Starting phenix.real_space_refine
on Fri Mar  6 18:55:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o5h_12736/03_2026/7o5h_12736.cif"
  }
  resolution = 3.1
  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=   0.006
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: 6
    Type Number    sf(0)   Gaussians
     P     964      5.49       5
     Mg    167      5.21       5
     S      59      5.16       5
     C   17729      2.51       5
     N    6377      2.21       5
     O    9140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 34436
  Number of models: 1
  Model: ""
    Number of chains: 22
    Chain: "V"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1955
          Classifications: {'peptide': 251}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 231}
    Chain: "A"
      Number of atoms: 20726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 964, 20726
          Classifications: {'RNA': 964}
          Modifications used: {'rna2p_pur': 78, 'rna2p_pyr': 44, 'rna3p_pur': 485, 'rna3p_pyr': 357}
          Link IDs: {'rna2p': 121, 'rna3p': 842}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1760
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 7, 'TRANS': 217}
    Chain: "D"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1643
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 198}
    Chain: "E"
      Number of atoms: 1165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1165
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 5, 'TRANS': 152}
    Chain: "F"
      Number of atoms: 839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 839
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 979
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "K"
      Number of atoms: 877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 877
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
    Chain: "L"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 955
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 115}
    Chain: "O"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 702
          Classifications: {'peptide': 87}
          Link IDs: {'TRANS': 86}
    Chain: "P"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 641
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 2, 'TRANS': 76}
    Chain: "R"
      Number of atoms: 456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 456
          Classifications: {'peptide': 55}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "T"
      Number of atoms: 670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 670
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "U"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 252
          Classifications: {'peptide': 30}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
    Chain: "A"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 161
          Unusual residues: {' MG': 161}
          Classifications: {'undetermined': 161}
          Link IDs: {None: 160}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "U"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  29871  SG  CYS K 121      97.455  45.225 110.621  1.00 55.55           S

  Time building chain proxies: 6.80, per 1000 atoms: 0.20
  Number of scatterers: 34436
  At special positions: 0
  Unit cell: (168.19, 191.82, 159.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      59     16.00
     P     964     15.00
     Mg    167     11.99
     O    9140      8.00
     N    6377      7.00
     C   17729      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: 2.44
  Conformation dependent library (CDL) restraints added in 820.4 milliseconds
  

