Starting phenix.real_space_refine
on Mon Mar 18 16:46:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/03_2024/6vl6_21231.pdb"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C   13788      2.51       5
     N    3564      2.21       5
     O    4116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   85": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 21504
  Number of models: 1
  Model: ""
    Number of chains: 24
    Chain: "A"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "B"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "C"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "N"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "D"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "O"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "E"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "P"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "F"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "Q"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "G"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "R"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "S"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "I"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "T"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "J"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "U"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "K"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "V"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "L"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "W"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "M"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 981
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "X"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
  Time building chain proxies: 10.62, per 1000 atoms: 0.49
  Number of scatterers: 21504
  At special positions: 0
  Unit cell: (162.15, 158.7, 156.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    4116      8.00
     N    3564      7.00
     C   13788      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  - 3.50
        Amino acid           : False - 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=0, symmetry=0
  Time building additional restraints: 8.54
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  5184 Ramachandran restraints generated.
    2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4944

  Finding SS restraints...
    Secondary structure from input PDB file:
      156 helices and 0 sheets defined
      90.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 20
    Processing helix  chain 'A' and resid 22 through 36
    Processing helix  chain 'A' and resid 40 through 55
    Processing helix  chain 'A' and resid 56 through 71
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 90 through 105
    Processing helix  chain 'A' and resid 108 through 122
    Processing helix  chain 'B' and resid 3 through 16
    Processing helix  chain 'B' and resid 18 through 33
    Processing helix  chain 'B' and resid 36 through 50
    Processing helix  chain 'B' and resid 52 through 67
    Processing helix  chain 'B' and resid 70 through 84
    Processing helix  chain 'B' and resid 86 through 99
    Processing helix  chain 'C' and resid 5 through 20
    Processing helix  chain 'C' and resid 22 through 36
    Processing helix  chain 'C' and resid 40 through 55
    Processing helix  chain 'C' and resid 56 through 71
    Processing helix  chain 'C' and resid 74 through 88
    Processing helix  chain 'C' and resid 90 through 105
    Processing helix  chain 'C' and resid 108 through 122
    Processing helix  chain 'N' and resid 3 through 16
    Processing helix  chain 'N' and resid 18 through 33
    Processing helix  chain 'N' and resid 36 through 50
    Processing helix  chain 'N' and resid 52 through 67
    Processing helix  chain 'N' and resid 70 through 84
    Processing helix  chain 'N' and resid 86 through 99
    Processing helix  chain 'D' and resid 5 through 20
    Processing helix  chain 'D' and resid 22 through 36
    Processing helix  chain 'D' and resid 40 through 55
    Processing helix  chain 'D' and resid 56 through 71
    Processing helix  chain 'D' and resid 74 through 88
    Processing helix  chain 'D' and resid 90 through 105
    Processing helix  chain 'D' and resid 108 through 122
    Processing helix  chain 'O' and resid 3 through 16
    Processing helix  chain 'O' and resid 18 through 33
    Processing helix  chain 'O' and resid 36 through 50
    Processing helix  chain 'O' and resid 52 through 67
    Processing helix  chain 'O' and resid 70 through 84
    Processing helix  chain 'O' and resid 86 through 99
    Processing helix  chain 'E' and resid 5 through 20
    Processing helix  chain 'E' and resid 22 through 36
    Processing helix  chain 'E' and resid 40 through 55
    Processing helix  chain 'E' and resid 56 through 71
    Processing helix  chain 'E' and resid 74 through 88
    Processing helix  chain 'E' and resid 90 through 105
    Processing helix  chain 'E' and resid 108 through 122
    Processing helix  chain 'P' and resid 3 through 16
    Processing helix  chain 'P' and resid 18 through 33
    Processing helix  chain 'P' and resid 36 through 50
    Processing helix  chain 'P' and resid 52 through 67
    Processing helix  chain 'P' and resid 70 through 84
    Processing helix  chain 'P' and resid 86 through 99
    Processing helix  chain 'F' and resid 5 through 20
    Processing helix  chain 'F' and resid 22 through 36
    Processing helix  chain 'F' and resid 40 through 55
    Processing helix  chain 'F' and resid 56 through 71
