Starting phenix.real_space_refine
on Thu Jul  2 14:28:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e93_47752/07_2026/9e93_47752.map"
  }
  resolution = 3.58
  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=  -0.026 sd=   0.342
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
     Zn      4      6.06       5
     P      36      5.49       5
     S      50      5.16       5
     C    5427      2.51       5
     N    1587      2.21       5
     O    1669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8773
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "C"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 194
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 8}
    Chain: "D"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 173
          Classifications: {'DNA': 2, 'RNA': 8}
          Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 9}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 3
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'  A%5*END:plan': 1, '  A%5*END:plan2': 1, '  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 1508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1508
          Classifications: {'peptide': 181}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 194
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 8}
    Chain: "H"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 173
          Classifications: {'DNA': 2, 'RNA': 8}
          Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 9}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 3
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'  A%5*END:plan': 1, '  A%5*END:plan2': 1, '  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 1508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1508
          Classifications: {'peptide': 181}
          Link IDs: {'PTRANS': 10, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "o"
      Number of atoms: 1138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1138
          Classifications: {'peptide': 137}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 133}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "p"
      Number of atoms: 1367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1367
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 8, 'TRANS': 155}
          Chain breaks: 1
    Chain: "s"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1147
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 134}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "t"
      Number of atoms: 1367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1367
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 8, 'TRANS': 155}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "p"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "t"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1066  SG  CYS A  85      72.287  55.628  49.334  1.00 67.15           S
  ATOM   1084  SG  CYS A  88      73.419  55.035  47.951  1.00 65.88           S
  ATOM   2941  SG  CYS E  85      41.143  56.096  49.407  1.00 65.73           S
  ATOM   2959  SG  CYS E  88      39.736  56.696  48.097  1.00 63.94           S
  ATOM   5812  SG  CYS p 114      60.812  88.006  60.028  1.00 94.13           S
  ATOM   5959  SG  CYS p 133      63.366  88.061  59.934  1.00 95.31           S
  ATOM   8326  SG  CYS t 114      52.648  25.185  60.311  1.00 94.09           S
  ATOM   8473  SG  CYS t 133      49.640  24.842  59.811  1.00 94.64           S

  Time building chain proxies: 2.30, per 1000 atoms: 0.26
  Number of scatterers: 8773
  At special positions: 0
  Unit cell: (112.59, 110.97, 95.58, 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)
     Zn      4     29.99
     S      50     16.00
     P      36     15.00
     O    1669      8.00
     N    1587      7.00
     C    5427      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 444.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 300 "
        pdb="ZN    ZN A 300 " - pdb=" ND1 HIS A  54 "
        pdb="ZN    ZN A 300 " - pdb=" SG  CYS A  85 "
        pdb="ZN    ZN A 300 " - pdb=" SG  CYS A  88 "
      pdb="  ZN E 300 "
        pdb="ZN    ZN E 300 " - pdb=" SG  CYS E  85 "
        pdb="ZN    ZN E 300 " - pdb=" SG  CYS E  88 "
        pdb="ZN    ZN E 300 " - pdb=" ND1 HIS E  54 "
      pdb="  ZN p 201 "
        pdb="ZN    ZN p 201 " - pdb=" SG  CYS p 133 "
        pdb="ZN    ZN p 201 " - pdb=" NE2 HIS p 108 "
        pdb="ZN    ZN p 201 " - pdb=" SG  CYS p 114 "
      pdb="  ZN t 201 "
        pdb="ZN    ZN t 201 " - pdb=" SG  CYS t 114 "
        pdb="ZN    ZN t 201 " - pdb=" SG  CYS t 133 "
        pdb="ZN    ZN t 201 " - pdb=" NE2 HIS t 108 "


  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1846

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      41.0% alpha, 26.1% beta
      16 base pairs and 17 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 13
    Processing helix  chain 'A' and resid 54 through 66
    Processing helix  chain 'A' and resid 85 through 99
    Processing helix  chain 'A' and resid 116 through 129
    Processing helix  chain 'A' and resid 137 through 147
    Processing helix  chain 'A' and resid 158 through 182
      removed outlier: 4.010A  pdb=" N   MET A 162 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   ALA A 172 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE A 173 " --> pdb=" O   ASN A 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 5 through 13
    Processing helix  chain 'E' and resid 54 through 66
    Processing helix  chain 'E' and resid 85 through 99
    Processing helix  chain 'E' and resid 116 through 129
    Processing helix  chain 'E' and resid 137 through 149
    Processing helix  chain 'E' and resid 158 through 182
      removed outlier: 3.849A  pdb=" N   MET E 162 " --> pdb=" O   ASP E 158 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ALA E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 8 through 15
      removed outlier: 3.675A  pdb=" N   GLU o  13 " --> pdb=" O   ARG o   9 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 15 through 24
      removed outlier: 3.894A  pdb=" N   ARG o  19 " --> pdb=" O   GLU o  15 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU o  24 " --> pdb=" O   LYS o  20 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 36 through 50
