Starting phenix.real_space_refine
on Thu Mar 13 18:28:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6o_35201/03_2025/8i6o_35201.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.047
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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    5876      2.51       5
     N    1498      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9084
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2299
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2299
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "E"
      Number of atoms: 1126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1126
          Classifications: {'peptide': 150}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 148}
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 64
  Time building chain proxies: 7.04, per 1000 atoms: 0.77
  Number of scatterers: 9084
  At special positions: 0
  Unit cell: (78.455, 81.77, 233.155, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1690      8.00
     N    1498      7.00
     C    5876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2186

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      61.9% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 3.735A  pdb=" N   HIS A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 84
      removed outlier: 3.887A  pdb=" N   SER A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 4.407A  pdb=" N   TRP A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN A  91 " --> pdb=" O   GLY A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 91'
    Processing helix  chain 'A' and resid 105 through 118
    Processing helix  chain 'A' and resid 129 through 142
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.673A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 234
      removed outlier: 3.859A  pdb=" N   ARG A 196 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   GLY A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ARG A 234 " --> pdb=" O   HIS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 244
    Processing helix  chain 'A' and resid 247 through 272
      Proline residue:  A 254  - end of helix
    Processing helix  chain 'A' and resid 273 through 293
      removed outlier: 3.891A  pdb=" N   GLY A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   SER A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASN A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
    Processing helix  chain 'B' and resid 41 through 49
      removed outlier: 4.117A  pdb=" N   LEU B  45 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.554A  pdb=" N   GLN B  80 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE B  81 " --> pdb=" O   ARG B  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 77 through 81'
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 101 through 108
      removed outlier: 3.931A  pdb=" N   GLN B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 125
      removed outlier: 3.907A  pdb=" N   ILE B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LYS B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 151
      removed outlier: 4.036A  pdb=" N   ALA B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 186
      removed outlier: 3.863A  pdb=" N   SER B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 186 " --> pdb=" O   ASP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'C' and resid 36 through 54
    Processing helix  chain 'C' and resid 60 through 75
      removed outlier: 3.748A  pdb=" N   GLY C  67 " --> pdb=" O   CYS C  63 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU C  70 " --> pdb=" O   MET C  66 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      Proline residue:  C  73  - end of helix
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 105 through 119
    Processing helix  chain 'C' and resid 129 through 140
      removed outlier: 3.989A  pdb=" N   GLN C 140 " --> pdb=" O   GLU C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 180
      removed outlier: 4.019A  pdb=" N   GLU C 180 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 195
    Processing helix  chain 'C' and resid 197 through 233
      removed outlier: 3.547A  pdb=" N   LEU C 201 " --> pdb=" O   LEU C 197 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS C 202 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE C 227 " --> pdb=" O   VAL C 223 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN C 233 " --> pdb=" O   LEU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 244
    Processing helix  chain 'C' and resid 247 through 292
      removed outlier: 3.786A  pdb=" N   VAL C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG C 252 " --> pdb=" O   ASP C 248 " (cutoff:3.500A)
      Proline residue:  C 254  - end of helix