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3214

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 15 sheets defined
      46.6% alpha, 18.9% beta
      317 base pairs and 590 stacking pairs defined.
    Time for finding SS restraints: 5.57
  Creating SS restraints...
    Processing helix  chain 'V' and resid 22 through 34
    Processing helix  chain 'V' and resid 51 through 56
      removed outlier: 3.846A  pdb=" N   VAL V  55 " --> pdb=" O   LEU V  51 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 68 through 77
    Processing helix  chain 'V' and resid 96 through 105
      removed outlier: 4.495A  pdb=" N   LEU V 100 " --> pdb=" O   ASN V  96 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA V 101 " --> pdb=" O   PHE V  97 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU V 102 " --> pdb=" O   GLY V  98 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 115 through 128
      removed outlier: 4.439A  pdb=" N   THR V 120 " --> pdb=" O   TYR V 116 " (cutoff:3.500A)
      Proline residue:  V 121  - end of helix
    Processing helix  chain 'V' and resid 141 through 150
    Processing helix  chain 'V' and resid 158 through 167
      removed outlier: 4.308A  pdb=" N   TYR V 167 " --> pdb=" O   MET V 163 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 177 through 179
      No H-bonds generated for 'chain 'V' and resid 177 through 179'
    Processing helix  chain 'V' and resid 206 through 218
    Processing helix  chain 'V' and resid 219 through 221
      No H-bonds generated for 'chain 'V' and resid 219 through 221'
    Processing helix  chain 'V' and resid 224 through 229
    Processing helix  chain 'V' and resid 234 through 241
    Processing helix  chain 'V' and resid 248 through 252
    Processing helix  chain 'V' and resid 253 through 268
    Processing helix  chain 'B' and resid 5 through 13
    Processing helix  chain 'B' and resid 24 through 29
      Proline residue:  B  29  - end of helix
    Processing helix  chain 'B' and resid 42 through 63
      removed outlier: 3.587A  pdb=" N   THR B  46 " --> pdb=" O   ASN B  42 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      Proline residue:  B  48  - end of helix
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 4.359A  pdb=" N   GLU B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B  85 " --> pdb=" O   LYS B  81 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER B  86 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 123
      removed outlier: 3.621A  pdb=" N   SER B 121 " --> pdb=" O   LEU B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 149
    Processing helix  chain 'B' and resid 150 through 152
      No H-bonds generated for 'chain 'B' and resid 150 through 152'
    Processing helix  chain 'B' and resid 169 through 180
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.626A  pdb=" N   GLY B 195 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 227
      removed outlier: 3.762A  pdb=" N   THR B 220 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLN B 227 " --> pdb=" O   GLU B 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 16
      removed outlier: 4.207A  pdb=" N   LEU D  11 " --> pdb=" O   PRO D   7 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER D  12 " --> pdb=" O   LYS D   8 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 27 through 32
      removed outlier: 3.778A  pdb=" N   LYS D  31 " --> pdb=" O   ALA D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 43
      removed outlier: 4.456A  pdb=" N   ALA D  43 " --> pdb=" O   GLN D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 66
    Processing helix  chain 'D' and resid 68 through 82
    Processing helix  chain 'D' and resid 85 through 96
    Processing helix  chain 'D' and resid 97 through 105
    Processing helix  chain 'D' and resid 110 through 120
    Processing helix  chain 'D' and resid 147 through 150
    Processing helix  chain 'D' and resid 152 through 165
      removed outlier: 3.752A  pdb=" N   LYS D 156 " --> pdb=" O   GLN D 152 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU D 160 " --> pdb=" O   LYS D 156 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU D 161 " --> pdb=" O   ALA D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 206
    Processing helix  chain 'E' and resid 55 through 69
      removed outlier: 3.597A  pdb=" N   ARG E  69 " --> pdb=" O   GLU E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 119
      removed outlier: 3.676A  pdb=" N   ALA E 113 " --> pdb=" O   GLY E 109 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 132 through 146
      removed outlier: 3.712A  pdb=" N   ASN E 146 " --> pdb=" O   ASP E 142 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 149 through 157
    Processing helix  chain 'E' and resid 160 through 165
    Processing helix  chain 'F' and resid 12 through 16
      removed outlier: 4.934A  pdb=" N   GLU F  16 " --> pdb=" O   ASP F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 32
      removed outlier: 3.518A  pdb=" N   ARG F  24 " --> pdb=" O   GLY F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 80
      removed outlier: 3.551A  pdb=" N   ILE F  71 " --> pdb=" O   PRO F  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 5 through 20
      removed outlier: 3.524A  pdb=" N   ASP H   9 " --> pdb=" O   ASP H   5 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 44
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'H' and resid 94 through 99
      removed outlier: 3.679A  pdb=" N   ALA H  97 " --> pdb=" O   LYS H  94 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 113 through 120
    Processing helix  chain 'K' and resid 48 through 51
      removed outlier: 3.879A  pdb=" N   GLY K  51 " --> pdb=" O   GLY K  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 48 through 51'
    Processing helix  chain 'K' and resid 59 through 75
      removed outlier: 3.615A  pdb=" N   ALA K  63 " --> pdb=" O   THR K  59 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLU K  68 " --> pdb=" O   GLN K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 76 through 78
      No H-bonds generated for 'chain 'K' and resid 76 through 78'
    Processing helix  chain 'K' and resid 92 through 103
      removed outlier: 3.574A  pdb=" N   THR K  96 " --> pdb=" O   GLY K  92 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE K  97 " --> pdb=" O   ARG K  93 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 3 through 10
    Processing helix  chain 'L' and resid 113 through 117
    Processing helix  chain 'O' and resid 4 through 16
    Processing helix  chain 'O' and resid 24 through 46
      removed outlier: 4.263A  pdb=" N   GLY O  41 " --> pdb=" O   ASN O  37 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   HIS O  42 " --> pdb=" O   HIS O  38 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 74
      removed outlier: 3.750A  pdb=" N   GLY O  55 " --> pdb=" O   HIS O  51 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 74 through 86
    Processing helix  chain 'P' and resid 53 through 63
    Processing helix  chain 'P' and resid 68 through 82
    Processing helix  chain 'Q' and resid 49 through 52
      removed outlier: 3.929A  pdb=" N   GLU Q  52 " --> pdb=" O   GLU Q  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Q' and resid 49 through 52'
    Processing helix  chain 'R' and resid 25 through 31
      removed outlier: 3.805A  pdb=" N   ASN R  31 " --> pdb=" O   ALA R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 46
      removed outlier: 3.587A  pdb=" N   THR R  45 " --> pdb=" O   PRO R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 48 through 65
    Processing helix  chain 'T' and resid 4 through 42
      removed outlier: 3.506A  pdb=" N   ARG T  24 " --> pdb=" O   HIS T  20 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 43 through 64
      removed outlier: 3.622A  pdb=" N   ALA T  47 " --> pdb=" O   ASP T  43 " (cutoff:3.500A)
      Proline residue:  T  56  - end of helix
    Processing helix  chain 'T' and resid 68 through 87
    Processing helix  chain 'U' and resid 29 through 36
      removed outlier: 3.578A  pdb=" N   ARG U  33 " --> pdb=" O   LEU U  29 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ARG U  34 " --> pdb=" O   ALA U  30 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 40 through 55
    Processing sheet with id=AA1, first strand: chain 'V' and resid 19 through 20
    Processing sheet with id=AA2, first strand: chain 'V' and resid 85 through 89
      removed outlier: 3.546A  pdb=" N   PHE V 111 " --> pdb=" O   VAL V  42 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE V  44 " --> pdb=" O   PHE V 111 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU V 108 " --> pdb=" O   ASP V 135 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   HIS V 137 " --> pdb=" O   LEU V 108 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL V 110 " --> pdb=" O   HIS V 137 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   MET V 139 " --> pdb=" O   VAL V 110 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ALA V 134 " --> pdb=" O   PRO V 196 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ARG V 193 " --> pdb=" O   PRO V 172 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   VAL V 195 " --> pdb=" O   VAL V 170 " (cutoff:3.500A)
      removed outlier: 5.599A  pdb=" N   VAL V 170 " --> pdb=" O   VAL V 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19
      removed outlier: 5.552A  pdb=" N   PHE B  16 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ILE B  41 " --> pdb=" O   PHE B  16 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   HIS B  18 " --> pdb=" O   HIS B  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92
      removed outlier: 6.268A  pdb=" N   LEU B  68 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   ILE B 164 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   VAL B  70 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   VAL B 183 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   ILE B 200 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ALA B 185 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 129
      removed outlier: 3.849A  pdb=" N   ASP D 141 " --> pdb=" O   PHE D 182 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 24
      removed outlier: 5.001A  pdb=" N   GLU E  13 " --> pdb=" O   GLY E  40 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   GLY E  40 " --> pdb=" O   GLU E  13 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   LEU E  15 " --> pdb=" O   VAL E  38 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL E  38 " --> pdb=" O   LEU E  15 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 88
      removed outlier: 6.465A  pdb=" N   ILE E 106 " --> pdb=" O   ALA E 125 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   ALA E 127 " --> pdb=" O   ILE E 106 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 51
      removed outlier: 5.000A  pdb=" N   ILE F  36 " --> pdb=" O   GLU F  65 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   GLU F  65 " --> pdb=" O   ILE F  36 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG F  38 " --> pdb=" O   ASN F  63 " (cutoff:3.500A)
      removed outlier: 5.488A  pdb=" N   TYR F  59 " --> pdb=" O   TRP F  42 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ARG F  44 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ALA F  57 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   GLN F  46 " --> pdb=" O   HIS F  55 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   HIS F  55 " --> pdb=" O   GLN F  46 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   HIS F   3 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   ARG F  86 " --> pdb=" O   MET F   9 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28
    Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77
    Processing sheet with id=AB2, first strand: chain 'H' and resid 74 through 77
      removed outlier: 6.845A  pdb=" N   VAL H 103 " --> pdb=" O   ILE H 126 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   TYR H 128 " --> pdb=" O   ILE H 101 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   ILE H 101 " --> pdb=" O   TYR H 128 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 41 through 46
      removed outlier: 6.681A  pdb=" N   ILE K  34 " --> pdb=" O   LEU K  42 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   TRP K  44 " --> pdb=" O   VAL K  32 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   VAL K  32 " --> pdb=" O   TRP K  44 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   THR K  46 " --> pdb=" O   THR K  30 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   THR K  30 " --> pdb=" O   THR K  46 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU K  82 " --> pdb=" O   ILE K 107 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASN K 109 " --> pdb=" O   LEU K  82 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 62 through 66
      removed outlier: 3.545A  pdb=" N   ARG L  36 " --> pdb=" O   ARG L  54 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ARG L  56 " --> pdb=" O   CYS L  34 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   CYS L  34 " --> pdb=" O   ARG L  56 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS L  30 " --> pdb=" O   ILE L  82 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   SER L  78 " --> pdb=" O   CYS L  34 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'P' and resid 50 through 52
      removed outlier: 6.638A  pdb=" N   VAL P  19 " --> pdb=" O   VAL P  36 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   PHE P  38 " --> pdb=" O   TYR P  17 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TYR P  17 " --> pdb=" O   PHE P  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'Q' and resid 8 through 14
      removed outlier: 7.521A  pdb=" N   GLN Q   9 " --> pdb=" O   GLU Q  26 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   GLU Q  26 " --> pdb=" O   GLN Q   9 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL Q  22 " --> pdb=" O   VAL Q  13 " (cutoff:3.500A)
      removed outlier: 9.476A  pdb=" N   LYS Q  71 " --> pdb=" O   LYS Q  43 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   HIS Q  45 " --> pdb=" O   LYS Q  71 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   TRP Q  73 " --> pdb=" O   HIS Q  45 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU Q  75 " --> pdb=" O   HIS Q  47 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   LEU Q  75 " --> pdb=" O   ARG Q  62 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   ARG Q  62 " --> pdb=" O   LEU Q  75 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG Q  77 " --> pdb=" O   GLU Q  60 " (cutoff:3.500A)