      removed outlier: 4.517A  pdb=" N   ALA o  42 " --> pdb=" O   GLU o  38 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ARG o  43 " --> pdb=" O   GLU o  39 " (cutoff:3.500A)
    Processing helix  chain 'o' and resid 129 through 135
    Processing helix  chain 'o' and resid 136 through 149
      removed outlier: 3.889A  pdb=" N   GLN o 140 " --> pdb=" O   ASP o 136 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 14 through 31
    Processing helix  chain 'p' and resid 99 through 112
      removed outlier: 3.750A  pdb=" N   HIS p 110 " --> pdb=" O   LEU p 106 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE p 112 " --> pdb=" O   HIS p 108 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 118 through 126
      removed outlier: 3.550A  pdb=" N   THR p 123 " --> pdb=" O   ALA p 119 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 135 through 139
      removed outlier: 3.873A  pdb=" N   HIS p 139 " --> pdb=" O   GLN p 136 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 144 through 154
    Processing helix  chain 'p' and resid 165 through 170
      removed outlier: 3.649A  pdb=" N   LEU p 169 " --> pdb=" O   SER p 165 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 8 through 13
    Processing helix  chain 's' and resid 15 through 24
    Processing helix  chain 's' and resid 36 through 50
      removed outlier: 4.017A  pdb=" N   ALA s  42 " --> pdb=" O   GLU s  38 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ARG s  43 " --> pdb=" O   GLU s  39 " (cutoff:3.500A)
    Processing helix  chain 's' and resid 129 through 135
    Processing helix  chain 's' and resid 136 through 147
      removed outlier: 3.954A  pdb=" N   GLN s 140 " --> pdb=" O   ASP s 136 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 14 through 30
    Processing helix  chain 't' and resid 99 through 110
      removed outlier: 3.931A  pdb=" N   HIS t 110 " --> pdb=" O   LEU t 106 " (cutoff:3.500A)
    Processing helix  chain 't' and resid 118 through 125
    Processing helix  chain 't' and resid 146 through 154
    Processing helix  chain 't' and resid 165 through 171
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 48
      removed outlier: 3.624A  pdb=" N   GLY A  45 " --> pdb=" O   TYR A  32 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LEU A  29 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A  81 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN A  75 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 48
      removed outlier: 3.624A  pdb=" N   GLY A  45 " --> pdb=" O   TYR A  32 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   LEU A  29 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A  81 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN A  75 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   SER A 109 " --> pdb=" O   CYS A  78 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   LEU A  80 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 45 through 46
      removed outlier: 3.859A  pdb=" N   GLY E  45 " --> pdb=" O   TYR E  32 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR E  32 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLN E  75 " --> pdb=" O   THR E  35 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   TYR E  74 " --> pdb=" O   ASN E 103 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   ARG E 105 " --> pdb=" O   TYR E  74 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   VAL E  76 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   PHE E 107 " --> pdb=" O   VAL E  76 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   CYS E  78 " --> pdb=" O   PHE E 107 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   SER E 109 " --> pdb=" O   CYS E  78 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   LEU E  80 " --> pdb=" O   SER E 109 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'o' and resid 27 through 28
    Processing sheet with id=AA5, first strand: chain 'o' and resid 64 through 70
      removed outlier: 20.859A  pdb=" N   TRP p   5 " --> pdb=" O   LYS p  91 " (cutoff:3.500A)
      removed outlier: 18.335A  pdb=" N   LYS p  91 " --> pdb=" O   TRP p   5 " (cutoff:3.500A)
      removed outlier: 14.273A  pdb=" N   VAL p   7 " --> pdb=" O   TRP p  89 " (cutoff:3.500A)
      removed outlier: 11.274A  pdb=" N   TRP p  89 " --> pdb=" O   VAL p   7 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ILE p   9 " --> pdb=" O   ILE p  87 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ILE p  87 " --> pdb=" O   ILE p   9 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLN p  83 " --> pdb=" O   VAL p  13 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY p  84 " --> pdb=" O   TYR p  69 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS p  63 " --> pdb=" O   ARG p  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'o' and resid 64 through 70
      removed outlier: 20.859A  pdb=" N   TRP p   5 " --> pdb=" O   LYS p  91 " (cutoff:3.500A)
      removed outlier: 18.335A  pdb=" N   LYS p  91 " --> pdb=" O   TRP p   5 " (cutoff:3.500A)
      removed outlier: 14.273A  pdb=" N   VAL p   7 " --> pdb=" O   TRP p  89 " (cutoff:3.500A)
      removed outlier: 11.274A  pdb=" N   TRP p  89 " --> pdb=" O   VAL p   7 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ILE p   9 " --> pdb=" O   ILE p  87 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   ILE p  87 " --> pdb=" O   ILE p   9 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLN p  83 " --> pdb=" O   VAL p  13 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'o' and resid 86 through 87
      removed outlier: 4.035A  pdb=" N   TYR o  96 " --> pdb=" O   ASP o  87 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   VAL o  95 " --> pdb=" O   ILE o 114 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS o 124 " --> pdb=" O   LYS o 111 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 's' and resid 27 through 28
      removed outlier: 3.821A  pdb=" N   ASP s 120 " --> pdb=" O   ASP s 115 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS s  98 " --> pdb=" O   TYR s  85 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TYR s  85 " --> pdb=" O   LYS s  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 's' and resid 56 through 58
      removed outlier: 3.542A  pdb=" N   MET t   8 " --> pdb=" O   GLN s  67 " (cutoff:3.500A)
