Starting phenix.real_space_refine
on Wed Mar  4 16:24:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nn6_0458/03_2026/6nn6_0458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nn6_0458/03_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nn6_0458/03_2026/6nn6_0458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nn6_0458/03_2026/6nn6_0458.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nn6_0458/03_2026/6nn6_0458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nn6_0458/03_2026/6nn6_0458.map"
  }
  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-dev-5986/lib/python3.9/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: 2.81, per 1000 atoms: 0.19
  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: 0.87
  Conformation dependent library (CDL) restraints added in 448.3 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: 2.19
  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: 2.98

  Time building geometry restraints manager: 1.20 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=" 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=" C   LEU H 101 "
       pdb=" N   LEU H 102 "
    ideal  model  delta    sigma   weight residual
    1.331  1.231  0.100 2.83e-02 1.25e+03 1.26e+01
  bond pdb=" C   LEU G 108 "
       pdb=" N   PRO G 109 "
    ideal  model  delta    sigma   weight residual
    1.333  1.304  0.030 1.01e-02 9.80e+03 8.75e+00
  bond pdb=" C   GLN C  24 "
       pdb=" N   PHE C  25 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.47e-02 4.63e+03 6.67e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.481 -0.059 3.00e-02 1.11e+03 3.89e+00
  ... (remaining 15998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 20730
        1.66 -     3.31: 1859
        3.31 -     4.97: 239
        4.97 -     6.62: 27
        6.62 -     8.28: 22
  Bond angle restraints: 22877
  Sorted by residual:
  angle pdb=" N   VAL C  27 "
        pdb=" CA  VAL C  27 "
        pdb=" C   VAL C  27 "
      ideal   model   delta    sigma   weight residual
     113.43  108.54    4.89 1.09e+00 8.42e-01 2.01e+01
  angle pdb=" C   THR D 115 "
        pdb=" N   LYS D 116 "
        pdb=" CA  LYS D 116 "
      ideal   model   delta    sigma   weight residual
     120.28  126.19   -5.91 1.34e+00 5.57e-01 1.94e+01
  angle pdb=" N   ARG K 282 "
        pdb=" CA  ARG K 282 "
        pdb=" C   ARG K 282 "
      ideal   model   delta    sigma   weight residual
     114.04  109.04    5.00 1.24e+00 6.50e-01 1.63e+01
  angle pdb=" N   ILE L  36 "
        pdb=" CA  ILE L  36 "
        pdb=" C   ILE L  36 "
      ideal   model   delta    sigma   weight residual
     109.02  105.28    3.74 9.30e-01 1.16e+00 1.62e+01
  angle pdb=" C   ALA G 103 "
        pdb=" N   GLN G 104 "
        pdb=" CA  GLN G 104 "
      ideal   model   delta    sigma   weight residual
     122.40  127.97   -5.57 1.45e+00 4.76e-01 1.47e+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: 1825
       0.052 -    0.103: 639
       0.103 -    0.155: 112
       0.155 -    0.207: 12
       0.207 -    0.259: 1
  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=" 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
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.00e+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:             2.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.790
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
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= 0.426
  Angle     :  1.016   8.280  22877  Z= 0.597
  Chirality :  0.051   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
  covalent geometry    : bond        0.00972 (16003)
  covalent geometry    : angle       1.01570 (22877)
  hydrogen bonds       : bond        0.34078 (  637)
  hydrogen bonds       : angle      10.56686 ( 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  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.9345 (m) cc_final: 0.8720 (p)
REVERT: B   53 GLU cc_start: 0.8396 (tp30) cc_final: 0.8048 (tp30)
REVERT: C   91 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8035 (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: 0.8673 (mttm)
REVERT: D   42 TYR cc_start: 0.7942 (t80) cc_final: 0.7541 (t80)
REVERT: D   87 SER cc_start: 0.8668 (m) cc_final: 0.8441 (t)
REVERT: E  122 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9085 (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: 0.8429 (mm-40)
REVERT: H   32 THR cc_start: 0.7817 (p) cc_final: 0.7519 (p)
REVERT: H   43 LYS cc_start: 0.9214 (mttt) cc_final: 0.8842 (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: 0.8635 (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: 0.6289 (m-30)
