Starting phenix.real_space_refine
on Sat Aug 23 06:46:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dne_27564/08_2025/8dne_27564.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    6841      2.51       5
     N    1609      2.21       5
     O    1795      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10281
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2976
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2131
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 11, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2979
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 11, 'TRANS': 358}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2131
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 11, 'TRANS': 243}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.04, per 1000 atoms: 0.20
  Number of scatterers: 10281
  At special positions: 0
  Unit cell: (91.8, 85.32, 136.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1795      8.00
     N    1609      7.00
     C    6841      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 265.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 10 sheets defined
      52.0% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 26
      removed outlier: 3.603A  pdb=" N   ILE A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   PHE A  26 " --> pdb=" O   LYS A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 99 through 112
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 3.557A  pdb=" N   ILE A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   GLU A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   SER A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 143 through 157
      removed outlier: 3.702A  pdb=" N   HIS A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 191
      removed outlier: 3.597A  pdb=" N   GLY A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 207
      removed outlier: 3.581A  pdb=" N   VAL A 204 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 240
    Processing helix  chain 'B' and resid 3 through 18
    Processing helix  chain 'B' and resid 21 through 47
      removed outlier: 3.959A  pdb=" N   ILE B  25 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TRP B  26 " --> pdb=" O   VAL B  22 " (cutoff:3.500A)
      Proline residue:  B  32  - end of helix
      removed outlier: 4.431A  pdb=" N   HIS B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 82
      Proline residue:  B  70  - end of helix
    Processing helix  chain 'B' and resid 83 through 88
      removed outlier: 3.658A  pdb=" N   GLU B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B  88 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 83 through 88'
    Processing helix  chain 'B' and resid 88 through 93
      removed outlier: 3.733A  pdb=" N   THR B  93 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 126
      removed outlier: 3.732A  pdb=" N   VAL B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 138
      removed outlier: 5.123A  pdb=" N   TYR B 138 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 163
      removed outlier: 3.872A  pdb=" N   ALA B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLY B 155 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET B 156 " --> pdb=" O   PHE B 152 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 180
      removed outlier: 3.948A  pdb=" N   GLY B 173 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE B 180 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 201
      removed outlier: 3.511A  pdb=" N   LEU B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 223 through 256
      Proline residue:  B 235  - end of helix
      removed outlier: 3.579A  pdb=" N   LEU B 248 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   LYS B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   ASP B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 27
      removed outlier: 4.105A  pdb=" N   LEU C  21 " --> pdb=" O   PRO C  17 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 68
    Processing helix  chain 'C' and resid 99 through 112
    Processing helix  chain 'C' and resid 114 through 129
      removed outlier: 4.974A  pdb=" N   SER C 124 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ILE C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   GLU C 127 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   PHE C 128 " --> pdb=" O   SER C 124 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER C 129 " --> pdb=" O   ILE C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 137
      removed outlier: 4.229A  pdb=" N   ASN C 136 " --> pdb=" O   ASP C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 142
      removed outlier: 3.527A  pdb=" N   TYR C 142 " --> pdb=" O   LEU C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 157
    Processing helix  chain 'C' and resid 173 through 190
      removed outlier: 3.528A  pdb=" N   LYS C 190 " --> pdb=" O   GLU C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 208
      removed outlier: 4.010A  pdb=" N   VAL C 204 " --> pdb=" O   ASP C 200 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS C 205 " --> pdb=" O   MET C 201 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE C 206 " --> pdb=" O   ASN C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 239
    Processing helix  chain 'D' and resid 3 through 17
    Processing helix  chain 'D' and resid 26 through 44
      Proline residue:  D  32  - end of helix
    Processing helix  chain 'D' and resid 55 through 82
      Proline residue:  D  70  - end of helix
      removed outlier: 3.613A  pdb=" N   THR D  82 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 93
