Starting phenix.real_space_refine
on Sun Dec 29 10:32:04 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dne_27564/12_2024/8dne_27564.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dne_27564/12_2024/8dne_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_27564/12_2024/8dne_27564.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dne_27564/12_2024/8dne_27564.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dne_27564/12_2024/8dne_27564.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dne_27564/12_2024/8dne_27564.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.065
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.44, per 1000 atoms: 0.63
  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.12
  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: 2.90

  Time building geometry restraints manager: 3.19 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 393 or resid 501 throug \ 
h 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.660
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.340
-------------------------------------------------------------------------------
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= 0.224
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (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
 TRP   0.052   0.002   TRP D  31 
 HIS   0.004   0.001   HIS D  45 
 PHE   0.018   0.001   PHE C  30 
 TYR   0.021   0.001   TYR B 150 
 ARG   0.006   0.000   ARG A 263 

*********************** 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  : 1.129 
Fit side-chains
REVERT: B  187 TYR cc_start: 0.8141 (p90) cc_final: 0.7819 (p90)
REVERT: C  317 MET cc_start: 0.7857 (mtp) cc_final: 0.7651 (mtp)
REVERT: C  362 TRP cc_start: 0.7203 (t60) cc_final: 0.6447 (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: 0.1999
  time to fit residues: 51.0967
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  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 93 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 97 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    0.3980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
B  53 HIS
B 223 HIS
C  56 ASN
C 230 GLN
** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10544  Z= 0.165
  Angle     :  0.557   7.879  14269  Z= 0.294
  Chirality :  0.042   0.168   1605
  Planarity :  0.004   0.048   1737
  Dihedral  :  8.104  85.044   1411
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.18 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.24), residues: 1235
  helix:  1.23 (0.22), residues: 586
  sheet:  0.74 (0.37), residues: 199
  loop : -1.50 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP D  31 
 HIS   0.006   0.001   HIS B  53 
 PHE   0.022   0.001   PHE D  72 
 TYR   0.014   0.001   TYR D 150 
 ARG   0.005   0.000   ARG D  11 

*********************** 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
  160 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 155
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.5317 (ptt-90) cc_final: 0.4982 (ptp90)
REVERT: B   80 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7418 (ttm170)
REVERT: B  110 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: B  187 TYR cc_start: 0.8414 (p90) cc_final: 0.8017 (p90)
REVERT: C  362 TRP cc_start: 0.7074 (t60) cc_final: 0.6400 (m-90)
REVERT: D    8 GLU cc_start: 0.7612 (tp30) cc_final: 0.6748 (tp30)
REVERT: D   87 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6830 (tm-30)
REVERT: D  175 PHE cc_start: 0.8430 (t80) cc_final: 0.8033 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 157
  average time/residue: 0.2090
  time to fit residues: 48.1062
Evaluate side-chains
  135 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   chunk 76 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 112 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.9582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1975

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= 0.350
  Angle     :  0.640   8.395  14269  Z= 0.334
  Chirality :  0.045   0.180   1605
  Planarity :  0.004   0.049   1737
  Dihedral  :  8.873  89.812   1411
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.93 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.24), residues: 1235
  helix:  1.12 (0.22), residues: 588
  sheet:  0.59 (0.37), residues: 199
  loop : -1.55 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  31 
 HIS   0.005   0.001   HIS D 212 
 PHE   0.026   0.002   PHE D 255 
 TYR   0.030   0.002   TYR B 150 
 ARG   0.005   0.000   ARG D  11 

