Starting phenix.real_space_refine
on Tue Jan 13 17:07:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ou0_17188/01_2026/8ou0_17188.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       5      5.49       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    5119      2.51       5
     N    1398      2.21       5
     O    1559      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8139
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3337
          Classifications: {'peptide': 426}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 11
    Chain: "D"
      Number of atoms: 164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 164
          Classifications: {'peptide': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 17}
    Chain: "C"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1236
          Classifications: {'peptide': 153}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 148}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3341
          Classifications: {'peptide': 428}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.97, per 1000 atoms: 0.24
  Number of scatterers: 8139
  At special positions: 0
  Unit cell: (106.002, 80.181, 112.797, 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      57     16.00
     P       5     15.00
     Mg      1     11.99
     O    1559      8.00
     N    1398      7.00
     C    5119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  33 " - pdb=" SG  CYS C  58 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  81 " - pdb=" SG  CYS C 101 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 389.4 milliseconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      55.9% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 71 through 81
      removed outlier: 4.655A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 90
      No H-bonds generated for 'chain 'B' and resid 88 through 90'
    Processing helix  chain 'B' and resid 102 through 109
    Processing helix  chain 'B' and resid 110 through 129
      removed outlier: 4.421A  pdb=" N   ASP B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   CYS B 129 " --> pdb=" O   GLU B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 4.034A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 3.638A  pdb=" N   ASN B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   GLU B 196 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 240
      removed outlier: 3.584A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 243
      No H-bonds generated for 'chain 'B' and resid 241 through 243'
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 296
      removed outlier: 3.754A  pdb=" N   PHE B 296 " --> pdb=" O   THR B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.504A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASN B 339 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
      removed outlier: 3.650A  pdb=" N   PHE B 343 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 340 through 343'
    Processing helix  chain 'B' and resid 383 through 401
      removed outlier: 4.019A  pdb=" N   LEU B 387 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ARG B 401 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.507A  pdb=" N   GLY B 410 " --> pdb=" O   HIS B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 435
      removed outlier: 3.757A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 22
      removed outlier: 3.618A  pdb=" N   GLN C  22 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 37
    Processing helix  chain 'C' and resid 46 through 56
      removed outlier: 3.547A  pdb=" N   VAL C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 87
      removed outlier: 4.075A  pdb=" N   GLU C  85 " --> pdb=" O   CYS C  81 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C  86 " --> pdb=" O   GLN C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 106
    Processing helix  chain 'C' and resid 122 through 126
      removed outlier: 3.512A  pdb=" N   HIS C 125 " --> pdb=" O   VAL C 122 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU C 126 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 122 through 126'
    Processing helix  chain 'C' and resid 127 through 134
    Processing helix  chain 'C' and resid 137 through 140
    Processing helix  chain 'C' and resid 141 through 157
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 4.357A  pdb=" N   THR A  51 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
      removed outlier: 3.942A  pdb=" N   GLU A 113 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 110 through 113'
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.618A  pdb=" N   LEU A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   CYS A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.310A  pdb=" N   ALA A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 205 through 218
      removed outlier: 3.906A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.736A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 260
      removed outlier: 4.644A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.662A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   HIS A 283 " --> pdb=" O   GLU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 6.132A  pdb=" N   ALA A 299 " --> pdb=" O   PHE A 296 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 301 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
    Processing helix  chain 'A' and resid 383 through 401
      removed outlier: 4.198A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 412
      removed outlier: 4.347A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 437
      removed outlier: 3.957A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94
