Starting phenix.real_space_refine
on Mon Jul 28 12:38:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k2t_22644/07_2025/7k2t_22644.cif"
  }
  resolution = 3.6
  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=  -0.000 sd=   0.006
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    6842      2.51       5
     N    1607      2.21       5
     O    1790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10275
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 3005
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 12, 'TRANS': 361}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2082
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 248, 2082
          Classifications: {'peptide': 248}
          Link IDs: {'PTRANS': 11, 'TRANS': 236}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2993
          Classifications: {'peptide': 372}
          Link IDs: {'PTRANS': 12, 'TRANS': 359}
          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: 6.46, per 1000 atoms: 0.63
  Number of scatterers: 10275
  At special positions: 0
  Unit cell: (101.363, 79.0034, 138.629, 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    1790      8.00
     N    1607      7.00
     C    6842      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: 3.02
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 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 9 sheets defined
      50.3% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 27
    Processing helix  chain 'A' and resid 59 through 68
    Processing helix  chain 'A' and resid 101 through 112
      removed outlier: 3.828A  pdb=" N   TYR A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 3.706A  pdb=" N   GLU A 120 " --> pdb=" O   ARG A 116 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   GLU A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   SER A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLU A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 143 through 157
      removed outlier: 3.590A  pdb=" N   HIS A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 190
    Processing helix  chain 'A' and resid 200 through 207
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 314 through 318
    Processing helix  chain 'B' and resid 3 through 18
    Processing helix  chain 'B' and resid 21 through 47
      removed outlier: 4.065A  pdb=" N   TRP B  26 " --> pdb=" O   VAL B  22 " (cutoff:3.500A)
      Proline residue:  B  32  - end of helix
      removed outlier: 4.514A  pdb=" N   HIS B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 83
      removed outlier: 3.792A  pdb=" N   PHE B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      Proline residue:  B  70  - end of helix
      removed outlier: 3.827A  pdb=" N   THR B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLY B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 86
      No H-bonds generated for 'chain 'B' and resid 84 through 86'
    Processing helix  chain 'B' and resid 100 through 128
      removed outlier: 3.735A  pdb=" N   LEU B 120 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 138
      removed outlier: 3.929A  pdb=" N   LYS B 135 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 5.180A  pdb=" N   TYR B 138 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 163
      removed outlier: 3.663A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 157 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   VAL B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 180
      removed outlier: 3.767A  pdb=" N   GLY B 173 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLN B 177 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 201
      removed outlier: 3.885A  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
      removed outlier: 3.503A  pdb=" N   LEU B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
      removed outlier: 3.681A  pdb=" N   LEU B 248 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   LYS B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   ASP B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ASP B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 25
      removed outlier: 4.256A  pdb=" N   LEU C  21 " --> pdb=" O   PRO C  17 " (cutoff:3.500A)
      removed outlier: 4.078A  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 111
      removed outlier: 3.605A  pdb=" N   ASN C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 126
      removed outlier: 3.673A  pdb=" N   ASP C 119 " --> pdb=" O   ARG C 115 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   SER C 124 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 136
    Processing helix  chain 'C' and resid 143 through 158
    Processing helix  chain 'C' and resid 173 through 190
    Processing helix  chain 'C' and resid 200 through 205
    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
      removed outlier: 3.553A  pdb=" N   PHE D  43 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 82
      Proline residue:  D  70  - end of helix
    Processing helix  chain 'D' and resid 100 through 129
      removed outlier: 3.842A  pdb=" N   VAL D 104 " --> pdb=" O   GLU D 100 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR D 128 " --> pdb=" O   ILE D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 138
      removed outlier: 4.277A  pdb=" N   GLY D 133 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE D 134 " --> pdb=" O   PHE D 131 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   LYS D 135 " --> pdb=" O   GLU D 132 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   TYR D 138 " --> pdb=" O   LYS D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 165
