Starting phenix.real_space_refine
on Tue Jan 13 20:48:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vuj_32130/01_2026/7vuj_32130.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      49      5.16       5
     Cl      1      4.86       5
     C    5277      2.51       5
     N    1433      2.21       5
     O    1523      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 8286
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1943
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2295
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 12, 'TRANS': 266}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 29
          Unusual residues: {' MG': 1, 'GDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'7ZQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.28
  Number of scatterers: 8286
  At special positions: 0
  Unit cell: (82.16, 100.88, 134.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      49     16.00
     P       2     15.00
     Mg      1     11.99
     O    1523      8.00
     N    1433      7.00
     C    5277      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 0.77
  Conformation dependent library (CDL) restraints added in 329.1 milliseconds
  

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      41.6% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 3.906A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 62
      removed outlier: 4.011A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.511A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.898A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.902A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
      removed outlier: 3.597A  pdb=" N   ARG A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.586A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.873A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 27 through 53
      removed outlier: 3.906A  pdb=" N   SER R  34 " --> pdb=" O   VAL R  30 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU R  35 " --> pdb=" O   VAL R  31 " (cutoff:3.500A)
      Proline residue:  R  42  - end of helix
      removed outlier: 3.755A  pdb=" N   GLN R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 59
      removed outlier: 4.086A  pdb=" N   ARG R  58 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 91
      removed outlier: 4.247A  pdb=" N   ASN R  64 " --> pdb=" O   LYS R  60 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   ASP R  89 " --> pdb=" O   PHE R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 132
      removed outlier: 3.872A  pdb=" N   VAL R 106 " --> pdb=" O   LYS R 102 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 135 through 140
    Processing helix  chain 'R' and resid 141 through 161
      removed outlier: 3.583A  pdb=" N   LYS R 147 " --> pdb=" O   ALA R 143 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL R 152 " --> pdb=" O   VAL R 148 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   TYR R 153 " --> pdb=" O   ILE R 149 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE R 161 " --> pdb=" O   PHE R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 166
      removed outlier: 3.832A  pdb=" N   TRP R 165 " --> pdb=" O   PRO R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 192
      removed outlier: 3.623A  pdb=" N   HIS R 181 " --> pdb=" O   THR R 177 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL R 182 " --> pdb=" O   SER R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 213
      removed outlier: 3.576A  pdb=" N   SER R 197 " --> pdb=" O   LEU R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 222 through 253
      Proline residue:  R 243  - end of helix
    Processing helix  chain 'R' and resid 259 through 286
      removed outlier: 3.511A  pdb=" N   HIS R 264 " --> pdb=" O   ARG R 260 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   MET R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER R 267 " --> pdb=" O   VAL R 263 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   PHE R 282 " --> pdb=" O   THR R 278 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   PHE R 283 " --> pdb=" O   ALA R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 301
      removed outlier: 4.172A  pdb=" N   LYS R 301 " --> pdb=" O   ALA R 297 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.789A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE A 219 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   HIS A 352 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   LEU A 279 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.260A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63
      removed outlier: 6.885A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.670A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.449A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.830A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.175A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR B 243 " --> pdb=" O   ARG B 251 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.874A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU B 286 " --> pdb=" O   SER B 277 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.682A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU N  79 " --> pdb=" O   CYS N  22 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR N  69 " --> pdb=" O   GLN N  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60
      removed outlier: 3.829A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLN N  39 " --> pdb=" O   VAL N  93 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1068 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: 1.26

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1327
        1.31 -     1.44: 2381
        1.44 -     1.56: 4686