    Processing helix  chain 'F' and resid 74 through 88
    Processing helix  chain 'F' and resid 90 through 105
    Processing helix  chain 'F' and resid 108 through 122
    Processing helix  chain 'Q' and resid 3 through 16
    Processing helix  chain 'Q' and resid 18 through 33
    Processing helix  chain 'Q' and resid 36 through 50
    Processing helix  chain 'Q' and resid 52 through 67
    Processing helix  chain 'Q' and resid 70 through 84
    Processing helix  chain 'Q' and resid 86 through 99
    Processing helix  chain 'G' and resid 5 through 20
    Processing helix  chain 'G' and resid 22 through 36
    Processing helix  chain 'G' and resid 40 through 55
    Processing helix  chain 'G' and resid 56 through 71
    Processing helix  chain 'G' and resid 74 through 88
    Processing helix  chain 'G' and resid 90 through 105
    Processing helix  chain 'G' and resid 108 through 122
    Processing helix  chain 'R' and resid 3 through 16
    Processing helix  chain 'R' and resid 18 through 33
    Processing helix  chain 'R' and resid 36 through 50
    Processing helix  chain 'R' and resid 52 through 67
    Processing helix  chain 'R' and resid 70 through 84
    Processing helix  chain 'R' and resid 86 through 99
    Processing helix  chain 'H' and resid 5 through 20
    Processing helix  chain 'H' and resid 22 through 36
    Processing helix  chain 'H' and resid 40 through 55
    Processing helix  chain 'H' and resid 56 through 71
    Processing helix  chain 'H' and resid 74 through 88
    Processing helix  chain 'H' and resid 90 through 105
    Processing helix  chain 'H' and resid 108 through 122
    Processing helix  chain 'S' and resid 3 through 16
    Processing helix  chain 'S' and resid 18 through 33
    Processing helix  chain 'S' and resid 36 through 50
    Processing helix  chain 'S' and resid 52 through 67
    Processing helix  chain 'S' and resid 70 through 84
    Processing helix  chain 'S' and resid 86 through 99
    Processing helix  chain 'I' and resid 5 through 20
    Processing helix  chain 'I' and resid 22 through 36
    Processing helix  chain 'I' and resid 40 through 55
    Processing helix  chain 'I' and resid 56 through 71
    Processing helix  chain 'I' and resid 74 through 88
    Processing helix  chain 'I' and resid 90 through 105
    Processing helix  chain 'I' and resid 108 through 122
    Processing helix  chain 'T' and resid 3 through 16
    Processing helix  chain 'T' and resid 18 through 33
    Processing helix  chain 'T' and resid 36 through 50
    Processing helix  chain 'T' and resid 52 through 67
    Processing helix  chain 'T' and resid 70 through 84
    Processing helix  chain 'T' and resid 86 through 99
    Processing helix  chain 'J' and resid 5 through 20
    Processing helix  chain 'J' and resid 22 through 36
    Processing helix  chain 'J' and resid 40 through 55
    Processing helix  chain 'J' and resid 56 through 71
    Processing helix  chain 'J' and resid 74 through 88
    Processing helix  chain 'J' and resid 90 through 105
    Processing helix  chain 'J' and resid 108 through 122
    Processing helix  chain 'U' and resid 3 through 16
    Processing helix  chain 'U' and resid 18 through 33
    Processing helix  chain 'U' and resid 36 through 50
    Processing helix  chain 'U' and resid 52 through 67
    Processing helix  chain 'U' and resid 70 through 84
    Processing helix  chain 'U' and resid 86 through 99
    Processing helix  chain 'K' and resid 5 through 20
    Processing helix  chain 'K' and resid 22 through 36
    Processing helix  chain 'K' and resid 40 through 55
    Processing helix  chain 'K' and resid 56 through 71
    Processing helix  chain 'K' and resid 74 through 88
    Processing helix  chain 'K' and resid 90 through 105
    Processing helix  chain 'K' and resid 108 through 122
    Processing helix  chain 'V' and resid 3 through 16
    Processing helix  chain 'V' and resid 18 through 33
    Processing helix  chain 'V' and resid 36 through 50
    Processing helix  chain 'V' and resid 52 through 67
    Processing helix  chain 'V' and resid 70 through 84
    Processing helix  chain 'V' and resid 86 through 99
    Processing helix  chain 'L' and resid 5 through 20
    Processing helix  chain 'L' and resid 22 through 36
    Processing helix  chain 'L' and resid 40 through 55
    Processing helix  chain 'L' and resid 56 through 71
    Processing helix  chain 'L' and resid 74 through 88
    Processing helix  chain 'L' and resid 90 through 105
    Processing helix  chain 'L' and resid 108 through 122
    Processing helix  chain 'W' and resid 3 through 16
    Processing helix  chain 'W' and resid 18 through 33
    Processing helix  chain 'W' and resid 36 through 50
    Processing helix  chain 'W' and resid 52 through 67
    Processing helix  chain 'W' and resid 70 through 84
    Processing helix  chain 'W' and resid 86 through 99
    Processing helix  chain 'M' and resid 5 through 20
    Processing helix  chain 'M' and resid 22 through 36
    Processing helix  chain 'M' and resid 40 through 55
    Processing helix  chain 'M' and resid 56 through 71
    Processing helix  chain 'M' and resid 74 through 88
    Processing helix  chain 'M' and resid 90 through 105
    Processing helix  chain 'M' and resid 108 through 122
    Processing helix  chain 'X' and resid 3 through 16
    Processing helix  chain 'X' and resid 18 through 33
    Processing helix  chain 'X' and resid 36 through 50
    Processing helix  chain 'X' and resid 52 through 67
    Processing helix  chain 'X' and resid 70 through 84
    Processing helix  chain 'X' and resid 86 through 99