    666 hydrogen bonds defined for protein.
    1899 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      778 hydrogen bonds
      1242 hydrogen bond angles
      0 basepair planarities
      317 basepair parallelities
      590 stacking parallelities
  Total time for adding SS restraints: 12.86

  Time building geometry restraints manager: 3.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 6692
        1.33 -     1.45: 13488
        1.45 -     1.57: 14758
        1.57 -     1.69: 1920
        1.69 -     1.81: 105
  Bond restraints: 36963
  Sorted by residual:
  bond pdb=" C3'   A A 411 "
       pdb=" O3'   A A 411 "
    ideal  model  delta    sigma   weight residual
    1.427  1.445 -0.018 1.50e-02 4.44e+03 1.37e+00
  bond pdb=" CA  VAL F  18 "
       pdb=" CB  VAL F  18 "
    ideal  model  delta    sigma   weight residual
    1.539  1.545 -0.006 5.40e-03 3.43e+04 1.21e+00
  bond pdb=" CA  VAL B  47 "
       pdb=" CB  VAL B  47 "
    ideal  model  delta    sigma   weight residual
    1.539  1.544 -0.005 5.40e-03 3.43e+04 1.03e+00
  bond pdb=" C   VAL V 110 "
       pdb=" N   PHE V 111 "
    ideal  model  delta    sigma   weight residual
    1.333  1.345 -0.012 1.30e-02 5.92e+03 8.83e-01
  bond pdb=" CA  VAL H  72 "
       pdb=" CB  VAL H  72 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 6.75e-01
  ... (remaining 36958 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 54042
        1.07 -     2.13: 525
        2.13 -     3.20: 100
        3.20 -     4.26: 30
        4.26 -     5.33: 10
  Bond angle restraints: 54707
  Sorted by residual:
  angle pdb=" C3'   A A 411 "
        pdb=" O3'   A A 411 "
        pdb=" P     A A 412 "
      ideal   model   delta    sigma   weight residual
     120.20  125.15   -4.95 1.50e+00 4.44e-01 1.09e+01
  angle pdb=" C4'   A A 411 "
        pdb=" C3'   A A 411 "
        pdb=" O3'   A A 411 "
      ideal   model   delta    sigma   weight residual
     109.40  113.03   -3.63 1.50e+00 4.44e-01 5.84e+00
  angle pdb=" O3'   A A 411 "
        pdb=" C3'   A A 411 "
        pdb=" C2'   A A 411 "
      ideal   model   delta    sigma   weight residual
     109.50  113.02   -3.52 1.50e+00 4.44e-01 5.50e+00
  angle pdb=" C3'   C A1107 "
        pdb=" O3'   C A1107 "
        pdb=" P     G A1108 "
      ideal   model   delta    sigma   weight residual
     120.20  123.42   -3.22 1.50e+00 4.44e-01 4.60e+00
  angle pdb=" O3'   C A1107 "
        pdb=" C3'   C A1107 "
        pdb=" C2'   C A1107 "
      ideal   model   delta    sigma   weight residual
     113.70  116.70   -3.00 1.50e+00 4.44e-01 4.01e+00
  ... (remaining 54702 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 21079
       35.58 -    71.16: 2239
       71.16 -   106.74: 250
      106.74 -   142.32: 0
      142.32 -   177.89: 7
  Dihedral angle restraints: 23575
    sinusoidal: 18602
      harmonic: 4973
  Sorted by residual:
  dihedral pdb=" O4'   U A 365 "
           pdb=" C1'   U A 365 "
           pdb=" N1    U A 365 "
           pdb=" C2    U A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.36  146.64     1      1.50e+01 4.44e-03 7.83e+01
  dihedral pdb=" O4'   C A 754 "
           pdb=" C1'   C A 754 "
           pdb=" N1    C A 754 "
           pdb=" C2    C A 754 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   57.36  142.64     1      1.50e+01 4.44e-03 7.66e+01
  dihedral pdb=" O4'   C A 183 "
           pdb=" C1'   C A 183 "
           pdb=" N1    C A 183 "
           pdb=" C2    C A 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.11  177.89     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 23572 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 6324
       0.041 -    0.081: 399
       0.081 -    0.122: 163
       0.122 -    0.163: 12
       0.163 -    0.204: 1
  Chirality restraints: 6899
  Sorted by residual:
  chirality pdb=" C3'   A A 411 "
            pdb=" C4'   A A 411 "
            pdb=" O3'   A A 411 "
            pdb=" C2'   A A 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.54   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C3'   C A1107 "
            pdb=" C4'   C A1107 "
            pdb=" O3'   C A1107 "
            pdb=" C2'   C A1107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" C1'   U A 365 "
            pdb=" O4'   U A 365 "
            pdb=" C2'   U A 365 "
            pdb=" N1    U A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.31    0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 6896 not shown)

  Planarity restraints: 3369
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L  44 "   -0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO L  45 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO L  45 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L  45 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 138 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO D 139 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO D 139 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 139 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  80 "    0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO H  81 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO H  81 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H  81 "    0.016 5.00e-02 4.00e+02
  ... (remaining 3366 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 4
        1.99 -     2.72: 2835
        2.72 -     3.44: 46149
        3.44 -     4.17: 112281
        4.17 -     4.90: 155292
  Nonbonded interactions: 316561
  Sorted by model distance:
  nonbonded pdb="MG    MG A1632 "
            pdb="MG    MG A1696 "
     model   vdw
     1.262 1.300
  nonbonded pdb=" OP1   C A 504 "
            pdb="MG    MG A1725 "
     model   vdw
     1.933 2.170
  nonbonded pdb=" OP2   A A 195 "
            pdb="MG    MG A1642 "
     model   vdw
     1.976 2.170
  nonbonded pdb=" OP1   A A  59 "
            pdb="MG    MG A1621 "
     model   vdw
     1.983 2.170
  nonbonded pdb=" O4'   G A 713 "
            pdb="MG    MG A1708 "
     model   vdw
     2.009 2.170
  ... (remaining 316556 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.110
  Set scattering table:                    0.080
  Process input model:                     38.450
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
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      :  0.002   0.035  36963  Z= 0.095
  Angle     :  0.328   5.327  54707  Z= 0.176
  Chirality :  0.025   0.204   6899
  Planarity :  0.003   0.030   3369
  Dihedral  : 21.625 177.894  20361
  Min Nonbonded Distance : 1.262