*********************** 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
  169 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.8086 (tt) cc_final: 0.7785 (pt)
REVERT: A  263 ARG cc_start: 0.5296 (ptt-90) cc_final: 0.5013 (ptp90)
REVERT: A  315 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4816 (t80)
REVERT: B   80 ARG cc_start: 0.8009 (ttp-170) cc_final: 0.7807 (ttp-170)
REVERT: B  187 TYR cc_start: 0.8738 (p90) cc_final: 0.8102 (p90)
REVERT: C  362 TRP cc_start: 0.7271 (t60) cc_final: 0.6416 (m-90)
REVERT: D    8 GLU cc_start: 0.7753 (tp30) cc_final: 0.7083 (tp30)
REVERT: D   33 ILE cc_start: 0.8444 (mm) cc_final: 0.7967 (mp)
REVERT: D  179 PHE cc_start: 0.8663 (t80) cc_final: 0.8432 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 160
  average time/residue: 0.2155
  time to fit residues: 49.9053
Evaluate side-chains
  148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 TYR
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  321 VAL
Chi-restraints excluded: chain D residue  163 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2322

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= 0.263
  Angle     :  0.590   7.945  14269  Z= 0.309
  Chirality :  0.043   0.171   1605
  Planarity :  0.004   0.048   1737
  Dihedral  :  8.498  88.261   1411
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.79 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.24), residues: 1235
  helix:  1.13 (0.22), residues: 588
  sheet:  0.52 (0.36), residues: 200
  loop : -1.49 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  31 
 HIS   0.013   0.001   HIS B  53 
 PHE   0.024   0.002   PHE D 175 
 TYR   0.021   0.001   TYR B 150 
 ARG   0.004   0.000   ARG D  11 

*********************** 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
  175 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.8137 (tt) cc_final: 0.7753 (pt)
REVERT: A  263 ARG cc_start: 0.5409 (ptt-90) cc_final: 0.5071 (ptp90)
REVERT: A  315 TYR cc_start: 0.5557 (OUTLIER) cc_final: 0.4878 (t80)
REVERT: B  187 TYR cc_start: 0.8667 (p90) cc_final: 0.8024 (p90)
REVERT: C  123 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7555 (pm20)
REVERT: D    8 GLU cc_start: 0.7760 (tp30) cc_final: 0.7040 (tp30)
REVERT: D   33 ILE cc_start: 0.8471 (mm) cc_final: 0.7990 (mp)
REVERT: D   37 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7598 (mm)
REVERT: D  179 PHE cc_start: 0.8578 (t80) cc_final: 0.8297 (t80)
  outliers start: 25
  outliers final: 14
  residues processed: 163
  average time/residue: 0.1966
  time to fit residues: 47.9378
Evaluate side-chains
  154 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
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   61 SER
Chi-restraints excluded: chain B residue   75 SER
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain C residue   98 LEU
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   26 TRP
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  161 LEU
Chi-restraints excluded: chain D residue  163 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 89 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0270
   overall best weight:    1.0640

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10544  Z= 0.223
  Angle     :  0.573   7.970  14269  Z= 0.298
  Chirality :  0.043   0.173   1605
  Planarity :  0.004   0.047   1737
  Dihedral  :  8.113  88.337   1411
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.04 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.24), residues: 1235
  helix:  1.23 (0.22), residues: 590
  sheet:  0.63 (0.36), residues: 199
  loop : -1.50 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D  31 
 HIS   0.007   0.001   HIS B  53 
 PHE   0.029   0.001   PHE D  72 
 TYR   0.018   0.001   TYR B 150 
 ARG   0.004   0.000   ARG D  11 

*********************** 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
  171 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.283 
Fit side-chains
REVERT: A  139 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7800 (tp)
REVERT: A  165 ILE cc_start: 0.8125 (tt) cc_final: 0.7720 (pt)
REVERT: A  263 ARG cc_start: 0.5699 (ptt-90) cc_final: 0.5275 (ptp90)
REVERT: B   89 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8429 (ttpp)
REVERT: B  187 TYR cc_start: 0.8586 (p90) cc_final: 0.8020 (p90)
REVERT: C  123 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7518 (pm20)
REVERT: C  362 TRP cc_start: 0.7248 (t60) cc_final: 0.6298 (m100)
REVERT: D    8 GLU cc_start: 0.7776 (tp30) cc_final: 0.6644 (tp30)
REVERT: D   12 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7415 (mt0)
REVERT: D   33 ILE cc_start: 0.8399 (mm) cc_final: 0.7831 (mp)
REVERT: D   37 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7568 (mm)
REVERT: D   47 ILE cc_start: 0.5327 (OUTLIER) cc_final: 0.5008 (mp)
REVERT: D  179 PHE cc_start: 0.8532 (t80) cc_final: 0.8208 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 159
  average time/residue: 0.2181
  time to fit residues: 50.7322
Evaluate side-chains
  156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  234 LYS
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   75 SER
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  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  259 ILE
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  161 LEU
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 29 optimal weight:    0.7980
   chunk 119 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.8940

