Starting phenix.real_space_refine
on Wed Mar  4 18:49:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cgn_30358/03_2026/7cgn_30358.map"
  }
  resolution = 4.3
  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=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      68      5.16       5
     C   10164      2.51       5
     N    2666      2.21       5
     O    2950      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15854
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1934
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 7, 'TRANS': 249}
    Chain: "B"
      Number of atoms: 1995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1995
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 244}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 724
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "D"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1934
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 7, 'TRANS': 249}
    Chain: "E"
      Number of atoms: 1995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 1995
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 244}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "F"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 724
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
    Chain: "G"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1105
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1105
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1033
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "J"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1105
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1105
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1033
          Classifications: {'peptide': 144}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 137}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.16, per 1000 atoms: 0.20
  Number of scatterers: 15854
  At special positions: 0
  Unit cell: (104.352, 116.309, 150.006, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      68     16.00
     P       6     15.00
     O    2950      8.00
     N    2666      7.00
     C   10164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 632.6 milliseconds
  

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3824

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 20 sheets defined
      42.9% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 31
      removed outlier: 3.752A  pdb=" N   LEU A   9 " --> pdb=" O   ALA A   5 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS A  12 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE A  14 " --> pdb=" O   GLY A  10 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU A  17 " --> pdb=" O   GLY A  13 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A  19 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE A  20 " --> pdb=" O   THR A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 52
      removed outlier: 3.710A  pdb=" N   VAL A  45 " --> pdb=" O   ALA A  41 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG A  46 " --> pdb=" O   PRO A  42 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
      removed outlier: 3.804A  pdb=" N   ILE A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   PHE A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A  77 " --> pdb=" O   GLN A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 86
      No H-bonds generated for 'chain 'A' and resid 84 through 86'
    Processing helix  chain 'A' and resid 87 through 96
      removed outlier: 3.822A  pdb=" N   ALA A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU A  93 " --> pdb=" O   MET A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 126
      removed outlier: 3.705A  pdb=" N   VAL A 102 " --> pdb=" O   GLU A  98 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   THR A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 133
      removed outlier: 3.533A  pdb=" N   GLU A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 144 through 153
      removed outlier: 3.588A  pdb=" N   VAL A 152 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 174
      removed outlier: 4.001A  pdb=" N   LEU A 157 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ILE A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 191
      removed outlier: 3.686A  pdb=" N   TRP A 186 " --> pdb=" O   SER A 182 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA A 188 " --> pdb=" O   PHE A 184 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASN A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 221
      removed outlier: 4.022A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   THR A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP A 215 " --> pdb=" O   ILE A 211 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 258
      removed outlier: 4.136A  pdb=" N   SER A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL A 240 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   MET A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A 258 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.769A  pdb=" N   LEU B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
      removed outlier: 3.863A  pdb=" N   ALA B  74 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET B  75 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 71 through 75'
    Processing helix  chain 'B' and resid 76 through 84
    Processing helix  chain 'B' and resid 101 through 107
    Processing helix  chain 'B' and resid 109 through 114
    Processing helix  chain 'B' and resid 117 through 132
      removed outlier: 3.878A  pdb=" N   LYS B 128 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLU B 130 " --> pdb=" O   MET B 126 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL B 132 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 159
      removed outlier: 3.539A  pdb=" N   ARG B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ARG B 152 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 193
      removed outlier: 3.520A  pdb=" N   LYS B 185 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU B 189 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN B 191 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 209
    Processing helix  chain 'B' and resid 237 through 246
    Processing helix  chain 'C' and resid 25 through 31
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 80 through 88
      removed outlier: 3.669A  pdb=" N   LYS C  86 " --> pdb=" O   TYR C  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 31
      removed outlier: 3.752A  pdb=" N   LEU D   9 " --> pdb=" O   ALA D   5 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS D  12 " --> pdb=" O   SER D   8 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE D  14 " --> pdb=" O   GLY D  10 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU D  17 " --> pdb=" O   GLY D  13 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR D  19 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE D  20 " --> pdb=" O   THR D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 52
      removed outlier: 3.710A  pdb=" N   VAL D  45 " --> pdb=" O   ALA D  41 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG D  46 " --> pdb=" O   PRO D  42 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN D  47 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR D  49 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
      removed outlier: 3.803A  pdb=" N   ILE D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   PHE D  65 " --> pdb=" O   VAL D  61 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR D  75 " --> pdb=" O   GLY D  71 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL D  77 " --> pdb=" O   GLN D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 86
      No H-bonds generated for 'chain 'D' and resid 84 through 86'
    Processing helix  chain 'D' and resid 87 through 96
      removed outlier: 3.822A  pdb=" N   ALA D  92 " --> pdb=" O   GLY D  88 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU D  93 " --> pdb=" O   MET D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 126
      removed outlier: 3.705A  pdb=" N   VAL D 102 " --> pdb=" O   GLU D  98 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA D 104 " --> pdb=" O   GLY D 100 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA D 105 " --> pdb=" O   PRO D 101 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER D 114 " --> pdb=" O   GLY D 110 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   THR D 117 " --> pdb=" O   GLY D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 133
      removed outlier: 3.533A  pdb=" N   GLU D 133 " --> pdb=" O   LEU D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 143
    Processing helix  chain 'D' and resid 144 through 153
      removed outlier: 3.589A  pdb=" N   VAL D 152 " --> pdb=" O   PHE D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 174
      removed outlier: 4.000A  pdb=" N   LEU D 157 " --> pdb=" O   ILE D 153 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ILE D 161 " --> pdb=" O   LEU D 157 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA D 164 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   VAL D 173 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLY D 174 " --> pdb=" O   GLY D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 191
      removed outlier: 3.687A  pdb=" N   TRP D 186 " --> pdb=" O   SER D 182 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER D 187 " --> pdb=" O   GLY D 183 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA D 188 " --> pdb=" O   PHE D 184 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   MET D 189 " --> pdb=" O   PHE D 185 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASN D 191 " --> pdb=" O   SER D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 221
      removed outlier: 4.021A  pdb=" N   LEU D 203 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL D 208 " --> pdb=" O   ILE D 204 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE D 209 " --> pdb=" O   LYS D 205 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE D 211 " --> pdb=" O   VAL D 207 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   THR D 212 " --> pdb=" O   VAL D 208 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP D 215 " --> pdb=" O   ILE D 211 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN D 220 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 258
      removed outlier: 4.137A  pdb=" N   SER D 232 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL D 240 " --> pdb=" O   THR D 236 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU D 244 " --> pdb=" O   VAL D 240 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU D 247 " --> pdb=" O   SER D 243 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL D 252 " --> pdb=" O   GLY D 248 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   MET D 257 " --> pdb=" O   LEU D 253 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   PHE D 258 " --> pdb=" O   THR D 254 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 3.769A  pdb=" N   LEU E  51 " --> pdb=" O   LYS E  47 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 75
      removed outlier: 3.864A  pdb=" N   ALA E  74 " --> pdb=" O   ASN E  71 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   MET E  75 " --> pdb=" O   ILE E  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 71 through 75'
    Processing helix  chain 'E' and resid 76 through 84
    Processing helix  chain 'E' and resid 101 through 107
    Processing helix  chain 'E' and resid 109 through 114
    Processing helix  chain 'E' and resid 117 through 132
      removed outlier: 3.878A  pdb=" N   LYS E 128 " --> pdb=" O   THR E 124 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU E 130 " --> pdb=" O   MET E 126 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL E 132 " --> pdb=" O   LYS E 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 159
      removed outlier: 3.540A  pdb=" N   ARG E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ARG E 152 " --> pdb=" O   GLY E 148 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 176 through 193
      removed outlier: 3.520A  pdb=" N   LYS E 185 " --> pdb=" O   GLY E 181 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU E 189 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN E 191 " --> pdb=" O   ILE E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 209
    Processing helix  chain 'E' and resid 237 through 246
    Processing helix  chain 'F' and resid 25 through 31
    Processing helix  chain 'F' and resid 51 through 64
    Processing helix  chain 'F' and resid 80 through 88
      removed outlier: 3.669A  pdb=" N   LYS F  86 " --> pdb=" O   TYR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 26
      removed outlier: 3.540A  pdb=" N   TRP G   9 " --> pdb=" O   LYS G   5 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY G  11 " --> pdb=" O   GLU G   7 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU G  18 " --> pdb=" O   LEU G  14 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL G  24 " --> pdb=" O   ALA G  20 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS G  25 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 145 through 150
    Processing helix  chain 'H' and resid 9 through 28
      removed outlier: 3.985A  pdb=" N   PHE H  13 " --> pdb=" O   TRP H   9 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL H  24 " --> pdb=" O   ALA H  20 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS H  25 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LYS H  27 " --> pdb=" O   PHE H  23 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 144 through 152
      removed outlier: 3.759A  pdb=" N   PHE H 150 " --> pdb=" O   LEU H 146 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU H 151 " --> pdb=" O   ILE H 147 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR H 152 " --> pdb=" O   GLY H 148 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 5 through 28
      removed outlier: 4.028A  pdb=" N   TRP I   9 " --> pdb=" O   LYS I   5 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL I  10 " --> pdb=" O   ASN I   6 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE I  13 " --> pdb=" O   TRP I   9 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU I  22 " --> pdb=" O   LEU I  18 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 142 through 152
      removed outlier: 3.515A  pdb=" N   PHE I 150 " --> pdb=" O   LEU I 146 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 5 through 29
      removed outlier: 3.702A  pdb=" N   GLY J  11 " --> pdb=" O   GLU J   7 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 142 through 152
      removed outlier: 3.515A  pdb=" N   PHE J 150 " --> pdb=" O   LEU J 146 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 6 through 29
      removed outlier: 3.993A  pdb=" N   ALA K  28 " --> pdb=" O   VAL K  24 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA K  29 " --> pdb=" O   CYS K  25 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 142 through 152
      removed outlier: 4.568A  pdb=" N   LEU K 146 " --> pdb=" O   VAL K 142 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU K 151 " --> pdb=" O   ILE K 147 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 5 through 28
    Processing helix  chain 'L' and resid 143 through 151
      removed outlier: 3.565A  pdb=" N   PHE L 150 " --> pdb=" O   LEU L 146 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 32
      removed outlier: 6.033A  pdb=" N   ILE B  27 " --> pdb=" O   ASP B  13 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASP B  13 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  29 " --> pdb=" O   MET B  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90
      removed outlier: 6.721A  pdb=" N   SER B  88 " --> pdb=" O   MET B 167 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   ASP B 169 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU B  90 " --> pdb=" O   ASP B 169 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR B  37 " --> pdb=" O   CYS B 198 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   ILE B  36 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   TRP B 216 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA B  38 " --> pdb=" O   TRP B 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42
    Processing sheet with id=AA4, first strand: chain 'E' and resid 27 through 32
      removed outlier: 6.033A  pdb=" N   ILE E  27 " --> pdb=" O   ASP E  13 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ASP E  13 " --> pdb=" O   ILE E  27 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU E  29 " --> pdb=" O   MET E  11 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 87 through 90
      removed outlier: 6.720A  pdb=" N   SER E  88 " --> pdb=" O   MET E 167 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   ASP E 169 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU E  90 " --> pdb=" O   ASP E 169 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR E  37 " --> pdb=" O   CYS E 198 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   ILE E  36 " --> pdb=" O   HIS E 214 " (cutoff:3.500A)
      removed outlier: 8.358A  pdb=" N   TRP E 216 " --> pdb=" O   ILE E  36 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA E  38 " --> pdb=" O   TRP E 216 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 41 through 42
    Processing sheet with id=AA7, first strand: chain 'G' and resid 97 through 98
    Processing sheet with id=AA8, first strand: chain 'G' and resid 97 through 98
      removed outlier: 6.815A  pdb=" N   VAL G  58 " --> pdb=" O   VAL G  65 " (cutoff:3.500A)
      removed outlier: 10.119A  pdb=" N   VAL G  65 " --> pdb=" O   GLU G  87 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLU G  87 " --> pdb=" O   VAL G  65 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG G  67 " --> pdb=" O   GLU G  85 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU G  85 " --> pdb=" O   ARG G  67 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU G  42 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
      removed outlier: 9.455A  pdb=" N   ILE G 134 " --> pdb=" O   THR G  41 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   TYR G  43 " --> pdb=" O   ILE G 134 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 81 through 87
      removed outlier: 8.825A  pdb=" N   ILE H 134 " --> pdb=" O   THR H  41 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   TYR H  43 " --> pdb=" O   ILE H 134 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 63 through 67
      removed outlier: 6.864A  pdb=" N   VAL H  58 " --> pdb=" O   VAL H  65 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'I' and resid 39 through 40
    Processing sheet with id=AB3, first strand: chain 'I' and resid 63 through 68
      removed outlier: 3.686A  pdb=" N   VAL I  63 " --> pdb=" O   ILE I  60 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL I  58 " --> pdb=" O   VAL I  65 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ARG I  67 " --> pdb=" O   SER I  56 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   SER I  56 " --> pdb=" O   ARG I  67 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 81 through 87
      removed outlier: 3.634A  pdb=" N   LEU J  42 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ILE J 134 " --> pdb=" O   THR J  41 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   TYR J  43 " --> pdb=" O   ILE J 134 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'J' and resid 63 through 67
      removed outlier: 3.751A  pdb=" N   VAL J  63 " --> pdb=" O   ILE J  60 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL J  58 " --> pdb=" O   VAL J  65 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LEU J 114 " --> pdb=" O   PRO J  57 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER J  59 " --> pdb=" O   LEU J 114 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   VAL J 116 " --> pdb=" O   SER J  59 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 39 through 40
    Processing sheet with id=AB7, first strand: chain 'K' and resid 81 through 83
      removed outlier: 7.754A  pdb=" N   TYR K  43 " --> pdb=" O   ILE K 134 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 68
      removed outlier: 6.382A  pdb=" N   VAL K  58 " --> pdb=" O   VAL K  65 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ARG K  67 " --> pdb=" O   SER K  56 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   SER K  56 " --> pdb=" O   ARG K  67 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'K' and resid 63 through 68
      removed outlier: 6.382A  pdb=" N   VAL K  58 " --> pdb=" O   VAL K  65 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ARG K  67 " --> pdb=" O   SER K  56 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   SER K  56 " --> pdb=" O   ARG K  67 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 39 through 40
    Processing sheet with id=AC2, first strand: chain 'L' and resid 63 through 67
      removed outlier: 6.732A  pdb=" N   VAL L  58 " --> pdb=" O   VAL L  65 " (cutoff:3.500A)