      removed outlier: 3.655A  pdb=" N   ASN C 279 " --> pdb=" O   ALA C 275 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY C 283 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL C 286 " --> pdb=" O   ASN C 282 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ASN C 287 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR C 292 " --> pdb=" O   LEU C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 313
    Processing helix  chain 'C' and resid 319 through 332
      removed outlier: 3.938A  pdb=" N   ALA C 326 " --> pdb=" O   TRP C 322 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   HIS C 328 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG C 330 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 39
    Processing helix  chain 'D' and resid 40 through 49
      removed outlier: 3.696A  pdb=" N   ILE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU D  49 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 79
      removed outlier: 3.576A  pdb=" N   ARG D  79 " --> pdb=" O   PRO D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
    Processing helix  chain 'D' and resid 101 through 108
    Processing helix  chain 'D' and resid 110 through 126
      removed outlier: 3.710A  pdb=" N   GLU D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 151
      removed outlier: 3.909A  pdb=" N   ALA D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 186
      removed outlier: 4.077A  pdb=" N   GLU D 175 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 201
      removed outlier: 3.650A  pdb=" N   ALA D 201 " --> pdb=" O   ALA D 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 98
      removed outlier: 3.777A  pdb=" N   LEU E  57 " --> pdb=" O   VAL E  53 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN E  70 " --> pdb=" O   ASP E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 99 through 116
      removed outlier: 3.765A  pdb=" N   GLN E 103 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 126
      removed outlier: 3.844A  pdb=" N   LEU E 126 " --> pdb=" O   LEU E 122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 186
      removed outlier: 3.992A  pdb=" N   ILE E 169 " --> pdb=" O   VAL E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 200
      removed outlier: 4.068A  pdb=" N   ALA E 191 " --> pdb=" O   ARG E 187 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLN E 198 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLN E 199 " --> pdb=" O   LYS E 195 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA E 200 " --> pdb=" O   GLU E 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97
      removed outlier: 6.844A  pdb=" N   VAL A 158 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LEU A 127 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   SER A 160 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ALA A 125 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   THR A 162 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21
      removed outlier: 5.443A  pdb=" N   VAL B   7 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   PHE B   4 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LEU B  60 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   GLN B   6 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   LYS B  58 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83
      removed outlier: 7.007A  pdb=" N   GLY B  82 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 211
      removed outlier: 7.307A  pdb=" N   THR B 209 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 128
      removed outlier: 3.504A  pdb=" N   GLN C 126 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL C 158 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLN C 186 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 8
      removed outlier: 3.927A  pdb=" N   GLU D   5 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS D  58 " --> pdb=" O   GLU D   5 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   VAL D   7 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   SER D  56 " --> pdb=" O   VAL D   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33
      removed outlier: 6.652A  pdb=" N   PHE D  32 " --> pdb=" O   LEU D 208 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG D 219 " --> pdb=" O   MET D 207 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 84
      removed outlier: 3.657A  pdb=" N   ASP D 162 " --> pdb=" O   VAL D  84 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ALA D 161 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1512 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: 2.32

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2982
        1.34 -     1.46: 1047
        1.46 -     1.58: 5159
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 9226
  Sorted by residual:
  bond pdb=" C   ILE E 144 "
