Starting phenix.real_space_refine
on Thu Dec  7 19:41:43 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pes_20331/12_2023/6pes_20331.pdb"
  }
  resolution = 3.6
  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
-------------------------------------------------------------------------------
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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    2515      2.51       5
     N     700      2.21       5
     O     825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Y PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Z PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 4040
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "B"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "C"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "E"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 441
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "W"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 367
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "V"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 367
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "X"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 367
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "Y"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 367
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "Z"
      Number of atoms: 367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 367
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
  Time building chain proxies: 2.33, per 1000 atoms: 0.58
  Number of scatterers: 4040
  At special positions: 0
  Unit cell: (73.485, 117.15, 43.665, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     825      8.00
     N     700      7.00
     C    2515      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: 1.57
  Conformation dependent library (CDL) restraints added in 991.2 milliseconds
  

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1000

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 64.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40
      removed outlier: 6.324A  pdb=" N   VAL B  37 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   VAL D  40 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR B  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   VAL A  37 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   VAL B  40 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   TYR A  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 57
      removed outlier: 6.442A  pdb=" N   THR B  44 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   GLY D  47 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   GLU B  46 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   VAL D  49 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 8.828A  pdb=" N   VAL B  48 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
      removed outlier: 9.174A  pdb=" N   GLY D  51 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   GLN B  50 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
      removed outlier: 7.620A  pdb=" N   ALA D  53 " --> pdb=" O   GLN B  50 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL B  52 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   VAL D  55 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   THR B  54 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   GLU D  57 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA B  56 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   THR A  44 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   GLY B  47 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 8.439A  pdb=" N   GLU A  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 8.193A  pdb=" N   VAL B  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 8.834A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 9.177A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   GLN A  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ALA B  53 " --> pdb=" O   GLN A  50 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   VAL B  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   THR A  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   GLU B  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL C  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL A  49 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLN C  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL E  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL C  49 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLN E  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 66
      removed outlier: 6.538A  pdb=" N   GLU B  61 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   THR D  64 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL B  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   VAL D  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASN B  65 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   GLU A  61 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   THR B  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   VAL B  66 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASN A  65 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.543A  pdb=" N   VAL B  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 74 through 83