      removed outlier: 8.294A  pdb=" N   VAL B  93 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLY B 134 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL B   5 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   SER B 140 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   MET B 166 " --> pdb=" O   GLU B 200 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   TYR B 202 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   THR B 168 " --> pdb=" O   TYR B 202 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   ILE B 204 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   SER B 170 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   THR B 201 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   CYS B 203 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      removed outlier: 10.425A  pdb=" N   PHE B 272 " --> pdb=" O   CYS B 203 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR B 314 " --> pdb=" O   ASN B 380 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.408A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   GLU A   3 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLY A 134 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.374A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ILE A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   ILE A 171 " --> pdb=" O   ILE A 137 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ALA A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273
      removed outlier: 6.794A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   CYS A 376 " --> pdb=" O   MET A 317 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   MET A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2706
        1.34 -     1.47: 1948
        1.47 -     1.59: 3570
        1.59 -     1.71: 8
        1.71 -     1.84: 88
  Bond restraints: 8320
  Sorted by residual:
  bond pdb=" C5  GDP B 501 "
       pdb=" C4  GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.490  1.467  0.023 2.00e-02 2.50e+03 1.35e+00
  bond pdb=" CG  PRO C 119 "
       pdb=" CD  PRO C 119 "
    ideal  model  delta    sigma   weight residual
    1.512  1.487  0.025 2.70e-02 1.37e+03 8.69e-01
  bond pdb=" CB  CYS C 101 "
       pdb=" SG  CYS C 101 "
    ideal  model  delta    sigma   weight residual
    1.808  1.838 -0.030 3.30e-02 9.18e+02 8.03e-01
  bond pdb=" CA  VAL C 105 "
       pdb=" C   VAL C 105 "
    ideal  model  delta    sigma   weight residual
    1.519  1.529 -0.010 1.14e-02 7.69e+03 7.21e-01
  bond pdb=" CB  LYS C  79 "
       pdb=" CG  LYS C  79 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.01e-01
  ... (remaining 8315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 10965
        1.34 -     2.68: 249
        2.68 -     4.02: 57
        4.02 -     5.36: 14
        5.36 -     6.70: 7
  Bond angle restraints: 11292
  Sorted by residual:
  angle pdb=" C   MET B 259 "
        pdb=" N   VAL B 260 "
        pdb=" CA  VAL B 260 "
      ideal   model   delta    sigma   weight residual
     122.59  120.21    2.38 7.20e-01 1.93e+00 1.09e+01
  angle pdb=" CA  CYS C 101 "
        pdb=" CB  CYS C 101 "
        pdb=" SG  CYS C 101 "
      ideal   model   delta    sigma   weight residual
     114.40  121.10   -6.70 2.30e+00 1.89e-01 8.49e+00
  angle pdb=" CA  CYS C  81 "
        pdb=" CB  CYS C  81 "
        pdb=" SG  CYS C  81 "
      ideal   model   delta    sigma   weight residual
     114.40  120.33   -5.93 2.30e+00 1.89e-01 6.64e+00
  angle pdb=" CA  TYR C 118 "
        pdb=" CB  TYR C 118 "
        pdb=" CG  TYR C 118 "
      ideal   model   delta    sigma   weight residual
     113.90  118.41   -4.51 1.80e+00 3.09e-01 6.27e+00
  angle pdb=" N   VAL B 260 "
        pdb=" CA  VAL B 260 "
        pdb=" C   VAL B 260 "
      ideal   model   delta    sigma   weight residual
     107.76  110.17   -2.41 1.01e+00 9.80e-01 5.71e+00
  ... (remaining 11287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.32: 4718
       27.32 -    54.64: 225
       54.64 -    81.96: 21
       81.96 -   109.28: 5
      109.28 -   136.59: 2
  Dihedral angle restraints: 4971
    sinusoidal: 1994
      harmonic: 2977
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -32.00  136.59     1      2.00e+01 2.50e-03 4.14e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -44.89  114.15     1      2.00e+01 2.50e-03 3.38e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  166.78  107.35     1      2.00e+01 2.50e-03 3.12e+01
  ... (remaining 4968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 758
       0.030 -    0.059: 306
       0.059 -    0.089: 107
       0.089 -    0.118: 65
       0.118 -    0.148: 8
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" CA  TYR C 118 "
            pdb=" N   TYR C 118 "
            pdb=" C   TYR C 118 "
            pdb=" CB  TYR C 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" CB  ILE B 347 "
            pdb=" CA  ILE B 347 "
            pdb=" CG1 ILE B 347 "
            pdb=" CG2 ILE B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE B 378 "
            pdb=" N   ILE B 378 "
            pdb=" C   ILE B 378 "
            pdb=" CB  ILE B 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 1241 not shown)

  Planarity restraints: 1465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 118 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO C 119 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 119 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 119 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 145 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.60e+00
        pdb=" C   THR A 145 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   THR A 145 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY A 146 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 183 "    0.018 5.00e-02 4.00e+02   2.76e-02 1.22e+00
        pdb=" N   PRO A 184 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 184 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 184 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1462 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 73
        2.64 -     3.21: 7213
        3.21 -     3.77: 11908
        3.77 -     4.34: 15614
        4.34 -     4.90: 27078
  Nonbonded interactions: 61886
  Sorted by model distance:
  nonbonded pdb=" O1B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.080 2.170
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.110 2.170
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG  SER B 190 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" OH  TYR A 399 "