       pdb=" O   ILE E 144 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.017 1.29e-02 6.01e+03 1.82e+00
  bond pdb=" CA  GLU D 163 "
       pdb=" CB  GLU D 163 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.33e+00
  bond pdb=" CG  GLU C 114 "
       pdb=" CD  GLU C 114 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.27e+00
  bond pdb=" CD  GLU C 114 "
       pdb=" OE1 GLU C 114 "
    ideal  model  delta    sigma   weight residual
    1.249  1.228  0.021 1.90e-02 2.77e+03 1.18e+00
  bond pdb=" N   LYS D 130 "
       pdb=" CA  LYS D 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.40e-01
  ... (remaining 9221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 12157
        1.86 -     3.72: 239
        3.72 -     5.57: 45
        5.57 -     7.43: 8
        7.43 -     9.29: 3
  Bond angle restraints: 12452
  Sorted by residual:
  angle pdb=" N   VAL C 319 "
        pdb=" CA  VAL C 319 "
        pdb=" C   VAL C 319 "
      ideal   model   delta    sigma   weight residual
     111.62  108.52    3.10 7.90e-01 1.60e+00 1.54e+01
  angle pdb=" N   GLU C 114 "
        pdb=" CA  GLU C 114 "
        pdb=" CB  GLU C 114 "
      ideal   model   delta    sigma   weight residual
     110.28  116.11   -5.83 1.55e+00 4.16e-01 1.41e+01
  angle pdb=" C   ARG C 113 "
        pdb=" N   GLU C 114 "
        pdb=" CA  GLU C 114 "
      ideal   model   delta    sigma   weight residual
     120.31  115.50    4.81 1.52e+00 4.33e-01 1.00e+01
  angle pdb=" CB  LYS E 173 "
        pdb=" CG  LYS E 173 "
        pdb=" CD  LYS E 173 "
      ideal   model   delta    sigma   weight residual
     111.30  118.02   -6.72 2.30e+00 1.89e-01 8.53e+00
  angle pdb=" N   GLY C  58 "
        pdb=" CA  GLY C  58 "
        pdb=" C   GLY C  58 "
      ideal   model   delta    sigma   weight residual
     111.10  107.05    4.05 1.46e+00 4.69e-01 7.70e+00
  ... (remaining 12447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4961
       17.96 -    35.92: 561
       35.92 -    53.88: 87
       53.88 -    71.84: 21
       71.84 -    89.81: 8
  Dihedral angle restraints: 5638
    sinusoidal: 2242
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CA  LEU C 316 "
           pdb=" C   LEU C 316 "
           pdb=" N   GLY C 317 "
           pdb=" CA  GLY C 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  PRO E 131 "
           pdb=" C   PRO E 131 "
           pdb=" N   GLU E 132 "
           pdb=" CA  GLU E 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.09   19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  HIS B  19 "
           pdb=" C   HIS B  19 "
           pdb=" N   GLU B  20 "
           pdb=" CA  GLU B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.70   17.30     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 5635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 951
       0.032 -    0.063: 347
       0.063 -    0.095: 126
       0.095 -    0.127: 53
       0.127 -    0.158: 5
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CB  ILE E 169 "
            pdb=" CA  ILE E 169 "
            pdb=" CG1 ILE E 169 "
            pdb=" CG2 ILE E 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CG  LEU E 183 "
            pdb=" CB  LEU E 183 "
            pdb=" CD1 LEU E 183 "
            pdb=" CD2 LEU E 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  GLN E 172 "
            pdb=" N   GLN E 172 "
            pdb=" C   GLN E 172 "
            pdb=" CB  GLN E 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 153 "    0.036 5.00e-02 4.00e+02   5.41e-02 4.68e+00
        pdb=" N   PRO A 154 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 154 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 154 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 109 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO B 110 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 110 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 110 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 134 "   -0.029 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 135 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 135 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 135 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1556 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 133
        2.69 -     3.24: 9205
        3.24 -     3.79: 13611
        3.79 -     4.35: 16723
        4.35 -     4.90: 26606
  Nonbonded interactions: 66278
  Sorted by model distance:
  nonbonded pdb=" O   GLN E 151 "
            pdb=" OG  SER E 154 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER C 105 "
            pdb=" OD1 ASN C 107 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OE1 GLN B   6 "
            pdb=" OG  SER B  22 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   ARG D  27 "
            pdb=" OG1 THR D 189 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD1 ASP A 101 "