REVERT: K  189 ASP cc_start: 0.7951 (m-30) cc_final: 0.7277 (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: 0.4829 (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: 0.6991 (mp10)
REVERT: K  291 MET cc_start: 0.8538 (ptp) cc_final: 0.8209 (ptp)
REVERT: L   51 GLU cc_start: 0.7849 (tt0) cc_final: 0.7308 (mp0)
  outliers start: 8
  outliers final: 3
  residues processed: 368
  average time/residue: 0.1839
  time to fit residues: 88.2639
Evaluate side-chains
  249 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 246
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
A 125 GLN
C 110 ASN
D  67 ASN
E  68 GLN
E  76 GLN
G  84 GLN
G 104 GLN
H  67 ASN
H  95 GLN
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: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.129168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.093935 restraints weight = 43744.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093556 restraints weight = 31721.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093675 restraints weight = 29463.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.093777 restraints weight = 24478.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093880 restraints weight = 22756.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  16003  Z= 0.209
  Angle     :  0.682   7.439  22877  Z= 0.397
  Chirality :  0.040   0.187   2589
  Planarity :  0.005   0.038   1901
  Dihedral  : 30.630 175.972   4451
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 10.47 %
    Favored  : 86.08 %
  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: -2.85 (0.22), residues: 1129
  helix: -2.18 (0.17), residues: 636
  sheet: -0.89 (0.60), residues: 78
  loop : -1.26 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  35 
 TYR   0.017   0.002   TYR F  51 
 PHE   0.019   0.001   PHE L  45 
 TRP   0.008   0.001   TRP K 205 
 HIS   0.009   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (16003)
  covalent geometry    : angle       0.68222 (22877)
  hydrogen bonds       : bond        0.08841 (  637)
  hydrogen bonds       : angle       4.17783 ( 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
  329 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 295
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.9417 (m) cc_final: 0.8887 (p)
REVERT: B   24 ASP cc_start: 0.6364 (t0) cc_final: 0.6103 (t0)
REVERT: B   64 ASN cc_start: 0.9290 (m-40) cc_final: 0.8999 (m-40)
REVERT: D   42 TYR cc_start: 0.7834 (t80) cc_final: 0.7580 (t80)
REVERT: D   86 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7540 (mtm-85)
REVERT: D   87 SER cc_start: 0.8799 (m) cc_final: 0.8327 (t)
REVERT: E   97 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6662 (mt-10)
REVERT: G   38 ASN cc_start: 0.8339 (m-40) cc_final: 0.8044 (m110)
REVERT: G   59 THR cc_start: 0.9454 (p) cc_final: 0.9027 (m)
REVERT: G   75 LYS cc_start: 0.8270 (mttm) cc_final: 0.7993 (mtpp)
REVERT: K   71 MET cc_start: 0.5982 (mmm) cc_final: 0.4943 (mmm)
REVERT: K  108 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6830 (tpt170)
REVERT: K  147 MET cc_start: 0.7067 (tmm) cc_final: 0.5769 (mtt)
REVERT: K  206 MET cc_start: 0.6148 (mmm) cc_final: 0.5613 (ppp)
REVERT: K  282 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7900 (ttm-80)
  outliers start: 34
  outliers final: 17
  residues processed: 309
  average time/residue: 0.1502
  time to fit residues: 64.2683
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  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 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   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   39 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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    0.1980
   chunk 81 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  85 GLN
A 108 ASN
C  94 ASN
E  68 GLN
E  93 GLN
G  84 GLN
H  63 ASN
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.129317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093980 restraints weight = 43851.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093811 restraints weight = 33594.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.093801 restraints weight = 29443.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.093882 restraints weight = 25243.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094005 restraints weight = 22560.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3343
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3343 r_free = 0.3343    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3343
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16003  Z= 0.182
  Angle     :  0.613   5.935  22877  Z= 0.356
  Chirality :  0.038   0.184   2589
  Planarity :  0.004   0.048   1901