            pdb=" OE1 GLU A 415 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OG1 THR B 109 "
            pdb=" OE1 GLU B 411 "
     model   vdw
     2.207 3.040
  ... (remaining 61881 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.110
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
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      :  0.002   0.030   8322  Z= 0.118
  Angle     :  0.539   6.701  11296  Z= 0.280
  Chirality :  0.041   0.148   1244
  Planarity :  0.003   0.042   1465
  Dihedral  : 15.274 136.594   3049
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.45 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.28), residues: 1015
  helix:  2.05 (0.24), residues: 502
  sheet:  0.67 (0.48), residues: 154
  loop : -1.22 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  65 
 TYR   0.009   0.001   TYR B 161 
 PHE   0.008   0.001   PHE B 169 
 TRP   0.009   0.001   TRP B 346 
 HIS   0.006   0.001   HIS C 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8320)
  covalent geometry    : angle       0.53547 (11292)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       3.32897 (    4)
  hydrogen bonds       : bond        0.12331 (  405)
  hydrogen bonds       : angle       5.48068 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.315 
Fit side-chains
REVERT: C   15 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7774 (mtpt)
REVERT: C   31 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7572 (tm-30)
REVERT: C  150 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7482 (mttp)
REVERT: A   90 GLU cc_start: 0.7669 (pp20) cc_final: 0.7441 (tm-30)
REVERT: A  113 GLU cc_start: 0.7149 (pm20) cc_final: 0.6879 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0991
  time to fit residues: 19.8177
Evaluate side-chains
  129 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 336 GLN
** A  18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  35 GLN

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 = 0.122399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.098848 restraints weight = 12267.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.101994 restraints weight = 7239.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.104120 restraints weight = 5086.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.105532 restraints weight = 3977.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.106272 restraints weight = 3357.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8322  Z= 0.115
  Angle     :  0.539   6.683  11296  Z= 0.272
  Chirality :  0.041   0.125   1244
  Planarity :  0.004   0.042   1465
  Dihedral  :  7.696 136.829   1136
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.25 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  8.17 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.28), residues: 1015
  helix:  2.17 (0.24), residues: 503
  sheet:  0.67 (0.49), residues: 144
  loop : -1.12 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.021   0.001   TYR C 118 
 PHE   0.016   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.011   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8320)
  covalent geometry    : angle       0.53661 (11292)
  SS BOND              : bond        0.00345 (    2)
  SS BOND              : angle       2.97243 (    4)
  hydrogen bonds       : bond        0.04420 (  405)
  hydrogen bonds       : angle       4.29425 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 140
  time to evaluate  : 0.321 
Fit side-chains
REVERT: C   31 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7661 (tm-30)
REVERT: C   85 GLU cc_start: 0.7883 (tp30) cc_final: 0.7601 (tp30)
REVERT: C  130 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7219 (mt-10)
REVERT: A  113 GLU cc_start: 0.7196 (pm20) cc_final: 0.6916 (pm20)
REVERT: A  254 GLU cc_start: 0.4223 (tp30) cc_final: 0.4003 (tp30)
  outliers start: 7
  outliers final: 5
  residues processed: 143
  average time/residue: 0.0936
  time to fit residues: 18.3475
Evaluate side-chains
  135 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  335 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
B  37 HIS
B 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.122177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.098871 restraints weight = 12236.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.101914 restraints weight = 7332.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.103921 restraints weight = 5202.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.105274 restraints weight = 4115.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.106231 restraints weight = 3483.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8322  Z= 0.113
  Angle     :  0.527   6.973  11296  Z= 0.265
  Chirality :  0.041   0.137   1244
  Planarity :  0.003   0.041   1465
  Dihedral  :  7.658 137.333   1136
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 12.71 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.28), residues: 1015
  helix:  2.16 (0.24), residues: 504
  sheet:  0.80 (0.49), residues: 142
  loop : -1.10 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.019   0.001   TYR C 118 
 PHE   0.014   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.010   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8320)
  covalent geometry    : angle       0.52447 (11292)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       2.81363 (    4)
  hydrogen bonds       : bond        0.04299 (  405)
  hydrogen bonds       : angle       4.14165 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C   31 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: C   85 GLU cc_start: 0.7881 (tp30) cc_final: 0.7602 (tp30)
REVERT: C  130 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7239 (mt-10)
REVERT: A  183 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7007 (mt-10)
REVERT: A  254 GLU cc_start: 0.3874 (tp30) cc_final: 0.3641 (tp30)
REVERT: A  290 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7893 (tm-30)
  outliers start: 7
  outliers final: 6
  residues processed: 135
  average time/residue: 0.1018
  time to fit residues: 18.6643
Evaluate side-chains
  132 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  335 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0570