      removed outlier: 3.826A  pdb=" N   SER D 151 " --> pdb=" O   MET D 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   THR D 160 " --> pdb=" O   MET D 156 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   VAL D 163 " --> pdb=" O   GLY D 159 " (cutoff:3.500A)
      removed outlier: 3.863A  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: 3.513A  pdb=" N   LYS D 198 " --> pdb=" O   PRO D 194 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU D 199 " --> pdb=" O   PHE D 195 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE D 200 " --> pdb=" O   VAL D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 217
      removed outlier: 4.445A  pdb=" N   VAL D 208 " --> pdb=" O   PRO D 204 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU D 214 " --> pdb=" O   SER D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 233
      removed outlier: 3.505A  pdb=" N   LEU D 227 " --> pdb=" O   HIS D 223 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA D 233 " --> pdb=" O   GLY D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 240
    Processing helix  chain 'D' and resid 242 through 247
    Processing helix  chain 'D' and resid 248 through 253
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 43
      removed outlier: 6.411A  pdb=" N   LYS A   9 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LYS A  38 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   VAL A   7 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE A  40 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   PHE A   5 " --> pdb=" O   ILE A  40 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU A  42 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ARG A   3 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   VAL A   7 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 6.293A  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: 3.673A  pdb=" N   VAL A 197 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   HIS A 215 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   ILE A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265
      removed outlier: 6.560A  pdb=" N   ASP A 285 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   VAL A 262 " --> pdb=" O   GLU A 283 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLU A 283 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   LEU A 264 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   PHE A 281 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A 282 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 286 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA A 288 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN C 390 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276
      removed outlier: 5.975A  pdb=" N   SER A 276 " --> pdb=" O   ASN A 372 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   PHE A 374 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   CYS A 367 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   HIS A 350 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL A 296 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ASP A 303 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ASP A 308 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 392
      removed outlier: 3.742A  pdb=" N   ASN A 390 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   THR C 331 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG A 392 " --> pdb=" O   LEU C 329 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU C 329 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLU C 261 " --> pdb=" O   ASP C 285 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   GLU C 287 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   ILE C 259 " --> pdb=" O   GLU C 287 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 44
      removed outlier: 6.343A  pdb=" N   LYS C   9 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LYS C  38 " --> pdb=" O   VAL C   7 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   VAL C   7 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE C  40 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE C   5 " --> pdb=" O   ILE C  40 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU C  42 " --> pdb=" O   ARG C   3 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ARG C   3 " --> pdb=" O   LEU C  42 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 53
      removed outlier: 6.469A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   LEU C 214 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL C  53 " --> pdb=" O   LEU C 214 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   HIS C 215 " --> pdb=" O   ILE C 219 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   ILE C 219 " --> pdb=" O   HIS C 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 87
      removed outlier: 3.702A  pdb=" N   ILE C 164 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU C  87 " --> pdb=" O   ILE C 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 276
      removed outlier: 4.513A  pdb=" N   SER C 276 " --> pdb=" O   ASN C 372 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   PHE C 374 " --> pdb=" O   SER C 276 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ALA C 297 " --> pdb=" O   ASN C 313 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ASN C 313 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ILE C 299 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLY C 311 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ILE C 301 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)

    500 hydrogen bonds defined for protein.