    1764 hydrogen bonds defined for protein.
    5292 hydrogen bond angles 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: 7.17

  Time building geometry restraints manager: 9.13 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 4212
        1.32 -     1.44: 6379
        1.44 -     1.56: 11225
        1.56 -     1.68: 84
        1.68 -     1.81: 72
  Bond restraints: 21972
  Sorted by residual:
  bond pdb=" NE1 TRP O  40 "
       pdb=" CE2 TRP O  40 "
    ideal  model  delta    sigma   weight residual
    1.370  1.326  0.044 1.10e-02 8.26e+03 1.58e+01
  bond pdb=" NE1 TRP U  40 "
       pdb=" CE2 TRP U  40 "
    ideal  model  delta    sigma   weight residual
    1.370  1.327  0.043 1.10e-02 8.26e+03 1.56e+01
  bond pdb=" NE1 TRP Q  40 "
       pdb=" CE2 TRP Q  40 "
    ideal  model  delta    sigma   weight residual
    1.370  1.327  0.043 1.10e-02 8.26e+03 1.56e+01
  bond pdb=" NE1 TRP N  40 "
       pdb=" CE2 TRP N  40 "
    ideal  model  delta    sigma   weight residual
    1.370  1.327  0.043 1.10e-02 8.26e+03 1.56e+01
  bond pdb=" NE1 TRP B  40 "
       pdb=" CE2 TRP B  40 "
    ideal  model  delta    sigma   weight residual
    1.370  1.327  0.043 1.10e-02 8.26e+03 1.55e+01
  ... (remaining 21967 not shown)

  Histogram of bond angle deviations from ideal:
      100.69 -   107.32: 729
      107.32 -   113.96: 10697
      113.96 -   120.59: 11702
      120.59 -   127.22: 6428
      127.22 -   133.85: 168
  Bond angle restraints: 29724
  Sorted by residual:
  angle pdb=" C   ASP S  33 "
        pdb=" N   PRO S  34 "
        pdb=" CA  PRO S  34 "
      ideal   model   delta    sigma   weight residual
     119.82  128.00   -8.18 9.80e-01 1.04e+00 6.97e+01
  angle pdb=" C   ASP T  33 "
        pdb=" N   PRO T  34 "
        pdb=" CA  PRO T  34 "
      ideal   model   delta    sigma   weight residual
     119.82  128.00   -8.18 9.80e-01 1.04e+00 6.96e+01
  angle pdb=" C   ASP N  33 "
        pdb=" N   PRO N  34 "
        pdb=" CA  PRO N  34 "
      ideal   model   delta    sigma   weight residual
     119.82  127.99   -8.17 9.80e-01 1.04e+00 6.95e+01
  angle pdb=" C   ASP R  33 "
        pdb=" N   PRO R  34 "
        pdb=" CA  PRO R  34 "
      ideal   model   delta    sigma   weight residual
     119.82  127.99   -8.17 9.80e-01 1.04e+00 6.95e+01
  angle pdb=" C   ASP W  33 "
        pdb=" N   PRO W  34 "
        pdb=" CA  PRO W  34 "
      ideal   model   delta    sigma   weight residual
     119.82  127.98   -8.16 9.80e-01 1.04e+00 6.93e+01
  ... (remaining 29719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 12386
       17.11 -    34.22: 539
       34.22 -    51.33: 107
       51.33 -    68.43: 48
       68.43 -    85.54: 12
  Dihedral angle restraints: 13092
    sinusoidal: 5196
      harmonic: 7896
  Sorted by residual:
  dihedral pdb=" CB  MET L  17 "
           pdb=" CG  MET L  17 "
           pdb=" SD  MET L  17 "
           pdb=" CE  MET L  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   99.36  -39.36     3      1.50e+01 4.44e-03 6.97e+00
  dihedral pdb=" CB  MET F  17 "
           pdb=" CG  MET F  17 "
           pdb=" SD  MET F  17 "
           pdb=" CE  MET F  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   99.35  -39.35     3      1.50e+01 4.44e-03 6.97e+00
  dihedral pdb=" CB  MET J  17 "
           pdb=" CG  MET J  17 "
           pdb=" SD  MET J  17 "
           pdb=" CE  MET J  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   99.35  -39.35     3      1.50e+01 4.44e-03 6.97e+00
  ... (remaining 13089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1719
       0.065 -    0.130: 773
       0.130 -    0.195: 398
       0.195 -    0.260: 49
       0.260 -    0.325: 25
  Chirality restraints: 2964
  Sorted by residual:
  chirality pdb=" CA  ASN E  80 "
            pdb=" N   ASN E  80 "
            pdb=" C   ASN E  80 "
            pdb=" CB  ASN E  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CA  ASN J  80 "
            pdb=" N   ASN J  80 "
            pdb=" C   ASN J  80 "
            pdb=" CB  ASN J  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  ASN K  80 "
            pdb=" N   ASN K  80 "
            pdb=" C   ASN K  80 "
            pdb=" CB  ASN K  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 2961 not shown)