      removed outlier: 19.980A  pdb=" N   TRP t   5 " --> pdb=" O   LYS t  91 " (cutoff:3.500A)
      removed outlier: 17.563A  pdb=" N   LYS t  91 " --> pdb=" O   TRP t   5 " (cutoff:3.500A)
      removed outlier: 14.290A  pdb=" N   VAL t   7 " --> pdb=" O   TRP t  89 " (cutoff:3.500A)
      removed outlier: 11.488A  pdb=" N   TRP t  89 " --> pdb=" O   VAL t   7 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ILE t   9 " --> pdb=" O   ILE t  87 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ILE t  87 " --> pdb=" O   ILE t   9 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN t  83 " --> pdb=" O   VAL t  13 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   TRP t  70 " --> pdb=" O   ILE t  51 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   ILE t  51 " --> pdb=" O   TRP t  70 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU t  54 " --> pdb=" O   ARG t  41 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 's' and resid 56 through 58
      removed outlier: 3.542A  pdb=" N   MET t   8 " --> pdb=" O   GLN s  67 " (cutoff:3.500A)
      removed outlier: 19.980A  pdb=" N   TRP t   5 " --> pdb=" O   LYS t  91 " (cutoff:3.500A)
      removed outlier: 17.563A  pdb=" N   LYS t  91 " --> pdb=" O   TRP t   5 " (cutoff:3.500A)
      removed outlier: 14.290A  pdb=" N   VAL t   7 " --> pdb=" O   TRP t  89 " (cutoff:3.500A)
      removed outlier: 11.488A  pdb=" N   TRP t  89 " --> pdb=" O   VAL t   7 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ILE t   9 " --> pdb=" O   ILE t  87 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ILE t  87 " --> pdb=" O   ILE t   9 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLN t  83 " --> pdb=" O   VAL t  13 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1137 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      17 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2737
        1.34 -     1.46: 1618
        1.46 -     1.58: 4558
        1.58 -     1.69: 70
        1.69 -     1.81: 66
  Bond restraints: 9049
  Sorted by residual:
  bond pdb=" C   SER t 130 "
       pdb=" N   PRO t 131 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 8.36e-01
  bond pdb=" CG  PRO A  22 "
       pdb=" CD  PRO A  22 "
    ideal  model  delta    sigma   weight residual
    1.512  1.495  0.017 2.70e-02 1.37e+03 3.79e-01
  bond pdb=" P     A H  10 "
       pdb=" O5'   A H  10 "
    ideal  model  delta    sigma   weight residual
    1.593  1.599 -0.006 1.00e-02 1.00e+04 3.73e-01
  bond pdb=" P     A D  10 "
       pdb=" O5'   A D  10 "
    ideal  model  delta    sigma   weight residual
    1.593  1.599 -0.006 1.00e-02 1.00e+04 3.46e-01
  bond pdb=" CB  PRO o 100 "
       pdb=" CG  PRO o 100 "
    ideal  model  delta    sigma   weight residual
    1.492  1.520 -0.028 5.00e-02 4.00e+02 3.11e-01
  ... (remaining 9044 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 12106
        1.10 -     2.20: 199
        2.20 -     3.30: 48
        3.30 -     4.40: 6
        4.40 -     5.50: 9
  Bond angle restraints: 12368
  Sorted by residual:
  angle pdb=" C2'   U H   2 "
        pdb=" C1'   U H   2 "
        pdb=" N1    U H   2 "
      ideal   model   delta    sigma   weight residual
     112.00  114.81   -2.81 1.50e+00 4.44e-01 3.52e+00
  angle pdb=" C1'   U H   2 "
        pdb=" N1    U H   2 "
        pdb=" C2    U H   2 "
      ideal   model   delta    sigma   weight residual
     117.70  119.92   -2.22 1.20e+00 6.94e-01 3.44e+00
  angle pdb=" CG1 ILE t 159 "
        pdb=" CB  ILE t 159 "
        pdb=" CG2 ILE t 159 "
      ideal   model   delta    sigma   weight residual
     110.70  105.53    5.17 3.00e+00 1.11e-01 2.97e+00
  angle pdb=" N1    U H   2 "
        pdb=" C6    U H   2 "
        pdb=" C5    U H   2 "
      ideal   model   delta    sigma   weight residual
     122.70  123.54   -0.84 5.00e-01 4.00e+00 2.81e+00
  angle pdb=" C2    U H   2 "
        pdb=" N1    U H   2 "
        pdb=" C6    U H   2 "
      ideal   model   delta    sigma   weight residual
     121.00  120.01    0.99 6.00e-01 2.78e+00 2.74e+00
  ... (remaining 12363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 4995
       15.03 -    30.06: 317
       30.06 -    45.10: 96
       45.10 -    60.13: 57
       60.13 -    75.16: 43
  Dihedral angle restraints: 5508
    sinusoidal: 2669
      harmonic: 2839
  Sorted by residual:
  dihedral pdb=" CA  GLU o 130 "
           pdb=" CB  GLU o 130 "
           pdb=" CG  GLU o 130 "
           pdb=" CD  GLU o 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.61   53.61     3      1.50e+01 4.44e-03 9.22e+00
  dihedral pdb=" CA  ILE t 128 "
           pdb=" CB  ILE t 128 "
           pdb=" CG1 ILE t 128 "
           pdb=" CD1 ILE t 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  113.23  -53.23     3      1.50e+01 4.44e-03 9.19e+00
  dihedral pdb=" N   LEU p 169 "
           pdb=" CA  LEU p 169 "
           pdb=" CB  LEU p 169 "
           pdb=" CG  LEU p 169 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.76   50.76     3      1.50e+01 4.44e-03 8.94e+00
  ... (remaining 5505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1021
       0.034 -    0.068: 198
       0.068 -    0.102: 67
       0.102 -    0.135: 32
       0.135 -    0.169: 1
  Chirality restraints: 1319
  Sorted by residual:
  chirality pdb=" CB  ILE t 159 "
            pdb=" CA  ILE t 159 "
            pdb=" CG1 ILE t 159 "
            pdb=" CG2 ILE t 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  ILE p  66 "
            pdb=" N   ILE p  66 "
            pdb=" C   ILE p  66 "
            pdb=" CB  ILE p  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  chirality pdb=" CA  ILE t  66 "
            pdb=" N   ILE t  66 "
            pdb=" C   ILE t  66 "
            pdb=" CB  ILE t  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1316 not shown)

  Planarity restraints: 1466
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U H   2 "   -0.024 2.00e-02 2.50e+03   2.41e-02 1.30e+01
        pdb=" N1    U H   2 "    0.059 2.00e-02 2.50e+03
        pdb=" C2    U H   2 "   -0.032 2.00e-02 2.50e+03
        pdb=" O2    U H   2 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    U H   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    U H   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U H   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    U H   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    U H   2 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS t 160 "    0.048 5.00e-02 4.00e+02   7.25e-02 8.40e+00