            pdb=" OG1 THR A 104 "
     model   vdw
     2.262 3.040
  ... (remaining 66273 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             25.580
  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:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.850
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.060
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
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      :  0.003   0.035   9226  Z= 0.185
  Angle     :  0.664   9.289  12452  Z= 0.348
  Chirality :  0.041   0.158   1482
  Planarity :  0.004   0.054   1559
  Dihedral  : 15.305  89.805   3452
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  1.84 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1186
  helix:  1.61 (0.21), residues: 696
  sheet: -1.53 (0.67), residues: 66
  loop : -2.34 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  90 
 HIS   0.007   0.001   HIS E 130 
 PHE   0.020   0.001   PHE E 155 
 TYR   0.014   0.001   TYR E 114 
 ARG   0.000   0.000   ARG E 104 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.8636 (m-30) cc_final: 0.8331 (m-30)
REVERT: B  163 GLU cc_start: 0.8195 (tp30) cc_final: 0.7945 (tp30)
REVERT: B  196 ASP cc_start: 0.8807 (t0) cc_final: 0.8122 (p0)
REVERT: B  207 MET cc_start: 0.8162 (ptp) cc_final: 0.7544 (ptm)
REVERT: B  209 THR cc_start: 0.8036 (m) cc_final: 0.7627 (t)
REVERT: C  124 GLU cc_start: 0.8257 (pp20) cc_final: 0.8010 (pp20)
REVERT: D  116 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8756 (pttm)
REVERT: D  169 ASP cc_start: 0.8462 (t0) cc_final: 0.8214 (t0)
REVERT: E  169 ILE cc_start: 0.8959 (tp) cc_final: 0.8754 (tp)
  outliers start: 6
  outliers final: 6
  residues processed: 171
  average time/residue: 0.1939
  time to fit residues: 47.3956
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  148 ARG
Chi-restraints excluded: chain E residue  186 ARG
Chi-restraints excluded: chain E residue  194 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  19 HIS
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.143479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.100391 restraints weight = 21338.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.103394 restraints weight = 10789.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.105252 restraints weight = 7124.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9226  Z= 0.236
  Angle     :  0.651   7.685  12452  Z= 0.332
  Chirality :  0.041   0.140   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  6.221  58.133   1234
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.11 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.25), residues: 1186
  helix:  1.76 (0.21), residues: 705
  sheet: -1.59 (0.66), residues: 64
  loop : -2.52 (0.26), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 318 
 HIS   0.008   0.001   HIS D  36 
 PHE   0.016   0.001   PHE E 155 
 TYR   0.011   0.001   TYR E 140 
 ARG   0.000   0.000   ARG E  99 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 LYS cc_start: 0.8276 (mmtm) cc_final: 0.8042 (mmtp)
REVERT: B  207 MET cc_start: 0.8320 (ptp) cc_final: 0.7534 (ptm)
REVERT: B  209 THR cc_start: 0.8117 (m) cc_final: 0.7701 (t)
REVERT: C  103 LYS cc_start: 0.8050 (tppt) cc_final: 0.7678 (pttt)
REVERT: C  167 ASP cc_start: 0.7863 (p0) cc_final: 0.7596 (m-30)
REVERT: D  116 LYS cc_start: 0.8962 (ptpp) cc_final: 0.8654 (pttm)
REVERT: D  169 ASP cc_start: 0.8032 (t0) cc_final: 0.7598 (t0)
REVERT: E  143 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6603 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1913
  time to fit residues: 40.0274
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  186 ARG
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0670
   chunk 36 optimal weight:    0.0000
   chunk 42 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3922

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.130684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088436 restraints weight = 19924.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.091019 restraints weight = 10639.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092653 restraints weight = 7215.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9226  Z= 0.186
  Angle     :  0.600   8.470  12452  Z= 0.302
  Chirality :  0.039   0.161   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  5.614  55.188   1226
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.14 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1186
  helix:  1.95 (0.21), residues: 708
  sheet: -1.90 (0.68), residues: 57
  loop : -2.43 (0.26), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.006   0.001   HIS D  88 
 PHE   0.014   0.001   PHE E 155 
 TYR   0.013   0.001   TYR E 114 
 ARG   0.000   0.000   ARG E 148 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7873 (mmtp)