      removed outlier: 3.616A  pdb=" N   PHE D  92 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   THR D  93 " --> pdb=" O   LYS D  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 88 through 93'
    Processing helix  chain 'D' and resid 100 through 129
      removed outlier: 3.628A  pdb=" N   VAL D 106 " --> pdb=" O   PHE D 102 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ASN D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY D 117 " --> pdb=" O   ASN D 113 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR D 128 " --> pdb=" O   ILE D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 133 through 138
      removed outlier: 4.900A  pdb=" N   TYR D 138 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 165
      removed outlier: 3.963A  pdb=" N   SER D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLY D 155 " --> pdb=" O   SER D 151 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR D 160 " --> pdb=" O   MET D 156 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL D 163 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   PHE D 164 " --> pdb=" O   THR D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 180
    Processing helix  chain 'D' and resid 193 through 201
      removed outlier: 3.962A  pdb=" N   LEU D 199 " --> pdb=" O   PHE D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 217
      removed outlier: 4.362A  pdb=" N   VAL D 208 " --> pdb=" O   PRO D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 233
    Processing helix  chain 'D' and resid 233 through 256
      removed outlier: 3.520A  pdb=" N   LEU D 248 " --> pdb=" O   PHE D 244 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   LYS D 250 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ASP D 251 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43
      removed outlier: 7.110A  pdb=" N   LEU A  34 " --> pdb=" O   LYS A  12 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   LYS A  12 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  10 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LYS A  10 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LYS A  38 " --> pdb=" O   TRP A   8 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   TRP A   8 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   ILE A  40 " --> pdb=" O   ASP A   6 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   VAL A   7 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   LYS A  75 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87
      removed outlier: 6.588A  pdb=" N   VAL A  85 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP A 166 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   LEU A  87 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   PHE A 163 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   VAL A 197 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ILE A 165 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU A  50 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLY A  51 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   LEU A 214 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A  53 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ALA A 211 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   GLU A 222 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   LEU A 213 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265
      removed outlier: 5.200A  pdb=" N   ILE A 259 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   GLU A 287 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA A 288 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASN C 390 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU C 388 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276
      removed outlier: 5.999A  pdb=" N   PHE A 274 " --> pdb=" O   VAL A 371 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY A 373 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   HIS A 350 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL A 296 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASP A 303 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ASP A 308 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293
    Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394
      removed outlier: 3.549A  pdb=" N   LYS C 333 " --> pdb=" O   GLU A 388 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASN A 390 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR C 331 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 392 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE A 394 " --> pdb=" O   LYS C 327 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   LYS C 327 " --> pdb=" O   ILE A 394 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU C 261 " --> pdb=" O   ASP C 285 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   GLU C 287 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   ILE C 259 " --> pdb=" O   GLU C 287 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 44
      removed outlier: 3.569A  pdb=" N   GLU C  32 " --> pdb=" O   TYR C  13 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LYS C   9 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LYS C  38 " --> pdb=" O   VAL C   7 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   VAL C   7 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE C  40 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   PHE C   5 " --> pdb=" O   ILE C  40 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LEU C  42 " --> pdb=" O   ARG C   3 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   ARG C   3 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   VAL C   7 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   LYS C  75 " --> pdb=" O   VAL C   7 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 87