  Dihedral  : 30.177 176.447   4443
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.04 %
    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: -1.56 (0.23), residues: 1129
  helix: -0.95 (0.19), residues: 636
  sheet: -0.97 (0.59), residues: 78
  loop : -0.89 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 265 
 TYR   0.015   0.002   TYR H  40 
 PHE   0.011   0.001   PHE B 100 
 TRP   0.014   0.001   TRP K 228 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (16003)
  covalent geometry    : angle       0.61259 (22877)
  hydrogen bonds       : bond        0.08035 (  637)
  hydrogen bonds       : angle       3.68871 ( 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
  293 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 259
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9040 (t160) cc_final: 0.8629 (t0)
REVERT: B   24 ASP cc_start: 0.6011 (t0) cc_final: 0.4952 (t0)
REVERT: D   86 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7664 (mtm-85)
REVERT: D   87 SER cc_start: 0.8845 (m) cc_final: 0.8318 (t)
REVERT: D   90 THR cc_start: 0.8855 (p) cc_final: 0.8557 (t)
REVERT: E   97 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6476 (mt-10)
REVERT: F   91 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8938 (ttpp)
REVERT: G   59 THR cc_start: 0.9477 (p) cc_final: 0.9099 (m)
REVERT: G   75 LYS cc_start: 0.8268 (mttm) cc_final: 0.7979 (mtpp)
REVERT: K   55 MET cc_start: -0.1515 (mmp) cc_final: -0.1758 (mmt)
REVERT: K   71 MET cc_start: 0.6016 (mmm) cc_final: 0.5176 (mmm)
REVERT: K  108 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6823 (tpt170)
REVERT: K  143 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1690 (tt)
REVERT: K  147 MET cc_start: 0.6729 (tmm) cc_final: 0.5683 (mtt)
REVERT: K  198 MET cc_start: 0.3648 (mmm) cc_final: 0.2247 (mmm)
REVERT: K  206 MET cc_start: 0.6157 (mmm) cc_final: 0.5604 (ppp)
REVERT: K  212 LYS cc_start: 0.2752 (tptt) cc_final: 0.1857 (tptm)
  outliers start: 34
  outliers final: 16
  residues processed: 275
  average time/residue: 0.1410
  time to fit residues: 54.1579
Evaluate side-chains
  249 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 230
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  108 LEU
Chi-restraints excluded: chain C residue  114 VAL
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 E residue   97 GLU
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue   84 GLN
Chi-restraints excluded: chain K residue  143 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 134 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0270
   chunk 50 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0010
   chunk 64 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.3646

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  68 GLN
L  40 GLN
** 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 = 0.4044 r_free = 0.4044 target = 0.132053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.096687 restraints weight = 43464.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.096310 restraints weight = 32269.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.096455 restraints weight = 31018.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096629 restraints weight = 25400.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.096658 restraints weight = 23425.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16003  Z= 0.146
  Angle     :  0.567   5.905  22877  Z= 0.330
  Chirality :  0.036   0.159   2589
  Planarity :  0.004   0.045   1901
  Dihedral  : 29.838 174.572   4439
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.16 %
    Favored  : 80.79 %
  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: -0.79 (0.24), residues: 1129
  helix: -0.21 (0.20), residues: 637
  sheet: -0.96 (0.59), residues: 80
  loop : -0.69 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 203 
 TYR   0.015   0.001   TYR H  40 
 PHE   0.011   0.001   PHE K 159 
 TRP   0.010   0.001   TRP K 205 
 HIS   0.005   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (16003)
  covalent geometry    : angle       0.56720 (22877)
  hydrogen bonds       : bond        0.07533 (  637)
  hydrogen bonds       : angle       3.35346 ( 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
  301 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 271
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.8938 (mm) cc_final: 0.8649 (mp)
REVERT: A  108 ASN cc_start: 0.8978 (t160) cc_final: 0.8707 (t0)
REVERT: B   45 ARG cc_start: 0.8396 (tpt-90) cc_final: 0.8065 (ttt180)
REVERT: C   38 ASN cc_start: 0.8256 (t0) cc_final: 0.7861 (p0)
REVERT: D   76 GLU cc_start: 0.8697 (tp30) cc_final: 0.8240 (mm-30)