  Planarity restraints: 3888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR V  59 "   -0.044 2.00e-02 2.50e+03   2.22e-02 9.84e+00
        pdb=" CG  TYR V  59 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR V  59 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR V  59 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR V  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR V  59 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR V  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR V  59 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R  59 "    0.044 2.00e-02 2.50e+03   2.21e-02 9.75e+00
        pdb=" CG  TYR R  59 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR R  59 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR R  59 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR R  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR R  59 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR R  59 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR R  59 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR T  59 "   -0.044 2.00e-02 2.50e+03   2.21e-02 9.73e+00
        pdb=" CG  TYR T  59 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TYR T  59 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR T  59 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR T  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR T  59 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR T  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR T  59 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 3885 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 10121
        2.92 -     3.42: 23687
        3.42 -     3.91: 39439
        3.91 -     4.41: 49797
        4.41 -     4.90: 71062
  Nonbonded interactions: 194106
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  99 "
            pdb=" OD2 ASP O  88 "
     model   vdw
     2.431 2.520
  nonbonded pdb=" NZ  LYS C  99 "
            pdb=" OD2 ASP N  88 "
     model   vdw
     2.431 2.520
  nonbonded pdb=" NZ  LYS L  99 "
            pdb=" OD2 ASP W  88 "
     model   vdw
     2.431 2.520
  nonbonded pdb=" NZ  LYS A  99 "
            pdb=" OD2 ASP B  88 "
     model   vdw
     2.431 2.520
  nonbonded pdb=" NZ  LYS H  99 "
            pdb=" OD2 ASP S  88 "
     model   vdw
     2.431 2.520
  ... (remaining 194101 not shown)

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

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
}
pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
  selection = chain 'S'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
}
Set refine NCS operators
  NCS operators will be refined.
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:             5.880
  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:          18.830
  Check model and map are aligned:         0.260
  Set scattering table:                    0.160
  Process input model:                     54.780
  Find NCS groups from input model:        1.720
  Set up NCS constraints:                  0.200
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   84.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
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      :  0.019   0.086  21972  Z= 1.185
  Angle     :  1.456   8.182  29724  Z= 1.015
  Chirality :  0.089   0.325   2964
  Planarity :  0.008   0.041   3888
  Dihedral  : 11.376  85.543   8148
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.14), residues: 2592
  helix:  0.53 (0.09), residues: 2412
  sheet:  None (None), residues: 0
  loop : -1.42 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.006   TRP B  40 
 TYR   0.044   0.008   TYR V  59 
 ARG   0.006   0.001   ARG R  32 

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

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

  5184 Ramachandran restraints generated.
    2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5184 Ramachandran restraints generated.
    2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.9149 (mmt) cc_final: 0.8679 (mtm)
REVERT: A   32 LEU cc_start: 0.9706 (mt) cc_final: 0.9105 (tp)
REVERT: A  108 ASN cc_start: 0.9462 (t0) cc_final: 0.8999 (t0)
REVERT: A  110 ASP cc_start: 0.9268 (m-30) cc_final: 0.8932 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.2528
  time to fit residues: 10.1358
Evaluate side-chains
  14 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.120 
Evaluate side-chains
  31 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   11 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8664 (mt-10)
REVERT: B   33 ASP cc_start: 0.9175 (t0) cc_final: 0.8910 (t0)
REVERT: B   36 ASN cc_start: 0.9184 (t0) cc_final: 0.8950 (t0)
REVERT: B   67 ASP cc_start: 0.9240 (t0) cc_final: 0.9023 (t0)
REVERT: B   86 LYS cc_start: 0.9005 (mptt) cc_final: 0.8735 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.3474
  time to fit residues: 11.1738
Evaluate side-chains
  17 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 212 optimal weight:    2.9990
   chunk 191 optimal weight:    1.9990
   chunk 105 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 197 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 147 optimal weight:   10.0000
   chunk 228 optimal weight:    0.0570
   overall best weight:    1.0502
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
Q  50 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  21972  Z= 0.210
  Angle     :  0.588   5.688  29724  Z= 0.314
  Chirality :  0.041   0.143   2964
  Planarity :  0.005   0.035   3888
  Dihedral  :  3.885  13.196   3072
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  2.98 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.14), residues: 2592
  helix:  1.16 (0.09), residues: 2436
  sheet:  None (None), residues: 0
  loop : -1.31 (0.47), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP U  74 
 TYR   0.015   0.002   TYR I  64 
 ARG   0.006   0.001   ARG O  32 