      removed outlier: 4.346A  pdb=" N   ASP C 166 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   PHE C 163 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL C 197 " --> pdb=" O   PHE C 163 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ILE C 165 " --> pdb=" O   VAL C 197 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL C  49 " --> pdb=" O   ARG C 210 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   ILE C 212 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   LEU C 214 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL C  53 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLU C 221 " --> pdb=" O   LEU C 213 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 276
      removed outlier: 6.619A  pdb=" N   PHE C 274 " --> pdb=" O   VAL C 371 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   GLY C 373 " --> pdb=" O   PHE C 274 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313
      removed outlier: 6.714A  pdb=" N   ILE C 301 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   GLY C 311 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ILE C 299 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ASN C 313 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ALA C 297 " --> pdb=" O   ASN C 313 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1443 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: 1.87

  Time building geometry restraints manager: 1.00 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: 3019
        1.34 -     1.46: 1762
        1.46 -     1.57: 5707
        1.57 -     1.69: 10
        1.69 -     1.81: 46
  Bond restraints: 10544
  Sorted by residual:
  bond pdb=" N   ILE C 135 "
       pdb=" CA  ILE C 135 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.28e+00
  bond pdb=" N   VAL D 186 "
       pdb=" CA  VAL D 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.41e-02 5.03e+03 6.38e+00
  bond pdb=" N   VAL B 186 "
       pdb=" CA  VAL B 186 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.51e+00
  bond pdb=" N   TYR D 187 "
       pdb=" CA  TYR D 187 "
    ideal  model  delta    sigma   weight residual
    1.455  1.483 -0.028 1.21e-02 6.83e+03 5.30e+00
  bond pdb=" O5' ATP C 502 "
       pdb=" PA  ATP C 502 "
    ideal  model  delta    sigma   weight residual
    1.579  1.602 -0.023 1.10e-02 8.26e+03 4.52e+00
  ... (remaining 10539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 13977
        1.91 -     3.82: 238
        3.82 -     5.73: 45
        5.73 -     7.64: 3
        7.64 -     9.55: 6
  Bond angle restraints: 14269
  Sorted by residual:
  angle pdb=" PA  ATP A 502 "
        pdb=" O3A ATP A 502 "
        pdb=" PB  ATP A 502 "
      ideal   model   delta    sigma   weight residual
     136.83  127.51    9.32 1.00e+00 1.00e+00 8.69e+01
  angle pdb=" PB  ATP A 502 "
        pdb=" O3B ATP A 502 "
        pdb=" PG  ATP A 502 "
      ideal   model   delta    sigma   weight residual
     139.87  131.01    8.86 1.00e+00 1.00e+00 7.85e+01
  angle pdb=" PB  ATP C 502 "
        pdb=" O3B ATP C 502 "
        pdb=" PG  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     139.87  131.87    8.00 1.00e+00 1.00e+00 6.39e+01
  angle pdb=" N   ILE D  47 "
        pdb=" CA  ILE D  47 "
        pdb=" C   ILE D  47 "
      ideal   model   delta    sigma   weight residual
     113.71  109.05    4.66 9.50e-01 1.11e+00 2.40e+01
  angle pdb=" C5' ATP A 502 "
        pdb=" O5' ATP A 502 "
        pdb=" PA  ATP A 502 "
      ideal   model   delta    sigma   weight residual
     121.27  116.98    4.29 1.00e+00 1.00e+00 1.84e+01
  ... (remaining 14264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5533
       17.98 -    35.95: 544
       35.95 -    53.93: 107
       53.93 -    71.90: 12
       71.90 -    89.88: 11
  Dihedral angle restraints: 6207
    sinusoidal: 2568
      harmonic: 3639
  Sorted by residual:
  dihedral pdb=" CA  ARG A  27 "
           pdb=" C   ARG A  27 "
           pdb=" N   LYS A  28 "
           pdb=" CA  LYS A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.12  -25.88     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  ASN C  95 "
           pdb=" C   ASN C  95 "
           pdb=" N   TYR C  96 "
           pdb=" CA  TYR C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.76  -18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ASP C 200 "
           pdb=" C   ASP C 200 "
           pdb=" N   MET C 201 "
           pdb=" CA  MET C 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.55  -17.45     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 6204 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1461
       0.074 -    0.147: 139
       0.147 -    0.221: 3
       0.221 -    0.294: 0
       0.294 -    0.368: 2
  Chirality restraints: 1605
  Sorted by residual:
  chirality pdb=" CA  VAL D 186 "
            pdb=" N   VAL D 186 "
            pdb=" C   VAL D 186 "
            pdb=" CB  VAL D 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.81   -0.37 2.00e-01 2.50e+01 3.38e+00
  chirality pdb=" CA  VAL B 186 "
            pdb=" N   VAL B 186 "
            pdb=" C   VAL B 186 "
            pdb=" CB  VAL B 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CB  ILE C 135 "
            pdb=" CA  ILE C 135 "
            pdb=" CG1 ILE C 135 "
            pdb=" CG2 ILE C 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.63e-01
  ... (remaining 1602 not shown)

  Planarity restraints: 1737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  31 "   -0.020 2.00e-02 2.50e+03   1.97e-02 9.71e+00