    1437 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: 2.86

  Time building geometry restraints manager: 3.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3058
        1.34 -     1.46: 2468
        1.46 -     1.58: 4957
        1.58 -     1.69: 10
        1.69 -     1.81: 46
  Bond restraints: 10539
  Sorted by residual:
  bond pdb=" C4  ATP A 501 "
       pdb=" C5  ATP A 501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.30e+01
  bond pdb=" C4  ATP C 501 "
       pdb=" C5  ATP C 501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.85e+01
  bond pdb=" C5  ATP C 501 "
       pdb=" C6  ATP C 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.480 -0.071 1.00e-02 1.00e+04 5.09e+01
  bond pdb=" C5  ATP A 501 "
       pdb=" C6  ATP A 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.87e+01
  bond pdb=" C5  ATP A 501 "
       pdb=" N7  ATP A 501 "
    ideal  model  delta    sigma   weight residual
    1.387  1.341  0.046 1.00e-02 1.00e+04 2.09e+01
  ... (remaining 10534 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.34: 14219
        4.34 -     8.68: 40
        8.68 -    13.02: 2
       13.02 -    17.36: 0
       17.36 -    21.69: 4
  Bond angle restraints: 14265
  Sorted by residual:
  angle pdb=" PB  ATP C 501 "
        pdb=" O3B ATP C 501 "
        pdb=" PG  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     139.87  118.18   21.69 1.00e+00 1.00e+00 4.71e+02
  angle pdb=" PB  ATP A 501 "
        pdb=" O3B ATP A 501 "
        pdb=" PG  ATP A 501 "
      ideal   model   delta    sigma   weight residual
     139.87  119.92   19.95 1.00e+00 1.00e+00 3.98e+02
  angle pdb=" PA  ATP C 501 "
        pdb=" O3A ATP C 501 "
        pdb=" PB  ATP C 501 "
      ideal   model   delta    sigma   weight residual
     136.83  118.26   18.57 1.00e+00 1.00e+00 3.45e+02
  angle pdb=" PA  ATP A 501 "
        pdb=" O3A ATP A 501 "
        pdb=" PB  ATP A 501 "
      ideal   model   delta    sigma   weight residual
     136.83  118.49   18.34 1.00e+00 1.00e+00 3.36e+02
  angle pdb=" C5  ATP A 501 "
        pdb=" C4  ATP A 501 "
        pdb=" N3  ATP A 501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.57    8.23 1.00e+00 1.00e+00 6.77e+01
  ... (remaining 14260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 5543
       17.55 -    35.09: 547
       35.09 -    52.64: 84
       52.64 -    70.19: 22
       70.19 -    87.73: 11
  Dihedral angle restraints: 6207
    sinusoidal: 2571
      harmonic: 3636
  Sorted by residual:
  dihedral pdb=" CA  LEU C  98 "
           pdb=" C   LEU C  98 "
           pdb=" N   SER C  99 "
           pdb=" CA  SER C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.18  -17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  TYR B  18 "
           pdb=" C   TYR B  18 "
           pdb=" N   ALA B  19 "
           pdb=" CA  ALA B  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.92  -17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  LYS D  50 "
           pdb=" C   LYS D  50 "
           pdb=" N   LEU D  51 "
           pdb=" CA  LEU D  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.48   16.52     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 6204 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1124
       0.042 -    0.084: 363
       0.084 -    0.126: 106
       0.126 -    0.168: 11
       0.168 -    0.210: 1
  Chirality restraints: 1605
  Sorted by residual:
  chirality pdb=" CB  ILE C 219 "
            pdb=" CA  ILE C 219 "
            pdb=" CG1 ILE C 219 "
            pdb=" CG2 ILE C 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  ILE C 212 "
            pdb=" N   ILE C 212 "
            pdb=" C   ILE C 212 "
            pdb=" CB  ILE C 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.92e-01
  chirality pdb=" CA  ILE A 363 "
            pdb=" N   ILE A 363 "
            pdb=" C   ILE A 363 "
            pdb=" CB  ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 1602 not shown)

  Planarity restraints: 1735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 132 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.71e+00
        pdb=" C   ASP C 132 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ASP C 132 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP C 133 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 339 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 340 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 340 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 340 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 146 "   -0.006 2.00e-02 2.50e+03   1.28e-02 1.64e+00
        pdb=" C   LEU D 146 "    0.022 2.00e-02 2.50e+03
        pdb=" O   LEU D 146 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   MET D 147 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1732 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.54: 71
        2.54 -     3.13: 8222
        3.13 -     3.72: 15256
        3.72 -     4.31: 21819
        4.31 -     4.90: 37083
  Nonbonded interactions: 82451
  Sorted by model distance:
  nonbonded pdb=" O1G ATP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.955 2.170
  nonbonded pdb=" O1G ATP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     2.042 2.170
  nonbonded pdb=" O1B ATP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.079 2.170
  nonbonded pdb=" O1B ATP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     2.134 2.170
  nonbonded pdb=" OG  SER A  61 "
            pdb="MG    MG A 502 "
     model   vdw
     2.180 2.170
  ... (remaining 82446 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 241 or resid 255 through 395 or resid 501 throug \ 