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

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

  4934 Ramachandran restraints generated.
    2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4934 Ramachandran restraints generated.
    2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.091 
Fit side-chains
REVERT: I  108 ASN cc_start: 0.9230 (t0) cc_final: 0.8782 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1042
  time to fit residues: 3.6603
Evaluate side-chains
  17 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.123 
Evaluate side-chains
  26 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   15 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9104 (mmmt)
REVERT: Q   33 ASP cc_start: 0.9413 (t0) cc_final: 0.9102 (t0)
REVERT: Q   36 ASN cc_start: 0.9082 (t0) cc_final: 0.8312 (t0)
REVERT: Q   52 ASP cc_start: 0.8597 (t0) cc_final: 0.8376 (t0)
REVERT: Q   70 ASN cc_start: 0.9223 (t0) cc_final: 0.8659 (t0)
REVERT: Q   86 LYS cc_start: 0.9136 (mptt) cc_final: 0.8805 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.2328
  time to fit residues: 6.3927
Evaluate side-chains
  18 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 190 optimal weight:    2.9990
   chunk 155 optimal weight:    0.4980
   chunk 63 optimal weight:    9.9990
   chunk 229 optimal weight:    1.9990
   chunk 247 optimal weight:    4.9990
   chunk 204 optimal weight:    6.9990
   chunk 227 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 183 optimal weight:    6.9990
   overall best weight:    1.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  21972  Z= 0.232
  Angle     :  0.706  14.254  29724  Z= 0.344
  Chirality :  0.046   0.363   2964
  Planarity :  0.004   0.024   3888
  Dihedral  :  4.098  14.732   3072
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.79 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.15), residues: 2592
  helix:  0.97 (0.09), residues: 2436
  sheet:  None (None), residues: 0
  loop : -1.58 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP U  74 
 TYR   0.011   0.002   TYR L  23 
 ARG   0.004   0.001   ARG K 107 

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

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

  4502 Ramachandran restraints generated.
    2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4502 Ramachandran restraints generated.
    2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.104 
Fit side-chains
REVERT: L   37 ASP cc_start: 0.9375 (t70) cc_final: 0.9153 (t0)
REVERT: L   68 LEU cc_start: 0.9633 (pp) cc_final: 0.9397 (mt)
REVERT: L  108 ASN cc_start: 0.9413 (t0) cc_final: 0.9130 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1055
  time to fit residues: 3.0064
Evaluate side-chains
  14 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.106 
Evaluate side-chains
  24 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N   11 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: N   15 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9068 (mmmt)
REVERT: N   36 ASN cc_start: 0.8982 (t0) cc_final: 0.8292 (t0)
REVERT: N   38 GLU cc_start: 0.8526 (pm20) cc_final: 0.8209 (pm20)
REVERT: N   70 ASN cc_start: 0.9129 (t0) cc_final: 0.8495 (t0)
REVERT: N   86 LYS cc_start: 0.9183 (mptt) cc_final: 0.8895 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2312
  time to fit residues: 5.8421
Evaluate side-chains
  17 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 226 optimal weight:    4.9990
   chunk 172 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 109 optimal weight:    0.0170
   chunk 153 optimal weight:    0.9980
   chunk 230 optimal weight:    4.9990
   chunk 243 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 218 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.3822
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.5366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  21972  Z= 0.222
  Angle     :  0.650   9.254  29724  Z= 0.329
  Chirality :  0.043   0.250   2964
  Planarity :  0.003   0.033   3888
  Dihedral  :  4.068  13.368   3072
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.15), residues: 2592
  helix:  1.01 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.80 (0.43), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.012   0.001   TYR F  64 
 ARG   0.004   0.001   ARG D  19 

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

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

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.120 
Fit side-chains
REVERT: J   17 MET cc_start: 0.9213 (mmp) cc_final: 0.8693 (mmm)
REVERT: J  108 ASN cc_start: 0.9228 (t0) cc_final: 0.8813 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0661
  time to fit residues: 1.8041
Evaluate side-chains
  10 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.111 
Evaluate side-chains
  22 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   36 ASN cc_start: 0.9153 (t0) cc_final: 0.8396 (t0)
REVERT: Q   67 ASP cc_start: 0.9393 (t0) cc_final: 0.9041 (t0)
REVERT: Q   70 ASN cc_start: 0.9141 (t0) cc_final: 0.8319 (t0)
REVERT: Q   72 GLU cc_start: 0.8770 (pm20) cc_final: 0.8491 (pm20)
REVERT: Q   86 LYS cc_start: 0.9122 (mptt) cc_final: 0.8811 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2684
  time to fit residues: 6.2118
Evaluate side-chains
  17 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 202 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0570
   chunk 181 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0270
   chunk 207 optimal weight:    2.9990
   chunk 168 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 218 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7560
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.5502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  21972  Z= 0.186
  Angle     :  0.655   6.910  29724  Z= 0.339
  Chirality :  0.040   0.154   2964
  Planarity :  0.003   0.019   3888
  Dihedral  :  4.058  12.517   3072
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.15), residues: 2592
  helix:  0.87 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.82 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP U  74 
 TYR   0.011   0.001   TYR D  91 
 ARG   0.003   0.001   ARG E  19 