        pdb=" CG  TRP D  31 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  31 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  31 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  31 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  31 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  31 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  31 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 193 "   -0.041 5.00e-02 4.00e+02   6.27e-02 6.28e+00
        pdb=" N   PRO D 194 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO D 194 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 194 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B  31 "    0.041 5.00e-02 4.00e+02   6.21e-02 6.17e+00
        pdb=" N   PRO B  32 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1734 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 28
        2.41 -     3.03: 6180
        3.03 -     3.65: 15115
        3.65 -     4.28: 21782
        4.28 -     4.90: 37041
  Nonbonded interactions: 80146
  Sorted by model distance:
  nonbonded pdb="MG    MG C 501 "
            pdb=" O1G ATP C 502 "
     model   vdw
     1.785 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O1G ATP A 502 "
     model   vdw
     1.995 2.170
  nonbonded pdb="MG    MG A 501 "
            pdb=" O1B ATP A 502 "
     model   vdw
     2.020 2.170
  nonbonded pdb=" O   SER D 119 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OH  TYR D 206 "
            pdb=" O   ASP D 221 "
     model   vdw
     2.219 3.040
  ... (remaining 80141 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 240 or resid 254 through 350 or resid 363 throug \ 
h 393 or resid 501 through 502))
  selection = (chain 'C' and (resid 1 through 350 or resid 363 through 502))
}
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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.220
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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      :  0.004   0.038  10544  Z= 0.174
  Angle     :  0.654   9.547  14269  Z= 0.382
  Chirality :  0.044   0.368   1605
  Planarity :  0.004   0.063   1737
  Dihedral  : 14.834  89.879   3875
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.24), residues: 1235
  helix:  0.40 (0.22), residues: 574
  sheet:  0.67 (0.37), residues: 198
  loop : -1.42 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 263 
 TYR   0.021   0.001   TYR B 150 
 PHE   0.018   0.001   PHE C  30 
 TRP   0.052   0.002   TRP D  31 
 HIS   0.004   0.001   HIS D  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10544)
  covalent geometry    : angle       0.65364 (14269)
  hydrogen bonds       : bond        0.19205 (  498)
  hydrogen bonds       : angle       7.55797 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.377 
Fit side-chains
REVERT: B  187 TYR cc_start: 0.8141 (p90) cc_final: 0.7820 (p90)
REVERT: C  317 MET cc_start: 0.7857 (mtp) cc_final: 0.7650 (mtp)
REVERT: C  362 TRP cc_start: 0.7203 (t60) cc_final: 0.6448 (m-90)
REVERT: D   87 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6585 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0760
  time to fit residues: 19.9374
Evaluate side-chains
  138 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  53 HIS
C  56 ASN
C 230 GLN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.166102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.132628 restraints weight = 15798.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.135052 restraints weight = 10311.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.138100 restraints weight = 7320.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.138457 restraints weight = 6142.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138648 restraints weight = 5506.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10544  Z= 0.157
  Angle     :  0.586   7.981  14269  Z= 0.310
  Chirality :  0.043   0.174   1605
  Planarity :  0.004   0.050   1737
  Dihedral  :  8.586  88.453   1411
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 10.80 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.24), residues: 1235
  helix:  1.09 (0.22), residues: 586
  sheet:  0.68 (0.37), residues: 199
  loop : -1.58 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  11 
 TYR   0.020   0.001   TYR B 150 
 PHE   0.032   0.001   PHE D  72 
 TRP   0.028   0.002   TRP D  31 
 HIS   0.006   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (10544)
  covalent geometry    : angle       0.58555 (14269)
  hydrogen bonds       : bond        0.05589 (  498)
  hydrogen bonds       : angle       5.17866 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5345 (ptt-90) cc_final: 0.4984 (ptp90)
REVERT: B   80 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7659 (ttp-170)
REVERT: B  178 ILE cc_start: 0.8511 (pt) cc_final: 0.8266 (mt)
REVERT: B  187 TYR cc_start: 0.8559 (p90) cc_final: 0.8065 (p90)
REVERT: B  243 TYR cc_start: 0.7147 (t80) cc_final: 0.6924 (t80)
REVERT: C  236 MET cc_start: 0.7959 (mmt) cc_final: 0.7732 (mmm)
REVERT: C  362 TRP cc_start: 0.7205 (t60) cc_final: 0.6406 (m-90)
REVERT: D    8 GLU cc_start: 0.7829 (tp30) cc_final: 0.6981 (tp30)
REVERT: D   87 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6913 (tm-30)
REVERT: D  175 PHE cc_start: 0.8394 (t80) cc_final: 0.8025 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 158
  average time/residue: 0.0862
  time to fit residues: 19.8714
Evaluate side-chains
  139 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain C residue  228 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 84 optimal weight:    0.0670
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
B 223 HIS
