Starting phenix.real_space_refine
on Sat Sep 12 08:48:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nn6_0458/09_2026/6nn6_0458.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      27      5.16       5
     C    8631      2.51       5
     N    2781      2.21       5
     O    3398      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15125
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 804
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 2671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2671
          Classifications: {'peptide': 328}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 309}
    Chain: "L"
      Number of atoms: 593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 593
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LEU L  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU L  73 " occ=0.45
    residue:
      pdb=" N   ARG L  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  74 " occ=0.45
  Time building chain proxies: 3.08, per 1000 atoms: 0.20
  Number of scatterers: 15125
  At special positions: 0
  Unit cell: (124.2, 117.72, 116.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P     288     15.00
     O    3398      8.00
     N    2781      7.00
     C    8631      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 498.0 milliseconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 10 sheets defined
      56.5% alpha, 5.4% beta
      115 base pairs and 212 stacking pairs defined.
    Time for finding SS restraints: 1.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 3.599A  pdb=" N   ARG A  49 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 4.035A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLN A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 87 through 114
      removed outlier: 3.625A  pdb=" N   LEU A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ALA A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ILE A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.809A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.775A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.579A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 4.084A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR B  88 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
      removed outlier: 4.024A  pdb=" N   ARG C  35 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.506A  pdb=" N   GLU C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU C  63 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN C  68 " --> pdb=" O   GLU C  64 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA C  69 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ARG C  71 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASP C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.551A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN C  84 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 49
      removed outlier: 3.583A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 84
      removed outlier: 3.715A  pdb=" N   ILE D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   MET D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL D  66 " --> pdb=" O   MET D  62 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA D  81 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS D  82 " --> pdb=" O   SER D  78 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR D  83 " --> pdb=" O   ARG D  79 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.360A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN D  95 " --> pdb=" O   SER D  91 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG D  99 " --> pdb=" O   GLN D  95 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.603A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA D 124 " --> pdb=" O   CYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 4.125A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 75
      removed outlier: 3.808A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 86 through 114
      removed outlier: 3.684A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU E 105 " --> pdb=" O   VAL E 101 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 131
      removed outlier: 4.002A  pdb=" N   ARG E 129 " --> pdb=" O   GLN E 125 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 42
      removed outlier: 3.568A  pdb=" N   ARG F  40 " --> pdb=" O   ARG F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 76
      removed outlier: 3.902A  pdb=" N   GLU F  63 " --> pdb=" O   LYS F  59 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 4.094A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
      removed outlier: 3.659A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 34
      removed outlier: 3.573A  pdb=" N   HIS G  31 " --> pdb=" O   VAL G  27 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 71
      removed outlier: 3.841A  pdb=" N   VAL G  54 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG G  71 " --> pdb=" O   GLY G  67 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.773A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLN G  84 " --> pdb=" O   PRO G  80 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN G  89 " --> pdb=" O   LEU G  85 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
      removed outlier: 3.688A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 47
      removed outlier: 3.765A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR H  42 " --> pdb=" O   ALA H  38 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS H  43 " --> pdb=" O   ILE H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 74
      removed outlier: 3.874A  pdb=" N   MET H  62 " --> pdb=" O   ALA H  58 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER H  64 " --> pdb=" O   SER H  60 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ASN H  67 " --> pdb=" O   ASN H  63 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ASP H  68 " --> pdb=" O   SER H  64 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLU H  71 " --> pdb=" O   ASN H  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 76 through 83
      removed outlier: 3.810A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 102
      removed outlier: 4.040A  pdb=" N   LEU H 100 " --> pdb=" O   THR H  96 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU H 101 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.564A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   HIS H 109 " --> pdb=" O   GLU H 105 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA H 117 " --> pdb=" O   GLU H 113 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA H 124 " --> pdb=" O   CYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 32 through 45