REVERT: D   86 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7589 (mtm-85)
REVERT: D   87 SER cc_start: 0.8720 (m) cc_final: 0.8316 (t)
REVERT: E   90 MET cc_start: 0.8120 (mmp) cc_final: 0.7909 (mmt)
REVERT: G   75 LYS cc_start: 0.8159 (mttm) cc_final: 0.7911 (mtpp)
REVERT: H   93 GLU cc_start: 0.8647 (mp0) cc_final: 0.8193 (mp0)
REVERT: H  113 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7529 (mp0)
REVERT: K   71 MET cc_start: 0.6271 (mmm) cc_final: 0.5462 (mmm)
REVERT: K  108 ARG cc_start: 0.7132 (ttm110) cc_final: 0.6656 (tpt90)
REVERT: K  147 MET cc_start: 0.6768 (tmm) cc_final: 0.5957 (mtt)
REVERT: K  198 MET cc_start: 0.3239 (mmm) cc_final: 0.2032 (mmm)
REVERT: K  212 LYS cc_start: 0.2700 (tptt) cc_final: 0.1815 (tptm)
  outliers start: 30
  outliers final: 16
  residues processed: 286
  average time/residue: 0.1486
  time to fit residues: 59.0843
Evaluate side-chains
  245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 227
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   79 ILE
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   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain H residue  113 GLU
Chi-restraints excluded: chain K residue  139 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 137 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 127 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 126 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0970
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
E  68 GLN
K 168 GLN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.131717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.096423 restraints weight = 42725.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.095804 restraints weight = 33452.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.095863 restraints weight = 29506.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.096252 restraints weight = 24861.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.096208 restraints weight = 23040.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16003  Z= 0.144
  Angle     :  0.561   8.959  22877  Z= 0.322
  Chirality :  0.035   0.137   2589
  Planarity :  0.003   0.040   1901
  Dihedral  : 29.646 175.294   4439
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.17 %
    Favored  : 79.88 %
  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: -0.18 (0.25), residues: 1129
  helix:  0.38 (0.21), residues: 633
  sheet: -0.90 (0.59), residues: 80
  loop : -0.54 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 203 
 TYR   0.016   0.001   TYR H  40 
 PHE   0.019   0.001   PHE L  45 
 TRP   0.007   0.001   TRP K  89 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (16003)
  covalent geometry    : angle       0.56068 (22877)
  hydrogen bonds       : bond        0.07276 (  637)
  hydrogen bonds       : angle       3.23794 ( 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
  281 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 252
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9041 (t160) cc_final: 0.8793 (t0)
REVERT: C   38 ASN cc_start: 0.8215 (t0) cc_final: 0.7878 (p0)
REVERT: D   76 GLU cc_start: 0.8731 (tp30) cc_final: 0.8301 (mm-30)
REVERT: D   86 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7504 (mtm-85)
REVERT: D   87 SER cc_start: 0.8750 (m) cc_final: 0.8278 (t)
REVERT: E   90 MET cc_start: 0.8096 (mmp) cc_final: 0.7887 (mmt)
REVERT: E   94 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7280 (mm-30)
REVERT: G   75 LYS cc_start: 0.8153 (mttm) cc_final: 0.7916 (mtpp)
REVERT: H   62 MET cc_start: 0.9172 (mmm) cc_final: 0.8770 (mmp)
REVERT: H   93 GLU cc_start: 0.8531 (mp0) cc_final: 0.8123 (mp0)
REVERT: K   71 MET cc_start: 0.6489 (mmm) cc_final: 0.5699 (mmm)
REVERT: K  108 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6647 (tpt90)
REVERT: K  147 MET cc_start: 0.6692 (tmm) cc_final: 0.6008 (mtt)
REVERT: K  198 MET cc_start: 0.3408 (mmm) cc_final: 0.2156 (mmm)
REVERT: K  295 GLU cc_start: 0.6657 (tp30) cc_final: 0.6437 (tp30)
  outliers start: 29
  outliers final: 18
  residues processed: 266
  average time/residue: 0.1450
  time to fit residues: 53.5404
Evaluate side-chains
  252 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 233
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   79 ILE
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   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 G residue   16 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   54 ILE
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:    4.9990
   chunk 137 optimal weight:    5.9990
   chunk 129 optimal weight:   10.0000
   chunk 75 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 136 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E 113 HIS