h 502))
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and (resid 2 through 47 or resid 55 through 256))
}

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=0.15 max=1.00 mean=0.98
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:             0.890
  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:                    0.110
  Process input model:                     25.690
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  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:2.650
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
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      :  0.005   0.079  10539  Z= 0.287
  Angle     :  0.775  21.694  14265  Z= 0.529
  Chirality :  0.044   0.210   1605
  Planarity :  0.003   0.032   1735
  Dihedral  : 14.489  87.734   3875
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  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: -3.30 (0.21), residues: 1231
  helix: -1.83 (0.19), residues: 604
  sheet: -1.78 (0.33), residues: 185
  loop : -2.65 (0.25), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  71 
 HIS   0.012   0.001   HIS D 213 
 PHE   0.017   0.002   PHE D 179 
 TYR   0.013   0.001   TYR D  63 
 ARG   0.002   0.000   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18686 (  500)
  hydrogen bonds       : angle       7.78720 ( 1437)
  covalent geometry    : bond        0.00513 (10539)
  covalent geometry    : angle       0.77504 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7241 (tt0) cc_final: 0.6880 (tp30)
REVERT: A  365 ASN cc_start: 0.6626 (p0) cc_final: 0.6421 (p0)
REVERT: C  121 LYS cc_start: 0.8879 (mttt) cc_final: 0.8568 (mtpp)
REVERT: C  123 GLU cc_start: 0.6424 (mp0) cc_final: 0.6019 (mp0)
REVERT: C  146 MET cc_start: 0.8748 (mtp) cc_final: 0.8130 (mtm)
REVERT: C  263 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.6332 (mtp85)
REVERT: C  350 HIS cc_start: 0.7044 (p90) cc_final: 0.6842 (p-80)
REVERT: C  368 ASN cc_start: 0.7508 (t0) cc_final: 0.6704 (m-40)
REVERT: C  388 GLU cc_start: 0.8141 (tt0) cc_final: 0.7646 (tt0)
REVERT: D    8 GLU cc_start: 0.8220 (tp30) cc_final: 0.7521 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2758
  time to fit residues: 84.6161
Evaluate side-chains
  155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS
A 199 HIS
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 HIS
B 223 HIS
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 189 GLN
C 272 ASN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 313 ASN
D 113 ASN
D 177 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110421 restraints weight = 14916.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112025 restraints weight = 10345.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113311 restraints weight = 8803.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3305
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3305 r_free = 0.3305    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10539  Z= 0.216
  Angle     :  0.650   8.798  14265  Z= 0.333
  Chirality :  0.045   0.155   1605
  Planarity :  0.004   0.035   1735
  Dihedral  :  9.062  84.367   1408
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.49 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.85 (0.23), residues: 1231
  helix: -0.45 (0.20), residues: 620
  sheet: -1.20 (0.33), residues: 200
  loop : -2.26 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  71 
 HIS   0.011   0.001   HIS D 213 
 PHE   0.028   0.002   PHE B 131 
 TYR   0.022   0.001   TYR C 142 
 ARG   0.003   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04869 (  500)
  hydrogen bonds       : angle       5.40857 ( 1437)
  covalent geometry    : bond        0.00511 (10539)
  covalent geometry    : angle       0.64959 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 173
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8635 (m-80)
REVERT: B  156 MET cc_start: 0.8741 (tpp) cc_final: 0.8454 (tpp)
REVERT: C  146 MET cc_start: 0.8947 (mtp) cc_final: 0.8660 (mtm)
REVERT: C  263 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6569 (mtp85)
REVERT: C  340 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8483 (Cg_endo)
REVERT: C  368 ASN cc_start: 0.7329 (t0) cc_final: 0.6952 (m-40)
REVERT: D    8 GLU cc_start: 0.8352 (tp30) cc_final: 0.7779 (tp30)
REVERT: D   98 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7928 (tpp80)
REVERT: D  218 ASN cc_start: 0.8497 (t0) cc_final: 0.8279 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 187
  average time/residue: 0.3287
  time to fit residues: 86.3938
Evaluate side-chains
  160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 1.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  308 ASP
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   90 LEU
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain D residue   47 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0770
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.3196

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110268 restraints weight = 15008.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110529 restraints weight = 10154.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.111902 restraints weight = 9459.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10539  Z= 0.115
  Angle     :  0.562   8.109  14265  Z= 0.286
  Chirality :  0.043   0.151   1605
  Planarity :  0.004   0.054   1735
  Dihedral  :  8.179  73.219   1408
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.45 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.05 (0.24), residues: 1231
  helix:  0.20 (0.21), residues: 612
  sheet: -0.81 (0.34), residues: 202