      removed outlier: 3.628A  pdb=" N   ILE K  37 " --> pdb=" O   ALA K  33 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE K  38 " --> pdb=" O   ALA K  34 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 48 through 57
      removed outlier: 3.641A  pdb=" N   LEU K  53 " --> pdb=" O   PRO K  49 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA K  54 " --> pdb=" O   ASP K  50 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN K  57 " --> pdb=" O   LEU K  53 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 67 through 90
      removed outlier: 3.576A  pdb=" N   LEU K  74 " --> pdb=" O   SER K  70 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA K  81 " --> pdb=" O   LYS K  77 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASP K  83 " --> pdb=" O   ASN K  79 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER K  84 " --> pdb=" O   ARG K  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 103 through 118
      removed outlier: 3.680A  pdb=" N   HIS K 109 " --> pdb=" O   GLY K 105 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU K 111 " --> pdb=" O   LEU K 107 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLN K 112 " --> pdb=" O   ARG K 108 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 122 through 127
      removed outlier: 3.637A  pdb=" N   ASN K 127 " --> pdb=" O   LYS K 124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 140 through 151
      removed outlier: 3.890A  pdb=" N   VAL K 144 " --> pdb=" O   SER K 140 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA K 145 " --> pdb=" O   PHE K 141 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 175
    Processing helix  chain 'K' and resid 189 through 209
      removed outlier: 4.300A  pdb=" N   THR K 197 " --> pdb=" O   LYS K 193 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE K 202 " --> pdb=" O   MET K 198 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS K 207 " --> pdb=" O   ARG K 203 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   TYR K 209 " --> pdb=" O   TRP K 205 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 227 through 233
      removed outlier: 3.880A  pdb=" N   ARG K 231 " --> pdb=" O   GLU K 227 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA K 233 " --> pdb=" O   ARG K 229 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 257
    Processing helix  chain 'K' and resid 286 through 289
      removed outlier: 3.686A  pdb=" N   THR K 289 " --> pdb=" O   ASP K 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 286 through 289'
    Processing helix  chain 'K' and resid 319 through 331
      removed outlier: 4.259A  pdb=" N   GLU K 323 " --> pdb=" O   ARG K 319 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN K 324 " --> pdb=" O   THR K 320 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LYS K 330 " --> pdb=" O   PHE K 326 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 34
    Processing helix  chain 'L' and resid 37 through 39
      No H-bonds generated for 'chain 'L' and resid 37 through 39'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.943A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.498A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.173A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 7.116A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.837A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'K' and resid 6 through 9
      removed outlier: 3.603A  pdb=" N   LEU K   9 " --> pdb=" O   ALA K  18 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ALA K  18 " --> pdb=" O   LEU K   9 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 218 through 220
      removed outlier: 5.792A  pdb=" N   GLY K 184 " --> pdb=" O   GLU K 219 " (cutoff:3.500A)
      removed outlier: 8.483A  pdb=" N   VAL K 185 " --> pdb=" O   PHE K 159 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   ASP K 161 " --> pdb=" O   VAL K 185 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE K 266 " --> pdb=" O   HIS K 315 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 16
      removed outlier: 3.642A  pdb=" N   VAL L   5 " --> pdb=" O   ILE L  13 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU L  15 " --> pdb=" O   ILE L   3 " (cutoff:3.500A)
      removed outlier: 9.416A  pdb=" N   LEU L  67 " --> pdb=" O   GLN L   2 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   PHE L   4 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   LEU L  69 " --> pdb=" O   PHE L   4 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LYS L   6 " --> pdb=" O   LEU L  69 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   LEU L  71 " --> pdb=" O   LYS L   6 " (cutoff:3.500A)

    366 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      271 hydrogen bonds
      486 hydrogen bond angles
      0 basepair planarities
      115 basepair parallelities
      212 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2821
        1.33 -     1.45: 5116
        1.45 -     1.57: 7443
        1.57 -     1.69: 576
        1.69 -     1.82: 47
  Bond restraints: 16003
  Sorted by residual:
  bond pdb=" C3'  DG I -30 "
       pdb=" C2'  DG I -30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 8.00e-03 1.56e+04 1.90e+01
  bond pdb=" C3'  DA I -54 "
       pdb=" O3'  DA I -54 "
    ideal  model  delta    sigma   weight residual
    1.435  1.381  0.054 1.30e-02 5.92e+03 1.76e+01
  bond pdb=" C3'  DC I -63 "
       pdb=" C2'  DC I -63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.54e+01
  bond pdb=" C   LEU A  65 "
       pdb=" N   PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.336  1.381 -0.046 1.23e-02 6.61e+03 1.37e+01
  bond pdb=" C3'  DC J  37 "
       pdb=" C2'  DC J  37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.37e+01
  ... (remaining 15998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 20066
        1.66 -     3.31: 2485
        3.31 -     4.97: 265
        4.97 -     6.62: 37
        6.62 -     8.28: 24
  Bond angle restraints: 22877
  Sorted by residual:
  angle pdb=" O4'  DT J -59 "
        pdb=" C4'  DT J -59 "
        pdb=" C3'  DT J -59 "
      ideal   model   delta    sigma   weight residual
     106.00  102.43    3.57 6.00e-01 2.78e+00 3.53e+01
  angle pdb=" O4'  DC J  52 "
        pdb=" C4'  DC J  52 "
        pdb=" C3'  DC J  52 "
      ideal   model   delta    sigma   weight residual
     106.00  102.83    3.17 6.00e-01 2.78e+00 2.80e+01
  angle pdb=" O4'  DC I -63 "