        pdb=" N   PRO t 161 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO t 161 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO t 161 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS p 160 "   -0.046 5.00e-02 4.00e+02   6.98e-02 7.79e+00
        pdb=" N   PRO p 161 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO p 161 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO p 161 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1463 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1666
        2.78 -     3.31: 8100
        3.31 -     3.84: 14522
        3.84 -     4.37: 16512
        4.37 -     4.90: 27896
  Nonbonded interactions: 68696
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU E 121 "
            pdb=" OH  TYR p  30 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR E  35 "
            pdb=" O   GLN E  75 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   PHE s  32 "
            pdb=" NH1 ARG s  40 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" O   ASN E  15 "
            pdb=" ND2 ASN E 169 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" O   ASP o   7 "
            pdb=" OG  SER o  10 "
     model   vdw
     2.413 3.040
  ... (remaining 68691 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'o'
  selection = (chain 's' and resid 7 through 153)
}
ncs_group {
  reference = chain 'p'
  selection = chain 't'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.400
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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   0.028   9061  Z= 0.079
  Angle     :  0.398   5.503  12368  Z= 0.218
  Chirality :  0.035   0.169   1319
  Planarity :  0.007   0.079   1466
  Dihedral  : 13.952  75.160   3662
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  0.34 (0.28), residues: 945
  helix:  1.60 (0.28), residues: 363
  sheet: -0.48 (0.40), residues: 171
  loop : -0.66 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG t 121 
 TYR   0.009   0.001   TYR t  94 
 PHE   0.007   0.001   PHE E  59 
 TRP   0.009   0.001   TRP t  70 
 HIS   0.004   0.000   HIS t 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00156 /  0.08 ( 9049)
  covalent geometry    : angle       0.39762 /  0.22 (12368)
  hydrogen bonds       : bond        0.17560 / 17.19 (  407)
  hydrogen bonds       : angle       7.68717 /  7.19 ( 1225)
  metal coordination   : bond        0.00274 /  0.18 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 367
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 VAL cc_start: 0.7586 (t) cc_final: 0.7159 (p)
REVERT: E  136 MET cc_start: 0.7744 (mtp) cc_final: 0.7123 (mtp)
REVERT: E  158 ASP cc_start: 0.7701 (p0) cc_final: 0.7392 (p0)
REVERT: o  120 ASP cc_start: 0.7706 (t0) cc_final: 0.7384 (t0)
REVERT: p   12 GLN cc_start: 0.8701 (mp10) cc_final: 0.8459 (mp10)
REVERT: s  118 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7626 (ttp80)
REVERT: s  141 GLN cc_start: 0.8090 (mt0) cc_final: 0.7842 (mt0)
REVERT: t   16 MET cc_start: 0.7777 (mtm) cc_final: 0.7485 (mtm)
REVERT: t   83 GLN cc_start: 0.7905 (mt0) cc_final: 0.7547 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 367
  average time/residue: 0.1637
  time to fit residues: 73.5735
Evaluate side-chains
  263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.0370
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.9060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  15 ASN
A  37 GLN
A  38 ASN
A  97 GLN
E  49 ASN
E 101 HIS
o   8 GLN
o  45 GLN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  37 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.082377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.072205 restraints weight = 28666.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.074096 restraints weight = 15406.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.075337 restraints weight = 9945.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.076185 restraints weight = 7267.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.076801 restraints weight = 5774.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9061  Z= 0.199
  Angle     :  0.673  10.388  12368  Z= 0.349
  Chirality :  0.042   0.176   1319
  Planarity :  0.006   0.068   1466
  Dihedral  : 13.696  73.616   1623
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.14 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  0.21 (0.27), residues: 945
  helix:  1.31 (0.27), residues: 363
  sheet: -0.33 (0.43), residues: 154
  loop : -0.64 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 105 
 TYR   0.025   0.002   TYR t  94 
 PHE   0.014   0.002   PHE t 112 
 TRP   0.017   0.002   TRP s 113 
 HIS   0.008   0.001   HIS p 108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.20 ( 9049)
  covalent geometry    : angle       0.67276 /  0.35 (12368)
  hydrogen bonds       : bond        0.04012 /  3.92 (  407)
  hydrogen bonds       : angle       5.57308 /  5.44 ( 1225)
  metal coordination   : bond        0.00626 /  0.41 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 270
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  136 MET cc_start: 0.8160 (mtp) cc_final: 0.7832 (mtm)
REVERT: p   15 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7580 (tpp80)
REVERT: p   83 GLN cc_start: 0.8206 (mm110) cc_final: 0.7966 (mm110)
REVERT: p  121 ARG cc_start: 0.7729 (mmp-170) cc_final: 0.7488 (mmp80)
REVERT: s  120 ASP cc_start: 0.7892 (t0) cc_final: 0.7219 (t0)
REVERT: t    5 TRP cc_start: 0.7713 (m100) cc_final: 0.7490 (m100)
REVERT: t   45 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7086 (tt0)
REVERT: t   83 GLN cc_start: 0.8033 (mt0) cc_final: 0.7787 (mt0)
  outliers start: 27
  outliers final: 22
  residues processed: 283
  average time/residue: 0.1606
  time to fit residues: 55.8223
Evaluate side-chains
  274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 252
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  117 LYS
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   28 LYS
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   80 HIS
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   37 HIS