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

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

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.118 
Fit side-chains
REVERT: L   17 MET cc_start: 0.9160 (mmp) cc_final: 0.8900 (mmm)
REVERT: L   37 ASP cc_start: 0.9364 (t0) cc_final: 0.9120 (t0)
REVERT: L  108 ASN cc_start: 0.9364 (t0) cc_final: 0.9046 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1289
  time to fit residues: 2.5135
Evaluate side-chains
  12 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.115 
Evaluate side-chains
  24 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   11 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: Q   36 ASN cc_start: 0.9148 (t0) cc_final: 0.8489 (t0)
REVERT: Q   67 ASP cc_start: 0.9402 (t0) cc_final: 0.9105 (t0)
REVERT: Q   70 ASN cc_start: 0.9210 (t0) cc_final: 0.8488 (t0)
REVERT: Q   72 GLU cc_start: 0.8743 (pm20) cc_final: 0.8464 (pm20)
REVERT: Q   86 LYS cc_start: 0.8999 (mptt) cc_final: 0.8710 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2801
  time to fit residues: 7.0536
Evaluate side-chains
  17 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 219 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0070
   chunk 143 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 243 optimal weight:    2.9990
   chunk 202 optimal weight:    4.9990
   chunk 112 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 128 optimal weight:    4.9990
   overall best weight:    0.8400
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** J  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.5552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  21972  Z= 0.265
  Angle     :  0.730  11.951  29724  Z= 0.356
  Chirality :  0.040   0.144   2964
  Planarity :  0.003   0.018   3888
  Dihedral  :  4.054  13.827   3072
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  0.00 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.15), residues: 2592
  helix:  0.81 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.78 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.009   0.001   TYR K  23 
 ARG   0.007   0.001   ARG W  62 

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

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

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4262 Ramachandran restraints generated.
    2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 16
  time to evaluate  : 0.117 
Fit side-chains
REVERT: J   61 ILE cc_start: 0.9307 (mt) cc_final: 0.9022 (mt)
REVERT: J   65 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.9120 (pp30)
REVERT: J  108 ASN cc_start: 0.9236 (t0) cc_final: 0.8865 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1381
  time to fit residues: 2.6747
Evaluate side-chains
  12 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 11
  time to evaluate  : 0.116 
Evaluate side-chains
  22 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   36 ASN cc_start: 0.9156 (t0) cc_final: 0.8439 (t0)
REVERT: Q   38 GLU cc_start: 0.8433 (pm20) cc_final: 0.8187 (pm20)
REVERT: Q   67 ASP cc_start: 0.9408 (t0) cc_final: 0.9118 (t0)
REVERT: Q   70 ASN cc_start: 0.9214 (t0) cc_final: 0.8395 (t0)
REVERT: Q   86 LYS cc_start: 0.9000 (mptt) cc_final: 0.8713 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2522
  time to fit residues: 5.8532
Evaluate side-chains
  18 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 235 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 138 optimal weight:    2.9990
   chunk 178 optimal weight:    0.0980
   chunk 137 optimal weight:    0.7980
   chunk 205 optimal weight:    4.9990
   chunk 136 optimal weight:    0.0970
   chunk 242 optimal weight:    0.8980
   chunk 152 optimal weight:    3.9990
   chunk 148 optimal weight:    7.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.4378
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** L  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  21972  Z= 0.265
  Angle     :  0.730  11.951  29724  Z= 0.356
  Chirality :  0.040   0.144   2964
  Planarity :  0.003   0.018   3888
  Dihedral  :  4.054  13.827   3072
  Min Nonbonded Distance : 1.438

Molprobity Statistics.
  All-atom Clashscore : 23.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.15), residues: 2592
  helix:  0.81 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.78 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.009   0.001   TYR K  23 
 ARG   0.007   0.001   ARG B  62 