   chunk 15 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8502

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

Flipped N/Q/H residues before XYZ refinement:
B 349 ASN
A  31 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.118673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095404 restraints weight = 12548.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.098398 restraints weight = 7487.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.100362 restraints weight = 5294.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.101738 restraints weight = 4188.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.102453 restraints weight = 3544.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8322  Z= 0.163
  Angle     :  0.567   7.476  11296  Z= 0.287
  Chirality :  0.043   0.127   1244
  Planarity :  0.004   0.042   1465
  Dihedral  :  7.791 138.170   1136
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.17 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.28), residues: 1015
  helix:  2.13 (0.24), residues: 501
  sheet:  0.66 (0.46), residues: 153
  loop : -1.28 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.020   0.001   TYR C 118 
 PHE   0.014   0.001   PHE B 377 
 TRP   0.013   0.001   TRP B 346 
 HIS   0.010   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8320)
  covalent geometry    : angle       0.56435 (11292)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       2.92629 (    4)
  hydrogen bonds       : bond        0.05312 (  405)
  hydrogen bonds       : angle       4.20149 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: C   31 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: C  130 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7211 (mt-10)
REVERT: C  149 MET cc_start: 0.6542 (mmt) cc_final: 0.6311 (mmt)
REVERT: A   18 ASN cc_start: 0.7691 (t0) cc_final: 0.7409 (t0)
REVERT: A  254 GLU cc_start: 0.4290 (tp30) cc_final: 0.3897 (tp30)
REVERT: A  290 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: A  391 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8151 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 144
  average time/residue: 0.0973
  time to fit residues: 19.1113
Evaluate side-chains
  140 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  238 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  391 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.0980
   chunk 79 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 32 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 53 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.120837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.097451 restraints weight = 12348.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.100480 restraints weight = 7373.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.102518 restraints weight = 5218.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.103775 restraints weight = 4116.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.104752 restraints weight = 3508.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8322  Z= 0.117
  Angle     :  0.530   8.012  11296  Z= 0.266
  Chirality :  0.041   0.125   1244
  Planarity :  0.003   0.041   1465
  Dihedral  :  7.713 138.389   1136
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.42 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.28), residues: 1015
  helix:  2.17 (0.24), residues: 504
  sheet:  0.64 (0.46), residues: 152
  loop : -1.18 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.015   0.001   TYR C 118 
 PHE   0.012   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.012   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8320)
  covalent geometry    : angle       0.52723 (11292)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       2.86549 (    4)
  hydrogen bonds       : bond        0.04458 (  405)
  hydrogen bonds       : angle       4.05107 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B  269 MET cc_start: 0.7359 (ptt) cc_final: 0.7156 (ttp)
REVERT: C   31 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: C   76 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7310 (mt-10)
REVERT: C  130 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7191 (mt-10)
REVERT: C  149 MET cc_start: 0.6495 (mmt) cc_final: 0.6229 (mmt)
REVERT: A  168 GLU cc_start: 0.7752 (mp0) cc_final: 0.7510 (mp0)
REVERT: A  254 GLU cc_start: 0.4135 (tp30) cc_final: 0.3589 (tp30)
REVERT: A  290 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: A  391 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8123 (tp)
  outliers start: 14
  outliers final: 11
  residues processed: 137
  average time/residue: 0.0958
  time to fit residues: 17.9004
Evaluate side-chains
  137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  398 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 27 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C  95 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.120817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.097594 restraints weight = 12295.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.100622 restraints weight = 7361.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.102644 restraints weight = 5198.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.103970 restraints weight = 4092.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.104926 restraints weight = 3467.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8322  Z= 0.118
  Angle     :  0.533   8.652  11296  Z= 0.266
  Chirality :  0.041   0.139   1244
  Planarity :  0.003   0.040   1465
  Dihedral  :  7.655 138.674   1136
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.44 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.28), residues: 1015
  helix:  2.16 (0.24), residues: 505
  sheet:  0.65 (0.46), residues: 153
  loop : -1.21 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  34 
 TYR   0.014   0.001   TYR C 118 
 PHE   0.011   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.011   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8320)
  covalent geometry    : angle       0.53064 (11292)
