  At special positions: 0
  Unit cell: (55.59, 62.13, 30.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     224      8.00
     N     224      7.00
     C     864      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=24, symmetry=0
  Number of additional bonds: simple=24, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 14.4 milliseconds
  

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  192

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...

    No hydrogen bonds defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.00

  Time building geometry restraints manager: 0.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.17 -     1.25: 160
        1.25 -     1.32: 64
        1.32 -     1.39: 264
        1.39 -     1.46: 192
        1.46 -     1.54: 640
  Bond restraints: 1320
  Sorted by residual:
  bond pdb=" C53 UQ4 W   1 "
       pdb=" N52 UQ4 W   1 "
    ideal  model  delta    sigma   weight residual
    1.342  1.511 -0.169 2.00e-02 2.50e+03 7.11e+01
  bond pdb=" C53 UQ4 K   1 "
       pdb=" N52 UQ4 K   1 "
    ideal  model  delta    sigma   weight residual
    1.342  1.511 -0.169 2.00e-02 2.50e+03 7.11e+01
  bond pdb=" C53 UQ4 N   1 "
       pdb=" N52 UQ4 N   1 "
    ideal  model  delta    sigma   weight residual
    1.342  1.511 -0.169 2.00e-02 2.50e+03 7.10e+01
  bond pdb=" C53 UQ4 E   1 "
       pdb=" N52 UQ4 E   1 "
    ideal  model  delta    sigma   weight residual
    1.342  1.511 -0.169 2.00e-02 2.50e+03 7.10e+01
  bond pdb=" C53 UQ4 B   1 "
       pdb=" N52 UQ4 B   1 "
    ideal  model  delta    sigma   weight residual
    1.342  1.510 -0.168 2.00e-02 2.50e+03 7.09e+01
  ... (remaining 1315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 1344
        1.78 -     3.57: 208
        3.57 -     5.35: 104
        5.35 -     7.14: 72
        7.14 -     8.92: 24
  Bond angle restraints: 1752
  Sorted by residual:
  angle pdb=" C50 UQ4 Q 101 "
        pdb=" C02 UQ4 Q 101 "
        pdb=" O01 UQ4 Q 101 "
      ideal   model   delta    sigma   weight residual
     126.87  117.95    8.92 3.00e+00 1.11e-01 8.85e+00
  angle pdb=" C50 UQ4 H 101 "
        pdb=" C02 UQ4 H 101 "
        pdb=" O01 UQ4 H 101 "
      ideal   model   delta    sigma   weight residual
     126.87  117.95    8.92 3.00e+00 1.11e-01 8.85e+00
  angle pdb=" C50 UQ4 K 101 "
        pdb=" C02 UQ4 K 101 "
        pdb=" O01 UQ4 K 101 "
      ideal   model   delta    sigma   weight residual
     126.87  117.97    8.90 3.00e+00 1.11e-01 8.80e+00
  angle pdb=" C50 UQ4 W 101 "
        pdb=" C02 UQ4 W 101 "
        pdb=" O01 UQ4 W 101 "
      ideal   model   delta    sigma   weight residual
     126.87  117.97    8.90 3.00e+00 1.11e-01 8.80e+00
  angle pdb=" C50 UQ4 B 101 "
        pdb=" C02 UQ4 B 101 "
        pdb=" O01 UQ4 B 101 "
      ideal   model   delta    sigma   weight residual
     126.87  117.97    8.90 3.00e+00 1.11e-01 8.79e+00
  ... (remaining 1747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.54: 384
       14.54 -    29.08: 64
       29.08 -    43.62: 64
       43.62 -    58.16: 24
       58.16 -    72.70: 16
  Dihedral angle restraints: 552
    sinusoidal: 288
      harmonic: 264
  Sorted by residual:
  dihedral pdb=" CA  LEU E   4 "
           pdb=" CB  LEU E   4 "
           pdb=" CG  LEU E   4 "
           pdb=" CD1 LEU E   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  144.08   35.92     3      1.50e+01 4.44e-03 6.19e+00
  dihedral pdb=" CA  LEU N   4 "
           pdb=" CB  LEU N   4 "
           pdb=" CG  LEU N   4 "
           pdb=" CD1 LEU N   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  144.08   35.92     3      1.50e+01 4.44e-03 6.19e+00
  dihedral pdb=" CA  LEU K   4 "
           pdb=" CB  LEU K   4 "
           pdb=" CG  LEU K   4 "
           pdb=" CD1 LEU K   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  144.10   35.90     3      1.50e+01 4.44e-03 6.18e+00
  ... (remaining 549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.038: 120
       0.038 -    0.075: 48
       0.075 -    0.112: 16
       0.112 -    0.149: 0
       0.149 -    0.185: 8
  Chirality restraints: 192
  Sorted by residual:
  chirality pdb=" CG  LEU R   4 "
            pdb=" CB  LEU R   4 "
            pdb=" CD1 LEU R   4 "
            pdb=" CD2 LEU R   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CG  LEU I   4 "
            pdb=" CB  LEU I   4 "
            pdb=" CD1 LEU I   4 "
            pdb=" CD2 LEU I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CG  LEU L   4 "
            pdb=" CB  LEU L   4 "
            pdb=" CD1 LEU L   4 "
            pdb=" CD2 LEU L   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.47e-01
  ... (remaining 189 not shown)

  Planarity restraints: 136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU I   4 "   -0.002 2.00e-02 2.50e+03   3.39e-03 1.15e-01
        pdb=" C   LEU I   4 "    0.006 2.00e-02 2.50e+03
        pdb=" O   LEU I   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" N   LEU I   5 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R   4 "    0.002 2.00e-02 2.50e+03   3.39e-03 1.15e-01
        pdb=" C   LEU R   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" O   LEU R   4 "    0.002 2.00e-02 2.50e+03
        pdb=" N   LEU R   5 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU X   4 "    0.002 2.00e-02 2.50e+03   3.34e-03 1.12e-01
        pdb=" C   LEU X   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" O   LEU X   4 "    0.002 2.00e-02 2.50e+03
        pdb=" N   LEU X   5 "    0.002 2.00e-02 2.50e+03
  ... (remaining 133 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 48
        2.72 -     3.26: 1116
        3.26 -     3.81: 2110
        3.81 -     4.35: 2730
        4.35 -     4.90: 4930
  Nonbonded interactions: 10934
  Sorted by model distance:
  nonbonded pdb=" O58 UQ4 I   1 "
            pdb=" O58 UQ4 R   1 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O58 UQ4 C   1 "
            pdb=" O58 UQ4 U   1 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O58 UQ4 F   1 "
            pdb=" O58 UQ4 O   1 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O58 UQ4 L   1 "
            pdb=" O58 UQ4 X   1 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" N52 UQ4 M   1 "
            pdb=" O01 UQ4 M   1 "
     model   vdw
     2.420 3.120
  ... (remaining 10929 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'X'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'T'
  selection = chain 'W'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.010
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.030
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.050   0.169   1344  Z= 2.763
  Angle     :  2.197   8.924   1752  Z= 0.752
  Chirality :  0.056   0.185    192
  Planarity :  0.001   0.003    136
  Dihedral  : 26.689  72.701    360
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 29.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -9.60 (0.20), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -7.31 (0.15), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.04854 ( 1320)
  covalent geometry    : angle       2.19652 ( 1752)
  Misc. bond           : bond        0.10220 (   24)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.025 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0154
  time to fit residues: 0.6624
Evaluate side-chains
  5 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 5
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.045480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.044050 restraints weight = 10630.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.044486 restraints weight = 4065.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.044700 restraints weight = 2107.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.044850 restraints weight = 1283.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.044938 restraints weight = 877.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.7197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.196   1344  Z= 3.279
  Angle     :  5.811  28.032   1752  Z= 2.047
  Chirality :  0.181   0.632    192
  Planarity :  0.013   0.029    136
  Dihedral  : 26.417  86.806    168
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 62.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 29.17 %
    Favored  : 70.83 %
  Rotamer:
    Outliers : 35.42 %
    Allowed  : 35.42 %
    Favored  : 29.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.49 (0.54), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.47 (0.41), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07489 ( 1320)
  covalent geometry    : angle       5.81112 ( 1752)
  Misc. bond           : bond        0.00810 (   24)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 0
  time to evaluate  : 0.036 
Fit side-chains
REVERT: I    2 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9285 (tp)
REVERT: N    5 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9247 (tp)
REVERT: Q    4 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9361 (tt)
REVERT: R    2 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9249 (tp)
  outliers start: 34
  outliers final: 22
  residues processed: 34
  average time/residue: 0.0172
  time to fit residues: 0.7903
Evaluate side-chains
  26 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 0
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain G residue    4 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain I residue    2 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    3 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.047612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.045846 restraints weight = 10928.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.046409 restraints weight = 4122.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.046706 restraints weight = 2175.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 15)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.046855 restraints weight = 1361.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.046984 restraints weight = 976.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.7842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.199   1344  Z= 3.271
  Angle     :  5.988  34.413   1752  Z= 2.093
  Chirality :  0.171   0.539    192
  Planarity :  0.014   0.033    136
  Dihedral  : 26.773  89.751    168
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 74.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 38.54 %
    Allowed  : 39.58 %
    Favored  : 21.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.55 (0.59), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.51 (0.45), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07471 ( 1320)
  covalent geometry    : angle       5.98796 ( 1752)
  Misc. bond           : bond        0.00884 (   24)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 0
  time to evaluate  : 0.039 
Fit side-chains
   revert: symmetry clash
REVERT: N    5 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9282 (tp)
REVERT: Q    4 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9312 (tt)
  outliers start: 37
  outliers final: 21
  residues processed: 37
  average time/residue: 0.0144
  time to fit residues: 0.7220
Evaluate side-chains
  23 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 0