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain t residue   67 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
o  45 GLN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 140 ASN
p 158 GLN
s  37 HIS
t  12 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.081069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.070992 restraints weight = 28408.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.072875 restraints weight = 15362.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.074110 restraints weight = 9905.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.074912 restraints weight = 7238.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.075439 restraints weight = 5800.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9061  Z= 0.158
  Angle     :  0.612   6.749  12368  Z= 0.315
  Chirality :  0.040   0.185   1319
  Planarity :  0.005   0.059   1466
  Dihedral  : 13.752  73.536   1623
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.34 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  0.17 (0.27), residues: 945
  helix:  1.27 (0.27), residues: 362
  sheet: -0.61 (0.39), residues: 181
  loop : -0.52 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  20 
 TYR   0.023   0.002   TYR t 147 
 PHE   0.015   0.002   PHE E 148 
 TRP   0.018   0.002   TRP s 113 
 HIS   0.007   0.001   HIS s  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.16 ( 9049)
  covalent geometry    : angle       0.61250 /  0.32 (12368)
  hydrogen bonds       : bond        0.03851 /  3.67 (  407)
  hydrogen bonds       : angle       5.25849 /  5.12 ( 1225)
  metal coordination   : bond        0.00310 /  0.20 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 263
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 TYR cc_start: 0.7291 (m-10) cc_final: 0.6994 (m-10)
REVERT: E  136 MET cc_start: 0.8386 (mtp) cc_final: 0.8065 (mtt)
REVERT: o   45 GLN cc_start: 0.7647 (tp40) cc_final: 0.7093 (tp-100)
REVERT: o  109 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7867 (mt)
REVERT: o  144 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7618 (mm-30)
REVERT: s   20 LYS cc_start: 0.7782 (tttt) cc_final: 0.7572 (tmtt)
  outliers start: 31
  outliers final: 21
  residues processed: 275
  average time/residue: 0.1499
  time to fit residues: 51.2085
Evaluate side-chains
  273 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 251
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue  125 LEU
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   80 HIS
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   37 HIS
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   95 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  15 ASN
A  37 GLN
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 140 ASN
s  37 HIS
** s  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s 141 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.077649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.067600 restraints weight = 29190.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.069445 restraints weight = 15678.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.070646 restraints weight = 10148.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.071394 restraints weight = 7426.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.071945 restraints weight = 6001.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9061  Z= 0.199
  Angle     :  0.647   7.634  12368  Z= 0.335
  Chirality :  0.041   0.215   1319
  Planarity :  0.005   0.046   1466
  Dihedral  : 13.706  73.456   1623
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.27 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.04 (0.27), residues: 945
  helix:  0.81 (0.26), residues: 381
  sheet: -0.59 (0.38), residues: 183
  loop : -0.45 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG o  43 
 TYR   0.022   0.002   TYR A  32 
 PHE   0.016   0.002   PHE o  18 
 TRP   0.020   0.002   TRP s 113 
 HIS   0.020   0.001   HIS s  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.20 ( 9049)
  covalent geometry    : angle       0.64730 /  0.33 (12368)
  hydrogen bonds       : bond        0.04007 /  3.84 (  407)
  hydrogen bonds       : angle       5.04457 /  4.93 ( 1225)
  metal coordination   : bond        0.00419 /  0.26 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 259
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7567 (pm20) cc_final: 0.7280 (pm20)
REVERT: E   51 LYS cc_start: 0.7780 (tppt) cc_final: 0.7257 (tppt)
REVERT: E  146 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: o   49 ARG cc_start: 0.6685 (ptt180) cc_final: 0.6365 (ptt90)
REVERT: o  109 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7968 (mt)
REVERT: o  144 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7583 (mm-30)
REVERT: o  147 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8063 (ttp80)
REVERT: p   14 ASP cc_start: 0.7397 (t0) cc_final: 0.6496 (t0)
REVERT: p  121 ARG cc_start: 0.7687 (mmp-170) cc_final: 0.7449 (mmp80)
REVERT: s   20 LYS cc_start: 0.7877 (tttt) cc_final: 0.7661 (tmtt)
  outliers start: 34
  outliers final: 28
  residues processed: 275
  average time/residue: 0.1503
  time to fit residues: 51.1855
Evaluate side-chains
  278 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 249
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue    7 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   16 GLU
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   80 HIS
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   23 ARG
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** s  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
t  12 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.077080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.067004 restraints weight = 28622.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.068870 restraints weight = 15290.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.070069 restraints weight = 9800.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.070821 restraints weight = 7157.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.071404 restraints weight = 5779.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9061  Z= 0.169
  Angle     :  0.638   7.706  12368  Z= 0.324
  Chirality :  0.042   0.240   1319
  Planarity :  0.005   0.057   1466
  Dihedral  : 13.746  73.426   1623