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

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

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.126 
Fit side-chains
REVERT: L   37 ASP cc_start: 0.9383 (t0) cc_final: 0.9171 (t0)
REVERT: L  108 ASN cc_start: 0.9366 (t0) cc_final: 0.9049 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1331
  time to fit residues: 2.4357
Evaluate side-chains
  11 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.117 
Evaluate side-chains
  23 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   15 LYS cc_start: 0.9499 (mmpt) cc_final: 0.9068 (mmmt)
REVERT: V   33 ASP cc_start: 0.9451 (t0) cc_final: 0.9157 (t0)
REVERT: V   36 ASN cc_start: 0.9166 (t0) cc_final: 0.8439 (t0)
REVERT: V   67 ASP cc_start: 0.9402 (t0) cc_final: 0.9187 (t0)
REVERT: V   70 ASN cc_start: 0.9061 (t0) cc_final: 0.8209 (t0)
REVERT: V   86 LYS cc_start: 0.9110 (mptt) cc_final: 0.8684 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2337
  time to fit residues: 5.6477
Evaluate side-chains
  19 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 150 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 145 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 165 optimal weight:    0.5980
   chunk 120 optimal weight:    0.0020
   chunk 22 optimal weight:    0.8980
   chunk 190 optimal weight:    0.6980
   chunk 220 optimal weight:    0.7980
   overall best weight:    0.5588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** L  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.5628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  21972  Z= 0.265
  Angle     :  0.730  11.951  29724  Z= 0.356
  Chirality :  0.040   0.144   2964
  Planarity :  0.003   0.018   3888
  Dihedral  :  4.054  13.827   3072
  Min Nonbonded Distance : 1.438

Molprobity Statistics.
  All-atom Clashscore : 23.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.15), residues: 2592
  helix:  0.81 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.78 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.009   0.001   TYR K  23 
 ARG   0.007   0.001   ARG W  62 

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

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

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.177 
Fit side-chains
REVERT: L   37 ASP cc_start: 0.9383 (t0) cc_final: 0.9171 (t0)
REVERT: L  108 ASN cc_start: 0.9365 (t0) cc_final: 0.9049 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1718
  time to fit residues: 3.1783
Evaluate side-chains
  11 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.137 
Evaluate side-chains
  22 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q   36 ASN cc_start: 0.9167 (t0) cc_final: 0.8439 (t0)
REVERT: Q   38 GLU cc_start: 0.8449 (pm20) cc_final: 0.8212 (pm20)
REVERT: Q   70 ASN cc_start: 0.9178 (t0) cc_final: 0.8395 (t0)
REVERT: Q   86 LYS cc_start: 0.8968 (mptt) cc_final: 0.8708 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.3799
  time to fit residues: 8.8199
Evaluate side-chains
  18 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 232 optimal weight:    0.1980
   chunk 212 optimal weight:    9.9990
   chunk 226 optimal weight:    4.9990
   chunk 136 optimal weight:    0.4980
   chunk 98 optimal weight:    9.9990
   chunk 177 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9980
   chunk 204 optimal weight:   20.0000
   chunk 214 optimal weight:    2.9990
   chunk 225 optimal weight:    3.9990
   chunk 148 optimal weight:    0.0980
   overall best weight:    0.9582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** L  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  21972  Z= 0.240
  Angle     :  0.733  10.566  29724  Z= 0.366
  Chirality :  0.042   0.185   2964
  Planarity :  0.004   0.035   3888
  Dihedral  :  4.090  11.991   3072
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.15), residues: 2592
  helix:  0.63 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.73 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.008   0.001   TYR L  23 
 ARG   0.002   0.000   ARG W  62 

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

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

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.117 
Fit side-chains
REVERT: L   37 ASP cc_start: 0.9388 (t0) cc_final: 0.9173 (t0)
REVERT: L  108 ASN cc_start: 0.9369 (t0) cc_final: 0.9053 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1375
  time to fit residues: 2.5192
Evaluate side-chains
  11 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.113 
Evaluate side-chains
  23 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   33 ASP cc_start: 0.9452 (t0) cc_final: 0.9161 (t0)
REVERT: V   36 ASN cc_start: 0.9154 (t0) cc_final: 0.8438 (t0)
REVERT: V   67 ASP cc_start: 0.9313 (t70) cc_final: 0.9079 (t0)
REVERT: V   70 ASN cc_start: 0.8921 (t0) cc_final: 0.8219 (t0)
REVERT: V   86 LYS cc_start: 0.9107 (mptt) cc_final: 0.8683 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2353
  time to fit residues: 5.6910
Evaluate side-chains
  16 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 252
   random chunks:
   chunk 239 optimal weight:    0.0010
   chunk 146 optimal weight:    0.0060
   chunk 113 optimal weight:    1.9990
   chunk 166 optimal weight:    0.8980
   chunk 251 optimal weight:    3.9990
   chunk 231 optimal weight:    9.9990
   chunk 199 optimal weight:    0.0020
   chunk 20 optimal weight:    0.9990
   chunk 154 optimal weight:    0.0980
   chunk 122 optimal weight:    0.6980
   chunk 158 optimal weight:    1.9990
   overall best weight:    0.1610
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** L  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  21972  Z= 0.240
  Angle     :  0.733  10.566  29724  Z= 0.366
  Chirality :  0.042   0.185   2964
  Planarity :  0.004   0.035   3888
  Dihedral  :  4.090  11.991   3072
  Min Nonbonded Distance : 1.690

Molprobity Statistics.
  All-atom Clashscore : 23.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.15), residues: 2592
  helix:  0.63 (0.10), residues: 2436
  sheet:  None (None), residues: 0
  loop : -2.73 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U  74 
 TYR   0.008   0.001   TYR L  23 
 ARG   0.002   0.000   ARG W  62 