        pdb=" C1'  DC I -63 "
        pdb=" N1   DC I -63 "
      ideal   model   delta    sigma   weight residual
     108.00  111.51   -3.51 7.00e-01 2.04e+00 2.52e+01
  angle pdb=" C4'  DC I -63 "
        pdb=" O4'  DC I -63 "
        pdb=" C1'  DC I -63 "
      ideal   model   delta    sigma   weight residual
     110.10  105.32    4.78 1.00e+00 1.00e+00 2.29e+01
  angle pdb=" O4'  DA J  -1 "
        pdb=" C4'  DA J  -1 "
        pdb=" C3'  DA J  -1 "
      ideal   model   delta    sigma   weight residual
     106.00  103.15    2.85 6.00e-01 2.78e+00 2.25e+01
  ... (remaining 22872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 7467
       35.46 -    70.91: 1377
       70.91 -   106.37: 42
      106.37 -   141.82: 5
      141.82 -   177.28: 1
  Dihedral angle restraints: 8892
    sinusoidal: 5543
      harmonic: 3349
  Sorted by residual:
  dihedral pdb=" CA  LEU D 100 "
           pdb=" C   LEU D 100 "
           pdb=" N   LEU D 101 "
           pdb=" CA  LEU D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.22  -29.78     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  ILE F  29 "
           pdb=" C   ILE F  29 "
           pdb=" N   THR F  30 "
           pdb=" CA  THR F  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.34  -23.66     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  SER H  60 "
           pdb=" C   SER H  60 "
           pdb=" N   ILE H  61 "
           pdb=" CA  ILE H  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.30   21.70     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 8889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1651
       0.052 -    0.103: 739
       0.103 -    0.155: 180
       0.155 -    0.207: 17
       0.207 -    0.259: 2
  Chirality restraints: 2589
  Sorted by residual:
  chirality pdb=" CB  ILE K 279 "
            pdb=" CA  ILE K 279 "
            pdb=" CG1 ILE K 279 "
            pdb=" CG2 ILE K 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" C3'  DC I -29 "
            pdb=" C4'  DC I -29 "
            pdb=" O3'  DC I -29 "
            pdb=" C2'  DC I -29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.52   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  LEU A  65 "
            pdb=" N   LEU A  65 "
            pdb=" C   LEU A  65 "
            pdb=" CB  LEU A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2586 not shown)

  Planarity restraints: 1901
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  40 "   -0.022 2.00e-02 2.50e+03   2.12e-02 8.96e+00
        pdb=" CG  TYR H  40 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  40 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  40 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  40 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  40 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  40 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H  40 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER K 132 "    0.040 5.00e-02 4.00e+02   6.09e-02 5.94e+00
        pdb=" N   PRO K 133 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO K 133 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO K 133 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.040 5.00e-02 4.00e+02   5.98e-02 5.72e+00
        pdb=" N   PRO G  80 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1898 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 978
        2.70 -     3.25: 13268
        3.25 -     3.80: 27575
        3.80 -     4.35: 34217
        4.35 -     4.90: 49936
  Nonbonded interactions: 125974
  Sorted by model distance:
  nonbonded pdb=" O   ILE E  62 "
            pdb=" O   ARG E  63 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE2 GLU C  56 "
            pdb=" NH2 ARG K 282 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OH  TYR K 136 "
            pdb=" OE2 GLU K 138 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   LYS C  15 "
            pdb=" O   THR C  16 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O2   DC I  56 "
            pdb=" N2   DG J -56 "
     model   vdw
     2.284 3.120
  ... (remaining 125969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 101)
  selection = (chain 'F' and resid 25 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 15 through 118)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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=0.45 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:             3.230
  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:             0.020
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.970
  Find NCS groups from input model:        0.230
  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:             0.010
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
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      :  0.010   0.100  16003  Z= 0.743
  Angle     :  1.112   8.280  22877  Z= 0.834
  Chirality :  0.057   0.259   2589
  Planarity :  0.007   0.061   1901
  Dihedral  : 25.945 177.280   6728
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.81 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  1.73 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.04 (0.18), residues: 1129
  helix: -4.32 (0.09), residues: 622
  sheet: -1.07 (0.58), residues: 74
  loop : -1.83 (0.25), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 128 
 TYR   0.049   0.004   TYR H  40 
 PHE   0.022   0.003   PHE B 100 
 TRP   0.023   0.003   TRP K 228 
 HIS   0.020   0.003   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01019 /  0.74 (16003)
  covalent geometry    : angle       1.11206 /  0.83 (22877)
  hydrogen bonds       : bond        0.34078 / 22.46 (  637)
  hydrogen bonds       : angle      10.56686 /  7.09 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 364
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.8396 (tp30) cc_final: 0.8045 (tp30)
REVERT: C   91 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8036 (tp30)
REVERT: C   94 ASN cc_start: 0.8724 (t0) cc_final: 0.8483 (t0)
REVERT: C   95 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8671 (mttm)
REVERT: D   42 TYR cc_start: 0.7942 (t80) cc_final: 0.7548 (t80)
REVERT: D   87 SER cc_start: 0.8668 (m) cc_final: 0.8430 (t)
REVERT: E  122 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9084 (ptpp)
REVERT: F   59 LYS cc_start: 0.8846 (tttp) cc_final: 0.8639 (tttm)
REVERT: G   61 GLU cc_start: 0.8581 (tp30) cc_final: 0.8157 (tp30)
REVERT: G   74 LYS cc_start: 0.8904 (mppt) cc_final: 0.8395 (mmtp)
REVERT: G  112 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8430 (mm-40)