REVERT: B  207 MET cc_start: 0.8219 (ptp) cc_final: 0.7604 (ptm)
REVERT: B  209 THR cc_start: 0.8139 (m) cc_final: 0.7721 (t)
REVERT: C  114 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8761 (mp0)
REVERT: C  258 MET cc_start: 0.7544 (ttm) cc_final: 0.7252 (ttm)
REVERT: D  116 LYS cc_start: 0.9012 (ptpp) cc_final: 0.8729 (pttm)
REVERT: D  169 ASP cc_start: 0.7956 (t0) cc_final: 0.7505 (t0)
REVERT: E   97 ASP cc_start: 0.9200 (m-30) cc_final: 0.8890 (m-30)
REVERT: E  143 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.6662 (t80)
REVERT: E  169 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8747 (tp)
  outliers start: 25
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1928
  time to fit residues: 41.3346
Evaluate side-chains
  144 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  169 ILE
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 97 optimal weight:    0.0370
   chunk 113 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 50 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 114 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
C  95 GLN
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.130074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.087638 restraints weight = 19865.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090257 restraints weight = 10668.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091972 restraints weight = 7243.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9226  Z= 0.194
  Angle     :  0.607   7.857  12452  Z= 0.303
  Chirality :  0.039   0.159   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  5.350  59.617   1222
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 19.88 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1186
  helix:  1.96 (0.21), residues: 714
  sheet: -1.66 (0.70), residues: 52
  loop : -2.37 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D  88 
 PHE   0.008   0.001   PHE C 209 
 TYR   0.009   0.001   TYR E 114 
 ARG   0.000   0.000   ARG E 148 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8384 (t0) cc_final: 0.8126 (t0)
REVERT: A  164 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7810 (mmtp)
REVERT: B  207 MET cc_start: 0.8226 (ptp) cc_final: 0.7278 (ptm)
REVERT: B  209 THR cc_start: 0.8110 (m) cc_final: 0.7696 (t)
REVERT: C  114 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8790 (mp0)
REVERT: C  258 MET cc_start: 0.7598 (ttm) cc_final: 0.7303 (ttm)
REVERT: D  116 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8707 (pttm)
REVERT: D  123 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (pm20)
REVERT: D  169 ASP cc_start: 0.7870 (t0) cc_final: 0.7404 (t0)
REVERT: E   97 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8860 (m-30)
REVERT: E  143 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6728 (t80)
  outliers start: 34
  outliers final: 18
  residues processed: 156
  average time/residue: 0.1898
  time to fit residues: 42.2205
Evaluate side-chains
  150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   76 PHE
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  123 GLU
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 55 optimal weight:    0.4980
   chunk 109 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.141483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.102952 restraints weight = 21428.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.102681 restraints weight = 12612.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.103850 restraints weight = 8268.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9226  Z= 0.248
  Angle     :  0.635   9.825  12452  Z= 0.318
  Chirality :  0.040   0.160   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  5.059  50.193   1218
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 21.00 %
    Favored  : 74.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1186
  helix:  1.85 (0.21), residues: 717
  sheet: -1.82 (0.67), residues: 52
  loop : -2.36 (0.26), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 318 
 HIS   0.004   0.001   HIS C  41 
 PHE   0.015   0.001   PHE E 155 
 TYR   0.011   0.001   TYR A  37 
 ARG   0.000   0.000   ARG E 197 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8500 (t0) cc_final: 0.8198 (t0)
REVERT: A  164 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7700 (mmtp)
REVERT: B  143 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7782 (pt0)
REVERT: B  191 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8416 (tt)
REVERT: B  207 MET cc_start: 0.8137 (ptp) cc_final: 0.7483 (ptm)
REVERT: B  209 THR cc_start: 0.8035 (m) cc_final: 0.7601 (t)
REVERT: C  114 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8761 (mp0)
REVERT: C  258 MET cc_start: 0.7362 (ttm) cc_final: 0.7055 (ttm)
REVERT: D  116 LYS cc_start: 0.8966 (ptpp) cc_final: 0.8686 (pttm)