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

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

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4070 Ramachandran restraints generated.
    2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.103 
Fit side-chains
REVERT: L   37 ASP cc_start: 0.9388 (t0) cc_final: 0.9183 (t0)
REVERT: L  108 ASN cc_start: 0.9366 (t0) cc_final: 0.9051 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1314
  time to fit residues: 2.5354
Evaluate side-chains
  11 residues out of total 94 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.100 
Evaluate side-chains
  21 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   33 ASP cc_start: 0.9447 (t0) cc_final: 0.9161 (t0)
REVERT: V   36 ASN cc_start: 0.9156 (t0) cc_final: 0.8437 (t0)
REVERT: V   67 ASP cc_start: 0.9316 (t70) cc_final: 0.9079 (t0)
REVERT: V   70 ASN cc_start: 0.8931 (t0) cc_final: 0.8218 (t0)
REVERT: V   86 LYS cc_start: 0.9075 (mptt) cc_final: 0.8683 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.2444
  time to fit residues: 5.4530
Evaluate side-chains
  16 residues out of total 74 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs
    ncs_groups                  = ncs_groups)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine
    rms_angles_limit         = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine
    refine_sites                 = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__
    ignore_line_search_failed_maxfev=True))
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients
    x=self.x)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients
    grad                   = g_data)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads
    compute_gradients = True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8433 > 50:
  distance: 1 - 2:  11.846
  distance: 2 - 3:   5.252
  distance: 2 - 5:  27.429
  distance: 3 - 4:  10.584
  distance: 3 - 9:  17.244
  distance: 4 - 30:  14.371
  distance: 5 - 6:  32.146
  distance: 6 - 7:  13.310
  distance: 6 - 8:  19.675
  distance: 9 - 10:  14.227
  distance: 10 - 11:  13.928
  distance: 10 - 13:  37.944
  distance: 11 - 12:  15.009
  distance: 11 - 14:  29.451
  distance: 14 - 15:  23.628
  distance: 15 - 16:  17.229
  distance: 15 - 18:  36.560
  distance: 16 - 17:  22.856
  distance: 16 - 22:  29.638
  distance: 18 - 19:  31.272
  distance: 19 - 20:  29.276
  distance: 19 - 21:  50.009
  distance: 22 - 23:  13.242
  distance: 23 - 24:  37.942
  distance: 23 - 26:  31.099
  distance: 24 - 25:  27.826
  distance: 24 - 30:  26.389
  distance: 26 - 27:  37.341
  distance: 27 - 28:  33.357
  distance: 27 - 29:  27.077
  distance: 30 - 31:  18.946
  distance: 31 - 32:  24.648
  distance: 31 - 34:  28.385
  distance: 32 - 33:  33.723
  distance: 32 - 39:   8.614
  distance: 34 - 35:  10.736
  distance: 35 - 36:  10.103
  distance: 36 - 37:  23.478
  distance: 37 - 38:  30.683
  distance: 39 - 40:  10.595
  distance: 40 - 41:  22.249
  distance: 40 - 43:  12.138
  distance: 41 - 42:  31.368
  distance: 41 - 47:  35.396
  distance: 43 - 44:  23.024
  distance: 44 - 45:  38.039
  distance: 44 - 46:   7.768
  distance: 47 - 48:   9.494
  distance: 47 - 53:  10.177
  distance: 48 - 49:  24.451
  distance: 48 - 51:  16.319
  distance: 49 - 50:  33.925
  distance: 49 - 54:  33.157
  distance: 51 - 52:  29.584
  distance: 52 - 53:  14.191
  distance: 54 - 55:  18.516
  distance: 55 - 56:  33.153
  distance: 55 - 58:  22.673
  distance: 56 - 57:  19.651
  distance: 56 - 62:  14.377
  distance: 58 - 59:  24.571
  distance: 59 - 60:  27.902
  distance: 59 - 61:  28.440
  distance: 62 - 63:   6.904
  distance: 63 - 64:  27.509
  distance: 63 - 66:  23.625
  distance: 64 - 65:  26.847
  distance: 64 - 70:  42.818
  distance: 66 - 67:  16.966
  distance: 67 - 68:  27.691
  distance: 67 - 69:  22.728
  distance: 70 - 71:  15.018
  distance: 71 - 72:  31.766
  distance: 71 - 74:  31.844
  distance: 72 - 73:  48.399
  distance: 72 - 75:  21.271
  distance: 75 - 76:   7.314
  distance: 76 - 77:   6.635
  distance: 76 - 79:   7.064
  distance: 77 - 78:  14.885
  distance: 79 - 80:   7.766
  distance: 80 - 81:  19.870
  distance: 81 - 82:  17.890
  distance: 81 - 83:  12.732