    609 hydrogen bonds defined for protein.
    1782 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 5142
        1.35 -     1.47: 3629
        1.47 -     1.60: 7227
        1.60 -     1.72: 10
        1.72 -     1.84: 124
  Bond restraints: 16132
  Sorted by residual:
  bond pdb=" C4  ATP E 301 "
       pdb=" C5  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.91e+01
  bond pdb=" C4  ATP B 301 "
       pdb=" C5  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.388  1.471 -0.083 1.00e-02 1.00e+04 6.86e+01
  bond pdb=" C5  ATP E 301 "
       pdb=" C6  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.34e+01
  bond pdb=" C5  ATP B 301 "
       pdb=" C6  ATP B 301 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.33e+01
  bond pdb=" C8  ATP E 301 "
       pdb=" N7  ATP E 301 "
    ideal  model  delta    sigma   weight residual
    1.310  1.358 -0.048 1.00e-02 1.00e+04 2.30e+01
  ... (remaining 16127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.87: 21687
        3.87 -     7.75: 221
        7.75 -    11.62: 36
       11.62 -    15.49: 0
       15.49 -    19.37: 4
  Bond angle restraints: 21948
  Sorted by residual:
  angle pdb=" PB  ATP E 301 "
        pdb=" O3B ATP E 301 "
        pdb=" PG  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     139.87  120.50   19.37 1.00e+00 1.00e+00 3.75e+02
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  120.56   19.31 1.00e+00 1.00e+00 3.73e+02
  angle pdb=" PA  ATP E 301 "
        pdb=" O3A ATP E 301 "
        pdb=" PB  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     136.83  120.47   16.36 1.00e+00 1.00e+00 2.68e+02
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  120.51   16.32 1.00e+00 1.00e+00 2.66e+02
  angle pdb=" C5  ATP E 301 "
        pdb=" C4  ATP E 301 "
        pdb=" N3  ATP E 301 "
      ideal   model   delta    sigma   weight residual
     126.80  118.64    8.16 1.00e+00 1.00e+00 6.67e+01
  ... (remaining 21943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 8421
       17.12 -    34.23: 867
       34.23 -    51.35: 267
       51.35 -    68.47: 94
       68.47 -    85.59: 23
  Dihedral angle restraints: 9672
    sinusoidal: 3718
      harmonic: 5954
  Sorted by residual:
  dihedral pdb=" CA  GLN J 135 "
           pdb=" C   GLN J 135 "
           pdb=" N   ASP J 136 "
           pdb=" CA  ASP J 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.81   27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  ALA K 140 "
           pdb=" C   ALA K 140 "
           pdb=" N   MET K 141 "
           pdb=" CA  MET K 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.54   24.46     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  VAL J 142 "
           pdb=" C   VAL J 142 "
           pdb=" N   LEU J 143 "
           pdb=" CA  LEU J 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 9669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 2114
       0.064 -    0.129: 443
       0.129 -    0.193: 76
       0.193 -    0.257: 15
       0.257 -    0.321: 4
  Chirality restraints: 2652
  Sorted by residual:
  chirality pdb=" CB  ILE B 223 "
            pdb=" CA  ILE B 223 "
            pdb=" CG1 ILE B 223 "
            pdb=" CG2 ILE B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CB  ILE E 223 "
            pdb=" CA  ILE E 223 "
            pdb=" CG1 ILE E 223 "
            pdb=" CG2 ILE E 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CB  ILE J  60 "
            pdb=" CA  ILE J  60 "
            pdb=" CG1 ILE J  60 "
            pdb=" CG2 ILE J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.30e+00
  ... (remaining 2649 not shown)