REVERT: D  169 ASP cc_start: 0.8081 (t0) cc_final: 0.7627 (t0)
REVERT: E  143 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6765 (t80)
REVERT: E  150 GLU cc_start: 0.8011 (tp30) cc_final: 0.7752 (tp30)
  outliers start: 42
  outliers final: 28
  residues processed: 156
  average time/residue: 0.2048
  time to fit residues: 45.5766
Evaluate side-chains
  155 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   76 PHE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  162 ASP
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 105 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0770
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 90 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0170
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
D  99 ASN
D 126 ASN
E 180 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.128993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.086166 restraints weight = 19594.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088712 restraints weight = 10588.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.090299 restraints weight = 7243.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9226  Z= 0.182
  Angle     :  0.617  11.531  12452  Z= 0.307
  Chirality :  0.039   0.177   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  4.919  48.229   1218
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.75 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1186
  helix:  1.94 (0.21), residues: 715
  sheet: -1.65 (0.69), residues: 52
  loop : -2.37 (0.26), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 
 PHE   0.015   0.001   PHE E 155 
 TYR   0.009   0.001   TYR E 114 
 ARG   0.000   0.000   ARG E 148 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8440 (t0) cc_final: 0.8140 (t0)
REVERT: B  143 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7569 (pm20)
REVERT: B  207 MET cc_start: 0.8193 (ptp) cc_final: 0.7354 (ptm)
REVERT: B  209 THR cc_start: 0.8195 (m) cc_final: 0.7803 (t)
REVERT: C  114 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8781 (mp0)
REVERT: C  167 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.7560 (p0)
REVERT: C  258 MET cc_start: 0.7381 (ttm) cc_final: 0.7102 (ttm)
REVERT: D  116 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8756 (pttm)
REVERT: D  169 ASP cc_start: 0.7962 (t0) cc_final: 0.7473 (t0)
REVERT: E   97 ASP cc_start: 0.9123 (m-30) cc_final: 0.8811 (m-30)
REVERT: E  143 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6812 (t80)
REVERT: E  150 GLU cc_start: 0.8088 (tp30) cc_final: 0.7839 (tp30)
REVERT: E  168 ASP cc_start: 0.8184 (p0) cc_final: 0.7806 (p0)
  outliers start: 40
  outliers final: 28
  residues processed: 155
  average time/residue: 0.1991
  time to fit residues: 44.7665
Evaluate side-chains
  155 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain C residue   41 HIS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   76 PHE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  141 TYR
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 68 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0060
   chunk 99 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.4754

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.131400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.092359 restraints weight = 19874.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.094029 restraints weight = 11084.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.094105 restraints weight = 7663.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9226  Z= 0.191
  Angle     :  0.633  10.707  12452  Z= 0.311
  Chirality :  0.039   0.162   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  4.619  45.720   1214
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.98 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1186
  helix:  1.97 (0.21), residues: 715
  sheet: -1.65 (0.68), residues: 52
  loop : -2.35 (0.26), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  90 
 HIS   0.005   0.001   HIS B  15 
 PHE   0.020   0.001   PHE E 155 
 TYR   0.028   0.001   TYR B  11 
 ARG   0.000   0.000   ARG E 194 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 125
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8296 (t0) cc_final: 0.7748 (t0)
REVERT: A  164 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8198 (mmmt)
REVERT: B  143 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7877 (pt0)
REVERT: B  144 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8181 (pp30)
REVERT: B  207 MET cc_start: 0.7928 (ptp) cc_final: 0.7234 (ptm)
REVERT: B  209 THR cc_start: 0.8106 (m) cc_final: 0.7691 (t)
REVERT: C  114 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8890 (mp0)
REVERT: C  167 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7480 (p0)
REVERT: C  258 MET cc_start: 0.7439 (ttm) cc_final: 0.7154 (ttm)