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  3.07 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  1.09 (0.21), residues: 1702
  helix:  1.77 (0.20), residues: 682
  sheet:  0.14 (0.31), residues: 301
  loop :  0.07 (0.24), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R  63 
 TYR   0.007   0.001   TYR L  95 
 PHE   0.008   0.001   PHE V 111 
 TRP   0.007   0.001   TRP B  23 
 HIS   0.003   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 (36963)
  covalent geometry    : angle       0.32847 (54707)
  hydrogen bonds       : bond        0.22658 ( 1440)
  hydrogen bonds       : angle       8.55959 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 413
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   23 GLN cc_start: 0.6955 (tp40) cc_final: 0.6617 (tp-100)
REVERT: V   44 ILE cc_start: 0.6889 (mm) cc_final: 0.6495 (mt)
REVERT: V   48 LEU cc_start: 0.8249 (tp) cc_final: 0.7819 (tt)
REVERT: V  170 VAL cc_start: 0.8201 (t) cc_final: 0.7934 (p)
REVERT: V  257 TYR cc_start: 0.8370 (m-80) cc_final: 0.8024 (m-80)
REVERT: B  147 SER cc_start: 0.8068 (m) cc_final: 0.7784 (p)
REVERT: B  168 HIS cc_start: 0.7716 (t-90) cc_final: 0.6926 (t-90)
REVERT: B  170 HIS cc_start: 0.8659 (p-80) cc_final: 0.8294 (p-80)
REVERT: D   47 ARG cc_start: 0.6536 (mtt180) cc_final: 0.6311 (mtm-85)
REVERT: E  116 GLU cc_start: 0.6870 (tt0) cc_final: 0.6591 (tt0)
REVERT: E  145 GLU cc_start: 0.7349 (pp20) cc_final: 0.7081 (pp20)
REVERT: F   96 VAL cc_start: 0.8140 (m) cc_final: 0.7508 (m)
REVERT: H  114 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7674 (ttm170)
REVERT: O    6 GLU cc_start: 0.8143 (mp0) cc_final: 0.7850 (mp0)
REVERT: O   72 ARG cc_start: 0.6869 (ttp-110) cc_final: 0.6655 (ttm110)
REVERT: Q    9 GLN cc_start: 0.8117 (mt0) cc_final: 0.7849 (mt0)
REVERT: Q   43 LYS cc_start: 0.7529 (mtmt) cc_final: 0.7290 (mtpp)
REVERT: R   50 LYS cc_start: 0.8749 (tttt) cc_final: 0.8200 (ttmm)
REVERT: R   54 GLN cc_start: 0.7912 (mt0) cc_final: 0.7653 (mt0)
REVERT: T   28 MET cc_start: 0.8072 (ttp) cc_final: 0.7750 (ptm)
  outliers start: 14
  outliers final: 4
  residues processed: 427
  average time/residue: 0.2731
  time to fit residues: 174.8101
Evaluate side-chains
  299 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 295
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain F residue   36 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 197 optimal weight:    2.9990
   chunk 215 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 261 optimal weight:    0.9990
   chunk 248 optimal weight:    3.9990
   chunk 207 optimal weight:    0.9990
   chunk 155 optimal weight:    7.9990
   chunk 244 optimal weight:    0.9980
   chunk 183 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
V  78 HIS
V  90 GLN
** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
B  19 GLN
B  36 ASN
** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  52 ASN
K  15 GLN
K  64 GLN
L   5 ASN
O  62 GLN
P  18 GLN
** R  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T   3 ASN
T  20 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.064296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.051293 restraints weight = 140904.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.37
r_work: 0.2948 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  36963  Z= 0.167
  Angle     :  0.552   8.493  54707  Z= 0.283
  Chirality :  0.034   0.228   6899
  Planarity :  0.004   0.045   3369
  Dihedral  : 22.916 178.126  16988
  Min Nonbonded Distance : 1.173

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.92 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  1.02 (0.21), residues: 1702
  helix:  1.66 (0.20), residues: 694
  sheet:  0.24 (0.32), residues: 299
  loop : -0.01 (0.24), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K  69 
 TYR   0.013   0.001   TYR O  78 
 PHE   0.017   0.001   PHE K  61 
 TRP   0.010   0.001   TRP P  60 
 HIS   0.003   0.001   HIS V 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (36963)
  covalent geometry    : angle       0.55240 (54707)
  hydrogen bonds       : bond        0.06008 ( 1440)
  hydrogen bonds       : angle       4.07312 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 331
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   23 GLN cc_start: 0.7198 (tp40) cc_final: 0.6965 (tp-100)
REVERT: V   44 ILE cc_start: 0.6746 (mm) cc_final: 0.6341 (mt)
REVERT: V   48 LEU cc_start: 0.8158 (tp) cc_final: 0.7831 (tt)
REVERT: V  142 LYS cc_start: 0.7712 (tppt) cc_final: 0.7508 (tppt)
REVERT: V  170 VAL cc_start: 0.8313 (t) cc_final: 0.8031 (p)
REVERT: B  113 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7680 (tpt170)
REVERT: B  168 HIS cc_start: 0.7723 (t-90) cc_final: 0.6959 (t-90)
REVERT: E  142 ASP cc_start: 0.7446 (m-30) cc_final: 0.7144 (m-30)
REVERT: F   81 ASN cc_start: 0.7997 (t0) cc_final: 0.7793 (t0)
REVERT: Q    9 GLN cc_start: 0.8660 (mt0) cc_final: 0.8369 (mt0)
REVERT: Q   48 ASP cc_start: 0.8206 (t0) cc_final: 0.7883 (t70)
REVERT: R   50 LYS cc_start: 0.8884 (tttt) cc_final: 0.8451 (ttmm)
REVERT: T   39 ILE cc_start: 0.9010 (tp) cc_final: 0.8525 (mm)
REVERT: T   54 MET cc_start: 0.8459 (ttp) cc_final: 0.8132 (ttp)
REVERT: T   79 LEU cc_start: 0.8076 (mt) cc_final: 0.7603 (mt)
  outliers start: 31
  outliers final: 19
  residues processed: 349
  average time/residue: 0.2611
  time to fit residues: 137.3340
Evaluate side-chains
  307 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 288
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain F residue   36 ILE
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain K residue   20 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   10 LYS
Chi-restraints excluded: chain O residue   18 ASP
Chi-restraints excluded: chain R residue   42 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 227 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 141 optimal weight:   10.0000
   chunk 160 optimal weight:    0.3980
   chunk 80 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 144 optimal weight:    7.9990
   chunk 223 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** V  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
B  36 ASN
** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 109 ASN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  61 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.062486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.049335 restraints weight = 141286.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.43
r_work: 0.2887 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  36963  Z= 0.309
  Angle     :  0.649   8.302  54707  Z= 0.331
  Chirality :  0.039   0.233   6899
  Planarity :  0.005   0.049   3369
  Dihedral  : 23.052 176.353  16988
  Min Nonbonded Distance : 1.066