REVERT: H   32 THR cc_start: 0.7817 (p) cc_final: 0.7520 (p)
REVERT: H   43 LYS cc_start: 0.9214 (mttt) cc_final: 0.8841 (mttp)
REVERT: H   76 GLU cc_start: 0.8449 (tp30) cc_final: 0.8115 (tp30)
REVERT: H   87 SER cc_start: 0.8994 (m) cc_final: 0.8651 (p)
REVERT: K   71 MET cc_start: 0.5125 (mmm) cc_final: 0.4323 (mmm)
REVERT: K  149 ASP cc_start: 0.6601 (m-30) cc_final: 0.6291 (m-30)
REVERT: K  189 ASP cc_start: 0.7951 (m-30) cc_final: 0.7276 (p0)
REVERT: K  198 MET cc_start: 0.2109 (mmm) cc_final: 0.1409 (mmm)
REVERT: K  205 TRP cc_start: 0.5089 (m100) cc_final: 0.4828 (m100)
REVERT: K  206 MET cc_start: 0.6165 (mmm) cc_final: 0.5609 (ppp)
REVERT: K  252 GLN cc_start: 0.7306 (mt0) cc_final: 0.6990 (mp10)
REVERT: K  291 MET cc_start: 0.8538 (ptp) cc_final: 0.8212 (ptp)
REVERT: L   51 GLU cc_start: 0.7849 (tt0) cc_final: 0.7311 (mp0)
  outliers start: 8
  outliers final: 3
  residues processed: 368
  average time/residue: 0.1695
  time to fit residues: 82.7652
Evaluate side-chains
  251 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 248
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain K residue  282 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 108 ASN
A 125 GLN
C 110 ASN
D  67 ASN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E  76 GLN
G  84 GLN
G 104 GLN
H  67 ASN
K 109 HIS
K 113 GLN
K 259 ASN
K 315 HIS
L  40 GLN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  60 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.127570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093347 restraints weight = 43862.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.092005 restraints weight = 35237.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092547 restraints weight = 36330.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.092579 restraints weight = 28005.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.092607 restraints weight = 26915.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  16003  Z= 0.261
  Angle     :  0.883  10.475  22877  Z= 0.488
  Chirality :  0.056   0.314   2589
  Planarity :  0.006   0.041   1901
  Dihedral  : 31.028 174.374   4451
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 10.57 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.28 (0.21), residues: 1129
  helix: -2.55 (0.16), residues: 643
  sheet: -0.90 (0.58), residues: 77
  loop : -1.41 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  17 
 TYR   0.020   0.002   TYR E  99 
 PHE   0.026   0.002   PHE L  45 
 TRP   0.010   0.001   TRP K 208 
 HIS   0.008   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00534 /  0.26 (16003)
  covalent geometry    : angle       0.88259 /  0.49 (22877)
  hydrogen bonds       : bond        0.11332 /  7.16 (  637)
  hydrogen bonds       : angle       4.90829 /  3.36 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 273
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8692 (t0)
REVERT: A  118 THR cc_start: 0.9487 (m) cc_final: 0.8980 (p)
REVERT: A  120 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8061 (mtt)
REVERT: B   24 ASP cc_start: 0.6054 (t0) cc_final: 0.5465 (t0)
REVERT: B   53 GLU cc_start: 0.8155 (tp30) cc_final: 0.7609 (tp30)
REVERT: C   95 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8781 (mttm)
REVERT: D   42 TYR cc_start: 0.7916 (t80) cc_final: 0.7656 (t80)
REVERT: D   79 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7821 (mtp85)
REVERT: D   86 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7482 (mtm-85)
REVERT: D   87 SER cc_start: 0.8797 (m) cc_final: 0.8366 (t)
REVERT: E   63 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7679 (mmp-170)
REVERT: E  122 LYS cc_start: 0.9315 (ptpt) cc_final: 0.9082 (ptpp)
REVERT: G   74 LYS cc_start: 0.9000 (mppt) cc_final: 0.8748 (mtmm)
REVERT: K   55 MET cc_start: -0.1375 (mmp) cc_final: -0.1768 (mmt)
REVERT: K  108 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6950 (tpt170)
REVERT: K  198 MET cc_start: 0.1919 (mmm) cc_final: 0.0720 (mmm)
REVERT: K  206 MET cc_start: 0.6080 (mmm) cc_final: 0.5551 (ppp)
REVERT: K  282 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7820 (ttm-80)
REVERT: L   51 GLU cc_start: 0.7653 (tt0) cc_final: 0.7190 (mp0)
  outliers start: 39
  outliers final: 22
  residues processed: 295
  average time/residue: 0.1440
  time to fit residues: 58.9796
Evaluate side-chains
  269 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  108 ASN
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   84 GLN
Chi-restraints excluded: chain H residue  108 LYS
Chi-restraints excluded: chain K residue  275 LEU
Chi-restraints excluded: chain K residue  282 ARG
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 105 optimal weight:    6.9990
   chunk 85 optimal weight:   30.0000
   chunk 74 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 119 optimal weight:   10.0000
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 108 ASN
C  94 ASN
E  68 GLN
E 113 HIS
G  84 GLN
H  63 ASN
H  67 ASN
L  40 GLN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.128873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.093491 restraints weight = 44106.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.093711 restraints weight = 31836.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093576 restraints weight = 27162.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.093689 restraints weight = 23124.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093746 restraints weight = 21109.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16003  Z= 0.175
  Angle     :  0.721   8.130  22877  Z= 0.416
  Chirality :  0.050   0.261   2589
  Planarity :  0.004   0.035   1901
  Dihedral  : 30.791 178.766   4451
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.53 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.23), residues: 1129
  helix: -1.51 (0.18), residues: 639
  sheet: -1.14 (0.58), residues: 78
  loop : -1.03 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  95 
 TYR   0.019   0.002   TYR H  83 
 PHE   0.013   0.001   PHE B 100 
 TRP   0.016   0.002   TRP K 228 
 HIS   0.007   0.001   HIS G  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.17 (16003)
  covalent geometry    : angle       0.72066 /  0.42 (22877)
  hydrogen bonds       : bond        0.09634 /  6.10 (  637)
  hydrogen bonds       : angle       4.18785 /  2.88 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 270
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7965 (mtt)
REVERT: B   24 ASP cc_start: 0.5944 (t0) cc_final: 0.5369 (t0)
REVERT: B   43 VAL cc_start: 0.8683 (t) cc_final: 0.8467 (t)