  SS BOND              : bond        0.00419 (    2)
  SS BOND              : angle       2.82120 (    4)
  hydrogen bonds       : bond        0.04429 (  405)
  hydrogen bonds       : angle       4.00941 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: B  269 MET cc_start: 0.7738 (ptt) cc_final: 0.7380 (ttp)
REVERT: C   31 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7867 (tm-30)
REVERT: C   76 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7245 (mt-10)
REVERT: C  130 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7222 (mt-10)
REVERT: A  254 GLU cc_start: 0.4227 (tp30) cc_final: 0.3734 (tp30)
REVERT: A  290 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: A  391 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (tp)
  outliers start: 18
  outliers final: 13
  residues processed: 138
  average time/residue: 0.0970
  time to fit residues: 18.1184
Evaluate side-chains
  137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  425 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 83 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.095500 restraints weight = 12457.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.098499 restraints weight = 7414.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.100544 restraints weight = 5237.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.101859 restraints weight = 4115.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.102707 restraints weight = 3482.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8322  Z= 0.155
  Angle     :  0.562   9.056  11296  Z= 0.284
  Chirality :  0.042   0.133   1244
  Planarity :  0.004   0.039   1465
  Dihedral  :  7.724 138.961   1136
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.44 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.28), residues: 1015
  helix:  2.14 (0.24), residues: 500
  sheet:  0.51 (0.46), residues: 153
  loop : -1.26 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.012   0.001   TYR C 118 
 PHE   0.012   0.001   PHE B 377 
 TRP   0.012   0.001   TRP B 346 
 HIS   0.009   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8320)
  covalent geometry    : angle       0.55966 (11292)
  SS BOND              : bond        0.00472 (    2)
  SS BOND              : angle       3.02223 (    4)
  hydrogen bonds       : bond        0.05164 (  405)
  hydrogen bonds       : angle       4.12587 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: C    4 GLU cc_start: 0.7509 (pp20) cc_final: 0.7011 (pp20)
REVERT: C   31 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7970 (tm-30)
REVERT: C   76 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7402 (mt-10)
REVERT: C  130 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7198 (mt-10)
REVERT: A  254 GLU cc_start: 0.4375 (tp30) cc_final: 0.3805 (tp30)
REVERT: A  290 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: A  391 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8171 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 140
  average time/residue: 0.0925
  time to fit residues: 17.8291
Evaluate side-chains
  139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  425 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 83 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.4718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.123716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.100048 restraints weight = 12324.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.103309 restraints weight = 6950.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.105448 restraints weight = 4801.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.106900 restraints weight = 3758.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.107827 restraints weight = 3160.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8322  Z= 0.118
  Angle     :  0.548   9.229  11296  Z= 0.274
  Chirality :  0.041   0.134   1244
  Planarity :  0.003   0.039   1465
  Dihedral  :  7.654 139.361   1136
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.35 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.28), residues: 1015
  helix:  2.17 (0.24), residues: 504
  sheet:  0.56 (0.46), residues: 152
  loop : -1.21 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.012   0.001   TYR C 118 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.012   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8320)
  covalent geometry    : angle       0.54581 (11292)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       2.91749 (    4)
  hydrogen bonds       : bond        0.04418 (  405)
  hydrogen bonds       : angle       4.02498 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: C    4 GLU cc_start: 0.7540 (pp20) cc_final: 0.7029 (pp20)
REVERT: C   31 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: C   76 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7288 (mt-10)
REVERT: C  130 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7200 (mt-10)
REVERT: A  154 MET cc_start: 0.7841 (mtp) cc_final: 0.7571 (mtp)
REVERT: A  254 GLU cc_start: 0.4190 (tp30) cc_final: 0.3510 (mm-30)
REVERT: A  290 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: A  391 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8131 (tp)
  outliers start: 16
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0967
  time to fit residues: 16.9613
Evaluate side-chains
  135 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  425 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    0.4980
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0040
   chunk 79 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.4992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.120624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.097378 restraints weight = 12284.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.100439 restraints weight = 7338.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.102521 restraints weight = 5179.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.103868 restraints weight = 4060.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.104723 restraints weight = 3431.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8322  Z= 0.120