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.38 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.51 (0.20), residues: 1702
  helix:  1.28 (0.19), residues: 696
  sheet:  0.03 (0.32), residues: 282
  loop : -0.36 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  63 
 TYR   0.018   0.002   TYR V 157 
 PHE   0.012   0.002   PHE V 124 
 TRP   0.020   0.003   TRP B  23 
 HIS   0.006   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (36963)
  covalent geometry    : angle       0.64854 (54707)
  hydrogen bonds       : bond        0.06382 ( 1440)
  hydrogen bonds       : angle       4.06392 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 292
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   44 ILE cc_start: 0.6780 (mm) cc_final: 0.6398 (mt)
REVERT: V   48 LEU cc_start: 0.8220 (tp) cc_final: 0.7911 (tt)
REVERT: B   96 TRP cc_start: 0.8366 (t-100) cc_final: 0.8013 (t-100)
REVERT: B  168 HIS cc_start: 0.7735 (t-90) cc_final: 0.7281 (t-90)
REVERT: E  142 ASP cc_start: 0.7420 (m-30) cc_final: 0.7085 (m-30)
REVERT: F   75 GLU cc_start: 0.8183 (pp20) cc_final: 0.7965 (pp20)
REVERT: F   81 ASN cc_start: 0.8318 (t0) cc_final: 0.7955 (t0)
REVERT: O   48 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8453 (mtmm)
REVERT: Q    5 ILE cc_start: 0.8789 (pt) cc_final: 0.8344 (pt)
REVERT: Q   18 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: T   39 ILE cc_start: 0.8956 (tp) cc_final: 0.8609 (mm)
REVERT: T   54 MET cc_start: 0.8356 (ttp) cc_final: 0.8092 (ttp)
REVERT: T   79 LEU cc_start: 0.8175 (mt) cc_final: 0.7850 (mt)
  outliers start: 53
  outliers final: 48
  residues processed: 319
  average time/residue: 0.2497
  time to fit residues: 122.8370
Evaluate side-chains
  312 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 264
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   25 VAL
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   36 ILE
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   54 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   78 PHE
Chi-restraints excluded: chain F residue   82 ASP
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   10 MET
Chi-restraints excluded: chain H residue   26 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain K residue   20 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain O residue   18 ASP
Chi-restraints excluded: chain P residue   66 THR
Chi-restraints excluded: chain Q residue    8 LEU
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   81 LYS
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain R residue   44 ILE
Chi-restraints excluded: chain T residue   28 MET
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Chi-restraints excluded: chain T residue   83 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 250 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 255 optimal weight:    3.9990
   chunk 94 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 260 optimal weight:    2.9990
   chunk 203 optimal weight:    9.9990
   chunk 202 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** V  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
B  36 ASN
B 120 GLN
K  64 GLN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** 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 = 0.3419 r_free = 0.3419 target = 0.062755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.049679 restraints weight = 140210.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.40
r_work: 0.2897 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  36963  Z= 0.270
  Angle     :  0.611   8.084  54707  Z= 0.314
  Chirality :  0.038   0.233   6899
  Planarity :  0.005   0.048   3369
  Dihedral  : 23.065 176.941  16988
  Min Nonbonded Distance : 1.090

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 12.92 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.45 (0.20), residues: 1702
  helix:  1.30 (0.20), residues: 695
  sheet: -0.05 (0.31), residues: 286
  loop : -0.47 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG V 208 
 TYR   0.029   0.002   TYR V 157 
 PHE   0.012   0.002   PHE O  43 
 TRP   0.016   0.002   TRP B  23 
 HIS   0.007   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (36963)
  covalent geometry    : angle       0.61095 (54707)
  hydrogen bonds       : bond        0.05741 ( 1440)
  hydrogen bonds       : angle       3.98817 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 281
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   44 ILE cc_start: 0.6743 (mm) cc_final: 0.6328 (mt)
REVERT: V   48 LEU cc_start: 0.8192 (tp) cc_final: 0.7875 (tt)
REVERT: V  142 LYS cc_start: 0.7759 (tppt) cc_final: 0.7555 (tppt)
REVERT: V  157 TYR cc_start: 0.7948 (t80) cc_final: 0.7599 (t80)
REVERT: B   90 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5606 (m-10)
REVERT: B   96 TRP cc_start: 0.8337 (t-100) cc_final: 0.7955 (t-100)
REVERT: B  113 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7171 (tpm170)
REVERT: B  168 HIS cc_start: 0.7752 (t-90) cc_final: 0.7179 (t-90)
REVERT: E  142 ASP cc_start: 0.7441 (m-30) cc_final: 0.7088 (m-30)
REVERT: E  163 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: F   13 ASP cc_start: 0.7822 (m-30) cc_final: 0.7246 (t0)
REVERT: F   75 GLU cc_start: 0.8190 (pp20) cc_final: 0.7966 (pp20)
REVERT: F   81 ASN cc_start: 0.8395 (t0) cc_final: 0.8128 (t0)
REVERT: K   80 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7603 (mmmt)
REVERT: O   88 ARG cc_start: 0.7447 (mmm160) cc_final: 0.6486 (mmp80)
REVERT: Q   18 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7570 (mt-10)
REVERT: T   39 ILE cc_start: 0.8942 (tp) cc_final: 0.8571 (mm)
REVERT: T   54 MET cc_start: 0.8314 (ttp) cc_final: 0.8072 (ttp)
REVERT: T   79 LEU cc_start: 0.8084 (mt) cc_final: 0.7664 (mt)
  outliers start: 58
  outliers final: 53
  residues processed: 314
  average time/residue: 0.2426
  time to fit residues: 117.5389
Evaluate side-chains
  317 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 263
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   25 VAL
Chi-restraints excluded: chain V residue  136 MET
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   36 ILE
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   54 LEU
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   78 PHE
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   10 MET
Chi-restraints excluded: chain H residue   26 THR
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain K residue   20 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue  109 ASP
Chi-restraints excluded: chain O residue   18 ASP
Chi-restraints excluded: chain O residue   47 LYS
Chi-restraints excluded: chain P residue   53 ASP
Chi-restraints excluded: chain P residue   66 THR
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   61 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain R residue   44 ILE
Chi-restraints excluded: chain T residue   28 MET
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Chi-restraints excluded: chain T residue   83 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 231 optimal weight:    0.6980
   chunk 147 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 137 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 199 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 228 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** V  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
B  36 ASN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.063257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.050161 restraints weight = 141103.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.38
r_work: 0.2914 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  36963  Z= 0.214
  Angle     :  0.570   8.327  54707  Z= 0.295
  Chirality :  0.036   0.232   6899
  Planarity :  0.005   0.044   3369
  Dihedral  : 23.040 177.492  16988
  Min Nonbonded Distance : 1.106