  loop : -1.88 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.018   0.001   PHE B 131 
 TYR   0.018   0.001   TYR C 142 
 ARG   0.007   0.000   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  500)
  hydrogen bonds       : angle       5.00442 ( 1437)
  covalent geometry    : bond        0.00246 (10539)
  covalent geometry    : angle       0.56164 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 177
  time to evaluate  : 1.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 MET cc_start: 0.8185 (tmm) cc_final: 0.7864 (tmm)
REVERT: B   72 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8777 (m-80)
REVERT: C  146 MET cc_start: 0.8804 (mtp) cc_final: 0.8173 (mtm)
REVERT: C  158 THR cc_start: 0.8852 (m) cc_final: 0.8508 (m)
REVERT: C  220 ILE cc_start: 0.9251 (pt) cc_final: 0.9038 (pt)
REVERT: C  263 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6461 (mtp85)
REVERT: C  342 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7721 (mptt)
REVERT: C  368 ASN cc_start: 0.7634 (t0) cc_final: 0.7190 (m-40)
REVERT: D    8 GLU cc_start: 0.8304 (tp30) cc_final: 0.7750 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 189
  average time/residue: 0.3891
  time to fit residues: 103.9192
Evaluate side-chains
  167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 1.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  317 MET
Chi-restraints excluded: chain C residue  388 GLU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  183 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0670
   chunk 71 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 104 optimal weight:    3.9990
   overall best weight:    2.1924

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 350 HIS
D 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.101230 restraints weight = 15223.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.100829 restraints weight = 9946.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.101987 restraints weight = 9352.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10539  Z= 0.252
  Angle     :  0.654   8.942  14265  Z= 0.332
  Chirality :  0.045   0.149   1605
  Planarity :  0.004   0.034   1735
  Dihedral  :  8.006  69.396   1408
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.70 %
    Favored  : 81.18 %
  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: -0.99 (0.24), residues: 1231
  helix:  0.18 (0.21), residues: 626
  sheet: -0.78 (0.34), residues: 203
  loop : -1.80 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  27 
 HIS   0.009   0.001   HIS D 213 
 PHE   0.020   0.002   PHE C 163 
 TYR   0.023   0.002   TYR C 142 
 ARG   0.005   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  500)
  hydrogen bonds       : angle       5.03046 ( 1437)
  covalent geometry    : bond        0.00610 (10539)
  covalent geometry    : angle       0.65393 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8732 (pm20)
REVERT: B   72 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8704 (m-10)
REVERT: B  116 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8284 (mm)
REVERT: B  156 MET cc_start: 0.8689 (tpp) cc_final: 0.8419 (tpp)
REVERT: B  225 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6678 (t80)
REVERT: C  123 GLU cc_start: 0.5967 (mp0) cc_final: 0.5580 (mp0)
REVERT: C  146 MET cc_start: 0.8854 (mtp) cc_final: 0.8250 (mtm)
REVERT: C  212 ILE cc_start: 0.8969 (mm) cc_final: 0.8539 (tt)
REVERT: C  263 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6593 (mtp85)
REVERT: C  342 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7752 (mptt)
REVERT: D    8 GLU cc_start: 0.8442 (tp30) cc_final: 0.7753 (tp30)
REVERT: D   37 LEU cc_start: 0.9182 (mt) cc_final: 0.8950 (mp)
REVERT: D  218 ASN cc_start: 0.8543 (t0) cc_final: 0.8327 (t0)
  outliers start: 35
  outliers final: 22
  residues processed: 179
  average time/residue: 0.2248
  time to fit residues: 58.0266
Evaluate side-chains
  168 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 GLU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  308 ASP
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   40 ILE
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 81 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 107 ASN
A 199 HIS
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.133120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.108198 restraints weight = 14955.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.108304 restraints weight = 9982.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.109791 restraints weight = 9570.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3241
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3241 r_free = 0.3241    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10539  Z= 0.132
  Angle     :  0.565   8.430  14265  Z= 0.287
  Chirality :  0.043   0.150   1605
  Planarity :  0.003   0.028   1735
  Dihedral  :  7.680  68.697   1408
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.86 %
    Favored  : 80.29 %
  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: -0.62 (0.24), residues: 1231
  helix:  0.50 (0.21), residues: 619
  sheet: -0.45 (0.35), residues: 199
  loop : -1.70 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.019   0.001   PHE D  72 
 TYR   0.020   0.001   TYR C 142 
 ARG   0.002   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  500)
  hydrogen bonds       : angle       4.82986 ( 1437)
  covalent geometry    : bond        0.00299 (10539)
  covalent geometry    : angle       0.56457 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 LEU cc_start: 0.9256 (tp) cc_final: 0.8950 (tt)