REVERT: C   24 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8517 (mm110)
REVERT: C   91 GLU cc_start: 0.8265 (tp30) cc_final: 0.7641 (tp30)
REVERT: D   42 TYR cc_start: 0.7899 (t80) cc_final: 0.7668 (t80)
REVERT: D   59 MET cc_start: 0.8688 (tpt) cc_final: 0.8301 (tpp)
REVERT: D   86 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7501 (mtm-85)
REVERT: D   87 SER cc_start: 0.8825 (m) cc_final: 0.8386 (t)
REVERT: E  122 LYS cc_start: 0.9280 (ptpt) cc_final: 0.9047 (ptpp)
REVERT: G   74 LYS cc_start: 0.9084 (mppt) cc_final: 0.8745 (mtmm)
REVERT: G   75 LYS cc_start: 0.8319 (mttm) cc_final: 0.8016 (mtpp)
REVERT: G  112 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8544 (mm-40)
REVERT: H   62 MET cc_start: 0.9193 (mmm) cc_final: 0.8719 (mmp)
REVERT: H   87 SER cc_start: 0.9340 (m) cc_final: 0.9123 (p)
REVERT: K   55 MET cc_start: -0.1310 (mmp) cc_final: -0.1648 (mmt)
REVERT: K   71 MET cc_start: 0.5235 (mmm) cc_final: 0.4322 (mmm)
REVERT: K  108 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6760 (tpt170)
REVERT: K  198 MET cc_start: 0.1913 (mmm) cc_final: 0.0739 (mmm)
REVERT: K  206 MET cc_start: 0.6082 (mmm) cc_final: 0.5641 (ppp)
REVERT: K  212 LYS cc_start: 0.2911 (tptt) cc_final: 0.1855 (tptm)
REVERT: K  282 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (ttm-80)
REVERT: K  286 ASP cc_start: 0.8499 (t70) cc_final: 0.8215 (t70)
  outliers start: 30
  outliers final: 17
  residues processed: 282
  average time/residue: 0.1452
  time to fit residues: 57.4281
Evaluate side-chains
  267 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 247
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue  108 LYS
Chi-restraints excluded: chain K residue  275 LEU
Chi-restraints excluded: chain K residue  282 ARG
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 102 optimal weight:    0.0980
   chunk 99 optimal weight:   30.0000
   chunk 134 optimal weight:    7.9990
   chunk 101 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 71 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
G  38 ASN
G  84 GLN
H  67 ASN
** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 GLN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.129553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.093893 restraints weight = 43674.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.094263 restraints weight = 32550.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.094159 restraints weight = 26752.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.094228 restraints weight = 23661.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094297 restraints weight = 21486.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  16003  Z= 0.152
  Angle     :  0.680   7.535  22877  Z= 0.390
  Chirality :  0.048   0.258   2589
  Planarity :  0.004   0.035   1901
  Dihedral  : 30.632 179.153   4443
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.96 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.24), residues: 1129
  helix: -0.80 (0.20), residues: 637
  sheet: -1.10 (0.58), residues: 78
  loop : -0.90 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 265 
 TYR   0.022   0.001   TYR H  40 
 PHE   0.020   0.001   PHE K 159 
 TRP   0.025   0.002   TRP K 228 
 HIS   0.006   0.001   HIS K 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.15 (16003)
  covalent geometry    : angle       0.68001 /  0.39 (22877)
  hydrogen bonds       : bond        0.08822 /  5.55 (  637)
  hydrogen bonds       : angle       3.85698 /  2.67 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 255
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9157 (t0) cc_final: 0.8305 (t0)
REVERT: A  120 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7762 (mtt)
REVERT: C   91 GLU cc_start: 0.8100 (tp30) cc_final: 0.7583 (tp30)
REVERT: C   95 LYS cc_start: 0.8887 (mttm) cc_final: 0.8639 (mttm)
REVERT: D   76 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: D   86 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7538 (mtm-85)
REVERT: D   87 SER cc_start: 0.8829 (m) cc_final: 0.8416 (t)
REVERT: E   68 GLN cc_start: 0.8780 (tt0) cc_final: 0.8241 (tm-30)
REVERT: E   90 MET cc_start: 0.8252 (mmp) cc_final: 0.7985 (mmt)
REVERT: E  122 LYS cc_start: 0.9277 (ptpt) cc_final: 0.9004 (ptpp)
REVERT: G   75 LYS cc_start: 0.8206 (mttm) cc_final: 0.7762 (mtpp)
REVERT: G   99 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7669 (mmm160)
REVERT: H   87 SER cc_start: 0.9372 (m) cc_final: 0.9158 (p)
REVERT: K   71 MET cc_start: 0.5682 (mmm) cc_final: 0.4744 (mmm)
REVERT: K   96 MET cc_start: -0.1532 (mpp) cc_final: -0.1797 (mpp)
REVERT: K  108 ARG cc_start: 0.7193 (ttm110) cc_final: 0.6564 (tpt90)
REVERT: K  147 MET cc_start: 0.7185 (tmm) cc_final: 0.5777 (mtt)
REVERT: K  206 MET cc_start: 0.6084 (mmm) cc_final: 0.5612 (ppp)
REVERT: K  212 LYS cc_start: 0.2723 (tptt) cc_final: 0.1670 (tptm)
REVERT: K  252 GLN cc_start: 0.6636 (mt0) cc_final: 0.6402 (mt0)
REVERT: K  286 ASP cc_start: 0.8541 (t70) cc_final: 0.8196 (t70)
  outliers start: 25
  outliers final: 17
  residues processed: 266
  average time/residue: 0.1401
  time to fit residues: 52.5813
Evaluate side-chains
  258 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 239
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue  108 LYS
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  275 LEU
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 123 optimal weight:    0.7980
   chunk 137 optimal weight:    9.9990
   chunk 113 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 127 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 130 optimal weight:    0.5980
   chunk 126 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
K 168 GLN
** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.129427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.094216 restraints weight = 43643.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.093938 restraints weight = 34309.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.093924 restraints weight = 31369.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094081 restraints weight = 26490.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094107 restraints weight = 24228.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3346
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16003  Z= 0.161
  Angle     :  0.668   7.035  22877  Z= 0.381
  Chirality :  0.047   0.247   2589
  Planarity :  0.004   0.034   1901
  Dihedral  : 30.526 179.536   4439
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.85 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.24), residues: 1129