H  47 GLN
H  63 ASN
K 234 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 = 0.3958 r_free = 0.3958 target = 0.126247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.091186 restraints weight = 43951.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.090151 restraints weight = 36678.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.090398 restraints weight = 37740.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090495 restraints weight = 30197.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.090560 restraints weight = 27723.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.066  16003  Z= 0.361
  Angle     :  0.746   8.560  22877  Z= 0.415
  Chirality :  0.044   0.151   2589
  Planarity :  0.005   0.041   1901
  Dihedral  : 30.313 170.932   4439
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.58 %
    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: -0.68 (0.25), residues: 1129
  helix: -0.04 (0.20), residues: 636
  sheet: -1.21 (0.58), residues: 80
  loop : -0.72 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  23 
 TYR   0.035   0.003   TYR F  88 
 PHE   0.025   0.003   PHE L  45 
 TRP   0.006   0.001   TRP K 208 
 HIS   0.008   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00822 (16003)
  covalent geometry    : angle       0.74611 (22877)
  hydrogen bonds       : bond        0.08804 (  637)
  hydrogen bonds       : angle       4.21945 ( 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
  261 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9014 (t160) cc_final: 0.8753 (t0)
REVERT: A  118 THR cc_start: 0.9472 (m) cc_final: 0.9090 (p)
REVERT: C   92 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: D   59 MET cc_start: 0.8598 (tpt) cc_final: 0.8234 (tpp)
REVERT: D   86 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7876 (mtm-85)
REVERT: D   87 SER cc_start: 0.8833 (m) cc_final: 0.8338 (t)
REVERT: F   88 TYR cc_start: 0.8713 (m-10) cc_final: 0.8196 (m-10)
REVERT: G   75 LYS cc_start: 0.8478 (mttm) cc_final: 0.8024 (mtpp)
REVERT: G  112 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8593 (mm-40)
REVERT: H   59 MET cc_start: 0.8313 (tpt) cc_final: 0.8067 (tmm)
REVERT: H   93 GLU cc_start: 0.8658 (mp0) cc_final: 0.8019 (mp0)
REVERT: K   55 MET cc_start: -0.1428 (mmp) cc_final: -0.1631 (mmt)
REVERT: K   71 MET cc_start: 0.6260 (mmm) cc_final: 0.5440 (mmm)
REVERT: K  108 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7244 (tpt170)
REVERT: K  147 MET cc_start: 0.6525 (tmm) cc_final: 0.5855 (mtp)
REVERT: K  157 ASP cc_start: 0.2438 (OUTLIER) cc_final: 0.1855 (t70)
REVERT: K  212 LYS cc_start: 0.2503 (tptt) cc_final: 0.2053 (tptp)
  outliers start: 44
  outliers final: 34
  residues processed: 243
  average time/residue: 0.1340
  time to fit residues: 46.0738
Evaluate side-chains
  241 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 205
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   58 LEU
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   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   80 THR
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain K residue   74 LEU
Chi-restraints excluded: chain K residue  157 ASP
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:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 69 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 131 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  68 GLN
H  67 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 = 0.3974 r_free = 0.3974 target = 0.127638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089534 restraints weight = 42898.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.087535 restraints weight = 36451.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088429 restraints weight = 28603.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.088400 restraints weight = 25009.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.088476 restraints weight = 21238.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  16003  Z= 0.248
  Angle     :  0.656   8.818  22877  Z= 0.369
  Chirality :  0.039   0.154   2589
  Planarity :  0.004   0.039   1901
  Dihedral  : 30.103 172.809   4439
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.61 %
    Favored  : 76.73 %
  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: -0.39 (0.25), residues: 1129
  helix:  0.23 (0.21), residues: 631
  sheet: -1.23 (0.57), residues: 80
  loop : -0.60 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 231 
 TYR   0.021   0.002   TYR F  88 
 PHE   0.017   0.002   PHE L  45 
 TRP   0.026   0.002   TRP K 228 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (16003)