REVERT: D  116 LYS cc_start: 0.8995 (ptpp) cc_final: 0.8724 (pttm)
REVERT: D  169 ASP cc_start: 0.7905 (t0) cc_final: 0.7414 (t0)
REVERT: E   97 ASP cc_start: 0.9120 (m-30) cc_final: 0.8745 (m-30)
REVERT: E  143 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6874 (t80)
REVERT: E  150 GLU cc_start: 0.8138 (tp30) cc_final: 0.7873 (tp30)
REVERT: E  169 ILE cc_start: 0.8682 (tp) cc_final: 0.8469 (tp)
  outliers start: 38
  outliers final: 28
  residues processed: 151
  average time/residue: 0.1889
  time to fit residues: 41.2190
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue   41 HIS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  126 ASN
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0870
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0980
   chunk 102 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN
E 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.131999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091666 restraints weight = 20099.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095450 restraints weight = 11385.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095416 restraints weight = 7183.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9226  Z= 0.181
  Angle     :  0.638  12.663  12452  Z= 0.314
  Chirality :  0.039   0.170   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  4.606  43.801   1214
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.46 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1186
  helix:  2.02 (0.21), residues: 710
  sheet: -1.78 (0.65), residues: 57
  loop : -2.42 (0.26), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  90 
 HIS   0.004   0.001   HIS C  41 
 PHE   0.023   0.001   PHE E 155 
 TYR   0.012   0.001   TYR E 140 
 ARG   0.000   0.000   ARG E 194 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8248 (t0) cc_final: 0.7559 (t0)
REVERT: A  164 LYS cc_start: 0.8338 (mmpt) cc_final: 0.8074 (mmmt)
REVERT: B  143 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7596 (pm20)
REVERT: B  144 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8296 (pp30)
REVERT: B  196 ASP cc_start: 0.8695 (t0) cc_final: 0.8331 (t0)
REVERT: B  207 MET cc_start: 0.7959 (ptp) cc_final: 0.6969 (ptm)
REVERT: B  209 THR cc_start: 0.8109 (m) cc_final: 0.7736 (t)
REVERT: C  114 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8869 (mp0)
REVERT: C  167 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7424 (p0)
REVERT: C  172 GLU cc_start: 0.8981 (tp30) cc_final: 0.8487 (pt0)
REVERT: C  258 MET cc_start: 0.7342 (ttm) cc_final: 0.7075 (ttm)
REVERT: D  109 MET cc_start: 0.6830 (mmt) cc_final: 0.6565 (mmt)
REVERT: D  116 LYS cc_start: 0.8989 (ptpp) cc_final: 0.8710 (pttm)
REVERT: D  169 ASP cc_start: 0.7893 (t0) cc_final: 0.7400 (t0)
REVERT: E   97 ASP cc_start: 0.9135 (m-30) cc_final: 0.8746 (m-30)
REVERT: E  150 GLU cc_start: 0.8091 (tp30) cc_final: 0.7822 (tp30)
  outliers start: 40
  outliers final: 27
  residues processed: 162
  average time/residue: 0.1897
  time to fit residues: 43.5346
Evaluate side-chains
  163 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue   41 HIS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  141 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
B 195 HIS
E 180 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.129112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090091 restraints weight = 19809.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.091630 restraints weight = 11186.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.092708 restraints weight = 7307.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9226  Z= 0.247
  Angle     :  0.687  10.127  12452  Z= 0.338
  Chirality :  0.040   0.210   1482
  Planarity :  0.004   0.044   1559
  Dihedral  :  4.695  40.289   1214
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 24.39 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1186
  helix:  1.93 (0.21), residues: 717
  sheet: -1.91 (0.63), residues: 57
  loop : -2.38 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  90 
 HIS   0.004   0.001   HIS C  41 
 PHE   0.025   0.001   PHE E 155 
 TYR   0.012   0.001   TYR E 140 
 ARG   0.000   0.000   ARG E 186 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 130
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 LYS cc_start: 0.8355 (mmpt) cc_final: 0.8130 (mmmt)
REVERT: B  143 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7884 (pt0)
REVERT: B  144 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8127 (pp30)
REVERT: B  196 ASP cc_start: 0.8767 (t0) cc_final: 0.8022 (p0)
REVERT: B  207 MET cc_start: 0.8006 (ptp) cc_final: 0.7299 (ptm)
REVERT: B  209 THR cc_start: 0.8050 (m) cc_final: 0.7652 (t)
REVERT: C  114 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8887 (mp0)
REVERT: C  167 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7408 (p0)