      removed outlier: 6.361A  pdb=" N   VAL B  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   VAL D  77 " --> pdb=" O   VAL B  74 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ALA B  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   GLN D  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ALA B  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR D  81 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   LYS B  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 10.169A  pdb=" N   GLU D  83 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   VAL B  82 " --> pdb=" O   GLU D  83 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL A  74 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   VAL B  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ALA A  76 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   GLN B  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA A  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   THR B  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LYS A  80 " --> pdb=" O   THR B  81 " (cutoff:3.500A)
      removed outlier: 10.186A  pdb=" N   GLU B  83 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   VAL A  82 " --> pdb=" O   GLU B  83 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   THR A  81 " --> pdb=" O   LYS C  80 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL C  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   GLU A  83 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   THR C  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL E  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   GLU C  83 " --> pdb=" O   VAL E  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 96
      removed outlier: 6.641A  pdb=" N   ILE B  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ALA D  91 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   ALA B  90 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 10.207A  pdb=" N   GLY D  93 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   THR B  92 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 8.894A  pdb=" N   VAL D  95 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   PHE B  94 " --> pdb=" O   VAL D  95 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ALA B  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ALA A  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 10.233A  pdb=" N   GLY B  93 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   THR A  92 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   VAL B  95 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   PHE A  94 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ALA A  91 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   THR C  92 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLY A  93 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ALA C  91 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   THR E  92 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLY C  93 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'W' and resid 45 through 56
      removed outlier: 6.885A  pdb=" N   VAL V  48 " --> pdb=" O   GLY W  47 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL W  49 " --> pdb=" O   VAL V  48 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   GLN V  50 " --> pdb=" O   VAL W  49 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL X  48 " --> pdb=" O   GLY V  47 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL V  49 " --> pdb=" O   VAL X  48 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLN X  50 " --> pdb=" O   VAL V  49 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL Y  48 " --> pdb=" O   GLY X  47 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   VAL X  49 " --> pdb=" O   VAL Y  48 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   GLN Y  50 " --> pdb=" O   VAL X  49 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL Z  48 " --> pdb=" O   GLY Y  47 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL Y  49 " --> pdb=" O   VAL Z  48 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   GLN Z  50 " --> pdb=" O   VAL Y  49 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'W' and resid 61 through 66
    Processing sheet with id=AA9, first strand: chain 'W' and resid 69 through 71
    Processing sheet with id=AB1, first strand: chain 'W' and resid 74 through 83
      removed outlier: 8.950A  pdb=" N   VAL W  74 " --> pdb=" O   THR V  75 " (cutoff:3.500A)
      removed outlier: 10.095A  pdb=" N   VAL V  77 " --> pdb=" O   VAL W  74 " (cutoff:3.500A)
      removed outlier: 9.023A  pdb=" N   ALA W  76 " --> pdb=" O   VAL V  77 " (cutoff:3.500A)
      removed outlier: 10.255A  pdb=" N   GLN V  79 " --> pdb=" O   ALA W  76 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   ALA W  78 " --> pdb=" O   GLN V  79 " (cutoff:3.500A)
      removed outlier: 9.927A  pdb=" N   THR V  81 " --> pdb=" O   ALA W  78 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LYS W  80 " --> pdb=" O   THR V  81 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   GLU V  83 " --> pdb=" O   LYS W  80 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL W  82 " --> pdb=" O   GLU V  83 " (cutoff:3.500A)