C 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.161990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.126463 restraints weight = 15446.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.130793 restraints weight = 9040.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.133685 restraints weight = 6339.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.135715 restraints weight = 5019.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.137050 restraints weight = 4261.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10544  Z= 0.158
  Angle     :  0.573   7.912  14269  Z= 0.299
  Chirality :  0.043   0.175   1605
  Planarity :  0.004   0.049   1737
  Dihedral  :  8.518  87.986   1411
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.39 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.24), residues: 1235
  helix:  1.24 (0.22), residues: 587
  sheet:  0.72 (0.37), residues: 195
  loop : -1.61 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  11 
 TYR   0.021   0.001   TYR B 150 
 PHE   0.027   0.002   PHE D 255 
 TRP   0.023   0.002   TRP D  31 
 HIS   0.005   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10544)
  covalent geometry    : angle       0.57335 (14269)
  hydrogen bonds       : bond        0.04977 (  498)
  hydrogen bonds       : angle       4.79246 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.8069 (tt) cc_final: 0.7734 (pt)
REVERT: A  263 ARG cc_start: 0.5235 (ptt-90) cc_final: 0.4994 (ptp90)
REVERT: A  315 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.4622 (t80)
REVERT: B   80 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7784 (ttp-170)
REVERT: B  178 ILE cc_start: 0.8438 (pt) cc_final: 0.8227 (mt)
REVERT: B  187 TYR cc_start: 0.8685 (p90) cc_final: 0.8096 (p90)
REVERT: B  243 TYR cc_start: 0.7119 (t80) cc_final: 0.6895 (t80)
REVERT: D    8 GLU cc_start: 0.7855 (tp30) cc_final: 0.7132 (tp30)
REVERT: D   11 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7706 (ttm-80)
REVERT: D   33 ILE cc_start: 0.8372 (mm) cc_final: 0.8157 (mp)
REVERT: D   80 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8161 (ttm170)
REVERT: D   87 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7150 (tm-30)
REVERT: D  110 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8278 (mm-30)
REVERT: D  179 PHE cc_start: 0.8655 (t80) cc_final: 0.8320 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 163
  average time/residue: 0.0873
  time to fit residues: 21.0130
Evaluate side-chains
  146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 136
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  148 MET
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  321 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.162914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.128325 restraints weight = 16044.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132538 restraints weight = 9546.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135258 restraints weight = 6791.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.137113 restraints weight = 5445.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.138255 restraints weight = 4667.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10544  Z= 0.166
  Angle     :  0.572   7.901  14269  Z= 0.299
  Chirality :  0.043   0.170   1605
  Planarity :  0.004   0.047   1737
  Dihedral  :  8.375  88.521   1411
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.89 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.24), residues: 1235
  helix:  1.21 (0.22), residues: 588
  sheet:  0.74 (0.37), residues: 195
  loop : -1.59 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  11 
 TYR   0.021   0.001   TYR B 150 
 PHE   0.032   0.002   PHE D  72 
 TRP   0.032   0.002   TRP D  31 
 HIS   0.007   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10544)
  covalent geometry    : angle       0.57212 (14269)
  hydrogen bonds       : bond        0.04905 (  498)
  hydrogen bonds       : angle       4.67757 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.8100 (tt) cc_final: 0.7697 (pt)
REVERT: A  263 ARG cc_start: 0.5274 (ptt-90) cc_final: 0.5044 (ptp90)
REVERT: B  166 ARG cc_start: 0.8251 (mmt180) cc_final: 0.7948 (mmt180)
REVERT: B  178 ILE cc_start: 0.8486 (pt) cc_final: 0.8252 (mt)
REVERT: B  187 TYR cc_start: 0.8665 (p90) cc_final: 0.7998 (p90)
REVERT: C  236 MET cc_start: 0.7807 (mmt) cc_final: 0.7551 (mmm)
REVERT: C  362 TRP cc_start: 0.7214 (t60) cc_final: 0.6242 (m-90)
REVERT: D    8 GLU cc_start: 0.7834 (tp30) cc_final: 0.7086 (tp30)
REVERT: D   33 ILE cc_start: 0.8362 (mm) cc_final: 0.7843 (mt)
REVERT: D   87 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7016 (tm-30)
REVERT: D  179 PHE cc_start: 0.8585 (t80) cc_final: 0.8230 (t80)
  outliers start: 24
  outliers final: 14
  residues processed: 162
  average time/residue: 0.0848
  time to fit residues: 20.3800
Evaluate side-chains
  151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  148 MET
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain D residue   12 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.158162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.122037 restraints weight = 15963.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.126195 restraints weight = 9481.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129081 restraints weight = 6782.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.130987 restraints weight = 5396.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.132166 restraints weight = 4633.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10544  Z= 0.210
  Angle     :  0.623   7.748  14269  Z= 0.325
  Chirality :  0.045   0.175   1605
  Planarity :  0.004   0.050   1737
  Dihedral  :  8.310  82.701   1411