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain I residue    3 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    3 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.048073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.046264 restraints weight = 11198.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.046805 restraints weight = 4119.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.047117 restraints weight = 2120.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.047273 restraints weight = 1312.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.047389 restraints weight = 913.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.7981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.197   1344  Z= 3.259
  Angle     :  5.901  35.303   1752  Z= 2.069
  Chirality :  0.172   0.551    192
  Planarity :  0.015   0.049    136
  Dihedral  : 25.777  86.376    168
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 78.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 33.33 %
    Favored  : 66.67 %
  Rotamer:
    Outliers : 39.58 %
    Allowed  : 37.50 %
    Favored  : 22.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.50 (0.63), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.47 (0.48), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07445 ( 1320)
  covalent geometry    : angle       5.90054 ( 1752)
  Misc. bond           : bond        0.00878 (   24)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 0
  time to evaluate  : 0.042 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9331 (tt)
REVERT: H    5 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9418 (tp)
REVERT: N    5 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9263 (tp)
REVERT: Q    4 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9309 (tt)
  outliers start: 38
  outliers final: 25
  residues processed: 38
  average time/residue: 0.0259
  time to fit residues: 1.3090
Evaluate side-chains
  29 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 0
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain I residue    3 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain L residue    5 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    3 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    3 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.047884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.046030 restraints weight = 10564.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.046585 restraints weight = 3974.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.046896 restraints weight = 2053.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.047055 restraints weight = 1277.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.047210 restraints weight = 904.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.8091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.196   1344  Z= 3.255
  Angle     :  5.876  34.462   1752  Z= 2.064
  Chirality :  0.172   0.567    192
  Planarity :  0.015   0.051    136
  Dihedral  : 25.858  85.306    168
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 81.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 38.54 %
    Allowed  : 41.67 %
    Favored  : 19.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.29 (0.68), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.31 (0.52), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07435 ( 1320)
  covalent geometry    : angle       5.87647 ( 1752)
  Misc. bond           : bond        0.00900 (   24)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 0
  time to evaluate  : 0.023 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9338 (tp)
REVERT: H    4 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9337 (tt)
REVERT: H    5 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9279 (tp)
REVERT: N    5 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9270 (tp)
  outliers start: 37
  outliers final: 28
  residues processed: 37
  average time/residue: 0.0170
  time to fit residues: 0.8377
Evaluate side-chains
  32 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 0
  time to evaluate  : 0.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain I residue    3 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain L residue    5 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    3 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain R residue    3 LEU
Chi-restraints excluded: chain R residue    5 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.048036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.046209 restraints weight = 11066.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.046724 restraints weight = 4107.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.047086 restraints weight = 1999.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.047261 restraints weight = 1193.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.047409 restraints weight = 833.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.8206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.199   1344  Z= 3.247
  Angle     :  5.840  33.305   1752  Z= 2.047
  Chirality :  0.172   0.561    192
  Planarity :  0.015   0.049    136
  Dihedral  : 25.398  84.850    168
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 80.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 38.54 %
    Allowed  : 40.62 %
    Favored  : 20.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.29 (0.73), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.31 (0.56), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07427 ( 1320)
  covalent geometry    : angle       5.84019 ( 1752)
  Misc. bond           : bond        0.00876 (   24)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 0
  time to evaluate  : 0.025 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9306 (tp)
REVERT: H    4 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9309 (tt)
REVERT: H    5 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9273 (tp)
REVERT: N    5 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9308 (tp)