  Planarity restraints: 2762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  16 "   -0.024 2.00e-02 2.50e+03   2.39e-02 9.99e+00
        pdb=" CG  PHE E  16 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  16 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  16 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  16 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  16 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  16 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  16 "    0.024 2.00e-02 2.50e+03   2.38e-02 9.94e+00
        pdb=" CG  PHE B  16 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  16 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  16 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  16 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  16 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  16 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  41 "   -0.049 5.00e-02 4.00e+02   7.46e-02 8.89e+00
        pdb=" N   PRO B  42 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO B  42 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B  42 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 2759 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2668
        2.76 -     3.30: 14898
        3.30 -     3.83: 26061
        3.83 -     4.37: 28802
        4.37 -     4.90: 48214
  Nonbonded interactions: 120643
  Sorted by model distance:
  nonbonded pdb=" O   ALA K  69 "
            pdb=" N   ILE K  71 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" O   GLY A 110 "
            pdb=" OG  SER A 114 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLY D 110 "
            pdb=" OG  SER D 114 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   PRO B  42 "
            pdb=" CG  ASP E 176 "
     model   vdw
     2.242 3.270
  nonbonded pdb=" OG  SER I 100 "
            pdb=" O   ALA I 113 "
     model   vdw
     2.252 3.040
  ... (remaining 120638 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 36 through 152))
  selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 36 through 152))
  selection = chain 'I'
  selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 36 through 152))
  selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 36 through 152))
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.850
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
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      :  0.006   0.083  16132  Z= 0.321
  Angle     :  1.118  19.367  21948  Z= 0.678
  Chirality :  0.057   0.321   2652
  Planarity :  0.007   0.075   2762
  Dihedral  : 16.920  85.586   5848
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.44 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  :  9.75 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.60 (0.13), residues: 2056
  helix: -4.23 (0.08), residues: 801
  sheet: -3.05 (0.28), residues: 254
  loop : -3.41 (0.16), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  18 
 TYR   0.020   0.002   TYR H  40 
 PHE   0.054   0.002   PHE B  16 
 TRP   0.012   0.002   TRP B 216 
 HIS   0.006   0.001   HIS K  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 (16132)
  covalent geometry    : angle       1.11757 (21948)
  hydrogen bonds       : bond        0.33197 (  601)
  hydrogen bonds       : angle      10.71981 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  617 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 510
  time to evaluate  : 0.650 
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: A   81 TYR cc_start: 0.7525 (m-80) cc_final: 0.7269 (m-80)
REVERT: A  189 MET cc_start: 0.6996 (ttm) cc_final: 0.6658 (ttm)
REVERT: A  201 ASN cc_start: 0.8626 (t0) cc_final: 0.8267 (t0)
REVERT: A  251 PHE cc_start: 0.8406 (t80) cc_final: 0.7976 (t80)
REVERT: B   10 ASP cc_start: 0.7381 (t0) cc_final: 0.6881 (t0)
REVERT: B   20 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6744 (p0)
REVERT: B   89 MET cc_start: 0.7195 (mtp) cc_final: 0.6969 (mtp)
REVERT: B  100 MET cc_start: 0.7869 (mtt) cc_final: 0.7149 (mtt)
REVERT: B  172 PHE cc_start: 0.8292 (m-80) cc_final: 0.7812 (m-80)
REVERT: B  224 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (p)
REVERT: C   59 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8883 (tt)
REVERT: C   74 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7797 (mm)
REVERT: C   80 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8822 (mmmt)
REVERT: D   14 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8827 (tp)
REVERT: D  135 MET cc_start: 0.8937 (mmt) cc_final: 0.8686 (mmp)
REVERT: D  243 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9289 (t)
REVERT: E   28 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.6859 (t)
REVERT: E   29 LEU cc_start: 0.8551 (pp) cc_final: 0.8164 (pp)
REVERT: E   85 LYS cc_start: 0.8750 (mppt) cc_final: 0.8260 (mtpt)
REVERT: E  126 MET cc_start: 0.9343 (tpp) cc_final: 0.8887 (tpp)
REVERT: E  167 MET cc_start: 0.6955 (mtt) cc_final: 0.5823 (mtt)
REVERT: E  202 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (p)
REVERT: F   74 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7213 (tp)
REVERT: F   78 ASN cc_start: 0.8518 (p0) cc_final: 0.8305 (p0)
REVERT: F   79 ASP cc_start: 0.7664 (t0) cc_final: 0.7450 (t0)
REVERT: F   86 LYS cc_start: 0.8700 (pttt) cc_final: 0.8335 (tmtt)
REVERT: G   12 ILE cc_start: 0.8905 (mt) cc_final: 0.8278 (tp)
REVERT: G   40 TYR cc_start: 0.3456 (p90) cc_final: 0.3085 (p90)
REVERT: G   48 ASN cc_start: 0.4710 (t0) cc_final: 0.4154 (p0)
REVERT: G   81 ARG cc_start: 0.7324 (tmm160) cc_final: 0.6837 (ttp80)
REVERT: G   89 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7143 (mtm-85)
REVERT: G  145 ASP cc_start: 0.8790 (t0) cc_final: 0.8131 (p0)
REVERT: H   90 TYR cc_start: 0.4957 (m-80) cc_final: 0.4715 (m-10)
REVERT: H  130 ASP cc_start: 0.8383 (p0) cc_final: 0.7821 (p0)
REVERT: H  135 GLN cc_start: 0.6918 (mt0) cc_final: 0.6665 (mp-120)
REVERT: I   52 LEU cc_start: 0.3370 (tt) cc_final: 0.2828 (tt)
REVERT: I   88 GLN cc_start: 0.6454 (mt0) cc_final: 0.5425 (tm-30)
REVERT: J   53 LYS cc_start: 0.7304 (mptt) cc_final: 0.6974 (ptpt)
REVERT: K   88 GLN cc_start: 0.6898 (tp-100) cc_final: 0.6548 (pp30)
REVERT: K  109 GLU cc_start: 0.7961 (mp0) cc_final: 0.7689 (mp0)
  outliers start: 107
  outliers final: 15
  residues processed: 569
  average time/residue: 0.1396
  time to fit residues: 113.8153
Evaluate side-chains
  334 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 310
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 194 optimal weight:   10.0000
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 200 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
A  73 GLN
A 220 ASN
A 241 HIS
B 105 ASN
B 122 HIS
B 191 ASN
B 226 HIS
C  60 HIS
C  68 GLN
C  75 GLN
D  11 HIS
D  29 ASN
D 220 ASN
E  26 ASN
E 105 ASN
E 122 HIS
E 191 ASN
E 226 HIS
E 262 HIS
F  68 GLN
F  89 ASN
H  88 GLN
I  91 ASN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.115815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.087347 restraints weight = 51970.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088948 restraints weight = 34265.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.089337 restraints weight = 23831.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.089986 restraints weight = 18646.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.090086 restraints weight = 16457.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16132  Z= 0.164
  Angle     :  0.737   8.860  21948  Z= 0.379
  Chirality :  0.047   0.260   2652
  Planarity :  0.006   0.058   2762
  Dihedral  :  8.073  89.727   2296
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  8.90 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.53 %
    Favored  : 94.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.16), residues: 2056
  helix: -1.70 (0.15), residues: 836
  sheet: -2.53 (0.30), residues: 277
  loop : -3.29 (0.17), residues: 943