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 13.97 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.48 (0.20), residues: 1702
  helix:  1.35 (0.20), residues: 696
  sheet: -0.09 (0.31), residues: 288
  loop : -0.45 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG V 208 
 TYR   0.026   0.002   TYR V 157 
 PHE   0.012   0.001   PHE B 126 
 TRP   0.012   0.002   TRP B  23 
 HIS   0.005   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (36963)
  covalent geometry    : angle       0.57048 (54707)
  hydrogen bonds       : bond        0.05299 ( 1440)
  hydrogen bonds       : angle       3.87044 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 282
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: V   44 ILE cc_start: 0.6727 (mm) cc_final: 0.6300 (mt)
REVERT: V   48 LEU cc_start: 0.8255 (tp) cc_final: 0.7870 (tt)
REVERT: V  157 TYR cc_start: 0.8092 (t80) cc_final: 0.7741 (t80)
REVERT: B   90 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5845 (m-10)
REVERT: B   94 HIS cc_start: 0.6465 (m90) cc_final: 0.6207 (m170)
REVERT: B  168 HIS cc_start: 0.7795 (t-90) cc_final: 0.7195 (t-90)
REVERT: E   14 LYS cc_start: 0.8182 (mttt) cc_final: 0.7888 (mmtt)
REVERT: E   32 SER cc_start: 0.7040 (OUTLIER) cc_final: 0.6579 (m)
REVERT: E  142 ASP cc_start: 0.7467 (m-30) cc_final: 0.7090 (m-30)
REVERT: E  163 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: F   13 ASP cc_start: 0.7937 (m-30) cc_final: 0.7419 (t0)
REVERT: F   68 GLN cc_start: 0.7662 (mp10) cc_final: 0.7447 (mp10)
REVERT: F   75 GLU cc_start: 0.8163 (pp20) cc_final: 0.7933 (pp20)
REVERT: F   81 ASN cc_start: 0.8330 (t0) cc_final: 0.8033 (t0)
REVERT: K   74 VAL cc_start: 0.8856 (t) cc_final: 0.8627 (m)
REVERT: O   88 ARG cc_start: 0.7410 (mmm160) cc_final: 0.6460 (mmp80)
REVERT: Q   18 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7642 (mt-10)
REVERT: T   39 ILE cc_start: 0.8971 (tp) cc_final: 0.8597 (mm)
REVERT: T   61 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8349 (mp-120)
REVERT: T   79 LEU cc_start: 0.8042 (mt) cc_final: 0.7566 (mt)
  outliers start: 59
  outliers final: 50
  residues processed: 316
  average time/residue: 0.2472
  time to fit residues: 120.4154
Evaluate side-chains
  317 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 264
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   25 VAL
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue   90 PHE
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain D residue    5 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   36 ILE
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   54 LEU
Chi-restraints excluded: chain F residue   78 PHE
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   10 MET
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain K residue   20 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue  109 ASP
Chi-restraints excluded: chain O residue   18 ASP
Chi-restraints excluded: chain O residue   47 LYS
Chi-restraints excluded: chain P residue   53 ASP
Chi-restraints excluded: chain P residue   66 THR
Chi-restraints excluded: chain Q residue    8 LEU
Chi-restraints excluded: chain Q residue   28 PHE
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   38 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 247 optimal weight:    3.9990
   chunk 93 optimal weight:   10.0000
   chunk 170 optimal weight:    5.9990
   chunk 140 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 244 optimal weight:    3.9990
   chunk 216 optimal weight:    3.9990
   chunk 240 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 94 optimal weight:    8.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
** V  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
B  19 GLN
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  15 GLN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** 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 = 0.3412 r_free = 0.3412 target = 0.062478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.049440 restraints weight = 140322.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 1.47
r_work: 0.2891 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  36963  Z= 0.303
  Angle     :  0.639   8.707  54707  Z= 0.328
  Chirality :  0.039   0.234   6899
  Planarity :  0.005   0.046   3369
  Dihedral  : 23.092 177.307  16988
  Min Nonbonded Distance : 1.069

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 14.73 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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 (0.20), residues: 1702
  helix:  1.19 (0.20), residues: 695
  sheet: -0.15 (0.31), residues: 284
  loop : -0.62 (0.23), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG V 208 
 TYR   0.022   0.002   TYR V 157 
 PHE   0.013   0.002   PHE E  95 
 TRP   0.018   0.002   TRP B  23 
 HIS   0.005   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (36963)
  covalent geometry    : angle       0.63940 (54707)
  hydrogen bonds       : bond        0.05934 ( 1440)
  hydrogen bonds       : angle       4.02551 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 274
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   48 LEU cc_start: 0.8252 (tp) cc_final: 0.7878 (tt)
REVERT: V  157 TYR cc_start: 0.8167 (t80) cc_final: 0.7812 (t80)
REVERT: B  168 HIS cc_start: 0.7785 (t-90) cc_final: 0.7142 (t-90)
REVERT: E  142 ASP cc_start: 0.7388 (m-30) cc_final: 0.7044 (m-30)
REVERT: F   13 ASP cc_start: 0.7871 (m-30) cc_final: 0.7275 (t0)
REVERT: F   81 ASN cc_start: 0.8359 (t0) cc_final: 0.8062 (t0)
REVERT: O    6 GLU cc_start: 0.8922 (mp0) cc_final: 0.8505 (mp0)
REVERT: O   88 ARG cc_start: 0.7383 (mmm160) cc_final: 0.6388 (mmp80)
REVERT: T   39 ILE cc_start: 0.8978 (tp) cc_final: 0.8626 (mm)
REVERT: T   61 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8444 (mp-120)
REVERT: T   79 LEU cc_start: 0.8319 (mt) cc_final: 0.8035 (mt)
  outliers start: 67
  outliers final: 61
  residues processed: 315
  average time/residue: 0.2426
  time to fit residues: 118.7527
Evaluate side-chains
  327 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 265
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   25 VAL
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain D residue    5 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   36 ILE
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   54 LEU
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   78 PHE
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   10 MET
Chi-restraints excluded: chain H residue   26 THR
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain K residue   20 VAL
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain O residue   18 ASP
Chi-restraints excluded: chain O residue   47 LYS
Chi-restraints excluded: chain O residue   75 VAL
Chi-restraints excluded: chain P residue   53 ASP
Chi-restraints excluded: chain P residue   66 THR
Chi-restraints excluded: chain Q residue    8 LEU
Chi-restraints excluded: chain Q residue   28 PHE
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   38 ILE
Chi-restraints excluded: chain Q residue   61 ILE
Chi-restraints excluded: chain Q residue   81 LYS
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain R residue   44 ILE
Chi-restraints excluded: chain T residue   28 MET
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Chi-restraints excluded: chain T residue   83 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 248 optimal weight:    0.5980
   chunk 110 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0770
   chunk 22 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 247 optimal weight:    0.8980
   chunk 166 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 201 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
V  36 GLN
V 202 HIS
B  89 GLN
B 120 GLN
F  94 HIS
L  20 ASN
** R  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  70 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.065081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.052201 restraints weight = 141478.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 1.37
r_work: 0.2979 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  36963  Z= 0.108
  Angle     :  0.524   9.630  54707  Z= 0.272
  Chirality :  0.033   0.230   6899
  Planarity :  0.004   0.041   3369
  Dihedral  : 22.944 178.605  16988
  Min Nonbonded Distance : 1.154