      removed outlier: 8.942A  pdb=" N   VAL V  74 " --> pdb=" O   THR X  75 " (cutoff:3.500A)
      removed outlier: 10.084A  pdb=" N   VAL X  77 " --> pdb=" O   VAL V  74 " (cutoff:3.500A)
      removed outlier: 9.011A  pdb=" N   ALA V  76 " --> pdb=" O   VAL X  77 " (cutoff:3.500A)
      removed outlier: 10.241A  pdb=" N   GLN X  79 " --> pdb=" O   ALA V  76 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   ALA V  78 " --> pdb=" O   GLN X  79 " (cutoff:3.500A)
      removed outlier: 9.902A  pdb=" N   THR X  81 " --> pdb=" O   ALA V  78 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   LYS V  80 " --> pdb=" O   THR X  81 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   GLU X  83 " --> pdb=" O   LYS V  80 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL V  82 " --> pdb=" O   GLU X  83 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   VAL X  74 " --> pdb=" O   THR Y  75 " (cutoff:3.500A)
      removed outlier: 10.101A  pdb=" N   VAL Y  77 " --> pdb=" O   VAL X  74 " (cutoff:3.500A)
      removed outlier: 9.029A  pdb=" N   ALA X  76 " --> pdb=" O   VAL Y  77 " (cutoff:3.500A)
      removed outlier: 10.263A  pdb=" N   GLN Y  79 " --> pdb=" O   ALA X  76 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   ALA X  78 " --> pdb=" O   GLN Y  79 " (cutoff:3.500A)
      removed outlier: 9.946A  pdb=" N   THR Y  81 " --> pdb=" O   ALA X  78 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LYS X  80 " --> pdb=" O   THR Y  81 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   GLU Y  83 " --> pdb=" O   LYS X  80 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL X  82 " --> pdb=" O   GLU Y  83 " (cutoff:3.500A)
      removed outlier: 8.949A  pdb=" N   VAL Y  74 " --> pdb=" O   THR Z  75 " (cutoff:3.500A)
      removed outlier: 10.093A  pdb=" N   VAL Z  77 " --> pdb=" O   VAL Y  74 " (cutoff:3.500A)
      removed outlier: 9.022A  pdb=" N   ALA Y  76 " --> pdb=" O   VAL Z  77 " (cutoff:3.500A)
      removed outlier: 10.253A  pdb=" N   GLN Z  79 " --> pdb=" O   ALA Y  76 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   ALA Y  78 " --> pdb=" O   GLN Z  79 " (cutoff:3.500A)
      removed outlier: 9.926A  pdb=" N   THR Z  81 " --> pdb=" O   ALA Y  78 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LYS Y  80 " --> pdb=" O   THR Z  81 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   GLU Z  83 " --> pdb=" O   LYS Y  80 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   VAL Y  82 " --> pdb=" O   GLU Z  83 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'W' and resid 88 through 96
      removed outlier: 8.432A  pdb=" N   ALA W  89 " --> pdb=" O   ALA V  90 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   THR V  92 " --> pdb=" O   ALA W  89 " (cutoff:3.500A)
      removed outlier: 9.024A  pdb=" N   ALA W  91 " --> pdb=" O   THR V  92 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   PHE V  94 " --> pdb=" O   ALA W  91 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLY W  93 " --> pdb=" O   PHE V  94 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   LYS V  96 " --> pdb=" O   GLY W  93 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL W  95 " --> pdb=" O   LYS V  96 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   ALA V  89 " --> pdb=" O   ALA X  90 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   THR X  92 " --> pdb=" O   ALA V  89 " (cutoff:3.500A)
      removed outlier: 9.026A  pdb=" N   ALA V  91 " --> pdb=" O   THR X  92 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   PHE X  94 " --> pdb=" O   ALA V  91 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLY V  93 " --> pdb=" O   PHE X  94 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   LYS X  96 " --> pdb=" O   GLY V  93 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL V  95 " --> pdb=" O   LYS X  96 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   ALA X  89 " --> pdb=" O   ALA Y  90 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   THR Y  92 " --> pdb=" O   ALA X  89 " (cutoff:3.500A)
      removed outlier: 9.024A  pdb=" N   ALA X  91 " --> pdb=" O   THR Y  92 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   PHE Y  94 " --> pdb=" O   ALA X  91 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   GLY X  93 " --> pdb=" O   PHE Y  94 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LYS Y  96 " --> pdb=" O   GLY X  93 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   VAL X  95 " --> pdb=" O   LYS Y  96 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ALA Y  89 " --> pdb=" O   ALA Z  90 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   THR Z  92 " --> pdb=" O   ALA Y  89 " (cutoff:3.500A)
      removed outlier: 9.025A  pdb=" N   ALA Y  91 " --> pdb=" O   THR Z  92 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   PHE Z  94 " --> pdb=" O   ALA Y  91 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   GLY Y  93 " --> pdb=" O   PHE Z  94 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LYS Z  96 " --> pdb=" O   GLY Y  93 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL Y  95 " --> pdb=" O   LYS Z  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    124 hydrogen bonds defined for protein.
    372 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: 1.11