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  67 
 TYR   0.014   0.001   TYR G  78 
 PHE   0.020   0.002   PHE H  23 
 TRP   0.011   0.001   TRP E 216 
 HIS   0.007   0.001   HIS D  11 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (16132)
  covalent geometry    : angle       0.73729 (21948)
  hydrogen bonds       : bond        0.05035 (  601)
  hydrogen bonds       : angle       5.45895 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 408
  time to evaluate  : 0.605 
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: A  127 GLU cc_start: 0.8441 (pm20) cc_final: 0.7952 (pm20)
REVERT: A  153 ILE cc_start: 0.9356 (mm) cc_final: 0.9089 (mt)
REVERT: A  180 ILE cc_start: 0.8050 (mt) cc_final: 0.7465 (mt)
REVERT: A  201 ASN cc_start: 0.8615 (t0) cc_final: 0.8305 (t0)
REVERT: B   10 ASP cc_start: 0.7748 (t0) cc_final: 0.7367 (t0)
REVERT: B   89 MET cc_start: 0.7580 (mtp) cc_final: 0.7156 (mtp)
REVERT: B   91 PHE cc_start: 0.8400 (m-80) cc_final: 0.8120 (m-80)
REVERT: B  172 PHE cc_start: 0.8807 (m-80) cc_final: 0.8428 (m-80)
REVERT: C   40 THR cc_start: 0.8384 (t) cc_final: 0.7969 (m)
REVERT: C   68 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6612 (tm-30)
REVERT: D  127 GLU cc_start: 0.8299 (mp0) cc_final: 0.8070 (mp0)
REVERT: D  135 MET cc_start: 0.9090 (mmt) cc_final: 0.8873 (mmp)
REVERT: E   11 MET cc_start: 0.8566 (ptp) cc_final: 0.8200 (ptp)
REVERT: E   85 LYS cc_start: 0.8801 (mppt) cc_final: 0.8535 (mtpt)
REVERT: E   89 MET cc_start: 0.8628 (mmt) cc_final: 0.8408 (mmp)
REVERT: E  126 MET cc_start: 0.9239 (tpp) cc_final: 0.8991 (tpp)
REVERT: E  221 LYS cc_start: 0.8854 (mppt) cc_final: 0.8604 (mppt)
REVERT: F   26 LEU cc_start: 0.7806 (pt) cc_final: 0.7486 (tp)
REVERT: F   79 ASP cc_start: 0.8039 (t0) cc_final: 0.7780 (t0)
REVERT: F   86 LYS cc_start: 0.8878 (pttt) cc_final: 0.8432 (tmtt)
REVERT: F   93 ASP cc_start: 0.7459 (p0) cc_final: 0.6978 (t70)
REVERT: G   48 ASN cc_start: 0.4102 (t0) cc_final: 0.3719 (p0)
REVERT: G   72 THR cc_start: 0.5937 (t) cc_final: 0.4719 (p)
REVERT: G   81 ARG cc_start: 0.7739 (tmm160) cc_final: 0.7104 (ttp80)
REVERT: G  103 THR cc_start: 0.6729 (m) cc_final: 0.6137 (t)
REVERT: G  145 ASP cc_start: 0.8568 (t0) cc_final: 0.7733 (p0)
REVERT: J   53 LYS cc_start: 0.7329 (mptt) cc_final: 0.7033 (ptpt)
REVERT: K   88 GLN cc_start: 0.6700 (tp-100) cc_final: 0.6281 (pp30)
REVERT: K  109 GLU cc_start: 0.7580 (mp0) cc_final: 0.6930 (mp0)
REVERT: L   81 ARG cc_start: 0.6553 (ttp80) cc_final: 0.6108 (ttp80)
  outliers start: 6
  outliers final: 0
  residues processed: 413
  average time/residue: 0.1232
  time to fit residues: 75.5240
Evaluate side-chains
  290 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 123 optimal weight:    7.9990
   chunk 91 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 177 optimal weight:    5.9990
   chunk 158 optimal weight:    6.9990
   chunk 193 optimal weight:   20.0000
   chunk 168 optimal weight:    0.0470
   chunk 125 optimal weight:    0.0970
   chunk 106 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    1.5880

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
B 191 ASN
B 214 HIS
C   9 GLN
D  11 HIS
D  40 HIS
E 105 ASN
E 175 GLN
E 214 HIS
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   9 GLN
H 135 GLN
I  88 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.115660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.087147 restraints weight = 51916.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.088778 restraints weight = 33183.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.089789 restraints weight = 21292.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090167 restraints weight = 16717.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.090225 restraints weight = 15623.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16132  Z= 0.126
  Angle     :  0.673   8.907  21948  Z= 0.342
  Chirality :  0.046   0.272   2652
  Planarity :  0.005   0.061   2762
  Dihedral  :  7.471  86.038   2296
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.51 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  5.11 %
    Favored  : 94.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.84 (0.17), residues: 2056
  helix: -0.45 (0.18), residues: 830
  sheet: -2.26 (0.31), residues: 259
  loop : -3.16 (0.18), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  18 
 TYR   0.014   0.001   TYR L 111 
 PHE   0.043   0.001   PHE E  16 
 TRP   0.013   0.001   TRP D 215 
 HIS   0.006   0.001   HIS D  11 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (16132)
  covalent geometry    : angle       0.67307 (21948)
  hydrogen bonds       : bond        0.04167 (  601)
  hydrogen bonds       : angle       4.78225 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  399 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 397
  time to evaluate  : 0.592 
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: A  153 ILE cc_start: 0.9395 (mm) cc_final: 0.9114 (mt)
REVERT: A  198 ASP cc_start: 0.7440 (m-30) cc_final: 0.7206 (m-30)
REVERT: B   10 ASP cc_start: 0.7610 (t0) cc_final: 0.7341 (t0)
REVERT: B   75 MET cc_start: 0.7357 (ptp) cc_final: 0.7101 (ptp)
REVERT: B   89 MET cc_start: 0.7894 (mtp) cc_final: 0.7296 (mtp)
REVERT: B   91 PHE cc_start: 0.8232 (m-80) cc_final: 0.7971 (m-80)
REVERT: C   59 LEU cc_start: 0.9233 (mt) cc_final: 0.8889 (mm)
REVERT: D   50 ASN cc_start: 0.8626 (t0) cc_final: 0.8387 (t0)
REVERT: D   73 GLN cc_start: 0.8809 (tp40) cc_final: 0.8258 (tp-100)
REVERT: D  127 GLU cc_start: 0.8347 (mp0) cc_final: 0.8025 (mp0)
REVERT: E   11 MET cc_start: 0.8518 (ptp) cc_final: 0.8147 (ptp)
REVERT: E  105 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8482 (t0)
REVERT: E  126 MET cc_start: 0.9194 (tpp) cc_final: 0.8923 (tpp)
REVERT: E  170 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8257 (tm-30)
REVERT: E  237 ASP cc_start: 0.7944 (t70) cc_final: 0.7700 (t0)
REVERT: F   26 LEU cc_start: 0.7766 (pt) cc_final: 0.7431 (tp)
REVERT: F   86 LYS cc_start: 0.8826 (pttt) cc_final: 0.8402 (tmtt)
REVERT: F   93 ASP cc_start: 0.7357 (p0) cc_final: 0.6792 (t70)
REVERT: G  103 THR cc_start: 0.6369 (m) cc_final: 0.5713 (t)
REVERT: G  145 ASP cc_start: 0.8464 (t0) cc_final: 0.7614 (p0)
REVERT: J   53 LYS cc_start: 0.7334 (mptt) cc_final: 0.7021 (ptpt)
REVERT: K   88 GLN cc_start: 0.6658 (tp-100) cc_final: 0.6345 (pp30)
REVERT: K  109 GLU cc_start: 0.7467 (mp0) cc_final: 0.6846 (mp0)
REVERT: L   81 ARG cc_start: 0.6661 (ttp80) cc_final: 0.6171 (ttp80)
  outliers start: 2
  outliers final: 1
  residues processed: 399
  average time/residue: 0.1182
  time to fit residues: 70.3602
Evaluate side-chains
  288 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 286
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 168 optimal weight:    0.0770
   chunk 127 optimal weight:    7.9990
   chunk 202 optimal weight:   10.0000
   chunk 52 optimal weight:   20.0000
   chunk 153 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 13 optimal weight:    8.9990
   chunk 105 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.2940