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.25 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.74 (0.21), residues: 1702
  helix:  1.59 (0.20), residues: 701
  sheet:  0.05 (0.32), residues: 278
  loop : -0.35 (0.23), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG V 208 
 TYR   0.020   0.001   TYR V 157 
 PHE   0.027   0.001   PHE B  90 
 TRP   0.009   0.001   TRP P  60 
 HIS   0.002   0.001   HIS V 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (36963)
  covalent geometry    : angle       0.52382 (54707)
  hydrogen bonds       : bond        0.04632 ( 1440)
  hydrogen bonds       : angle       3.69056 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 298
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: V   36 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5967 (pm20)
REVERT: V   44 ILE cc_start: 0.6991 (mm) cc_final: 0.6562 (mt)
REVERT: V  142 LYS cc_start: 0.7714 (tppt) cc_final: 0.7465 (tppt)
REVERT: V  157 TYR cc_start: 0.8062 (t80) cc_final: 0.7736 (t80)
REVERT: B  113 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7163 (ttm110)
REVERT: B  118 GLU cc_start: 0.7082 (pp20) cc_final: 0.6809 (mt-10)
REVERT: B  159 ASP cc_start: 0.7586 (m-30) cc_final: 0.7309 (t0)
REVERT: B  168 HIS cc_start: 0.7773 (t-90) cc_final: 0.7080 (t-90)
REVERT: B  191 SER cc_start: 0.8893 (m) cc_final: 0.8591 (m)
REVERT: E   14 LYS cc_start: 0.7873 (mttt) cc_final: 0.7585 (mmtt)
REVERT: E  142 ASP cc_start: 0.7460 (m-30) cc_final: 0.7048 (m-30)
REVERT: E  159 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7164 (mtpt)
REVERT: E  163 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7641 (pt0)
REVERT: F   13 ASP cc_start: 0.7898 (m-30) cc_final: 0.7303 (t0)
REVERT: F   14 GLN cc_start: 0.9025 (mt0) cc_final: 0.8815 (pt0)
REVERT: F   81 ASN cc_start: 0.8266 (t0) cc_final: 0.7992 (t0)
REVERT: H   91 GLU cc_start: 0.7707 (pt0) cc_final: 0.7443 (pt0)
REVERT: K   74 VAL cc_start: 0.8894 (t) cc_final: 0.8657 (m)
REVERT: K   94 GLU cc_start: 0.7893 (pp20) cc_final: 0.7484 (pp20)
REVERT: O    6 GLU cc_start: 0.8932 (mp0) cc_final: 0.8532 (mp0)
REVERT: O   88 ARG cc_start: 0.7282 (mmm160) cc_final: 0.6393 (mmp80)
REVERT: T   39 ILE cc_start: 0.8958 (tp) cc_final: 0.8609 (mm)
REVERT: T   61 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8323 (mp-120)
REVERT: T   79 LEU cc_start: 0.8119 (mt) cc_final: 0.7763 (mt)
  outliers start: 45
  outliers final: 30
  residues processed: 330
  average time/residue: 0.2515
  time to fit residues: 127.5670
Evaluate side-chains
  298 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 266
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue   36 GLN
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue   79 VAL
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 129 optimal weight:   10.0000
   chunk 168 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 259 optimal weight:    0.0870
   chunk 56 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 256 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    3.0166

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

Flipped N/Q/H residues before XYZ refinement:
V 202 HIS
B 120 GLN
D  71 GLN
F  94 HIS
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  70 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.062784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.049738 restraints weight = 140922.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.41
r_work: 0.2898 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  36963  Z= 0.292
  Angle     :  0.632   9.904  54707  Z= 0.324
  Chirality :  0.038   0.232   6899
  Planarity :  0.005   0.043   3369
  Dihedral  : 23.031 177.602  16986
  Min Nonbonded Distance : 1.080

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.74 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.44 (0.20), residues: 1702
  helix:  1.35 (0.20), residues: 694
  sheet:  0.10 (0.32), residues: 268
  loop : -0.60 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 225 
 TYR   0.019   0.002   TYR V 157 
 PHE   0.022   0.002   PHE B  90 
 TRP   0.018   0.002   TRP B  23 
 HIS   0.006   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (36963)
  covalent geometry    : angle       0.63205 (54707)
  hydrogen bonds       : bond        0.05745 ( 1440)
  hydrogen bonds       : angle       3.93217 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 266
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: V  157 TYR cc_start: 0.8230 (t80) cc_final: 0.7922 (t80)
REVERT: V  241 MET cc_start: 0.7302 (mmm) cc_final: 0.7052 (tpp)
REVERT: B  118 GLU cc_start: 0.7029 (pp20) cc_final: 0.6777 (mt-10)
REVERT: B  168 HIS cc_start: 0.7804 (t-90) cc_final: 0.7107 (t-90)
REVERT: B  191 SER cc_start: 0.8915 (m) cc_final: 0.8602 (m)
REVERT: E  142 ASP cc_start: 0.7424 (m-30) cc_final: 0.7080 (m-30)
REVERT: E  163 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7673 (pt0)
REVERT: F   13 ASP cc_start: 0.7883 (m-30) cc_final: 0.7288 (t0)
REVERT: F   81 ASN cc_start: 0.8446 (t0) cc_final: 0.8052 (t0)
REVERT: K   74 VAL cc_start: 0.8925 (t) cc_final: 0.8634 (m)
REVERT: K  106 ARG cc_start: 0.6799 (ttt-90) cc_final: 0.6396 (ttt90)
REVERT: O    6 GLU cc_start: 0.8902 (mp0) cc_final: 0.8487 (mp0)
REVERT: O   26 GLU cc_start: 0.8840 (mp0) cc_final: 0.8544 (mp0)
REVERT: O   88 ARG cc_start: 0.7362 (mmm160) cc_final: 0.6350 (mmp80)
REVERT: T   39 ILE cc_start: 0.8964 (tp) cc_final: 0.8622 (mm)
REVERT: T   61 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8356 (mp-120)
REVERT: T   79 LEU cc_start: 0.8221 (mt) cc_final: 0.7880 (mt)
  outliers start: 46
  outliers final: 41
  residues processed: 297
  average time/residue: 0.2427
  time to fit residues: 112.0698
Evaluate side-chains
  304 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 262
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain D residue    5 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   10 MET
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue   79 VAL
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   38 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   54 MET
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 200 optimal weight:    0.5980
   chunk 210 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 160 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 194 optimal weight:    1.9990
   chunk 166 optimal weight:    1.9990
   chunk 141 optimal weight:    6.9990
   chunk 211 optimal weight:    3.9990
   chunk 152 optimal weight:    1.9990
   chunk 230 optimal weight:    3.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
V 165 GLN
V 202 HIS
F  94 HIS
L  20 ASN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** 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 = 0.3437 r_free = 0.3437 target = 0.063434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.050385 restraints weight = 140279.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.37
r_work: 0.2920 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  36963  Z= 0.191
  Angle     :  0.579  11.529  54707  Z= 0.300
  Chirality :  0.035   0.237   6899
  Planarity :  0.005   0.045   3369
  Dihedral  : 23.043 178.150  16986
  Min Nonbonded Distance : 1.102