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.23 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.24), residues: 1235
  helix:  1.06 (0.22), residues: 590
  sheet:  0.59 (0.37), residues: 196
  loop : -1.58 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  11 
 TYR   0.026   0.002   TYR B 150 
 PHE   0.028   0.002   PHE D 175 
 TRP   0.025   0.002   TRP D  31 
 HIS   0.009   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (10544)
  covalent geometry    : angle       0.62310 (14269)
  hydrogen bonds       : bond        0.05360 (  498)
  hydrogen bonds       : angle       4.73591 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5629 (ptt-90) cc_final: 0.5237 (ptp90)
REVERT: A  375 LYS cc_start: 0.8480 (tmmt) cc_final: 0.8140 (ttpp)
REVERT: B   54 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6444 (pm20)
REVERT: B   80 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7079 (ttm170)
REVERT: B  178 ILE cc_start: 0.8539 (pt) cc_final: 0.8225 (mt)
REVERT: B  187 TYR cc_start: 0.8673 (p90) cc_final: 0.7936 (p90)
REVERT: C  102 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8104 (mp0)
REVERT: C  362 TRP cc_start: 0.7391 (t60) cc_final: 0.6265 (m-90)
REVERT: D    8 GLU cc_start: 0.7988 (tp30) cc_final: 0.7012 (tp30)
REVERT: D   12 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7513 (mt0)
REVERT: D   33 ILE cc_start: 0.8356 (mm) cc_final: 0.7779 (mp)
REVERT: D   37 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7579 (mm)
REVERT: D   47 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.5168 (mp)
REVERT: D  179 PHE cc_start: 0.8610 (t80) cc_final: 0.8217 (t80)
  outliers start: 37
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0906
  time to fit residues: 22.3848
Evaluate side-chains
  164 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   72 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 110 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 118 optimal weight:    0.0970
   chunk 98 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.162362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.125790 restraints weight = 16006.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.130421 restraints weight = 9067.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133571 restraints weight = 6304.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.135618 restraints weight = 4934.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.136846 restraints weight = 4192.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10544  Z= 0.125
  Angle     :  0.546   8.044  14269  Z= 0.286
  Chirality :  0.042   0.172   1605
  Planarity :  0.004   0.043   1737
  Dihedral  :  7.618  78.576   1411
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.20 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.24), residues: 1235
  helix:  1.34 (0.22), residues: 595
  sheet:  0.70 (0.36), residues: 205
  loop : -1.54 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  11 
 TYR   0.017   0.001   TYR B  63 
 PHE   0.026   0.001   PHE D 175 
 TRP   0.024   0.002   TRP D  31 
 HIS   0.013   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10544)
  covalent geometry    : angle       0.54583 (14269)
  hydrogen bonds       : bond        0.04275 (  498)
  hydrogen bonds       : angle       4.49036 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5666 (ptt-90) cc_final: 0.5262 (ptp90)
REVERT: A  375 LYS cc_start: 0.8485 (tmmt) cc_final: 0.8064 (ttpp)
REVERT: B   47 ILE cc_start: 0.5340 (pt) cc_final: 0.4742 (tp)
REVERT: B   80 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7644 (ttp-170)
REVERT: B   89 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8333 (ttpp)
REVERT: B  178 ILE cc_start: 0.8499 (pt) cc_final: 0.8290 (mt)
REVERT: B  187 TYR cc_start: 0.8499 (p90) cc_final: 0.7847 (p90)
REVERT: C  102 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8179 (pm20)
REVERT: C  236 MET cc_start: 0.7942 (mmt) cc_final: 0.7705 (mmm)
REVERT: C  362 TRP cc_start: 0.7307 (t60) cc_final: 0.6290 (m100)
REVERT: D    8 GLU cc_start: 0.7996 (tp30) cc_final: 0.6820 (tp30)
REVERT: D   11 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7671 (ttp80)
REVERT: D   12 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7415 (mt0)
REVERT: D   33 ILE cc_start: 0.8389 (mm) cc_final: 0.8113 (mm)
REVERT: D   37 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7588 (mm)
REVERT: D   80 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8193 (ttm170)
REVERT: D  118 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7564 (tt)
  outliers start: 29
  outliers final: 16
  residues processed: 166
  average time/residue: 0.0918
  time to fit residues: 22.4649
Evaluate side-chains
  151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 101 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0020
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.3350

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

Flipped N/Q/H residues before XYZ refinement:
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.159701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.123154 restraints weight = 15822.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127621 restraints weight = 9110.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.130614 restraints weight = 6366.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.132618 restraints weight = 5025.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133975 restraints weight = 4278.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10544  Z= 0.172
  Angle     :  0.587   7.853  14269  Z= 0.306
  Chirality :  0.043   0.180   1605
  Planarity :  0.004   0.045   1737
  Dihedral  :  7.519  77.024   1411