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
B  62 HIS
B 191 ASN
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 175 GLN
** E 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  48 ASN
I  92 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.116531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.088312 restraints weight = 52730.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.088713 restraints weight = 37296.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.088945 restraints weight = 27244.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.089289 restraints weight = 24569.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.089432 restraints weight = 21724.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16132  Z= 0.116
  Angle     :  0.663   9.360  21948  Z= 0.331
  Chirality :  0.045   0.230   2652
  Planarity :  0.005   0.071   2762
  Dihedral  :  7.131  79.116   2296
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.37 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.52 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.18), residues: 2056
  helix:  0.16 (0.18), residues: 828
  sheet: -2.20 (0.30), residues: 279
  loop : -3.04 (0.18), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  97 
 TYR   0.015   0.001   TYR K  40 
 PHE   0.032   0.002   PHE E  16 
 TRP   0.008   0.001   TRP C  29 
 HIS   0.006   0.001   HIS B 262 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (16132)
  covalent geometry    : angle       0.66296 (21948)
  hydrogen bonds       : bond        0.03593 (  601)
  hydrogen bonds       : angle       4.52084 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 378
  time to evaluate  : 0.468 
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: A   89 MET cc_start: 0.7600 (mtt) cc_final: 0.6848 (tmm)
REVERT: A  127 GLU cc_start: 0.8329 (pm20) cc_final: 0.7861 (pm20)
REVERT: A  153 ILE cc_start: 0.9392 (mm) cc_final: 0.9078 (mt)
REVERT: A  198 ASP cc_start: 0.7084 (m-30) cc_final: 0.6705 (m-30)
REVERT: B   10 ASP cc_start: 0.7792 (t0) cc_final: 0.7427 (t0)
REVERT: B   29 LEU cc_start: 0.9098 (pp) cc_final: 0.8896 (pp)
REVERT: B   75 MET cc_start: 0.7349 (ptp) cc_final: 0.7091 (ptp)
REVERT: B   89 MET cc_start: 0.8091 (mtp) cc_final: 0.7677 (mtp)
REVERT: B  172 PHE cc_start: 0.8487 (m-80) cc_final: 0.8037 (m-80)
REVERT: B  190 LEU cc_start: 0.9013 (mt) cc_final: 0.8808 (mt)
REVERT: B  220 ASP cc_start: 0.8206 (t0) cc_final: 0.7114 (m-30)
REVERT: C    6 SER cc_start: 0.8914 (m) cc_final: 0.8599 (p)
REVERT: D  250 ASP cc_start: 0.8685 (t70) cc_final: 0.8335 (t70)
REVERT: E   11 MET cc_start: 0.8682 (ptp) cc_final: 0.8314 (ptp)
REVERT: E   29 LEU cc_start: 0.8967 (pp) cc_final: 0.8722 (pp)
REVERT: E   67 PHE cc_start: 0.8336 (t80) cc_final: 0.8091 (t80)
REVERT: E  108 TYR cc_start: 0.8678 (t80) cc_final: 0.8381 (t80)
REVERT: E  126 MET cc_start: 0.9255 (tpp) cc_final: 0.8929 (tpp)
REVERT: F   26 LEU cc_start: 0.7877 (pt) cc_final: 0.7582 (tp)
REVERT: F   79 ASP cc_start: 0.7532 (t0) cc_final: 0.7297 (t0)
REVERT: F   93 ASP cc_start: 0.7440 (p0) cc_final: 0.7054 (t70)
REVERT: G   81 ARG cc_start: 0.7602 (tmm160) cc_final: 0.6991 (ttp80)
REVERT: G  103 THR cc_start: 0.6402 (m) cc_final: 0.5722 (t)
REVERT: G  145 ASP cc_start: 0.8554 (t0) cc_final: 0.7752 (p0)
REVERT: I   91 ASN cc_start: 0.6518 (m-40) cc_final: 0.5986 (m-40)
REVERT: I  129 LYS cc_start: 0.6684 (ptpp) cc_final: 0.6169 (mtmt)
REVERT: J   53 LYS cc_start: 0.7352 (mptt) cc_final: 0.7067 (ptpt)
REVERT: J  141 MET cc_start: 0.1610 (pmm) cc_final: -0.0335 (ptp)
REVERT: K   56 SER cc_start: 0.6219 (m) cc_final: 0.5960 (m)
REVERT: K   88 GLN cc_start: 0.6605 (tp-100) cc_final: 0.6320 (pp30)
REVERT: K  109 GLU cc_start: 0.7495 (mp0) cc_final: 0.6761 (mp0)
REVERT: L   81 ARG cc_start: 0.6777 (ttp80) cc_final: 0.6245 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 379
  average time/residue: 0.1198
  time to fit residues: 67.9896
Evaluate side-chains
  286 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 143 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0370
   chunk 25 optimal weight:    4.9990
   chunk 186 optimal weight:   40.0000
   chunk 57 optimal weight:   20.0000
   chunk 74 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 199 optimal weight:   30.0000
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.3864