  Angle     :  0.549   9.598  11296  Z= 0.273
  Chirality :  0.041   0.134   1244
  Planarity :  0.003   0.036   1465
  Dihedral  :  7.582 139.907   1136
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.89 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.28), residues: 1015
  helix:  2.16 (0.24), residues: 506
  sheet:  0.58 (0.47), residues: 153
  loop : -1.25 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.012   0.001   TYR C 118 
 PHE   0.010   0.001   PHE B 377 
 TRP   0.012   0.001   TRP B 346 
 HIS   0.015   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8320)
  covalent geometry    : angle       0.54694 (11292)
  SS BOND              : bond        0.00454 (    2)
  SS BOND              : angle       2.83345 (    4)
  hydrogen bonds       : bond        0.04404 (  405)
  hydrogen bonds       : angle       4.00410 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: C    4 GLU cc_start: 0.7542 (pp20) cc_final: 0.7036 (pp20)
REVERT: C   31 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: C   76 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7326 (mt-10)
REVERT: C  130 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7204 (mt-10)
REVERT: A  254 GLU cc_start: 0.4255 (tp30) cc_final: 0.3663 (tp30)
REVERT: A  290 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A  392 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6461 (p0)
  outliers start: 20
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0984
  time to fit residues: 17.7731
Evaluate side-chains
  137 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain A residue   18 ASN
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  425 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0980
   chunk 75 optimal weight:    0.0770
   chunk 48 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.2516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.126069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102303 restraints weight = 12361.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105675 restraints weight = 6964.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107820 restraints weight = 4780.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109280 restraints weight = 3731.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110251 restraints weight = 3129.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8322  Z= 0.101
  Angle     :  0.537   9.733  11296  Z= 0.266
  Chirality :  0.040   0.132   1244
  Planarity :  0.003   0.035   1465
  Dihedral  :  7.355 140.939   1136
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.69 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.28), residues: 1015
  helix:  2.27 (0.24), residues: 503
  sheet:  0.64 (0.47), residues: 153
  loop : -1.23 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.013   0.001   TYR C 118 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.014   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8320)
  covalent geometry    : angle       0.53523 (11292)
  SS BOND              : bond        0.00424 (    2)
  SS BOND              : angle       2.61488 (    4)
  hydrogen bonds       : bond        0.03680 (  405)
  hydrogen bonds       : angle       3.89996 ( 1185)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: B  269 MET cc_start: 0.7156 (ttp) cc_final: 0.6953 (ttp)
REVERT: C    4 GLU cc_start: 0.7528 (pp20) cc_final: 0.7026 (pp20)
REVERT: C   15 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7819 (ttpt)
REVERT: C   31 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: C   76 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7252 (mt-10)
REVERT: C   79 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7307 (mmtm)
REVERT: C  130 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: A  254 GLU cc_start: 0.4019 (tp30) cc_final: 0.3438 (tp30)
REVERT: A  290 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: A  322 ASP cc_start: 0.7382 (t70) cc_final: 0.7056 (p0)
REVERT: A  392 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6355 (p0)
  outliers start: 15
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0947
  time to fit residues: 17.5302
Evaluate side-chains
  138 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  241 CYS
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain C residue   58 CYS
Chi-restraints excluded: chain C residue   76 GLU
Chi-restraints excluded: chain C residue   93 VAL
Chi-restraints excluded: chain A residue   18 ASN
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain A residue  425 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.0060
   chunk 74 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0570
   chunk 69 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.4114

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.098809 restraints weight = 12196.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.101957 restraints weight = 7079.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.104061 restraints weight = 4923.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.105507 restraints weight = 3832.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.106407 restraints weight = 3207.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8322  Z= 0.112
  Angle     :  0.552   9.749  11296  Z= 0.273
  Chirality :  0.041   0.132   1244
  Planarity :  0.003   0.035   1465
  Dihedral  :  7.310 142.232   1136
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.80 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.28), residues: 1015
  helix:  2.19 (0.24), residues: 506
  sheet:  0.64 (0.47), residues: 152
  loop : -1.21 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.012   0.001   TYR C 118 
 PHE   0.009   0.001   PHE B 377 
 TRP   0.011   0.001   TRP B 346 
 HIS   0.014   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8320)
  covalent geometry    : angle       0.54988 (11292)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       2.69490 (    4)
  hydrogen bonds       : bond        0.04033 (  405)
  hydrogen bonds       : angle       3.89966 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1392.82 seconds
wall clock time: 24 minutes 44.82 seconds (1484.82 seconds total)