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.38 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.24), residues: 1235
  helix:  1.28 (0.22), residues: 591
  sheet:  0.74 (0.37), residues: 196
  loop : -1.63 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  11 
 TYR   0.021   0.001   TYR B 150 
 PHE   0.028   0.002   PHE A 389 
 TRP   0.020   0.002   TRP D  31 
 HIS   0.005   0.001   HIS D  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10544)
  covalent geometry    : angle       0.58670 (14269)
  hydrogen bonds       : bond        0.04794 (  498)
  hydrogen bonds       : angle       4.55385 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5728 (ptt-90) cc_final: 0.5292 (ptp90)
REVERT: B   89 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8352 (ttpp)
REVERT: B  178 ILE cc_start: 0.8564 (pt) cc_final: 0.8274 (mt)
REVERT: B  187 TYR cc_start: 0.8597 (p90) cc_final: 0.7896 (p90)
REVERT: C  102 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8200 (pm20)
REVERT: C  236 MET cc_start: 0.7976 (mmt) cc_final: 0.7659 (mmm)
REVERT: C  362 TRP cc_start: 0.7304 (t60) cc_final: 0.6280 (m100)
REVERT: D    8 GLU cc_start: 0.8038 (tp30) cc_final: 0.6885 (tp30)
REVERT: D   11 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7719 (ttp80)
REVERT: D   12 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7493 (mt0)
REVERT: D   33 ILE cc_start: 0.8367 (mm) cc_final: 0.8107 (mm)
REVERT: D   37 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7602 (mm)
REVERT: D   80 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8208 (ttm170)
REVERT: D  118 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7429 (tt)
  outliers start: 34
  outliers final: 20
  residues processed: 156
  average time/residue: 0.0859
  time to fit residues: 20.1443
Evaluate side-chains
  154 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  172 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 103 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    0.1980
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  53 HIS
D 177 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.162972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.126607 restraints weight = 15742.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.131231 restraints weight = 8926.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.134323 restraints weight = 6204.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136374 restraints weight = 4881.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137743 restraints weight = 4145.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10544  Z= 0.119
  Angle     :  0.553   7.941  14269  Z= 0.288
  Chirality :  0.043   0.395   1605
  Planarity :  0.004   0.040   1737
  Dihedral  :  7.132  73.095   1411
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.45 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1235
  helix:  1.43 (0.22), residues: 597
  sheet:  0.84 (0.37), residues: 205
  loop : -1.63 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  11 
 TYR   0.016   0.001   TYR B  63 
 PHE   0.029   0.001   PHE D 175 
 TRP   0.021   0.001   TRP D  31 
 HIS   0.021   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10544)
  covalent geometry    : angle       0.55319 (14269)
  hydrogen bonds       : bond        0.04058 (  498)
  hydrogen bonds       : angle       4.44385 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5603 (ptt-90) cc_final: 0.5197 (ptp90)
REVERT: B   89 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8311 (ttpp)
REVERT: B  178 ILE cc_start: 0.8542 (pt) cc_final: 0.8313 (mt)
REVERT: B  187 TYR cc_start: 0.8469 (p90) cc_final: 0.7823 (p90)
REVERT: C  102 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8162 (pm20)
REVERT: C  362 TRP cc_start: 0.7294 (t60) cc_final: 0.6326 (m100)
REVERT: D    8 GLU cc_start: 0.7995 (tp30) cc_final: 0.6857 (tp30)
REVERT: D   12 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7448 (mt0)
REVERT: D   33 ILE cc_start: 0.8329 (mm) cc_final: 0.8076 (mm)
REVERT: D   37 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7557 (mm)
REVERT: D   80 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8090 (mtm180)
  outliers start: 26
  outliers final: 16
  residues processed: 152
  average time/residue: 0.0815
  time to fit residues: 18.5293
Evaluate side-chains
  151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   65 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0070
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   overall best weight:    0.8202

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

Flipped N/Q/H residues before XYZ refinement:
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.161690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.125008 restraints weight = 15807.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.129582 restraints weight = 9010.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.132650 restraints weight = 6285.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.134665 restraints weight = 4945.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.135919 restraints weight = 4220.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10544  Z= 0.134
  Angle     :  0.560   7.962  14269  Z= 0.293
  Chirality :  0.043   0.410   1605
  Planarity :  0.004   0.039   1737
  Dihedral  :  7.069  71.432   1411
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.54 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.24), residues: 1235
  helix:  1.47 (0.22), residues: 596
  sheet:  0.80 (0.37), residues: 200
  loop : -1.59 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  11 
 TYR   0.017   0.001   TYR B 150 
 PHE   0.032   0.001   PHE D 175 