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.00 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.06 (0.27), residues: 945
  helix:  0.76 (0.26), residues: 381
  sheet: -0.57 (0.38), residues: 183
  loop : -0.43 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG s  49 
 TYR   0.020   0.002   TYR t 147 
 PHE   0.011   0.002   PHE t 112 
 TRP   0.022   0.002   TRP E 115 
 HIS   0.004   0.001   HIS p  42 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 ( 9049)
  covalent geometry    : angle       0.63827 /  0.32 (12368)
  hydrogen bonds       : bond        0.03782 /  3.59 (  407)
  hydrogen bonds       : angle       4.93587 /  4.79 ( 1225)
  metal coordination   : bond        0.00311 /  0.20 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 257
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7549 (pm20) cc_final: 0.7284 (pm20)
REVERT: E  146 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7846 (tm-30)
REVERT: o   43 ARG cc_start: 0.6908 (ptp90) cc_final: 0.6551 (ptp90)
REVERT: o  144 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: s  149 ARG cc_start: 0.7352 (ptt90) cc_final: 0.7134 (ptm160)
REVERT: t   14 ASP cc_start: 0.7123 (m-30) cc_final: 0.6873 (m-30)
REVERT: t   16 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7856 (mtm)
  outliers start: 33
  outliers final: 25
  residues processed: 273
  average time/residue: 0.1505
  time to fit residues: 50.6779
Evaluate side-chains
  262 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue    7 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   16 GLU
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   62 THR
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 79 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** o  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 139 HIS
** p 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
p 158 GLN
s  37 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.076144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.066218 restraints weight = 28675.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.068018 restraints weight = 15235.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.069216 restraints weight = 9869.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.070012 restraints weight = 7219.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.070554 restraints weight = 5766.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.5208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085   9061  Z= 0.174
  Angle     :  0.666   8.535  12368  Z= 0.341
  Chirality :  0.041   0.215   1319
  Planarity :  0.005   0.052   1466
  Dihedral  : 13.751  73.401   1623
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 20.28 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.12 (0.27), residues: 945
  helix:  0.62 (0.26), residues: 382
  sheet: -0.48 (0.39), residues: 180
  loop : -0.44 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG s  19 
 TYR   0.018   0.002   TYR A  32 
 PHE   0.019   0.002   PHE E 148 
 TRP   0.024   0.002   TRP E 115 
 HIS   0.004   0.001   HIS p  42 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.17 ( 9049)
  covalent geometry    : angle       0.66580 /  0.34 (12368)
  hydrogen bonds       : bond        0.03896 /  3.74 (  407)
  hydrogen bonds       : angle       4.88395 /  4.75 ( 1225)
  metal coordination   : bond        0.00253 /  0.16 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 255
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLN cc_start: 0.7516 (pm20) cc_final: 0.7247 (pm20)
REVERT: E  146 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7883 (tm-30)
REVERT: o   43 ARG cc_start: 0.6890 (ptp90) cc_final: 0.6558 (ptp90)
REVERT: o  118 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7562 (ptm160)
REVERT: o  144 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7492 (mm-30)
REVERT: s    9 ARG cc_start: 0.6972 (mmm160) cc_final: 0.6532 (tpp-160)
REVERT: s  113 TRP cc_start: 0.8549 (p-90) cc_final: 0.8274 (p-90)
REVERT: t   16 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7976 (mtm)
  outliers start: 34
  outliers final: 29
  residues processed: 269
  average time/residue: 0.1606
  time to fit residues: 53.0002
Evaluate side-chains
  267 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 237
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue    7 GLU
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  129 VAL
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   37 HIS
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain s residue  109 ILE
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   85 VAL
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0000
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  37 HIS
s  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.076257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.066503 restraints weight = 28280.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.068316 restraints weight = 15022.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.069505 restraints weight = 9681.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.070264 restraints weight = 7055.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.070835 restraints weight = 5663.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.5357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9061  Z= 0.147
  Angle     :  0.657   7.905  12368  Z= 0.337
  Chirality :  0.040   0.214   1319
  Planarity :  0.005   0.069   1466
  Dihedral  : 13.794  73.494   1623
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.67 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.09 (0.27), residues: 945
  helix:  0.57 (0.26), residues: 382
  sheet: -0.34 (0.40), residues: 166
  loop : -0.40 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG o 131 
 TYR   0.018   0.002   TYR A  32 
 PHE   0.030   0.002   PHE E 148 
 TRP   0.027   0.002   TRP E 115 
 HIS   0.019   0.001   HIS s  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 9049)
  covalent geometry    : angle       0.65664 /  0.34 (12368)
  hydrogen bonds       : bond        0.03685 /  3.55 (  407)
  hydrogen bonds       : angle       4.85200 /  4.72 ( 1225)
  metal coordination   : bond        0.00234 /  0.15 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 247