REVERT: A  222 GLU cc_start: 0.7173 (tt0) cc_final: 0.6955 (tp30)
REVERT: A  241 ASN cc_start: 0.6137 (t0) cc_final: 0.5790 (m-40)
REVERT: B   72 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8734 (m-10)
REVERT: B  156 MET cc_start: 0.8823 (tpp) cc_final: 0.8568 (mmm)
REVERT: B  170 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: B  225 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6558 (t80)
REVERT: C   23 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8240 (pp20)
REVERT: C  146 MET cc_start: 0.8756 (mtp) cc_final: 0.8420 (mtt)
REVERT: C  212 ILE cc_start: 0.8971 (mm) cc_final: 0.8582 (tt)
REVERT: C  263 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6362 (mtp85)
REVERT: C  328 TYR cc_start: 0.6217 (m-80) cc_final: 0.5771 (m-80)
REVERT: C  342 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7833 (mptt)
REVERT: D    8 GLU cc_start: 0.8298 (tp30) cc_final: 0.7700 (tp30)
REVERT: D  175 PHE cc_start: 0.8779 (t80) cc_final: 0.8479 (t80)
  outliers start: 32
  outliers final: 19
  residues processed: 185
  average time/residue: 0.2205
  time to fit residues: 57.9853
Evaluate side-chains
  169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   23 GLU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  388 GLU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 104 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.8342

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 178 GLN
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.107902 restraints weight = 14912.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.109172 restraints weight = 9658.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110541 restraints weight = 8413.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10539  Z= 0.130
  Angle     :  0.554   9.249  14265  Z= 0.282
  Chirality :  0.042   0.148   1605
  Planarity :  0.003   0.027   1735
  Dihedral  :  7.386  63.581   1408
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.48 %
    Favored  : 79.04 %
  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: 1231
  helix:  0.68 (0.22), residues: 619
  sheet: -0.25 (0.37), residues: 185
  loop : -1.58 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.017   0.001   PHE D  72 
 TYR   0.017   0.001   TYR C 142 
 ARG   0.003   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  500)
  hydrogen bonds       : angle       4.70375 ( 1437)
  covalent geometry    : bond        0.00300 (10539)
  covalent geometry    : angle       0.55369 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 LEU cc_start: 0.9245 (tp) cc_final: 0.8936 (tt)
REVERT: A  222 GLU cc_start: 0.7229 (tt0) cc_final: 0.6977 (tp30)
REVERT: A  241 ASN cc_start: 0.6190 (t0) cc_final: 0.5880 (m-40)
REVERT: B   72 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8813 (m-10)
REVERT: B  116 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8149 (mm)
REVERT: B  156 MET cc_start: 0.8803 (tpp) cc_final: 0.8554 (tpp)
REVERT: B  170 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8083 (mm-30)
REVERT: B  225 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6531 (t80)
REVERT: C   23 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8250 (pp20)
REVERT: C  123 GLU cc_start: 0.5718 (mp0) cc_final: 0.5328 (mp0)
REVERT: C  146 MET cc_start: 0.8782 (mtp) cc_final: 0.8227 (mtm)
REVERT: C  263 ARG cc_start: 0.6854 (mtm-85) cc_final: 0.6135 (mtp85)
REVERT: C  328 TYR cc_start: 0.6083 (m-80) cc_final: 0.5846 (m-80)
REVERT: C  342 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7866 (mptt)
REVERT: C  379 PHE cc_start: 0.8528 (p90) cc_final: 0.8228 (p90)
REVERT: D    8 GLU cc_start: 0.8327 (tp30) cc_final: 0.7712 (tp30)
  outliers start: 39
  outliers final: 25
  residues processed: 180
  average time/residue: 0.2955
  time to fit residues: 77.9865
Evaluate side-chains
  177 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   23 GLU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  201 MET
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 115 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 ASN
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 350 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.134141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.108788 restraints weight = 15226.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.109077 restraints weight = 10173.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.110653 restraints weight = 9386.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3253
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10539  Z= 0.130
  Angle     :  0.554   9.147  14265  Z= 0.282
  Chirality :  0.042   0.183   1605
  Planarity :  0.003   0.032   1735
  Dihedral  :  7.253  60.542   1408
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.29 %
    Favored  : 78.32 %
  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: -0.22 (0.24), residues: 1231
  helix:  0.79 (0.22), residues: 619
  sheet: -0.13 (0.37), residues: 185
  loop : -1.49 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.016   0.001   PHE D  72 
 TYR   0.017   0.001   TYR C 142 
 ARG   0.002   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03656 (  500)
  hydrogen bonds       : angle       4.66158 ( 1437)
  covalent geometry    : bond        0.00301 (10539)
  covalent geometry    : angle       0.55406 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 157
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 LEU cc_start: 0.9252 (tp) cc_final: 0.8948 (tt)
REVERT: A  222 GLU cc_start: 0.7196 (tt0) cc_final: 0.6950 (tp30)
REVERT: A  241 ASN cc_start: 0.6231 (t0) cc_final: 0.5959 (m-40)
REVERT: A  365 ASN cc_start: 0.7871 (p0) cc_final: 0.7141 (p0)