 TRP   0.021   0.001   TRP D  31 
 HIS   0.005   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10544)
  covalent geometry    : angle       0.56032 (14269)
  hydrogen bonds       : bond        0.04235 (  498)
  hydrogen bonds       : angle       4.40309 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5653 (ptt-90) cc_final: 0.5217 (ptp90)
REVERT: B   89 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8336 (ttpp)
REVERT: B  178 ILE cc_start: 0.8599 (pt) cc_final: 0.8318 (mt)
REVERT: B  187 TYR cc_start: 0.8527 (p90) cc_final: 0.7850 (p90)
REVERT: C  102 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8161 (pm20)
REVERT: C  362 TRP cc_start: 0.7291 (t60) cc_final: 0.6272 (m100)
REVERT: D   11 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7984 (ttm-80)
REVERT: D   12 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7909 (mt0)
REVERT: D   33 ILE cc_start: 0.8347 (mm) cc_final: 0.8096 (mm)
REVERT: D   37 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7584 (mm)
REVERT: D   47 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5207 (mp)
REVERT: D   80 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8066 (mtm180)
REVERT: D  110 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8159 (mm-30)
REVERT: D  118 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7650 (tt)
  outliers start: 29
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0827
  time to fit residues: 18.7267
Evaluate side-chains
  155 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue    7 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.160461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124558 restraints weight = 15435.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.128890 restraints weight = 9163.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.131843 restraints weight = 6491.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133707 restraints weight = 5151.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.134840 restraints weight = 4431.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10544  Z= 0.161
  Angle     :  0.585   8.120  14269  Z= 0.306
  Chirality :  0.044   0.375   1605
  Planarity :  0.004   0.041   1737
  Dihedral  :  7.093  71.514   1411
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.25 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.24), residues: 1235
  helix:  1.43 (0.22), residues: 591
  sheet:  0.78 (0.37), residues: 200
  loop : -1.66 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  11 
 TYR   0.019   0.001   TYR B 150 
 PHE   0.035   0.001   PHE D 175 
 TRP   0.022   0.002   TRP D  31 
 HIS   0.006   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10544)
  covalent geometry    : angle       0.58486 (14269)
  hydrogen bonds       : bond        0.04554 (  498)
  hydrogen bonds       : angle       4.46605 ( 1443)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5534 (ptt-90) cc_final: 0.5129 (ptp90)
REVERT: B   89 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8360 (ttpp)
REVERT: B  178 ILE cc_start: 0.8627 (pt) cc_final: 0.8312 (mt)
REVERT: B  187 TYR cc_start: 0.8539 (p90) cc_final: 0.7828 (p90)
REVERT: C  102 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8153 (pm20)
REVERT: C  362 TRP cc_start: 0.7233 (t60) cc_final: 0.6122 (m100)
REVERT: D   11 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8021 (ttm-80)
REVERT: D   12 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7763 (mt0)
REVERT: D   33 ILE cc_start: 0.8312 (mm) cc_final: 0.8057 (mm)
REVERT: D   37 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7558 (mm)
REVERT: D   47 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.5249 (mp)
REVERT: D   80 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8084 (mtm180)
REVERT: D  118 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7870 (tt)
  outliers start: 27
  outliers final: 18
  residues processed: 155
  average time/residue: 0.0910
  time to fit residues: 20.9455
Evaluate side-chains
  159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  102 GLU
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue   12 GLN
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue  118 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 121 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.161802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.125262 restraints weight = 15773.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.129799 restraints weight = 8987.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.132873 restraints weight = 6278.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.134880 restraints weight = 4927.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136269 restraints weight = 4200.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10544  Z= 0.135
  Angle     :  0.564   8.119  14269  Z= 0.295
  Chirality :  0.043   0.399   1605
  Planarity :  0.004   0.041   1737
  Dihedral  :  6.962  70.129   1411
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.25 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.24), residues: 1235
  helix:  1.45 (0.22), residues: 596
  sheet:  0.91 (0.37), residues: 199
  loop : -1.67 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  11 
 TYR   0.017   0.001   TYR C 391 
 PHE   0.033   0.001   PHE D 175 
 TRP   0.024   0.001   TRP D  31 
 HIS   0.004   0.001   HIS D  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (10544)
  covalent geometry    : angle       0.56422 (14269)
  hydrogen bonds       : bond        0.04237 (  498)
  hydrogen bonds       : angle       4.38659 ( 1443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1634.43 seconds
wall clock time: 28 minutes 56.71 seconds (1736.71 seconds total)