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN
** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 214 HIS
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.116260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.086908 restraints weight = 52139.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.088719 restraints weight = 34124.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.089888 restraints weight = 21391.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.090174 restraints weight = 17871.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.090318 restraints weight = 15192.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16132  Z= 0.116
  Angle     :  0.645   9.287  21948  Z= 0.321
  Chirality :  0.045   0.195   2652
  Planarity :  0.005   0.058   2762
  Dihedral  :  6.783  77.759   2296
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.51 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.19), residues: 2056
  helix:  0.48 (0.19), residues: 841
  sheet: -2.08 (0.30), residues: 278
  loop : -2.95 (0.19), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  97 
 TYR   0.019   0.001   TYR B 261 
 PHE   0.032   0.001   PHE E  16 
 TRP   0.007   0.001   TRP D 195 
 HIS   0.005   0.001   HIS K  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (16132)
  covalent geometry    : angle       0.64478 (21948)
  hydrogen bonds       : bond        0.03398 (  601)
  hydrogen bonds       : angle       4.36716 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  381 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 381
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 MET cc_start: 0.7452 (mtt) cc_final: 0.6752 (tmm)
REVERT: A  153 ILE cc_start: 0.9462 (mm) cc_final: 0.9164 (mt)
REVERT: B   10 ASP cc_start: 0.7501 (t0) cc_final: 0.7296 (t0)
REVERT: B   75 MET cc_start: 0.7276 (ptp) cc_final: 0.7024 (ptp)
REVERT: B   89 MET cc_start: 0.8032 (mtp) cc_final: 0.7695 (mtp)
REVERT: B  172 PHE cc_start: 0.8436 (m-80) cc_final: 0.8059 (m-80)
REVERT: B  220 ASP cc_start: 0.8189 (t0) cc_final: 0.7026 (m-30)
REVERT: C    6 SER cc_start: 0.8775 (m) cc_final: 0.8479 (p)
REVERT: C   63 ASP cc_start: 0.8206 (m-30) cc_final: 0.8001 (m-30)
REVERT: D  250 ASP cc_start: 0.8558 (t70) cc_final: 0.8261 (t70)
REVERT: E   66 LEU cc_start: 0.7905 (tt) cc_final: 0.7329 (mt)
REVERT: E   67 PHE cc_start: 0.8278 (t80) cc_final: 0.8022 (t80)
REVERT: E  108 TYR cc_start: 0.8597 (t80) cc_final: 0.8260 (t80)
REVERT: E  126 MET cc_start: 0.9257 (tpp) cc_final: 0.8899 (tpp)
REVERT: E  128 LYS cc_start: 0.9327 (mtmm) cc_final: 0.8992 (mtmm)
REVERT: F   79 ASP cc_start: 0.7282 (t0) cc_final: 0.7056 (t0)
REVERT: F   93 ASP cc_start: 0.7354 (p0) cc_final: 0.6934 (t70)
REVERT: G   72 THR cc_start: 0.6788 (p) cc_final: 0.5570 (p)
REVERT: G   81 ARG cc_start: 0.7728 (tmm160) cc_final: 0.7107 (ttp80)
REVERT: G  103 THR cc_start: 0.6308 (m) cc_final: 0.5804 (t)
REVERT: G  145 ASP cc_start: 0.8443 (t0) cc_final: 0.7692 (p0)
REVERT: H   27 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6069 (mptt)
REVERT: H   90 TYR cc_start: 0.4168 (m-10) cc_final: 0.3589 (m-80)
REVERT: I  129 LYS cc_start: 0.6738 (ptpp) cc_final: 0.6447 (mtmm)
REVERT: J   53 LYS cc_start: 0.7338 (mptt) cc_final: 0.7038 (ptpt)
REVERT: K   56 SER cc_start: 0.6200 (m) cc_final: 0.5826 (m)
REVERT: K   88 GLN cc_start: 0.6757 (tp-100) cc_final: 0.6378 (pp30)
REVERT: K  109 GLU cc_start: 0.7372 (mp0) cc_final: 0.6624 (mp0)
REVERT: L   81 ARG cc_start: 0.6849 (ttp80) cc_final: 0.6322 (ttp80)
REVERT: L  141 MET cc_start: 0.4322 (pmm) cc_final: 0.3459 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 381
  average time/residue: 0.1212
  time to fit residues: 68.7724
Evaluate side-chains
  289 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 119 optimal weight:    7.9990
   chunk 141 optimal weight:    3.9990
   chunk 159 optimal weight:   30.0000
   chunk 126 optimal weight:    6.9990
   chunk 160 optimal weight:   20.0000
   chunk 63 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN
B 214 HIS
C  60 HIS
C  89 ASN
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN
H 149 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.112500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.083951 restraints weight = 52181.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.085531 restraints weight = 33098.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.086279 restraints weight = 21839.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.086934 restraints weight = 17918.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087028 restraints weight = 14888.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16132  Z= 0.165
  Angle     :  0.698   8.684  21948  Z= 0.351
  Chirality :  0.046   0.278   2652
  Planarity :  0.005   0.055   2762
  Dihedral  :  6.802  78.285   2296
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.48 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.73 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.19), residues: 2056
  helix:  0.57 (0.19), residues: 844
  sheet: -1.96 (0.30), residues: 276
  loop : -2.91 (0.19), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  97 
 TYR   0.024   0.002   TYR H 152 
 PHE   0.026   0.002   PHE E  16 
 TRP   0.020   0.002   TRP B 216 
 HIS   0.004   0.001   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (16132)
  covalent geometry    : angle       0.69772 (21948)
  hydrogen bonds       : bond        0.03736 (  601)
  hydrogen bonds       : angle       4.61601 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 359
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 MET cc_start: 0.7595 (mtt) cc_final: 0.6876 (tmm)
REVERT: B   10 ASP cc_start: 0.7603 (t0) cc_final: 0.7345 (t0)
REVERT: B   75 MET cc_start: 0.7445 (ptp) cc_final: 0.7055 (ptp)
REVERT: B   89 MET cc_start: 0.7901 (mtp) cc_final: 0.7491 (mtp)
REVERT: B   91 PHE cc_start: 0.8023 (m-80) cc_final: 0.7480 (m-80)
REVERT: B  220 ASP cc_start: 0.8040 (t0) cc_final: 0.7732 (t0)
REVERT: C    6 SER cc_start: 0.8849 (m) cc_final: 0.8519 (p)
REVERT: C   59 LEU cc_start: 0.9307 (mt) cc_final: 0.9037 (mm)
REVERT: D   56 MET cc_start: 0.7309 (mtm) cc_final: 0.6895 (ptt)
REVERT: D   84 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8006 (mm-30)
REVERT: D  250 ASP cc_start: 0.8633 (t70) cc_final: 0.8293 (t70)
REVERT: E  108 TYR cc_start: 0.8668 (t80) cc_final: 0.8346 (t80)
REVERT: E  126 MET cc_start: 0.9298 (tpp) cc_final: 0.8969 (tpp)
REVERT: F   68 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6291 (pp30)
REVERT: F   79 ASP cc_start: 0.7148 (t0) cc_final: 0.6875 (t0)
REVERT: F   93 ASP cc_start: 0.7465 (p0) cc_final: 0.7007 (t70)
REVERT: G   72 THR cc_start: 0.7065 (p) cc_final: 0.5402 (p)
REVERT: G   81 ARG cc_start: 0.7788 (tmm160) cc_final: 0.7218 (ttp80)
REVERT: G  118 PHE cc_start: 0.5420 (m-80) cc_final: 0.5199 (m-80)
REVERT: G  145 ASP cc_start: 0.8623 (t0) cc_final: 0.7662 (p0)
REVERT: H   27 LYS cc_start: 0.7011 (ttmt) cc_final: 0.6788 (ttpt)
REVERT: H   90 TYR cc_start: 0.4138 (m-10) cc_final: 0.3578 (m-80)
REVERT: J   53 LYS cc_start: 0.7200 (mptt) cc_final: 0.6952 (ptpt)
REVERT: J  141 MET cc_start: 0.1798 (pmm) cc_final: 0.0060 (ptp)
REVERT: K   88 GLN cc_start: 0.6771 (tp-100) cc_final: 0.6451 (pp30)
REVERT: K  109 GLU cc_start: 0.7359 (mp0) cc_final: 0.6626 (mp0)
REVERT: L   49 ILE cc_start: 0.7556 (pt) cc_final: 0.7313 (pt)
REVERT: L   81 ARG cc_start: 0.6898 (ttp80) cc_final: 0.6318 (ttp80)
REVERT: L  141 MET cc_start: 0.4663 (pmm) cc_final: 0.3800 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 361
  average time/residue: 0.1217
  time to fit residues: 65.3270
Evaluate side-chains
  278 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 197 optimal weight:   30.0000
   chunk 146 optimal weight:   30.0000
   chunk 188 optimal weight:    0.7980
   chunk 156 optimal weight:    4.9990
   chunk 158 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9980
   chunk 151 optimal weight:    8.9990
   chunk 129 optimal weight:   20.0000
   chunk 181 optimal weight:   30.0000
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
B 191 ASN
E 105 ASN
E 115 GLN
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN
H 149 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.113959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.085404 restraints weight = 51869.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.086898 restraints weight = 34483.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.087652 restraints weight = 21742.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.088125 restraints weight = 18073.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.088275 restraints weight = 16479.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16132  Z= 0.122
  Angle     :  0.664   9.534  21948  Z= 0.329
  Chirality :  0.046   0.282   2652
  Planarity :  0.005   0.080   2762
  Dihedral  :  6.659  77.809   2296
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.46 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.96 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.19), residues: 2056
  helix:  0.80 (0.19), residues: 842
  sheet: -1.83 (0.31), residues: 272
  loop : -2.87 (0.19), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 124 
 TYR   0.016   0.001   TYR B 261 
 PHE   0.026   0.001   PHE J  13 
 TRP   0.014   0.001   TRP B 216 
 HIS   0.004   0.001   HIS C  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (16132)
  covalent geometry    : angle       0.66409 (21948)
  hydrogen bonds       : bond        0.03333 (  601)
  hydrogen bonds       : angle       4.41658 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 373
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 MET cc_start: 0.7525 (mtt) cc_final: 0.6853 (tmm)
REVERT: B   10 ASP cc_start: 0.7674 (t0) cc_final: 0.7367 (t0)
REVERT: B   75 MET cc_start: 0.7347 (ptp) cc_final: 0.7060 (ptp)
REVERT: B   89 MET cc_start: 0.8062 (mtp) cc_final: 0.7644 (mtp)
REVERT: B   91 PHE cc_start: 0.8119 (m-80) cc_final: 0.7669 (m-80)
REVERT: C   59 LEU cc_start: 0.9283 (mt) cc_final: 0.8974 (mm)
REVERT: D   75 TYR cc_start: 0.7852 (t80) cc_final: 0.7611 (t80)
REVERT: D   84 GLU cc_start: 0.8694 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: D  122 LEU cc_start: 0.8968 (tp) cc_final: 0.8754 (tp)
REVERT: D  211 ILE cc_start: 0.9409 (mt) cc_final: 0.9167 (mt)
REVERT: D  250 ASP cc_start: 0.8654 (t70) cc_final: 0.8361 (t70)
REVERT: E   24 PHE cc_start: 0.8790 (m-80) cc_final: 0.8409 (m-80)
REVERT: E  108 TYR cc_start: 0.8553 (t80) cc_final: 0.8247 (t80)
REVERT: E  126 MET cc_start: 0.9262 (tpp) cc_final: 0.8951 (tpp)
REVERT: F   68 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6284 (pp30)
REVERT: F   79 ASP cc_start: 0.7166 (t0) cc_final: 0.6876 (t0)
REVERT: F   93 ASP cc_start: 0.7549 (p0) cc_final: 0.7029 (t70)
REVERT: G   72 THR cc_start: 0.7039 (p) cc_final: 0.5431 (p)
REVERT: G   81 ARG cc_start: 0.7731 (tmm160) cc_final: 0.7130 (ttp80)
REVERT: G  112 LEU cc_start: 0.6169 (tp) cc_final: 0.5279 (tt)
REVERT: G  145 ASP cc_start: 0.8566 (t0) cc_final: 0.7745 (p0)
REVERT: H   27 LYS cc_start: 0.6918 (ttmt) cc_final: 0.6036 (mptt)
REVERT: H   90 TYR cc_start: 0.4059 (m-10) cc_final: 0.3557 (m-80)
REVERT: I  129 LYS cc_start: 0.7023 (ptpp) cc_final: 0.6607 (mtmt)
REVERT: J   53 LYS cc_start: 0.7241 (mptt) cc_final: 0.6997 (ptpt)
REVERT: J  141 MET cc_start: 0.2197 (pmm) cc_final: 0.0660 (ptp)
REVERT: K   53 LYS cc_start: 0.7245 (ttpt) cc_final: 0.7039 (ttpt)
REVERT: K   56 SER cc_start: 0.6312 (m) cc_final: 0.6109 (m)
REVERT: K   88 GLN cc_start: 0.6624 (tp-100) cc_final: 0.6292 (pp30)
REVERT: K  109 GLU cc_start: 0.7171 (mp0) cc_final: 0.6416 (mp0)
REVERT: L   81 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6541 (ttp80)
REVERT: L  141 MET cc_start: 0.5489 (pmm) cc_final: 0.5242 (ttm)
  outliers start: 2
  outliers final: 0
  residues processed: 374
  average time/residue: 0.1143
  time to fit residues: 64.3159
Evaluate side-chains
  279 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 278
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 152 optimal weight:   20.0000
   chunk 196 optimal weight:    0.0010
   chunk 97 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 201 optimal weight:    7.9990
   chunk 162 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 171 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   overall best weight:    5.3994