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2647

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= 0.198
  Angle     :  0.553   7.943  14269  Z= 0.289
  Chirality :  0.042   0.175   1605
  Planarity :  0.004   0.044   1737
  Dihedral  :  7.713  83.058   1411
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.48 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1235
  helix:  1.35 (0.22), residues: 589
  sheet:  0.65 (0.36), residues: 200
  loop : -1.45 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP D  31 
 HIS   0.004   0.001   HIS D  45 
 PHE   0.030   0.001   PHE D 175 
 TYR   0.017   0.001   TYR B 150 
 ARG   0.009   0.000   ARG D  11 

*********************** 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
  173 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 1.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7773 (tp)
REVERT: A  165 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7648 (pt)
REVERT: A  184 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8140 (mt)
REVERT: A  263 ARG cc_start: 0.5622 (ptt-90) cc_final: 0.5227 (ptp90)
REVERT: A  375 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8128 (ttpp)
REVERT: B   89 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8460 (ttpp)
REVERT: B  187 TYR cc_start: 0.8552 (p90) cc_final: 0.7998 (p90)
REVERT: C  123 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7507 (pm20)
REVERT: C  236 MET cc_start: 0.7763 (mmt) cc_final: 0.7555 (mmm)
REVERT: C  362 TRP cc_start: 0.7317 (t60) cc_final: 0.6312 (m-90)
REVERT: D    8 GLU cc_start: 0.7725 (tp30) cc_final: 0.7321 (tp30)
REVERT: D   33 ILE cc_start: 0.8457 (mm) cc_final: 0.8169 (mm)
REVERT: D   37 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7565 (mm)
REVERT: D   47 ILE cc_start: 0.5495 (OUTLIER) cc_final: 0.5101 (mp)
REVERT: D  179 PHE cc_start: 0.8511 (t80) cc_final: 0.8201 (t80)
  outliers start: 31
  outliers final: 18
  residues processed: 163
  average time/residue: 0.2144
  time to fit residues: 51.0282
Evaluate side-chains
  156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  234 LYS
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   75 SER
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  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  161 LEU
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 115 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 87 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 119 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10544  Z= 0.194
  Angle     :  0.550   7.953  14269  Z= 0.287
  Chirality :  0.042   0.185   1605
  Planarity :  0.004   0.040   1737
  Dihedral  :  7.499  79.483   1411
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.84 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.24), residues: 1235
  helix:  1.39 (0.22), residues: 590
  sheet:  0.71 (0.36), residues: 200
  loop : -1.52 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  31 
 HIS   0.006   0.001   HIS B  53 
 PHE   0.030   0.001   PHE D 175 
 TYR   0.017   0.001   TYR B 150 
 ARG   0.005   0.000   ARG D  11 