  helix: -0.38 (0.20), residues: 640
  sheet: -1.07 (0.58), residues: 78
  loop : -0.78 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 203 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.015   0.001   PHE K 159 
 TRP   0.031   0.002   TRP K 228 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.16 (16003)
  covalent geometry    : angle       0.66806 /  0.38 (22877)
  hydrogen bonds       : bond        0.08556 /  5.40 (  637)
  hydrogen bonds       : angle       3.77668 /  2.63 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 241
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9202 (t0) cc_final: 0.8269 (t0)
REVERT: A  120 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7850 (mtt)
REVERT: C   91 GLU cc_start: 0.8238 (tp30) cc_final: 0.7694 (tp30)
REVERT: D   86 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7674 (mtm-85)
REVERT: D   87 SER cc_start: 0.8940 (m) cc_final: 0.8517 (t)
REVERT: E   94 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7450 (mm-30)
REVERT: E  122 LYS cc_start: 0.9286 (ptpt) cc_final: 0.9020 (ptpp)
REVERT: F   84 MET cc_start: 0.7365 (mmm) cc_final: 0.7059 (mmm)
REVERT: G   75 LYS cc_start: 0.8235 (mttm) cc_final: 0.7904 (mtpp)
REVERT: H   87 SER cc_start: 0.9375 (m) cc_final: 0.9152 (p)
REVERT: K   71 MET cc_start: 0.5672 (mmm) cc_final: 0.4743 (mmm)
REVERT: K   96 MET cc_start: -0.1388 (mpp) cc_final: -0.1672 (mpp)
REVERT: K  108 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6778 (tpt170)
REVERT: K  147 MET cc_start: 0.6918 (tmm) cc_final: 0.5770 (mtt)
REVERT: K  198 MET cc_start: 0.2924 (mmm) cc_final: 0.1705 (mmm)
REVERT: K  206 MET cc_start: 0.6097 (mmm) cc_final: 0.5587 (tmm)
REVERT: K  212 LYS cc_start: 0.2687 (tptt) cc_final: 0.1614 (tptm)
REVERT: K  252 GLN cc_start: 0.6522 (mt0) cc_final: 0.6254 (mt0)
REVERT: K  286 ASP cc_start: 0.8417 (t70) cc_final: 0.8036 (t70)
  outliers start: 35
  outliers final: 22
  residues processed: 256
  average time/residue: 0.1355
  time to fit residues: 48.8550
Evaluate side-chains
  255 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 231
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  275 LEU
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 137 optimal weight:   10.0000
   chunk 129 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 136 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    6.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
B  25 ASN
B  75 HIS
C  84 GLN
D  84 ASN
E  68 GLN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.121727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.087737 restraints weight = 44479.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.086095 restraints weight = 39480.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.086548 restraints weight = 42278.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.086553 restraints weight = 32433.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.086594 restraints weight = 31128.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.118  16003  Z= 0.645
  Angle     :  1.197  17.991  22877  Z= 0.618
  Chirality :  0.068   0.287   2589
  Planarity :  0.009   0.076   1901
  Dihedral  : 31.217 178.890   4439
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 21.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.91 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 15.85 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.23), residues: 1129
  helix: -1.36 (0.18), residues: 649
  sheet: -1.74 (0.56), residues: 75
  loop : -1.36 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG B  40 
 TYR   0.042   0.004   TYR A  99 
 PHE   0.037   0.004   PHE B 100 
 TRP   0.015   0.002   TRP K 228 
 HIS   0.019   0.004   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01426 /  0.64 (16003)
  covalent geometry    : angle       1.19694 /  0.62 (22877)
  hydrogen bonds       : bond        0.13580 /  9.00 (  637)
  hydrogen bonds       : angle       5.58257 /  3.88 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 208
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8559 (mt0) cc_final: 0.8249 (tt0)
REVERT: C   91 GLU cc_start: 0.8425 (tp30) cc_final: 0.8187 (tp30)
REVERT: D   87 SER cc_start: 0.8962 (m) cc_final: 0.8684 (t)
REVERT: E   94 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: E  131 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8580 (mtt180)
REVERT: G   39 TYR cc_start: 0.9027 (m-80) cc_final: 0.8812 (m-80)
REVERT: G  112 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8720 (mm-40)
REVERT: K   71 MET cc_start: 0.5246 (mmm) cc_final: 0.4310 (mmm)
REVERT: K   96 MET cc_start: -0.0751 (mpp) cc_final: -0.1215 (mpp)
REVERT: K  108 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7183 (tpt170)
REVERT: K  147 MET cc_start: 0.6861 (tmm) cc_final: 0.5798 (mtt)
REVERT: K  205 TRP cc_start: 0.4905 (m100) cc_final: 0.4662 (m100)
REVERT: K  252 GLN cc_start: 0.6608 (mt0) cc_final: 0.6184 (mp10)
  outliers start: 61
  outliers final: 43
  residues processed: 246
  average time/residue: 0.1543
  time to fit residues: 52.3374
Evaluate side-chains
  236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 THR
Chi-restraints excluded: chain H residue   42 TYR
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain H residue  108 LYS
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  275 LEU
Chi-restraints excluded: chain K residue  318 ASP
Chi-restraints excluded: chain K residue  329 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 83 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 131 optimal weight:    0.9980
   chunk 114 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  93 GLN
B  25 ASN
C  84 GLN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.127321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.092325 restraints weight = 43395.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.091610 restraints weight = 34218.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.091668 restraints weight = 34225.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091817 restraints weight = 27543.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091851 restraints weight = 25057.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3298
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16003  Z= 0.201
  Angle     :  0.745   8.192  22877  Z= 0.417
  Chirality :  0.050   0.264   2589
  Planarity :  0.004   0.038   1901
  Dihedral  : 30.902 177.562   4439
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.72 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.24), residues: 1129