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

Flipped N/Q/H residues before XYZ refinement:
** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 ASN
C  60 HIS
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.110132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.082247 restraints weight = 53618.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.082341 restraints weight = 38303.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.082761 restraints weight = 27023.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.083009 restraints weight = 23424.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.083196 restraints weight = 21883.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.5393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  16132  Z= 0.218
  Angle     :  0.789   8.464  21948  Z= 0.395
  Chirality :  0.049   0.296   2652
  Planarity :  0.006   0.068   2762
  Dihedral  :  7.013  81.394   2296
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.78 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.02 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.19), residues: 2056
  helix:  0.45 (0.18), residues: 858
  sheet: -1.73 (0.32), residues: 252
  loop : -2.90 (0.19), residues: 946

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 124 
 TYR   0.024   0.002   TYR B 261 
 PHE   0.020   0.002   PHE B  16 
 TRP   0.033   0.002   TRP B 216 
 HIS   0.007   0.002   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (16132)
  covalent geometry    : angle       0.78929 (21948)
  hydrogen bonds       : bond        0.04177 (  601)
  hydrogen bonds       : angle       4.92126 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 346
  time to evaluate  : 0.602 
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: A   17 LEU cc_start: 0.9195 (tp) cc_final: 0.8734 (mm)
REVERT: A   56 MET cc_start: 0.7865 (ttp) cc_final: 0.7630 (ttm)
REVERT: A   89 MET cc_start: 0.7708 (mtt) cc_final: 0.7063 (tmm)
REVERT: B   29 LEU cc_start: 0.9094 (pp) cc_final: 0.8886 (pp)
REVERT: B   89 MET cc_start: 0.8000 (mtp) cc_final: 0.7711 (mtp)
REVERT: B   91 PHE cc_start: 0.8098 (m-80) cc_final: 0.7655 (m-80)
REVERT: C    6 SER cc_start: 0.8936 (m) cc_final: 0.8588 (p)
REVERT: C   59 LEU cc_start: 0.9334 (mt) cc_final: 0.9114 (mm)
REVERT: D   56 MET cc_start: 0.7566 (mtp) cc_final: 0.7330 (ptt)
REVERT: D   90 LEU cc_start: 0.8634 (tp) cc_final: 0.8398 (tp)
REVERT: D  250 ASP cc_start: 0.8623 (t70) cc_final: 0.8275 (t70)
REVERT: E   39 ILE cc_start: 0.9125 (mm) cc_final: 0.8919 (mm)
REVERT: E  126 MET cc_start: 0.9248 (tpp) cc_final: 0.8988 (tpp)
REVERT: F   68 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6671 (pp30)
REVERT: F   79 ASP cc_start: 0.7047 (t0) cc_final: 0.6845 (t0)
REVERT: G   90 TYR cc_start: 0.6414 (m-80) cc_final: 0.5717 (m-80)
REVERT: G  109 GLU cc_start: 0.7161 (mp0) cc_final: 0.6538 (tp30)
REVERT: G  112 LEU cc_start: 0.6391 (tp) cc_final: 0.5531 (tp)
REVERT: G  145 ASP cc_start: 0.8602 (t0) cc_final: 0.7698 (p0)
REVERT: H   27 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6902 (ttpt)
REVERT: H   90 TYR cc_start: 0.4392 (m-10) cc_final: 0.3784 (m-10)
REVERT: I   55 ARG cc_start: 0.6099 (mmt180) cc_final: 0.5700 (mmm160)
REVERT: I   91 ASN cc_start: 0.8408 (p0) cc_final: 0.6792 (m-40)
REVERT: J   53 LYS cc_start: 0.7319 (mptt) cc_final: 0.7021 (ptpt)
REVERT: J  141 MET cc_start: 0.2688 (pmm) cc_final: 0.1301 (ptp)
REVERT: K   56 SER cc_start: 0.6428 (m) cc_final: 0.6196 (m)
REVERT: L   81 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6467 (ttp80)
REVERT: L  141 MET cc_start: 0.5504 (pmm) cc_final: 0.5269 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1142
  time to fit residues: 60.1130
Evaluate side-chains
  261 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 260
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 130 optimal weight:    5.9990
   chunk 165 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 141 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   chunk 55 optimal weight:   30.0000
   chunk 79 optimal weight:    0.6980
   chunk 196 optimal weight:    5.9990
   chunk 110 optimal weight:    6.9990
   overall best weight:    2.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN
B 191 ASN
B 214 HIS
C  60 HIS
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN
H 149 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.112338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083328 restraints weight = 52976.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.084555 restraints weight = 36073.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.085524 restraints weight = 23394.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.085909 restraints weight = 18826.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.085993 restraints weight = 16878.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16132  Z= 0.145
  Angle     :  0.717  10.263  21948  Z= 0.355
  Chirality :  0.047   0.330   2652
  Planarity :  0.005   0.090   2762
  Dihedral  :  6.869  78.358   2296
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.14 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.43 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.19), residues: 2056
  helix:  0.63 (0.19), residues: 859
  sheet: -1.93 (0.31), residues: 278
  loop : -2.78 (0.19), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  46 
 TYR   0.022   0.002   TYR B 261 
 PHE   0.023   0.002   PHE B  16 
 TRP   0.037   0.002   TRP B 216 
 HIS   0.006   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (16132)
  covalent geometry    : angle       0.71746 (21948)
  hydrogen bonds       : bond        0.03645 (  601)
  hydrogen bonds       : angle       4.59117 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 347
  time to evaluate  : 0.641 
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: A   17 LEU cc_start: 0.9153 (tp) cc_final: 0.8689 (mm)
REVERT: A   89 MET cc_start: 0.7655 (mtt) cc_final: 0.6980 (tmm)
REVERT: B   10 ASP cc_start: 0.7843 (t0) cc_final: 0.7288 (t0)
REVERT: B   75 MET cc_start: 0.7510 (ptp) cc_final: 0.6985 (ptp)
REVERT: B  220 ASP cc_start: 0.8158 (t0) cc_final: 0.7935 (t0)
REVERT: C    6 SER cc_start: 0.8937 (m) cc_final: 0.8576 (p)
REVERT: C   55 LEU cc_start: 0.9344 (tt) cc_final: 0.9111 (tt)
REVERT: C   59 LEU cc_start: 0.9332 (mt) cc_final: 0.9034 (mm)
REVERT: D  211 ILE cc_start: 0.9437 (mt) cc_final: 0.9211 (mt)
REVERT: D  250 ASP cc_start: 0.8658 (t70) cc_final: 0.8343 (t70)
REVERT: E  108 TYR cc_start: 0.8617 (t80) cc_final: 0.8342 (t80)
REVERT: E  126 MET cc_start: 0.9278 (tpp) cc_final: 0.9012 (tpp)
REVERT: F   68 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6617 (pp30)
REVERT: F   79 ASP cc_start: 0.7345 (t0) cc_final: 0.7022 (t0)
REVERT: F   97 ARG cc_start: 0.5826 (tmt170) cc_final: 0.5623 (mmp80)
REVERT: G  109 GLU cc_start: 0.7815 (mp0) cc_final: 0.6804 (tp30)
REVERT: G  112 LEU cc_start: 0.6270 (tp) cc_final: 0.5432 (tp)
REVERT: G  145 ASP cc_start: 0.8621 (t0) cc_final: 0.7812 (p0)
REVERT: H   27 LYS cc_start: 0.7056 (ttmt) cc_final: 0.6836 (ttpt)
REVERT: H   90 TYR cc_start: 0.4375 (m-10) cc_final: 0.3883 (m-80)
REVERT: H  152 TYR cc_start: 0.7952 (m-80) cc_final: 0.7699 (m-80)
REVERT: I   55 ARG cc_start: 0.5821 (mmt180) cc_final: 0.5472 (mmm160)
REVERT: I   91 ASN cc_start: 0.8194 (p0) cc_final: 0.7083 (m-40)
REVERT: J   53 LYS cc_start: 0.7395 (mptt) cc_final: 0.7099 (ptpt)
REVERT: J  141 MET cc_start: 0.2942 (pmm) cc_final: 0.1585 (ptp)
REVERT: K   53 LYS cc_start: 0.7120 (tmtt) cc_final: 0.6888 (tmtt)
REVERT: K   56 SER cc_start: 0.6353 (m) cc_final: 0.6054 (m)
REVERT: L   81 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6522 (ttp80)
REVERT: L  141 MET cc_start: 0.5860 (pmm) cc_final: 0.5562 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 348
  average time/residue: 0.1172
  time to fit residues: 61.6648
Evaluate side-chains
  277 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 127 optimal weight:    6.9990
   chunk 195 optimal weight:    0.4980
   chunk 110 optimal weight:   30.0000
   chunk 6 optimal weight:    1.9990
   chunk 171 optimal weight:    0.2980
   chunk 106 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0870
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN
C  60 HIS
D  73 GLN
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.113909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.085135 restraints weight = 52910.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.086154 restraints weight = 35700.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.087012 restraints weight = 25118.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.087436 restraints weight = 19651.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.087623 restraints weight = 18262.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.5733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16132  Z= 0.123
  Angle     :  0.716   9.890  21948  Z= 0.350
  Chirality :  0.046   0.386   2652
  Planarity :  0.005   0.083   2762
  Dihedral  :  6.726  78.868   2296
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.42 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.19), residues: 2056
  helix:  0.82 (0.19), residues: 848
  sheet: -1.85 (0.31), residues: 283
  loop : -2.84 (0.19), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  97 
 TYR   0.030   0.001   TYR A 222 
 PHE   0.023   0.001   PHE B  16 
 TRP   0.031   0.001   TRP B 216 
 HIS   0.007   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (16132)
  covalent geometry    : angle       0.71579 (21948)
  hydrogen bonds       : bond        0.03442 (  601)
  hydrogen bonds       : angle       4.42679 ( 1782)