REVERT: B   72 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8738 (m-10)
REVERT: B  156 MET cc_start: 0.8846 (tpp) cc_final: 0.8598 (tpp)
REVERT: B  170 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8016 (mm-30)
REVERT: B  225 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6534 (t80)
REVERT: C  146 MET cc_start: 0.8766 (mtp) cc_final: 0.8481 (mtt)
REVERT: C  212 ILE cc_start: 0.8918 (mm) cc_final: 0.8447 (tt)
REVERT: C  263 ARG cc_start: 0.6886 (mtm-85) cc_final: 0.5964 (mtp85)
REVERT: C  342 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7858 (mptt)
REVERT: C  379 PHE cc_start: 0.8556 (p90) cc_final: 0.8300 (p90)
REVERT: D    8 GLU cc_start: 0.8334 (tp30) cc_final: 0.7728 (tp30)
REVERT: D  232 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7989 (mt)
  outliers start: 38
  outliers final: 27
  residues processed: 182
  average time/residue: 0.2049
  time to fit residues: 53.4540
Evaluate side-chains
  173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 143
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  201 MET
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  308 ASP
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 120 optimal weight:    3.9990
   chunk 98 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 113 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 69 optimal weight:    0.0050
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.135509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.110031 restraints weight = 15047.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110903 restraints weight = 9816.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.112331 restraints weight = 8689.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3271 r_free = 0.3271    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10539  Z= 0.114
  Angle     :  0.550   8.860  14265  Z= 0.281
  Chirality :  0.042   0.176   1605
  Planarity :  0.003   0.030   1735
  Dihedral  :  7.067  57.192   1408
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.18 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.08 (0.24), residues: 1231
  helix:  0.87 (0.22), residues: 621
  sheet: -0.03 (0.38), residues: 185
  loop : -1.40 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.018   0.001   PHE D  72 
 TYR   0.015   0.001   TYR C 142 
 ARG   0.003   0.000   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  500)
  hydrogen bonds       : angle       4.61102 ( 1437)
  covalent geometry    : bond        0.00255 (10539)
  covalent geometry    : angle       0.55006 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7241 (tt0) cc_final: 0.6971 (tp30)
REVERT: A  241 ASN cc_start: 0.6213 (t0) cc_final: 0.5941 (m-40)
REVERT: A  365 ASN cc_start: 0.7785 (p0) cc_final: 0.7043 (p0)
REVERT: B   72 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8620 (m-10)
REVERT: B  156 MET cc_start: 0.8794 (tpp) cc_final: 0.8538 (tpp)
REVERT: B  170 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8021 (mm-30)
REVERT: B  225 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6517 (t80)
REVERT: C  123 GLU cc_start: 0.5700 (mp0) cc_final: 0.5386 (mp0)
REVERT: C  146 MET cc_start: 0.8716 (mtp) cc_final: 0.8490 (mtt)
REVERT: C  264 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7203 (mt)
REVERT: C  342 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7840 (mptt)
REVERT: C  379 PHE cc_start: 0.8520 (p90) cc_final: 0.8244 (p90)
REVERT: D    8 GLU cc_start: 0.8321 (tp30) cc_final: 0.7687 (tp30)
REVERT: D  232 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7983 (mt)
  outliers start: 33
  outliers final: 25
  residues processed: 175
  average time/residue: 0.2412
  time to fit residues: 60.6668
Evaluate side-chains
  174 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  201 MET
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain C residue  264 LEU
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  232 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 96 optimal weight:    0.0570
   chunk 13 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0370
   chunk 89 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 109 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 88 optimal weight:    9.9990
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
** A  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 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 = 0.3596 r_free = 0.3596 target = 0.136518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.111093 restraints weight = 15093.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.111974 restraints weight = 10135.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.113481 restraints weight = 8973.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10539  Z= 0.110
  Angle     :  0.548   8.707  14265  Z= 0.279
  Chirality :  0.042   0.164   1605
  Planarity :  0.003   0.027   1735
  Dihedral  :  6.898  55.926   1408
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.36 %
    Favored  : 78.06 %
  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:  0.05 (0.24), residues: 1231
  helix:  0.97 (0.22), residues: 621
  sheet:  0.07 (0.38), residues: 185
  loop : -1.33 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.016   0.001   PHE D  72 
 TYR   0.015   0.001   TYR B  18 
 ARG   0.002   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03395 (  500)
  hydrogen bonds       : angle       4.55888 ( 1437)
  covalent geometry    : bond        0.00245 (10539)
  covalent geometry    : angle       0.54757 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7205 (tt0) cc_final: 0.6949 (tp30)