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.16 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.49 (0.21), residues: 1702
  helix:  1.38 (0.20), residues: 694
  sheet:  0.08 (0.33), residues: 266
  loop : -0.54 (0.23), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG V 208 
 TYR   0.021   0.002   TYR V 157 
 PHE   0.023   0.001   PHE B  90 
 TRP   0.009   0.001   TRP B  23 
 HIS   0.004   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (36963)
  covalent geometry    : angle       0.57894 (54707)
  hydrogen bonds       : bond        0.05278 ( 1440)
  hydrogen bonds       : angle       3.85513 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 269
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: V  157 TYR cc_start: 0.8201 (t80) cc_final: 0.7898 (t80)
REVERT: V  241 MET cc_start: 0.7266 (mmm) cc_final: 0.7032 (tpp)
REVERT: B  168 HIS cc_start: 0.7796 (t-90) cc_final: 0.7078 (t-90)
REVERT: B  191 SER cc_start: 0.8895 (m) cc_final: 0.8588 (m)
REVERT: E  142 ASP cc_start: 0.7422 (m-30) cc_final: 0.7046 (m-30)
REVERT: E  163 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7704 (pt0)
REVERT: F   13 ASP cc_start: 0.7842 (m-30) cc_final: 0.7246 (t0)
REVERT: F   81 ASN cc_start: 0.8412 (t0) cc_final: 0.8013 (t0)
REVERT: K   74 VAL cc_start: 0.8902 (t) cc_final: 0.8622 (m)
REVERT: O    6 GLU cc_start: 0.8897 (mp0) cc_final: 0.8487 (mp0)
REVERT: O   26 GLU cc_start: 0.8834 (mp0) cc_final: 0.8544 (mp0)
REVERT: O   88 ARG cc_start: 0.7356 (mmm160) cc_final: 0.6358 (mmp80)
REVERT: T   39 ILE cc_start: 0.8969 (tp) cc_final: 0.8620 (mm)
REVERT: T   61 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8333 (mp-120)
REVERT: T   79 LEU cc_start: 0.8167 (mt) cc_final: 0.7858 (mt)
  outliers start: 40
  outliers final: 37
  residues processed: 296
  average time/residue: 0.2436
  time to fit residues: 111.8999
Evaluate side-chains
  298 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 260
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain D residue    5 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain O residue   75 VAL
Chi-restraints excluded: chain Q residue   21 ILE
Chi-restraints excluded: chain Q residue   28 PHE
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain U residue   29 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 193 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 155 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 169 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 233 optimal weight:    7.9990
   chunk 110 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
V 202 HIS
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  94 HIS
L  20 ASN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** 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 = 0.3416 r_free = 0.3416 target = 0.062642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.049593 restraints weight = 140774.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 1.47
r_work: 0.2896 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  36963  Z= 0.296
  Angle     :  0.651  10.560  54707  Z= 0.334
  Chirality :  0.039   0.265   6899
  Planarity :  0.005   0.043   3369
  Dihedral  : 23.094 177.976  16986
  Min Nonbonded Distance : 1.068

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.37 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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 (0.20), residues: 1702
  helix:  1.20 (0.20), residues: 698
  sheet: -0.08 (0.33), residues: 261
  loop : -0.73 (0.22), residues: 743

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  69 
 TYR   0.022   0.002   TYR V 157 
 PHE   0.019   0.002   PHE B  90 
 TRP   0.017   0.002   TRP B  23 
 HIS   0.005   0.001   HIS E  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (36963)
  covalent geometry    : angle       0.65108 (54707)
  hydrogen bonds       : bond        0.05921 ( 1440)
  hydrogen bonds       : angle       4.08430 ( 3141)

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

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

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3404 Ramachandran restraints generated.
    1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 264
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: V  142 LYS cc_start: 0.7691 (tppt) cc_final: 0.7439 (tppt)
REVERT: B  168 HIS cc_start: 0.7812 (t-90) cc_final: 0.7108 (t-90)
REVERT: E  142 ASP cc_start: 0.7386 (m-30) cc_final: 0.7038 (m-30)
REVERT: E  163 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7723 (pt0)
REVERT: F   13 ASP cc_start: 0.7848 (m-30) cc_final: 0.7253 (t0)
REVERT: F   81 ASN cc_start: 0.8401 (t0) cc_final: 0.8019 (t0)
REVERT: K   74 VAL cc_start: 0.8917 (t) cc_final: 0.8637 (m)
REVERT: O    6 GLU cc_start: 0.8877 (mp0) cc_final: 0.8481 (mp0)
REVERT: O   88 ARG cc_start: 0.7390 (mmm160) cc_final: 0.6401 (mmp80)
REVERT: T   39 ILE cc_start: 0.8977 (tp) cc_final: 0.8630 (mm)
REVERT: T   61 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8362 (mp-120)
REVERT: T   79 LEU cc_start: 0.8206 (mt) cc_final: 0.7872 (mt)
  outliers start: 45
  outliers final: 44
  residues processed: 295
  average time/residue: 0.2353
  time to fit residues: 107.5678
Evaluate side-chains
  304 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 259
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  161 SER
Chi-restraints excluded: chain V residue  199 THR
Chi-restraints excluded: chain V residue  204 VAL
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain D residue    5 LEU
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue  142 VAL
Chi-restraints excluded: chain D residue  143 VAL
Chi-restraints excluded: chain D residue  169 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   25 VAL
Chi-restraints excluded: chain E residue   32 SER
Chi-restraints excluded: chain E residue   34 THR
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain E residue   97 GLN
Chi-restraints excluded: chain E residue  131 THR
Chi-restraints excluded: chain E residue  165 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain H residue   62 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   76 GLN
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain K residue   32 VAL
Chi-restraints excluded: chain K residue   59 THR
Chi-restraints excluded: chain K residue  111 THR
Chi-restraints excluded: chain L residue    4 VAL
Chi-restraints excluded: chain L residue   56 ARG
Chi-restraints excluded: chain L residue   79 VAL
Chi-restraints excluded: chain L residue  109 ASP
Chi-restraints excluded: chain O residue   75 VAL
Chi-restraints excluded: chain Q residue   21 ILE
Chi-restraints excluded: chain Q residue   28 PHE
Chi-restraints excluded: chain Q residue   33 ILE
Chi-restraints excluded: chain Q residue   38 ILE
Chi-restraints excluded: chain R residue   33 ILE
Chi-restraints excluded: chain R residue   42 SER
Chi-restraints excluded: chain T residue   40 GLU
Chi-restraints excluded: chain T residue   61 GLN
Chi-restraints excluded: chain T residue   66 LEU
Chi-restraints excluded: chain T residue   75 HIS
Chi-restraints excluded: chain U residue   29 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 262
   random chunks:
   chunk 252 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 191 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    8.9990
   chunk 167 optimal weight:    0.7980
   chunk 216 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 202 HIS
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  94 HIS
L  20 ASN
** Q  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  74 HIS ** 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 = 0.3443 r_free = 0.3443 target = 0.063651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.050651 restraints weight = 140364.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.35
r_work: 0.2929 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  36963  Z= 0.163
  Angle     :  0.582  12.713  54707  Z= 0.303
  Chirality :  0.035   0.233   6899
  Planarity :  0.004   0.054   3369
  Dihedral  : 23.096 178.394  16986
  Min Nonbonded Distance : 1.109

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.85 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    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:  0.36 (0.21), residues: 1702
  helix:  1.28 (0.20), residues: 704
  sheet: -0.20 (0.33), residues: 257
  loop : -0.55 (0.23), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG F  24 
 TYR   0.034   0.002   TYR V 157 
 PHE   0.022   0.001   PHE B  90 
 TRP   0.009   0.001   TRP P  60 
 HIS   0.004   0.001   HIS V 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (36963)
  covalent geometry    : angle       0.58192 (54707)
  hydrogen bonds       : bond        0.05184 ( 1440)
  hydrogen bonds       : angle       3.90735 ( 3141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10037.68 seconds
wall clock time: 172 minutes 14.90 seconds (10334.90 seconds total)