  covalent geometry    : angle       0.65561 (22877)
  hydrogen bonds       : bond        0.07858 (  637)
  hydrogen bonds       : angle       3.84627 ( 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
  257 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 221
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   92 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7994 (tm-30)
REVERT: C  110 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7775 (p0)
REVERT: D   86 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7784 (mtm-85)
REVERT: D   87 SER cc_start: 0.8855 (m) cc_final: 0.8485 (t)
REVERT: E   90 MET cc_start: 0.8080 (mmp) cc_final: 0.7850 (mmt)
REVERT: G   75 LYS cc_start: 0.8528 (mttm) cc_final: 0.8022 (mtpp)
REVERT: G   99 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7506 (mmm160)
REVERT: G  112 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8666 (mm-40)
REVERT: H   90 THR cc_start: 0.9309 (p) cc_final: 0.8820 (t)
REVERT: H   93 GLU cc_start: 0.8610 (mp0) cc_final: 0.8106 (mp0)
REVERT: K   71 MET cc_start: 0.6365 (mmm) cc_final: 0.5587 (mmm)
REVERT: K  108 ARG cc_start: 0.7587 (ttm110) cc_final: 0.7072 (tpt170)
REVERT: K  147 MET cc_start: 0.6568 (tmm) cc_final: 0.5706 (mtp)
REVERT: K  197 THR cc_start: 0.4234 (OUTLIER) cc_final: 0.3880 (p)
REVERT: K  212 LYS cc_start: 0.2499 (tptt) cc_final: 0.2123 (tptp)
  outliers start: 36
  outliers final: 29
  residues processed: 239
  average time/residue: 0.1376
  time to fit residues: 46.3200
Evaluate side-chains
  238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   82 THR
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 C residue  115 LEU
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 E residue   60 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain K residue  197 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 114 optimal weight:    0.0670
   chunk 127 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
E  68 GLN
** 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 = 0.3986 r_free = 0.3986 target = 0.128448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.093674 restraints weight = 43395.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093471 restraints weight = 34368.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.093589 restraints weight = 34048.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093673 restraints weight = 28006.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.093724 restraints weight = 25669.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  16003  Z= 0.204
  Angle     :  0.628   8.483  22877  Z= 0.355
  Chirality :  0.038   0.156   2589
  Planarity :  0.004   0.037   1901
  Dihedral  : 29.968 173.370   4439
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 19.61 %
    Favored  : 76.42 %
  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: -0.13 (0.25), residues: 1129
  helix:  0.52 (0.21), residues: 620
  sheet: -1.15 (0.58), residues: 80
  loop : -0.61 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 200 
 TYR   0.021   0.002   TYR F  88 
 PHE   0.021   0.001   PHE K 159 
 TRP   0.026   0.002   TRP K 228 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (16003)
  covalent geometry    : angle       0.62780 (22877)
  hydrogen bonds       : bond        0.07637 (  637)
  hydrogen bonds       : angle       3.68010 ( 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
  261 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 222
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7742 (mtt)
REVERT: C  110 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7890 (p0)
REVERT: D   86 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7699 (mtm-85)
REVERT: D   87 SER cc_start: 0.8758 (m) cc_final: 0.8374 (t)
REVERT: E   90 MET cc_start: 0.8054 (mmp) cc_final: 0.7810 (mmt)
REVERT: G   75 LYS cc_start: 0.8496 (mttm) cc_final: 0.7994 (mtpp)
REVERT: G  112 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8671 (mm-40)
REVERT: H   90 THR cc_start: 0.9247 (p) cc_final: 0.8613 (t)
REVERT: H   93 GLU cc_start: 0.8540 (mp0) cc_final: 0.8161 (mp0)
REVERT: K   71 MET cc_start: 0.6477 (mmm) cc_final: 0.5588 (mmm)
REVERT: K  147 MET cc_start: 0.6517 (tmm) cc_final: 0.6063 (mtt)
REVERT: K  157 ASP cc_start: 0.2285 (OUTLIER) cc_final: 0.2019 (t70)
REVERT: K  212 LYS cc_start: 0.2786 (tptt) cc_final: 0.2396 (tptp)
REVERT: L    1 MET cc_start: 0.3645 (ttt) cc_final: 0.3437 (ttt)
  outliers start: 39
  outliers final: 31
  residues processed: 241
  average time/residue: 0.1387
  time to fit residues: 47.2935
Evaluate side-chains
  248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 213
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue   82 THR