*********************** 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
  166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 1.268 
Fit side-chains
REVERT: A  139 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7789 (tp)
REVERT: A  184 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8140 (mt)
REVERT: A  263 ARG cc_start: 0.5681 (ptt-90) cc_final: 0.5260 (ptp90)
REVERT: A  375 LYS cc_start: 0.8439 (tmmt) cc_final: 0.8104 (ttpp)
REVERT: B   89 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8463 (ttpp)
REVERT: B  187 TYR cc_start: 0.8533 (p90) cc_final: 0.7986 (p90)
REVERT: B  205 MET cc_start: 0.7478 (mmm) cc_final: 0.7120 (tpt)
REVERT: C  123 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7530 (pm20)
REVERT: C  362 TRP cc_start: 0.7248 (t60) cc_final: 0.6312 (m100)
REVERT: D    8 GLU cc_start: 0.7726 (tp30) cc_final: 0.6994 (tp30)
REVERT: D   12 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7490 (mt0)
REVERT: D   33 ILE cc_start: 0.8457 (mm) cc_final: 0.8143 (mm)
REVERT: D   37 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7570 (mm)
REVERT: D   47 ILE cc_start: 0.5418 (OUTLIER) cc_final: 0.5056 (mp)
REVERT: D   80 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7682 (mtm180)
  outliers start: 31
  outliers final: 21
  residues processed: 156
  average time/residue: 0.2062
  time to fit residues: 47.2730
Evaluate side-chains
  157 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  165 ILE
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  118 ILE
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  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  161 LEU
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 81 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.0182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10544  Z= 0.218
  Angle     :  0.571   7.855  14269  Z= 0.298
  Chirality :  0.043   0.191   1605
  Planarity :  0.004   0.041   1737
  Dihedral  :  7.322  75.409   1411
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.46 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1235
  helix:  1.39 (0.22), residues: 590
  sheet:  0.71 (0.36), residues: 200
  loop : -1.55 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D  31 
 HIS   0.005   0.001   HIS B  53 
 PHE   0.032   0.001   PHE D 175 
 TYR   0.018   0.001   TYR B 150 
 ARG   0.006   0.000   ARG D  11 

*********************** 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: 32
    poor density    : 131
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A  139 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (tp)
REVERT: A  184 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8140 (mt)
REVERT: A  263 ARG cc_start: 0.5697 (ptt-90) cc_final: 0.5276 (ptp90)
REVERT: A  375 LYS cc_start: 0.8426 (tmmt) cc_final: 0.8081 (ttpp)
REVERT: B   89 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8473 (ttpp)
REVERT: B  187 TYR cc_start: 0.8571 (p90) cc_final: 0.7956 (p90)
REVERT: B  205 MET cc_start: 0.7494 (mmm) cc_final: 0.7146 (tpt)
REVERT: C  123 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7539 (pm20)
REVERT: C  362 TRP cc_start: 0.7279 (t60) cc_final: 0.6350 (m100)
REVERT: D    8 GLU cc_start: 0.7772 (tp30) cc_final: 0.6728 (tp30)
REVERT: D   12 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7514 (mt0)
REVERT: D   33 ILE cc_start: 0.8455 (mm) cc_final: 0.8177 (mm)
REVERT: D   37 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7627 (mm)
REVERT: D   47 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5262 (mp)
REVERT: D   80 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7905 (mtm180)
REVERT: D  110 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7982 (mm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 152
  average time/residue: 0.2114
  time to fit residues: 46.8338
Evaluate side-chains
  157 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 1.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  234 LYS
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  118 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  147 MET
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  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  161 LEU
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 111 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 105 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10544  Z= 0.299
  Angle     :  0.606   7.744  14269  Z= 0.316
  Chirality :  0.044   0.187   1605
  Planarity :  0.004   0.044   1737
  Dihedral  :  7.401  73.385   1411
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.24), residues: 1235
  helix:  1.24 (0.22), residues: 591
  sheet:  0.63 (0.37), residues: 200
  loop : -1.58 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  31 
 HIS   0.022   0.002   HIS B  53 
 PHE   0.035   0.002   PHE D 175 
 TYR   0.020   0.001   TYR B 150 
 ARG   0.007   0.000   ARG D  11 