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: o  118 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7573 (ptm160)
REVERT: o  144 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: p   29 MET cc_start: 0.8243 (mmm) cc_final: 0.8035 (mtt)
REVERT: s  113 TRP cc_start: 0.8499 (p-90) cc_final: 0.8241 (p-90)
REVERT: t   16 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7985 (mtm)
  outliers start: 33
  outliers final: 27
  residues processed: 259
  average time/residue: 0.1479
  time to fit residues: 47.3814
Evaluate side-chains
  263 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 235
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue   95 VAL
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   16 MET
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   37 HIS
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain s residue  109 ILE
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
o  46 ASN
o 140 GLN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  37 HIS
** s 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.073943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.064210 restraints weight = 28380.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.065980 restraints weight = 15109.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.067152 restraints weight = 9773.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.067930 restraints weight = 7167.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.068451 restraints weight = 5750.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.5676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   9061  Z= 0.226
  Angle     :  0.729   9.926  12368  Z= 0.381
  Chirality :  0.042   0.216   1319
  Planarity :  0.007   0.180   1466
  Dihedral  : 13.732  73.395   1623
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.83 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.22 (0.27), residues: 945
  helix:  0.42 (0.26), residues: 381
  sheet: -0.38 (0.40), residues: 166
  loop : -0.44 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG o  19 
 TYR   0.018   0.002   TYR A  32 
 PHE   0.033   0.002   PHE s 127 
 TRP   0.036   0.002   TRP E 115 
 HIS   0.019   0.002   HIS s  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00529 /  0.23 ( 9049)
  covalent geometry    : angle       0.72930 /  0.38 (12368)
  hydrogen bonds       : bond        0.04165 /  3.99 (  407)
  hydrogen bonds       : angle       4.92400 /  4.79 ( 1225)
  metal coordination   : bond        0.00382 /  0.23 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 250
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: o   19 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7635 (mtm-85)
REVERT: o   43 ARG cc_start: 0.6981 (ptp90) cc_final: 0.6739 (ptp90)
REVERT: o  144 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: s  113 TRP cc_start: 0.8573 (p-90) cc_final: 0.8269 (p-90)
REVERT: s  141 GLN cc_start: 0.7692 (mm-40) cc_final: 0.6917 (mp10)
REVERT: t   14 ASP cc_start: 0.7102 (m-30) cc_final: 0.6860 (m-30)
REVERT: t   16 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7971 (mtm)
  outliers start: 36
  outliers final: 32
  residues processed: 264
  average time/residue: 0.1421
  time to fit residues: 46.4516
Evaluate side-chains
  276 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  151 HIS
Chi-restraints excluded: chain E residue   65 SER
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  130 GLN
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   16 GLU
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  129 VAL
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain s residue   37 HIS
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain s residue  109 ILE
Chi-restraints excluded: chain t residue    7 VAL
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   47 THR
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   72 LEU
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0070
   overall best weight:    0.7198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
o  37 HIS
o  46 ASN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** p 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  37 HIS
** s 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.074136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.064409 restraints weight = 28556.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.066205 restraints weight = 15214.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.067384 restraints weight = 9848.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.068172 restraints weight = 7207.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.068673 restraints weight = 5759.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.5802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9061  Z= 0.181
  Angle     :  0.742  12.030  12368  Z= 0.378
  Chirality :  0.041   0.215   1319
  Planarity :  0.007   0.153   1466
  Dihedral  : 13.810  73.469   1623
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.64 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.27 (0.27), residues: 945
  helix:  0.37 (0.26), residues: 380
  sheet: -0.35 (0.40), residues: 166
  loop : -0.48 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG o 131 
 TYR   0.018   0.002   TYR t 147 
 PHE   0.026   0.002   PHE s 127 
 TRP   0.044   0.002   TRP E 115 
 HIS   0.012   0.001   HIS s  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.18 ( 9049)
  covalent geometry    : angle       0.74155 /  0.38 (12368)
  hydrogen bonds       : bond        0.03880 /  3.71 (  407)
  hydrogen bonds       : angle       4.95676 /  4.91 ( 1225)
  metal coordination   : bond        0.00230 /  0.14 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 247
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: o   43 ARG cc_start: 0.6995 (ptp90) cc_final: 0.6717 (ptp90)
REVERT: o  144 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7367 (mm-30)
REVERT: s  113 TRP cc_start: 0.8535 (p-90) cc_final: 0.8231 (p-90)
REVERT: t   14 ASP cc_start: 0.7052 (m-30) cc_final: 0.6782 (m-30)
REVERT: t   16 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7766 (mpp)
  outliers start: 37
  outliers final: 31
  residues processed: 259
  average time/residue: 0.1512
  time to fit residues: 48.7247
Evaluate side-chains
  272 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 240