REVERT: C  172 GLU cc_start: 0.8974 (tp30) cc_final: 0.8477 (pt0)
REVERT: C  258 MET cc_start: 0.7471 (ttm) cc_final: 0.7178 (ttm)
REVERT: D  116 LYS cc_start: 0.9023 (ptpp) cc_final: 0.8712 (pttm)
REVERT: D  169 ASP cc_start: 0.8064 (t0) cc_final: 0.7592 (t0)
REVERT: E   93 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8689 (mmmt)
REVERT: E   97 ASP cc_start: 0.9121 (m-30) cc_final: 0.8610 (m-30)
REVERT: E  150 GLU cc_start: 0.8096 (tp30) cc_final: 0.7870 (tp30)
  outliers start: 36
  outliers final: 29
  residues processed: 155
  average time/residue: 0.1871
  time to fit residues: 41.4378
Evaluate side-chains
  160 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  141 TYR
Chi-restraints excluded: chain E residue  179 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0170
   chunk 16 optimal weight:    0.9980
   chunk 114 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN
E 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.135272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.099211 restraints weight = 20763.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.098923 restraints weight = 12417.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.100127 restraints weight = 8973.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9226  Z= 0.211
  Angle     :  0.680  10.907  12452  Z= 0.337
  Chirality :  0.040   0.219   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  4.684  38.003   1214
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.51 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1186
  helix:  1.93 (0.21), residues: 718
  sheet: -1.85 (0.65), residues: 57
  loop : -2.40 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  90 
 HIS   0.005   0.001   HIS B 195 
 PHE   0.026   0.001   PHE E 155 
 TYR   0.014   0.001   TYR E 140 
 ARG   0.000   0.000   ARG E 148 

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8041 (t0) cc_final: 0.7796 (t0)
REVERT: A  164 LYS cc_start: 0.8269 (mmpt) cc_final: 0.8024 (mmmt)
REVERT: B  143 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7894 (pt0)
REVERT: B  144 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8073 (pp30)
REVERT: B  196 ASP cc_start: 0.8703 (t0) cc_final: 0.7866 (p0)
REVERT: B  199 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8453 (mm)
REVERT: B  207 MET cc_start: 0.8100 (ptp) cc_final: 0.7431 (ptm)
REVERT: B  209 THR cc_start: 0.8071 (m) cc_final: 0.7630 (t)
REVERT: C  114 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8784 (mp0)
REVERT: C  167 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7449 (p0)
REVERT: C  172 GLU cc_start: 0.8806 (tp30) cc_final: 0.8493 (pt0)
REVERT: C  258 MET cc_start: 0.7191 (ttm) cc_final: 0.6907 (ttm)
REVERT: D  109 MET cc_start: 0.6821 (mmt) cc_final: 0.6611 (mmt)
REVERT: D  116 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8721 (pttm)
REVERT: D  169 ASP cc_start: 0.8103 (t0) cc_final: 0.7624 (t0)
REVERT: E   93 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8629 (mmmt)
REVERT: E   97 ASP cc_start: 0.9089 (m-30) cc_final: 0.8602 (m-30)
REVERT: E  150 GLU cc_start: 0.7936 (tp30) cc_final: 0.7698 (tp30)
  outliers start: 32
  outliers final: 27
  residues processed: 154
  average time/residue: 0.2118
  time to fit residues: 46.5880
Evaluate side-chains
  157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  235 ARG
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   32 PHE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  126 ASN
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  118 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 97 optimal weight:    0.2980
   chunk 71 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D 126 ASN
** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.134707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.099454 restraints weight = 20752.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098453 restraints weight = 12879.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.098921 restraints weight = 9813.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.286   9226  Z= 0.300
  Angle     :  0.993  59.054  12452  Z= 0.569
  Chirality :  0.042   0.548   1482
  Planarity :  0.004   0.075   1559
  Dihedral  :  4.735  37.989   1214
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.96 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.72 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.26), residues: 1186
  helix:  1.92 (0.21), residues: 718
  sheet: -1.85 (0.65), residues: 57
  loop : -2.39 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  90 
 HIS   0.005   0.001   HIS C  41 
 PHE   0.019   0.001   PHE E 155 
 TYR   0.076   0.002   TYR E 140 
 ARG   0.000   0.000   ARG E  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3815.34 seconds
wall clock time: 69 minutes 10.22 seconds (4150.22 seconds total)