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 C residue  115 LEU
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   60 LEU
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   63 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain K residue  157 ASP
Chi-restraints excluded: chain K residue  240 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 132 optimal weight:    0.0670
   chunk 84 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 120 optimal weight:    9.9990
   chunk 9 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
C  38 ASN
E  68 GLN
H  47 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 = 0.4031 r_free = 0.4031 target = 0.131468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096541 restraints weight = 43684.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.096255 restraints weight = 32877.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.096398 restraints weight = 30616.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.096470 restraints weight = 26524.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096541 restraints weight = 24081.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16003  Z= 0.150
  Angle     :  0.589  10.072  22877  Z= 0.333
  Chirality :  0.036   0.151   2589
  Planarity :  0.003   0.039   1901
  Dihedral  : 29.525 175.318   4439
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.73 %
    Favored  : 76.22 %
  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:  0.28 (0.26), residues: 1129
  helix:  0.91 (0.22), residues: 619
  sheet: -0.82 (0.60), residues: 80
  loop : -0.56 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  33 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.024   0.001   PHE K 159 
 TRP   0.022   0.001   TRP K 228 
 HIS   0.004   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (16003)
  covalent geometry    : angle       0.58894 (22877)
  hydrogen bonds       : bond        0.07315 (  637)
  hydrogen bonds       : angle       3.33515 ( 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
  262 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8685 (mmtm)
REVERT: A  120 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7588 (mtt)
REVERT: C   38 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7864 (p0)
REVERT: C   89 ASN cc_start: 0.8202 (m-40) cc_final: 0.7997 (m-40)
REVERT: C  110 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7811 (p0)
REVERT: D   86 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7579 (mtm-85)
REVERT: D   87 SER cc_start: 0.8642 (m) cc_final: 0.8355 (t)
REVERT: D   90 THR cc_start: 0.8926 (p) cc_final: 0.8590 (t)
REVERT: E   90 MET cc_start: 0.8077 (mmp) cc_final: 0.7846 (mmt)
REVERT: G   75 LYS cc_start: 0.8541 (mttm) cc_final: 0.8083 (mtpp)
REVERT: G  112 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8670 (mm-40)
REVERT: H   90 THR cc_start: 0.9257 (p) cc_final: 0.8518 (t)
REVERT: H   93 GLU cc_start: 0.8638 (mp0) cc_final: 0.8120 (mp0)
REVERT: K   71 MET cc_start: 0.6563 (mmm) cc_final: 0.5668 (mmm)
REVERT: K  108 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6942 (tpt170)
REVERT: K  147 MET cc_start: 0.6763 (tmm) cc_final: 0.6227 (mtt)
REVERT: K  157 ASP cc_start: 0.2178 (OUTLIER) cc_final: 0.1948 (t70)
REVERT: K  203 ARG cc_start: 0.6801 (ttp-110) cc_final: 0.6519 (ptp90)
REVERT: K  212 LYS cc_start: 0.2808 (tptt) cc_final: 0.2460 (tptp)
REVERT: K  322 LEU cc_start: 0.7985 (mp) cc_final: 0.7747 (mp)
  outliers start: 30
  outliers final: 19
  residues processed: 247
  average time/residue: 0.1388
  time to fit residues: 48.4155
Evaluate side-chains
  241 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
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   38 ASN
Chi-restraints excluded: chain C residue   79 ILE
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   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   63 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain K residue  157 ASP
Chi-restraints excluded: chain K residue  240 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 119 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 104 optimal weight:    7.9990
   chunk 127 optimal weight:    0.3980
   chunk 99 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
C  38 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
E  68 GLN
H  47 GLN
H  67 ASN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.130013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094426 restraints weight = 43290.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.094154 restraints weight = 33029.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.094251 restraints weight = 30015.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.094355 restraints weight = 26182.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.094439 restraints weight = 23598.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.5527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16003  Z= 0.174