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 725
        1.29 -     1.35: 625
        1.35 -     1.42: 110
        1.42 -     1.48: 689
        1.48 -     1.54: 1896
  Bond restraints: 4045
  Sorted by residual:
  bond pdb=" CB  VAL Z  66 "
       pdb=" CG2 VAL Z  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 1.00e+01
  bond pdb=" CB  VAL Y  66 "
       pdb=" CG2 VAL Y  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 1.00e+01
  bond pdb=" CB  VAL W  66 "
       pdb=" CG2 VAL W  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 9.95e+00
  bond pdb=" CB  VAL V  66 "
       pdb=" CG2 VAL V  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 9.87e+00
  bond pdb=" CB  VAL X  66 "
       pdb=" CG2 VAL X  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.418  0.103 3.30e-02 9.18e+02 9.82e+00
  ... (remaining 4040 not shown)

  Histogram of bond angle deviations from ideal:
      105.42 -   109.09: 402
      109.09 -   112.77: 2068
      112.77 -   116.45: 504
      116.45 -   120.13: 722
      120.13 -   123.81: 1769
  Bond angle restraints: 5465
  Sorted by residual:
  angle pdb=" C   THR Z  59 "
        pdb=" N   LYS Z  60 "
        pdb=" CA  LYS Z  60 "
      ideal   model   delta    sigma   weight residual
     122.93  119.54    3.39 1.51e+00 4.39e-01 5.05e+00
  angle pdb=" C   THR W  59 "
        pdb=" N   LYS W  60 "
        pdb=" CA  LYS W  60 "
      ideal   model   delta    sigma   weight residual
     122.93  119.54    3.39 1.51e+00 4.39e-01 5.03e+00
  angle pdb=" C   THR V  59 "
        pdb=" N   LYS V  60 "
        pdb=" CA  LYS V  60 "
      ideal   model   delta    sigma   weight residual
     122.93  119.55    3.38 1.51e+00 4.39e-01 5.00e+00
  angle pdb=" C   THR X  59 "
        pdb=" N   LYS X  60 "
        pdb=" CA  LYS X  60 "
      ideal   model   delta    sigma   weight residual
     122.93  119.57    3.36 1.51e+00 4.39e-01 4.96e+00
  angle pdb=" C   THR Y  59 "
        pdb=" N   LYS Y  60 "
        pdb=" CA  LYS Y  60 "
      ideal   model   delta    sigma   weight residual
     122.93  119.57    3.36 1.51e+00 4.39e-01 4.95e+00
  ... (remaining 5460 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.69: 2095
       12.69 -    25.39: 220
       25.39 -    38.08: 40
       38.08 -    50.77: 15
       50.77 -    63.46: 15
  Dihedral angle restraints: 2385
    sinusoidal: 800
      harmonic: 1585
  Sorted by residual:
  dihedral pdb=" CA  VAL E  48 "
           pdb=" C   VAL E  48 "
           pdb=" N   VAL E  49 "
           pdb=" CA  VAL E  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  VAL D  48 "
           pdb=" C   VAL D  48 "
           pdb=" N   VAL D  49 "
           pdb=" CA  VAL D  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.96   17.04     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  VAL C  48 "
           pdb=" C   VAL C  48 "
           pdb=" N   VAL C  49 "
           pdb=" CA  VAL C  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.97   17.03     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 2382 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 517
       0.052 -    0.103: 132
       0.103 -    0.155: 71
       0.155 -    0.206: 0
       0.206 -    0.258: 5
  Chirality restraints: 725
  Sorted by residual:
  chirality pdb=" CB  VAL Y  66 "
            pdb=" CA  VAL Y  66 "
            pdb=" CG1 VAL Y  66 "
            pdb=" CG2 VAL Y  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  VAL V  66 "
            pdb=" CA  VAL V  66 "
            pdb=" CG1 VAL V  66 "
            pdb=" CG2 VAL V  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  VAL X  66 "
            pdb=" CA  VAL X  66 "
            pdb=" CG1 VAL X  66 "
            pdb=" CG2 VAL X  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 722 not shown)

  Planarity restraints: 685
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS Y  60 "    0.020 2.00e-02 2.50e+03   4.04e-02 1.63e+01
        pdb=" C   LYS Y  60 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LYS Y  60 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLU Y  61 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS W  60 "    0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   LYS W  60 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LYS W  60 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLU W  61 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS X  60 "    0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   LYS X  60 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LYS X  60 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLU X  61 "    0.023 2.00e-02 2.50e+03
  ... (remaining 682 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 1854
        2.93 -     3.42: 3431
        3.42 -     3.91: 6356
        3.91 -     4.41: 6980
        4.41 -     4.90: 13933
  Nonbonded interactions: 32554
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS X  58 "
            pdb=" OE2 GLU X  61 "
     model   vdw
     2.432 2.520
  nonbonded pdb=" NZ  LYS W  58 "
            pdb=" OE2 GLU W  61 "
     model   vdw
     2.432 2.520
  nonbonded pdb=" NZ  LYS V  58 "
            pdb=" OE2 GLU V  61 "
     model   vdw
     2.432 2.520
  nonbonded pdb=" NZ  LYS Y  58 "
            pdb=" OE2 GLU Y  61 "
     model   vdw
     2.432 2.520
  nonbonded pdb=" NZ  LYS Z  58 "
            pdb=" OE2 GLU Z  61 "
     model   vdw
     2.433 2.520
  ... (remaining 32549 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'V'
  selection = chain 'W'
  selection = chain 'X'
  selection = chain 'Y'
  selection = chain 'Z'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.080
  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:             0.000
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     16.290
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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      :  0.009   0.104   4045  Z= 0.595
  Angle     :  0.704   3.394   5465  Z= 0.422
  Chirality :  0.060   0.258    725
  Planarity :  0.007   0.040    685
  Dihedral  : 12.873  63.461   1385
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.41 %
    Favored  : 86.59 %
  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: -1.79 (0.32), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.35 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.016   0.004   PHE W  94 
   TYR   0.002   0.001   TYR D  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1978
  time to fit residues: 19.0906
Evaluate side-chains
  69 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.486 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6395
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0070
   chunk 43 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 49 optimal weight:   30.0000
   overall best weight:    6.2006