  helix: -0.58 (0.20), residues: 630
  sheet: -1.66 (0.57), residues: 75
  loop : -0.99 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 203 
 TYR   0.029   0.002   TYR H  40 
 PHE   0.014   0.002   PHE L  45 
 TRP   0.016   0.001   TRP K 228 
 HIS   0.006   0.001   HIS K 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.20 (16003)
  covalent geometry    : angle       0.74455 /  0.42 (22877)
  hydrogen bonds       : bond        0.09145 /  5.83 (  637)
  hydrogen bonds       : angle       4.27482 /  2.97 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 236
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8519 (mt0) cc_final: 0.8206 (tt0)
REVERT: A  120 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7841 (mtt)
REVERT: B   27 GLN cc_start: 0.7971 (mp10) cc_final: 0.7610 (mp10)
REVERT: C   91 GLU cc_start: 0.8367 (tp30) cc_final: 0.8135 (tp30)
REVERT: D   86 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7881 (mtm-85)
REVERT: D   87 SER cc_start: 0.8900 (m) cc_final: 0.8478 (t)
REVERT: G  112 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8683 (mm-40)
REVERT: H   87 SER cc_start: 0.9412 (m) cc_final: 0.9192 (p)
REVERT: K   55 MET cc_start: -0.1712 (mmp) cc_final: -0.2286 (mmt)
REVERT: K   71 MET cc_start: 0.5217 (mmm) cc_final: 0.4289 (mmm)
REVERT: K   96 MET cc_start: -0.0726 (mpp) cc_final: -0.1185 (mpp)
REVERT: K  108 ARG cc_start: 0.7368 (ttm110) cc_final: 0.6886 (tpt170)
REVERT: K  147 MET cc_start: 0.6685 (tmm) cc_final: 0.5698 (mtt)
REVERT: K  198 MET cc_start: 0.3822 (mmm) cc_final: 0.2353 (mmm)
REVERT: K  252 GLN cc_start: 0.6559 (mt0) cc_final: 0.6206 (mp10)
  outliers start: 33
  outliers final: 22
  residues processed: 251
  average time/residue: 0.1431
  time to fit residues: 49.9684
Evaluate side-chains
  240 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  190 ILE
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 135 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 111 optimal weight:    9.9990
   chunk 114 optimal weight:   10.0000
   chunk 127 optimal weight:    7.9990
   chunk 72 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 24 optimal weight:    0.0980
   chunk 97 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   overall best weight:    5.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  25 ASN
C  68 ASN
C  84 GLN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.122230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088247 restraints weight = 44317.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.086040 restraints weight = 40594.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.086489 restraints weight = 46527.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.086647 restraints weight = 33364.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.086715 restraints weight = 31534.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3207
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3207 r_free = 0.3207    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.3207
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.095  16003  Z= 0.576
  Angle     :  1.106  15.782  22877  Z= 0.572
  Chirality :  0.064   0.367   2589
  Planarity :  0.008   0.061   1901
  Dihedral  : 31.151 176.292   4439
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 20.94
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.79 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.51 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.23), residues: 1129
  helix: -1.16 (0.19), residues: 634
  sheet: -1.92 (0.55), residues: 76
  loop : -1.31 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG D  33 
 TYR   0.051   0.004   TYR H  83 
 PHE   0.033   0.004   PHE B 100 
 TRP   0.017   0.002   TRP K 228 
 HIS   0.016   0.003   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01280 /  0.58 (16003)
  covalent geometry    : angle       1.10579 /  0.57 (22877)
  hydrogen bonds       : bond        0.12083 /  7.96 (  637)
  hydrogen bonds       : angle       5.40575 /  3.77 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 196
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8548 (mt0) cc_final: 0.8275 (tt0)
REVERT: D   87 SER cc_start: 0.8984 (m) cc_final: 0.8723 (t)
REVERT: E   94 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: F   52 GLU cc_start: 0.7374 (pm20) cc_final: 0.7136 (pm20)
REVERT: G   39 TYR cc_start: 0.8981 (m-80) cc_final: 0.8773 (m-80)
REVERT: G  112 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8700 (mm-40)
REVERT: K   55 MET cc_start: -0.0860 (mmp) cc_final: -0.1389 (mmt)
REVERT: K   71 MET cc_start: 0.5217 (mmm) cc_final: 0.4280 (mmm)
REVERT: K   96 MET cc_start: -0.0621 (mpp) cc_final: -0.1107 (mpp)
REVERT: K  147 MET cc_start: 0.6750 (tmm) cc_final: 0.5689 (mtt)
  outliers start: 49
  outliers final: 38
  residues processed: 224
  average time/residue: 0.1517
  time to fit residues: 47.3687
Evaluate side-chains
  231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  170 VAL
Chi-restraints excluded: chain K residue  190 ILE
Chi-restraints excluded: chain K residue  249 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9980
   chunk 84 optimal weight:   20.0000
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 81 optimal weight:   10.0000
   chunk 1 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 120 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.127810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.092960 restraints weight = 43289.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.092226 restraints weight = 33556.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.092404 restraints weight = 33698.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.092596 restraints weight = 26719.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.092614 restraints weight = 24218.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (13 function evaluations)
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16003  Z= 0.160
  Angle     :  0.733   9.455  22877  Z= 0.414
  Chirality :  0.049   0.275   2589
  Planarity :  0.005   0.042   1901
  Dihedral  : 30.831 173.960   4439
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.04 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.24), residues: 1129
  helix: -0.38 (0.20), residues: 629
  sheet: -1.83 (0.57), residues: 76
  loop : -0.98 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E  69 
 TYR   0.035   0.002   TYR H  83 
 PHE   0.019   0.002   PHE L  45 
 TRP   0.020   0.002   TRP K 228 
 HIS   0.005   0.001   HIS K 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.16 (16003)