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

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

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4112 Ramachandran restraints generated.
    2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 364
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LEU cc_start: 0.9187 (tp) cc_final: 0.8755 (mm)
REVERT: A   89 MET cc_start: 0.7594 (mtt) cc_final: 0.6824 (tmm)
REVERT: A  153 ILE cc_start: 0.9380 (mm) cc_final: 0.9138 (mt)
REVERT: B   10 ASP cc_start: 0.7641 (t0) cc_final: 0.7121 (t0)
REVERT: B   75 MET cc_start: 0.7544 (ptp) cc_final: 0.7163 (ptp)
REVERT: C    6 SER cc_start: 0.8952 (m) cc_final: 0.8593 (p)
REVERT: C   55 LEU cc_start: 0.9337 (tt) cc_final: 0.9103 (tt)
REVERT: C   59 LEU cc_start: 0.9333 (mt) cc_final: 0.9061 (mm)
REVERT: D  250 ASP cc_start: 0.8748 (t70) cc_final: 0.8450 (t70)
REVERT: E   39 ILE cc_start: 0.8840 (mm) cc_final: 0.8609 (mm)
REVERT: E  108 TYR cc_start: 0.8649 (t80) cc_final: 0.8313 (t80)
REVERT: E  126 MET cc_start: 0.9291 (tpp) cc_final: 0.8973 (tpp)
REVERT: E  216 TRP cc_start: 0.8388 (m100) cc_final: 0.7537 (m-10)
REVERT: F   68 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6633 (pp30)
REVERT: F   79 ASP cc_start: 0.7532 (t0) cc_final: 0.7147 (t0)
REVERT: G  109 GLU cc_start: 0.8016 (mp0) cc_final: 0.6861 (tp30)
REVERT: G  112 LEU cc_start: 0.6498 (tp) cc_final: 0.5613 (tt)
REVERT: G  145 ASP cc_start: 0.8647 (t0) cc_final: 0.7871 (p0)
REVERT: H   27 LYS cc_start: 0.6939 (ttmt) cc_final: 0.6129 (mptt)
REVERT: H  152 TYR cc_start: 0.8064 (m-80) cc_final: 0.7810 (m-80)
REVERT: I   55 ARG cc_start: 0.5604 (mmt180) cc_final: 0.5226 (mmm160)
REVERT: I   91 ASN cc_start: 0.8307 (p0) cc_final: 0.7026 (m-40)
REVERT: J   53 LYS cc_start: 0.7373 (mptt) cc_final: 0.7079 (ptpt)
REVERT: J  141 MET cc_start: 0.2895 (pmm) cc_final: 0.1486 (ptp)
REVERT: K   56 SER cc_start: 0.6259 (m) cc_final: 0.5898 (m)
REVERT: L   49 ILE cc_start: 0.7889 (pt) cc_final: 0.7605 (pt)
REVERT: L   81 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6491 (ttp80)
REVERT: L  141 MET cc_start: 0.5991 (pmm) cc_final: 0.5530 (ttt)
  outliers start: 2
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1194
  time to fit residues: 65.6230
Evaluate side-chains
  277 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 131 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 145 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 163 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0010
   overall best weight:    1.7994

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

Flipped N/Q/H residues before XYZ refinement:
A 201 ASN
B 191 ASN
** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.113507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.084808 restraints weight = 52990.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.086043 restraints weight = 34417.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.086872 restraints weight = 23076.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.087295 restraints weight = 18442.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.087264 restraints weight = 17222.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  16132  Z= 0.127
  Angle     :  0.720   9.564  21948  Z= 0.351
  Chirality :  0.046   0.177   2652
  Planarity :  0.005   0.085   2762
  Dihedral  :  6.668  78.764   2296
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.71 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.42 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.19), residues: 2056
  helix:  0.91 (0.19), residues: 838
  sheet: -1.75 (0.32), residues: 274
  loop : -2.74 (0.19), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  97 
 TYR   0.029   0.001   TYR J  90 
 PHE   0.023   0.002   PHE J  13 
 TRP   0.031   0.001   TRP B 216 
 HIS   0.005   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (16132)
  covalent geometry    : angle       0.71963 (21948)
  hydrogen bonds       : bond        0.03372 (  601)
  hydrogen bonds       : angle       4.41333 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2544.14 seconds
wall clock time: 44 minutes 41.07 seconds (2681.07 seconds total)