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
B  99 GLN
C  99 GLN
D  99 GLN
W  50 GLN
V  50 GLN
X  50 GLN
Y  50 GLN
Z  50 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   4045  Z= 0.276
  Angle     :  0.499   3.200   5465  Z= 0.290
  Chirality :  0.055   0.136    725
  Planarity :  0.002   0.015    685
  Dihedral  :  4.903  15.791    585
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 15.12 %
    Favored  : 79.76 %
  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: -1.90 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.011   0.003   PHE Z  94 
   TYR   0.004   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 21
  outliers final: 17
  residues processed: 91
  average time/residue: 0.1466
  time to fit residues: 16.9499
Evaluate side-chains
  93 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.429 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0409
  time to fit residues: 1.8338
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 15 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 34 optimal weight:   30.0000
   chunk 13 optimal weight:   20.0000
   chunk 50 optimal weight:    6.9990
   chunk 54 optimal weight:   40.0000
   chunk 44 optimal weight:   30.0000
   chunk 49 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0060
   overall best weight:    6.4004

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
B  99 GLN
D  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4045  Z= 0.275
  Angle     :  0.498   3.645   5465  Z= 0.286
  Chirality :  0.055   0.135    725
  Planarity :  0.002   0.013    685
  Dihedral  :  4.818  17.059    585
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.51 %
    Favored  : 78.54 %
  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: -2.00 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.51 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.021   0.003   PHE W  94 
   TYR   0.004   0.001   TYR E  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.427 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 78
  average time/residue: 0.1414
  time to fit residues: 14.2241
Evaluate side-chains
  77 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.460 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0438
  time to fit residues: 0.9926
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 49 optimal weight:   30.0000
   chunk 37 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 50 optimal weight:   30.0000
   chunk 53 optimal weight:    0.0010
   chunk 26 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   overall best weight:    6.9996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4045  Z= 0.301
  Angle     :  0.508   4.005   5465  Z= 0.291
  Chirality :  0.054   0.131    725
  Planarity :  0.002   0.011    685
  Dihedral  :  4.847  17.051    585
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 17.80 %
    Favored  : 77.80 %
  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: -2.20 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.019   0.003   PHE W  94 
   TYR   0.004   0.001   TYR E  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.453 
Fit side-chains
  outliers start: 18
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1516
  time to fit residues: 16.2182
Evaluate side-chains
  88 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.411 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0449
  time to fit residues: 1.5917
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:   30.0000
   chunk 30 optimal weight:   30.0000
   chunk 0 optimal weight:   30.0000
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 45 optimal weight:   30.0000
   chunk 36 optimal weight:   30.0000
   chunk 27 optimal weight:    0.0570
   chunk 47 optimal weight:   20.0000
   chunk 13 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   overall best weight:    8.0110

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   4045  Z= 0.335
  Angle     :  0.521   5.241   5465  Z= 0.299
  Chirality :  0.055   0.138    725
  Planarity :  0.002   0.014    685
  Dihedral  :  4.907  17.748    585
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 21.46 %
    Favored  : 76.59 %
  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: -2.42 (0.30), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.019   0.004   PHE W  94 
   TYR   0.002   0.001   TYR B  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.472 
Fit side-chains
  outliers start: 8
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1471
  time to fit residues: 15.6652
Evaluate side-chains
  76 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.433 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0384
  time to fit residues: 0.7111
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 47 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 31 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 4 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    9.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   4045  Z= 0.396
  Angle     :  0.551   4.812   5465  Z= 0.318
  Chirality :  0.056   0.134    725
  Planarity :  0.002   0.015    685
  Dihedral  :  5.044  18.240    585
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 20.24 %
    Favored  : 75.85 %
  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: -2.63 (0.30), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.00 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.020   0.004   PHE W  94 
   TYR   0.002   0.001   TYR B  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.456 
Fit side-chains
  outliers start: 16
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1536
  time to fit residues: 16.1651
Evaluate side-chains
  82 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.449 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0425
  time to fit residues: 1.4337
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 30 optimal weight:   30.0000
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:   30.0000
   chunk 29 optimal weight:   10.0000
   chunk 53 optimal weight:   20.0000
   chunk 33 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:   30.0000
   chunk 21 optimal weight:    0.4980
   chunk 31 optimal weight:   20.0000
   overall best weight:    4.8990