*********************** 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
  174 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 1.328 
Fit side-chains
REVERT: A  139 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7811 (tp)
REVERT: A  184 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8125 (mt)
REVERT: A  263 ARG cc_start: 0.5587 (ptt-90) cc_final: 0.5148 (ptp90)
REVERT: A  315 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5806 (t80)
REVERT: B   89 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8479 (ttpp)
REVERT: B  187 TYR cc_start: 0.8618 (p90) cc_final: 0.7918 (p90)
REVERT: B  205 MET cc_start: 0.7547 (mmm) cc_final: 0.7169 (tpt)
REVERT: C  123 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (pm20)
REVERT: C  362 TRP cc_start: 0.7194 (t60) cc_final: 0.6109 (m-90)
REVERT: D    8 GLU cc_start: 0.7765 (tp30) cc_final: 0.6843 (tp30)
REVERT: D   12 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7488 (mt0)
REVERT: D   33 ILE cc_start: 0.8427 (mm) cc_final: 0.8136 (mm)
REVERT: D   37 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7652 (mm)
REVERT: D   47 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5386 (mp)
REVERT: D   80 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7929 (mtm180)
REVERT: D  110 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8088 (mm-30)
  outliers start: 33
  outliers final: 21
  residues processed: 160
  average time/residue: 0.2132
  time to fit residues: 50.5048
Evaluate side-chains
  163 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  315 TYR
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  147 MET
Chi-restraints excluded: chain B residue  157 VAL
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  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  239 LEU
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  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 117 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 123 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
C 372 ASN
D  53 HIS
** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10544  Z= 0.219
  Angle     :  0.569   7.976  14269  Z= 0.298
  Chirality :  0.043   0.202   1605
  Planarity :  0.004   0.040   1737
  Dihedral  :  7.208  71.984   1411
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.27 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.24), residues: 1235
  helix:  1.37 (0.22), residues: 589
  sheet:  0.67 (0.37), residues: 200
  loop : -1.51 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  31 
 HIS   0.019   0.001   HIS B  53 
 PHE   0.037   0.001   PHE D 175 
 TYR   0.017   0.001   TYR C 391 
 ARG   0.005   0.000   ARG D  11 

********************** 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
  168 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 1.227 
Fit side-chains
REVERT: A  139 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7815 (tp)
REVERT: A  184 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: A  263 ARG cc_start: 0.5520 (ptt-90) cc_final: 0.5123 (ptp90)
REVERT: A  315 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5640 (t80)
REVERT: B   89 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8476 (ttpp)
REVERT: B  187 TYR cc_start: 0.8594 (p90) cc_final: 0.7915 (p90)
REVERT: B  205 MET cc_start: 0.7510 (mmm) cc_final: 0.7124 (tpt)
REVERT: C  123 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7515 (pm20)
REVERT: C  362 TRP cc_start: 0.7210 (t60) cc_final: 0.6124 (m-90)
REVERT: D    8 GLU cc_start: 0.7780 (tp30) cc_final: 0.6848 (tp30)
REVERT: D   12 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7460 (mt0)
REVERT: D   33 ILE cc_start: 0.8415 (mm) cc_final: 0.8065 (mm)
REVERT: D   37 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7604 (mm)
REVERT: D   80 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7906 (mtm180)
REVERT: D  110 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8042 (mm-30)
  outliers start: 29
  outliers final: 21
  residues processed: 155
  average time/residue: 0.2086
  time to fit residues: 47.3817
Evaluate side-chains
  162 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 VAL
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  315 TYR
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  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  123 GLU
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  239 LEU
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  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 90 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 101 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.3928 r_free = 0.3928 target = 0.157019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.121852 restraints weight = 15513.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126045 restraints weight = 9048.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.128863 restraints weight = 6394.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10544  Z= 0.321
  Angle     :  0.631   7.836  14269  Z= 0.329
  Chirality :  0.045   0.359   1605
  Planarity :  0.004   0.045   1737
  Dihedral  :  7.359  81.478   1411
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.36 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.24), residues: 1235
  helix:  1.18 (0.21), residues: 590
  sheet:  0.55 (0.37), residues: 200
  loop : -1.66 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  31 
 HIS   0.018   0.001   HIS B  53 
 PHE   0.038   0.002   PHE D 175 
 TYR   0.023   0.002   TYR B 150 
 ARG   0.005   0.000   ARG D  11 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1983.97 seconds
wall clock time: 37 minutes 24.03 seconds (2244.03 seconds total)