REVERT: Q    4 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9278 (tt)
  outliers start: 37
  outliers final: 23
  residues processed: 37
  average time/residue: 0.0178
  time to fit residues: 0.8754
Evaluate side-chains
  28 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 0
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain R residue    5 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.047822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046005 restraints weight = 10992.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.046579 restraints weight = 3911.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.046878 restraints weight = 1946.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.046997 restraints weight = 1172.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.047163 restraints weight = 881.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.8268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.199   1344  Z= 3.248
  Angle     :  5.843  33.267   1752  Z= 2.047
  Chirality :  0.172   0.550    192
  Planarity :  0.015   0.048    136
  Dihedral  : 25.417  84.928    168
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 78.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 38.54 %
    Allowed  : 37.50 %
    Favored  : 23.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.21 (0.79), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.25 (0.60), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07440 ( 1320)
  covalent geometry    : angle       5.84323 ( 1752)
  Misc. bond           : bond        0.00862 (   24)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 0
  time to evaluate  : 0.042 
Fit side-chains
   revert: symmetry clash
REVERT: E    5 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9309 (tp)
REVERT: H    4 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9324 (tt)
REVERT: H    5 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9287 (tp)
REVERT: N    5 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9279 (tp)
REVERT: Q    4 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9393 (tt)
  outliers start: 37
  outliers final: 26
  residues processed: 37
  average time/residue: 0.0229
  time to fit residues: 1.1129
Evaluate side-chains
  31 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 0
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain I residue    3 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain R residue    5 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Chi-restraints excluded: chain X residue    5 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.047559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.045771 restraints weight = 10841.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.046289 restraints weight = 3861.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.046607 restraints weight = 1902.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.046808 restraints weight = 1155.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.046951 restraints weight = 801.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.8305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.196   1344  Z= 3.246
  Angle     :  5.837  33.336   1752  Z= 2.044
  Chirality :  0.172   0.572    192
  Planarity :  0.015   0.048    136
  Dihedral  : 25.377  82.913    168
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 80.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 37.50 %
    Favored  : 62.50 %
  Rotamer:
    Outliers : 36.46 %
    Allowed  : 40.62 %
    Favored  : 22.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.21 (0.80), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.25 (0.61), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07437 ( 1320)
  covalent geometry    : angle       5.83702 ( 1752)
  Misc. bond           : bond        0.00849 (   24)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 0
  time to evaluate  : 0.044 
Fit side-chains
REVERT: E    5 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9290 (tt)
REVERT: H    4 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9286 (tt)
REVERT: H    5 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9232 (tp)
REVERT: N    5 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9236 (tp)
REVERT: Q    4 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9310 (tt)
  outliers start: 35
  outliers final: 25
  residues processed: 35
  average time/residue: 0.0243
  time to fit residues: 1.1158
Evaluate side-chains
  30 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 0
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain F residue    3 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain N residue    5 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain R residue    5 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Chi-restraints excluded: chain X residue    5 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.047376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.045595 restraints weight = 10861.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.046148 restraints weight = 3849.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.046483 restraints weight = 1926.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.046610 restraints weight = 1163.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.046752 restraints weight = 839.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.8313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.200   1344  Z= 3.244
  Angle     :  5.840  33.410   1752  Z= 2.047
  Chirality :  0.171   0.574    192
  Planarity :  0.015   0.048    136
  Dihedral  : 25.444  85.898    168
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 79.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 36.46 %