  covalent geometry    : angle       0.73348 /  0.41 (22877)
  hydrogen bonds       : bond        0.08931 /  5.68 (  637)
  hydrogen bonds       : angle       4.17742 /  2.91 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8482 (mt0) cc_final: 0.8185 (tt0)
REVERT: A  120 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7727 (mtt)
REVERT: B   27 GLN cc_start: 0.8118 (mp10) cc_final: 0.7830 (pm20)
REVERT: D   86 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7836 (mtm-85)
REVERT: D   87 SER cc_start: 0.8919 (m) cc_final: 0.8519 (t)
REVERT: E   68 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8408 (tt0)
REVERT: E  122 LYS cc_start: 0.9175 (ptpt) cc_final: 0.8838 (ptpp)
REVERT: G   99 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7587 (mmm160)
REVERT: G  112 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8638 (mm-40)
REVERT: K   55 MET cc_start: -0.1573 (mmp) cc_final: -0.2027 (mmt)
REVERT: K   71 MET cc_start: 0.5168 (mmm) cc_final: 0.4246 (mmm)
REVERT: K   96 MET cc_start: -0.0925 (mpp) cc_final: -0.1318 (mpp)
REVERT: K  147 MET cc_start: 0.6533 (tmm) cc_final: 0.5615 (mtt)
REVERT: K  198 MET cc_start: 0.3826 (mmm) cc_final: 0.2331 (mmm)
REVERT: K  212 LYS cc_start: 0.2165 (tptt) cc_final: 0.1551 (tptp)
  outliers start: 30
  outliers final: 23
  residues processed: 240
  average time/residue: 0.1411
  time to fit residues: 47.8712
Evaluate side-chains
  243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  190 ILE
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 119 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0020
   chunk 127 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  93 GLN
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.128401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.092597 restraints weight = 43646.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.092707 restraints weight = 32480.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.092568 restraints weight = 28386.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.092736 restraints weight = 23900.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092769 restraints weight = 21631.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16003  Z= 0.155
  Angle     :  0.709  11.171  22877  Z= 0.397
  Chirality :  0.047   0.280   2589
  Planarity :  0.004   0.064   1901
  Dihedral  : 30.579 174.985   4439
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.85 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.25), residues: 1129
  helix: -0.01 (0.21), residues: 623
  sheet: -1.79 (0.58), residues: 78
  loop : -0.92 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 203 
 TYR   0.041   0.002   TYR H  83 
 PHE   0.021   0.001   PHE L  45 
 TRP   0.015   0.001   TRP K 228 
 HIS   0.005   0.001   HIS K 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.15 (16003)
  covalent geometry    : angle       0.70867 /  0.40 (22877)
  hydrogen bonds       : bond        0.08383 /  5.33 (  637)
  hydrogen bonds       : angle       3.94708 /  2.74 ( 1572)

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 224
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.8512 (mt0) cc_final: 0.8232 (tt0)
REVERT: A  120 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7627 (mtt)
REVERT: B   27 GLN cc_start: 0.8260 (mp10) cc_final: 0.7995 (pm20)
REVERT: D   86 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7811 (mtm-85)
REVERT: D   87 SER cc_start: 0.8852 (m) cc_final: 0.8466 (t)
REVERT: E  122 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8793 (ptpp)
REVERT: F   91 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8859 (ttpp)
REVERT: G   99 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7646 (mmm160)
REVERT: G  112 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8608 (mm-40)
REVERT: H   83 TYR cc_start: 0.7424 (m-80) cc_final: 0.7077 (t80)
REVERT: K   55 MET cc_start: -0.1710 (mmp) cc_final: -0.2152 (mmt)
REVERT: K   71 MET cc_start: 0.5735 (mmm) cc_final: 0.4800 (mmm)
REVERT: K  147 MET cc_start: 0.6619 (tmm) cc_final: 0.5729 (mtt)
REVERT: K  198 MET cc_start: 0.3703 (mmm) cc_final: 0.2277 (mmm)
REVERT: K  212 LYS cc_start: 0.2354 (tptt) cc_final: 0.1752 (tptp)
  outliers start: 27
  outliers final: 21
  residues processed: 239
  average time/residue: 0.1424
  time to fit residues: 48.5186
Evaluate side-chains
  243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   85 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain K residue  144 VAL
Chi-restraints excluded: chain K residue  169 VAL
Chi-restraints excluded: chain K residue  190 ILE
Chi-restraints excluded: chain K residue  240 VAL
Chi-restraints excluded: chain K residue  267 VAL
Chi-restraints excluded: chain K residue  318 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 73 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 86 optimal weight:   20.0000
   chunk 82 optimal weight:   10.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 108 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
H  63 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.129090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.093332 restraints weight = 43704.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.093384 restraints weight = 32099.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.093326 restraints weight = 27758.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093469 restraints weight = 23938.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.093535 restraints weight = 21597.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.4736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16003  Z= 0.151
  Angle     :  0.686  12.548  22877  Z= 0.384
  Chirality :  0.046   0.277   2589
  Planarity :  0.004   0.044   1901
  Dihedral  : 30.452 175.270   4439
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.05 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.25), residues: 1129
  helix:  0.17 (0.21), residues: 622
  sheet: -1.68 (0.56), residues: 80
  loop : -0.79 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  67 
 TYR   0.032   0.002   TYR H  83 
 PHE   0.021   0.001   PHE L  45 
 TRP   0.014   0.001   TRP K 228 
 HIS   0.005   0.001   HIS K 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.15 (16003)
  covalent geometry    : angle       0.68637 /  0.38 (22877)
  hydrogen bonds       : bond        0.08160 /  5.15 (  637)
  hydrogen bonds       : angle       3.83256 /  2.65 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2463.83 seconds
wall clock time: 43 minutes 19.27 seconds (2599.27 seconds total)