  Angle     :  0.600   8.546  22877  Z= 0.339
  Chirality :  0.037   0.156   2589
  Planarity :  0.004   0.040   1901
  Dihedral  : 29.556 174.869   4439
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.34 %
    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:  0.26 (0.25), residues: 1129
  helix:  0.85 (0.21), residues: 626
  sheet: -0.80 (0.60), residues: 80
  loop : -0.53 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  72 
 TYR   0.023   0.002   TYR H  40 
 PHE   0.025   0.001   PHE L  45 
 TRP   0.026   0.001   TRP K 228 
 HIS   0.005   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (16003)
  covalent geometry    : angle       0.60018 (22877)
  hydrogen bonds       : bond        0.07323 (  637)
  hydrogen bonds       : angle       3.44908 ( 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
  247 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7760 (mtt)
REVERT: C   89 ASN cc_start: 0.8232 (m-40) cc_final: 0.8028 (m-40)
REVERT: C  110 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7884 (p0)
REVERT: D   86 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7697 (mtm-85)
REVERT: D   87 SER cc_start: 0.8744 (m) cc_final: 0.8350 (t)
REVERT: D   90 THR cc_start: 0.8704 (p) cc_final: 0.8387 (t)
REVERT: E   90 MET cc_start: 0.8158 (mmp) cc_final: 0.7940 (mmt)
REVERT: E   94 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: G   75 LYS cc_start: 0.8514 (mttm) cc_final: 0.8010 (mtpp)
REVERT: G  112 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8703 (mm-40)
REVERT: H   83 TYR cc_start: 0.7312 (m-80) cc_final: 0.7107 (t80)
REVERT: H   90 THR cc_start: 0.9292 (p) cc_final: 0.8549 (t)
REVERT: H   93 GLU cc_start: 0.8683 (mp0) cc_final: 0.8175 (mp0)
REVERT: K   55 MET cc_start: -0.1826 (mmp) cc_final: -0.2246 (mmt)
REVERT: K   71 MET cc_start: 0.6497 (mmm) cc_final: 0.5577 (mmm)
REVERT: K  108 ARG cc_start: 0.7367 (ttm110) cc_final: 0.7035 (tpt170)
REVERT: K  147 MET cc_start: 0.6532 (tmm) cc_final: 0.6101 (mtt)
REVERT: K  157 ASP cc_start: 0.2235 (OUTLIER) cc_final: 0.1980 (t70)
REVERT: K  322 LEU cc_start: 0.8045 (mp) cc_final: 0.7786 (mp)
  outliers start: 29
  outliers final: 22
  residues processed: 233
  average time/residue: 0.1355
  time to fit residues: 44.7587
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  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
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   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   80 LEU
Chi-restraints excluded: chain D residue   86 ARG
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   63 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain K residue  157 ASP
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  275 LEU
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:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
D  95 GLN
E  68 GLN
** 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 = 0.4017 r_free = 0.4017 target = 0.130485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.094859 restraints weight = 42767.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.094364 restraints weight = 32306.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.094495 restraints weight = 29226.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094582 restraints weight = 25072.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.094582 restraints weight = 23499.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.5701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16003  Z= 0.166
  Angle     :  0.592   8.233  22877  Z= 0.335
  Chirality :  0.036   0.156   2589
  Planarity :  0.004   0.040   1901
  Dihedral  : 29.432 175.193   4439
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.65 %
    Favored  : 75.61 %
  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:  0.23 (0.25), residues: 1129
  helix:  0.88 (0.21), residues: 632
  sheet: -0.79 (0.59), residues: 80
  loop : -0.65 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  72 
 TYR   0.021   0.002   TYR H  40 
 PHE   0.025   0.001   PHE L  45 
 TRP   0.023   0.001   TRP K 228 
 HIS   0.005   0.001   HIS K 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (16003)
  covalent geometry    : angle       0.59217 (22877)
  hydrogen bonds       : bond        0.07245 (  637)
  hydrogen bonds       : angle       3.40835 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2419.22 seconds
wall clock time: 42 minutes 21.00 seconds (2541.00 seconds total)