    Allowed  : 37.50 %
    Favored  : 26.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.25 (0.82), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.28 (0.63), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07436 ( 1320)
  covalent geometry    : angle       5.84006 ( 1752)
  Misc. bond           : bond        0.00838 (   24)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 0
  time to evaluate  : 0.042 
Fit side-chains
REVERT: E    5 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9291 (tt)
REVERT: H    4 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9298 (tt)
REVERT: H    5 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9240 (tp)
REVERT: Q    4 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9246 (tt)
  outliers start: 35
  outliers final: 24
  residues processed: 35
  average time/residue: 0.0214
  time to fit residues: 0.9983
Evaluate side-chains
  28 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 0
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain R residue    5 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Chi-restraints excluded: chain X residue    5 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.047307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.045455 restraints weight = 10881.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.046063 restraints weight = 3856.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.046387 restraints weight = 1921.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046524 restraints weight = 1161.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046524 restraints weight = 828.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.8327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.199   1344  Z= 3.243
  Angle     :  5.816  33.500   1752  Z= 2.038
  Chirality :  0.170   0.571    192
  Planarity :  0.015   0.049    136
  Dihedral  : 25.392  84.240    168
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 79.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 29.17 %
    Allowed  : 42.71 %
    Favored  : 28.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.35 (0.82), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.36 (0.63), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07433 ( 1320)
  covalent geometry    : angle       5.81613 ( 1752)
  Misc. bond           : bond        0.00838 (   24)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 0
  time to evaluate  : 0.045 
Fit side-chains
REVERT: E    5 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9284 (tt)
REVERT: H    4 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9290 (tt)
REVERT: H    5 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9236 (tp)
REVERT: Q    4 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9244 (tt)
  outliers start: 28
  outliers final: 24
  residues processed: 28
  average time/residue: 0.0210
  time to fit residues: 0.8016
Evaluate side-chains
  28 residues out of total 96 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 0
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain B residue    2 LEU
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain E residue    2 LEU
Chi-restraints excluded: chain E residue    3 LEU
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 LEU
Chi-restraints excluded: chain J residue    4 LEU
Chi-restraints excluded: chain K residue    3 LEU
Chi-restraints excluded: chain M residue    4 LEU
Chi-restraints excluded: chain N residue    2 LEU
Chi-restraints excluded: chain O residue    5 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain Q residue    2 LEU
Chi-restraints excluded: chain Q residue    3 LEU
Chi-restraints excluded: chain Q residue    4 LEU
Chi-restraints excluded: chain R residue    2 LEU
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain T residue    2 LEU
Chi-restraints excluded: chain T residue    3 LEU
Chi-restraints excluded: chain V residue    4 LEU
Chi-restraints excluded: chain W residue    2 LEU
Chi-restraints excluded: chain W residue    3 LEU
Chi-restraints excluded: chain X residue    2 LEU
Chi-restraints excluded: chain X residue    5 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    5.9990
   overall best weight:   50.0000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.047219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.045411 restraints weight = 10882.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.045972 restraints weight = 3819.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.046319 restraints weight = 1913.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046487 restraints weight = 1144.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.046606 restraints weight = 804.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.8328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.074   0.195   1344  Z= 3.240
  Angle     :  5.816  33.447   1752  Z= 2.038
  Chirality :  0.170   0.567    192
  Planarity :  0.015   0.047    136
  Dihedral  : 25.405  84.162    168
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 79.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 35.42 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 30.21 %
    Allowed  : 43.75 %
    Favored  : 26.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.78 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -8.34 (0.83), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -6.36 (0.63), residues: 48
Details of bonding type rmsd
  covalent geometry    : bond        0.07423 ( 1320)
  covalent geometry    : angle       5.81590 ( 1752)
  Misc. bond           : bond        0.00845 (   24)

===============================================================================
Job complete
usr+sys time: 213.48 seconds
wall clock time: 4 minutes 55.97 seconds (295.97 seconds total)