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

Flipped N/Q/H residues before XYZ refinement:
B  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4045  Z= 0.221
  Angle     :  0.477   4.806   5465  Z= 0.272
  Chirality :  0.054   0.132    725
  Planarity :  0.002   0.012    685
  Dihedral  :  4.587  16.132    585
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 20.24 %
    Favored  : 78.29 %
  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: -2.53 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.018   0.003   PHE W  94 
   TYR   0.002   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.444 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 77
  average time/residue: 0.1475
  time to fit residues: 14.5615
Evaluate side-chains
  78 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.427 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0467
  time to fit residues: 0.9976
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 36 optimal weight:   30.0000
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 49 optimal weight:   50.0000
   overall best weight:    7.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   4045  Z= 0.306
  Angle     :  0.526   9.154   5465  Z= 0.294
  Chirality :  0.055   0.131    725
  Planarity :  0.002   0.013    685
  Dihedral  :  4.769  17.438    585
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 20.73 %
    Favored  : 78.05 %
  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: -2.59 (0.30), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.020   0.003   PHE W  94 
   TYR   0.003   0.001   TYR E  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.408 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 69
  average time/residue: 0.1369
  time to fit residues: 12.3764
Evaluate side-chains
  72 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.472 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0403
  time to fit residues: 0.8507
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 44 optimal weight:   30.0000
   chunk 46 optimal weight:   30.0000
   chunk 49 optimal weight:   30.0000
   chunk 32 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 31 optimal weight:   20.0000
   overall best weight:    4.8386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4045  Z= 0.219
  Angle     :  0.498   8.433   5465  Z= 0.277
  Chirality :  0.054   0.131    725
  Planarity :  0.002   0.012    685
  Dihedral  :  4.545  15.550    585
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 20.98 %
    Favored  : 78.05 %
  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: -2.51 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.021   0.003   PHE X  94 
   TYR   0.002   0.001   TYR C  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.474 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 72
  average time/residue: 0.1431
  time to fit residues: 13.2277
Evaluate side-chains
  73 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.419 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0465
  time to fit residues: 0.7651
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 36 optimal weight:   30.0000
   chunk 54 optimal weight:    0.2980
   chunk 50 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:   30.0000
   chunk 46 optimal weight:   30.0000
   chunk 13 optimal weight:   10.0000
   overall best weight:    6.4588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4045  Z= 0.282
  Angle     :  0.518   8.191   5465  Z= 0.291
  Chirality :  0.054   0.131    725
  Planarity :  0.002   0.013    685
  Dihedral  :  4.699  16.955    585
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.20 %
    Favored  : 77.80 %
  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: -2.57 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.021   0.003   PHE W  94 
   TYR   0.002   0.001   TYR E  39 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.470 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1442
  time to fit residues: 13.2906
Evaluate side-chains
  68 residues out of total 410 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.463 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.6018
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:   30.0000
   chunk 43 optimal weight:   30.0000
   chunk 18 optimal weight:    7.9990
   chunk 44 optimal weight:   40.0000
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:   20.0000
   overall best weight:    5.5790

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

Flipped N/Q/H residues before XYZ refinement:
Y  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.187705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.163327 restraints weight = 4317.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.166696 restraints weight = 1861.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.168832 restraints weight = 1100.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4045  Z= 0.247
  Angle     :  0.510   8.085   5465  Z= 0.285
  Chirality :  0.054   0.147    725
  Planarity :  0.002   0.012    685
  Dihedral  :  4.643  17.031    585
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 23.17 %
    Favored  : 76.59 %
  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: -2.54 (0.31), residues: 570
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.24), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   PHE   0.029   0.004   PHE X  94 
   TYR   0.002   0.001   TYR E  39 

===============================================================================
Job complete
usr+sys time: 979.88 seconds
wall clock time: 18 minutes 47.49 seconds (1127.49 seconds total)