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  139 HIS
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain p residue  169 LEU
Chi-restraints excluded: chain s residue   23 ARG
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain s residue  109 ILE
Chi-restraints excluded: chain t residue    7 VAL
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   85 VAL
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Chi-restraints excluded: chain t residue  127 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0970
   chunk 70 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
o  37 HIS
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.073766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.064076 restraints weight = 28481.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.065864 restraints weight = 15175.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.067037 restraints weight = 9801.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.067807 restraints weight = 7162.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.068357 restraints weight = 5742.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.5920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9061  Z= 0.179
  Angle     :  0.755  11.711  12368  Z= 0.386
  Chirality :  0.042   0.215   1319
  Planarity :  0.007   0.184   1466
  Dihedral  : 13.825  73.478   1623
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.22 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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 (0.27), residues: 945
  helix:  0.36 (0.27), residues: 377
  sheet: -0.11 (0.42), residues: 152
  loop : -0.57 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG o 131 
 TYR   0.017   0.002   TYR t  94 
 PHE   0.022   0.002   PHE s 127 
 TRP   0.054   0.002   TRP E 115 
 HIS   0.007   0.001   HIS o  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.18 ( 9049)
  covalent geometry    : angle       0.75549 /  0.39 (12368)
  hydrogen bonds       : bond        0.03846 /  3.68 (  407)
  hydrogen bonds       : angle       4.97027 /  4.96 ( 1225)
  metal coordination   : bond        0.00224 /  0.14 (   12)

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

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

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1890 Ramachandran restraints generated.
    945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 243
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: o   43 ARG cc_start: 0.6997 (ptp90) cc_final: 0.6778 (ptp90)
REVERT: o  144 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: s   20 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7537 (tmtt)
REVERT: s  113 TRP cc_start: 0.8518 (p-90) cc_final: 0.8218 (p-90)
REVERT: s  118 ARG cc_start: 0.8529 (mtp180) cc_final: 0.7794 (ttp80)
REVERT: s  141 GLN cc_start: 0.7852 (mp10) cc_final: 0.7543 (mp10)
REVERT: t   14 ASP cc_start: 0.7046 (m-30) cc_final: 0.6785 (m-30)
REVERT: t   16 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7786 (mpp)
REVERT: t   83 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (mt0)
  outliers start: 35
  outliers final: 30
  residues processed: 258
  average time/residue: 0.1505
  time to fit residues: 48.4059
Evaluate side-chains
  265 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 233
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   46 TYR
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain o residue   73 TRP
Chi-restraints excluded: chain o residue   88 LEU
Chi-restraints excluded: chain o residue  109 ILE
Chi-restraints excluded: chain p residue   18 ILE
Chi-restraints excluded: chain p residue   53 SER
Chi-restraints excluded: chain p residue   99 ASP
Chi-restraints excluded: chain p residue  120 ILE
Chi-restraints excluded: chain p residue  159 ILE
Chi-restraints excluded: chain p residue  163 LEU
Chi-restraints excluded: chain p residue  169 LEU
Chi-restraints excluded: chain s residue   95 VAL
Chi-restraints excluded: chain s residue  109 ILE
Chi-restraints excluded: chain t residue    7 VAL
Chi-restraints excluded: chain t residue   16 MET
Chi-restraints excluded: chain t residue   18 ILE
Chi-restraints excluded: chain t residue   47 THR
Chi-restraints excluded: chain t residue   67 THR
Chi-restraints excluded: chain t residue   83 GLN
Chi-restraints excluded: chain t residue   95 SER
Chi-restraints excluded: chain t residue  120 ILE
Chi-restraints excluded: chain t residue  127 ARG
Chi-restraints excluded: chain t residue  159 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 93 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
o  37 HIS
o 140 GLN
** p  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
s  37 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.073035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.063423 restraints weight = 28451.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.065201 restraints weight = 15138.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.066371 restraints weight = 9746.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.067163 restraints weight = 7109.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.067667 restraints weight = 5657.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.6071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9061  Z= 0.187
  Angle     :  0.760  11.527  12368  Z= 0.387
  Chirality :  0.042   0.275   1319
  Planarity :  0.007   0.165   1466
  Dihedral  : 13.827  73.490   1623
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 23.52 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.33 (0.27), residues: 945
  helix:  0.28 (0.27), residues: 378
  sheet: -0.10 (0.43), residues: 152
  loop : -0.61 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG o 131 
 TYR   0.018   0.002   TYR t  94 
 PHE   0.019   0.002   PHE s 127 
 TRP   0.061   0.002   TRP E 115 
 HIS   0.008   0.001   HIS o  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.19 ( 9049)
  covalent geometry    : angle       0.76006 /  0.39 (12368)
  hydrogen bonds       : bond        0.03921 /  3.73 (  407)
  hydrogen bonds       : angle       4.94540 /  4.92 ( 1225)
  metal coordination   : bond        0.00262 /  0.16 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1978.15 seconds
wall clock time: 34 minutes 57.67 seconds (2097.67 seconds total)