REVERT: A  365 ASN cc_start: 0.7963 (p0) cc_final: 0.7203 (p0)
REVERT: B   72 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8681 (m-10)
REVERT: B  116 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8096 (mm)
REVERT: B  156 MET cc_start: 0.8815 (tpp) cc_final: 0.8561 (tpp)
REVERT: B  225 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6496 (t80)
REVERT: C  212 ILE cc_start: 0.8963 (mm) cc_final: 0.8622 (tt)
REVERT: C  276 SER cc_start: 0.7446 (m) cc_final: 0.7087 (t)
REVERT: C  342 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7715 (mptt)
REVERT: D    8 GLU cc_start: 0.8281 (tp30) cc_final: 0.7692 (tp30)
REVERT: D  232 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8162 (mt)
  outliers start: 29
  outliers final: 24
  residues processed: 171
  average time/residue: 0.2335
  time to fit residues: 57.5421
Evaluate side-chains
  172 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  201 MET
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 14 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 78 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 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 = 0.3586 r_free = 0.3586 target = 0.135694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110405 restraints weight = 15068.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110991 restraints weight = 10233.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112578 restraints weight = 9219.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       23 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10539  Z= 0.123
  Angle     :  0.563   8.929  14265  Z= 0.287
  Chirality :  0.042   0.161   1605
  Planarity :  0.003   0.028   1735
  Dihedral  :  6.848  55.342   1408
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.54 %
    Favored  : 77.70 %
  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:  0.09 (0.24), residues: 1231
  helix:  1.02 (0.22), residues: 616
  sheet:  0.10 (0.37), residues: 185
  loop : -1.33 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.031   0.001   PHE C 389 
 TYR   0.014   0.001   TYR C 142 
 ARG   0.002   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  500)
  hydrogen bonds       : angle       4.59984 ( 1437)
  covalent geometry    : bond        0.00284 (10539)
  covalent geometry    : angle       0.56316 (14265)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7197 (tt0) cc_final: 0.6936 (tp30)
REVERT: A  241 ASN cc_start: 0.6169 (t0) cc_final: 0.5618 (m-40)
REVERT: B   72 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8697 (m-10)
REVERT: B  116 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8114 (mm)
REVERT: B  156 MET cc_start: 0.8808 (tpp) cc_final: 0.8547 (tpp)
REVERT: B  225 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6520 (t80)
REVERT: C  123 GLU cc_start: 0.5518 (mp0) cc_final: 0.5223 (mp0)
REVERT: C  212 ILE cc_start: 0.8976 (mm) cc_final: 0.8673 (tt)
REVERT: C  342 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7845 (mptt)
REVERT: D    8 GLU cc_start: 0.8329 (tp30) cc_final: 0.7732 (tp30)
REVERT: D  232 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8172 (mt)
  outliers start: 31
  outliers final: 25
  residues processed: 167
  average time/residue: 0.2177
  time to fit residues: 52.2189
Evaluate side-chains
  174 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  344 THR
Chi-restraints excluded: chain B residue   72 PHE
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  118 ILE
Chi-restraints excluded: chain B residue  168 ILE
Chi-restraints excluded: chain B residue  174 VAL
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 TYR
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  132 ASP
Chi-restraints excluded: chain C residue  135 ILE
Chi-restraints excluded: chain C residue  156 ILE
Chi-restraints excluded: chain C residue  201 MET
Chi-restraints excluded: chain C residue  262 VAL
Chi-restraints excluded: chain D residue   47 ILE
Chi-restraints excluded: chain D residue   68 ILE
Chi-restraints excluded: chain D residue  118 ILE
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  183 THR
Chi-restraints excluded: chain D residue  188 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  240 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0060
   chunk 8 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 307 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 = 0.3584 r_free = 0.3584 target = 0.135547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110060 restraints weight = 14980.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110879 restraints weight = 9714.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.112278 restraints weight = 8498.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10539  Z= 0.123
  Angle     :  0.559   8.576  14265  Z= 0.285
  Chirality :  0.042   0.158   1605
  Planarity :  0.003   0.029   1735
  Dihedral  :  6.753  55.293   1408
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.63 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.16 (0.24), residues: 1231
  helix:  1.08 (0.22), residues: 615
  sheet:  0.13 (0.38), residues: 185
  loop : -1.29 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  71 
 HIS   0.008   0.001   HIS D  45 
 PHE   0.026   0.001   PHE C 389 
 TYR   0.017   0.001   TYR B  18 
 ARG   0.002   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  500)
  hydrogen bonds       : angle       4.58356 ( 1437)
  covalent geometry    : bond        0.00285 (10539)
  covalent geometry    : angle       0.55921 (14265)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3585.82 seconds
wall clock time: 66 minutes 51.55 seconds (4011.55 seconds total)