        1.56 -     1.69: 3
        1.69 -     1.81: 70
  Bond restraints: 8467
  Sorted by residual:
  bond pdb=" C7  7ZQ R 401 "
       pdb=" N1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.448 -0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" C9  7ZQ R 401 "
       pdb=" N2  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.444 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" C5  GDP A 402 "
       pdb=" C4  GDP A 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.389  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" C3' GDP A 402 "
       pdb=" C2' GDP A 402 "
    ideal  model  delta    sigma   weight residual
    1.524  1.447  0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C5  GDP A 402 "
       pdb=" C6  GDP A 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.419  0.071 2.00e-02 2.50e+03 1.27e+01
  ... (remaining 8462 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 11377
        3.02 -     6.05: 102
        6.05 -     9.07: 7
        9.07 -    12.10: 2
       12.10 -    15.12: 1
  Bond angle restraints: 11489
  Sorted by residual:
  angle pdb=" CA  LEU A 260 "
        pdb=" CB  LEU A 260 "
        pdb=" CG  LEU A 260 "
      ideal   model   delta    sigma   weight residual
     116.30  131.42  -15.12 3.50e+00 8.16e-02 1.87e+01
  angle pdb=" O5' GDP A 402 "
        pdb=" PA  GDP A 402 "
        pdb=" O3A GDP A 402 "
      ideal   model   delta    sigma   weight residual
     102.60  112.22   -9.62 3.00e+00 1.11e-01 1.03e+01
  angle pdb=" C8  GDP A 402 "
        pdb=" N9  GDP A 402 "
        pdb=" C4  GDP A 402 "
      ideal   model   delta    sigma   weight residual
     108.00  117.13   -9.13 3.00e+00 1.11e-01 9.26e+00
  angle pdb=" N   VAL R 150 "
        pdb=" CA  VAL R 150 "
        pdb=" C   VAL R 150 "
      ideal   model   delta    sigma   weight residual
     112.35  108.47    3.88 1.41e+00 5.03e-01 7.57e+00
  angle pdb=" N   GLY N  66 "
        pdb=" CA  GLY N  66 "
        pdb=" C   GLY N  66 "
      ideal   model   delta    sigma   weight residual
     115.61  110.97    4.64 1.74e+00 3.30e-01 7.13e+00
  ... (remaining 11484 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 4569
       17.58 -    35.17: 376
       35.17 -    52.75: 67
       52.75 -    70.34: 12
       70.34 -    87.92: 9
  Dihedral angle restraints: 5033
    sinusoidal: 2004
      harmonic: 3029
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.00  -75.00     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CA  PHE R  85 "
           pdb=" C   PHE R  85 "
           pdb=" N   LEU R  86 "
           pdb=" CA  LEU R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.81   25.19     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  LYS G  29 "
           pdb=" C   LYS G  29 "
           pdb=" N   VAL G  30 "
           pdb=" CA  VAL G  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.73  -24.27     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 5030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 856
       0.040 -    0.080: 325
       0.080 -    0.119: 94
       0.119 -    0.159: 17
       0.159 -    0.199: 4
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" C10 7ZQ R 401 "
            pdb=" C11 7ZQ R 401 "
            pdb=" C12 7ZQ R 401 "
            pdb=" N2  7ZQ R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.65    0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CG  LEU N  81 "
            pdb=" CB  LEU N  81 "
            pdb=" CD1 LEU N  81 "
            pdb=" CD2 LEU N  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.32e-01
  chirality pdb=" CA  ARG A 270 "
            pdb=" N   ARG A 270 "
            pdb=" C   ARG A 270 "
            pdb=" CB  ARG A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  ... (remaining 1293 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 321 "   -0.044 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO A 322 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 310 "   -0.040 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO A 311 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 311 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 311 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 100 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.72e+00
        pdb=" C   PRO R 100 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   PRO R 100 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP R 101 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 86
        2.55 -     3.14: 6767
        3.14 -     3.72: 13342
        3.72 -     4.31: 17609
        4.31 -     4.90: 29118
  Nonbonded interactions: 66922
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 276 "
            pdb=" CD1 ILE A 372 "
     model   vdw
     1.960 3.460
  nonbonded pdb=" O   PRO N  88 "
            pdb=" OG1 THR N  91 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OD1 ASN A 361 "
            pdb=" NH2 ARG A 364 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.198 3.120
  ... (remaining 66917 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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.620
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6297
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104   8469  Z= 0.220
  Angle     :  0.739  15.125  11493  Z= 0.378
  Chirality :  0.045   0.199   1296
  Planarity :  0.005   0.067   1452
  Dihedral  : 13.587  87.920   3067
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 19.69
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.97 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.27), residues: 1022
  helix:  0.81 (0.26), residues: 388
  sheet: -0.64 (0.37), residues: 216
  loop : -0.90 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 314 
 TYR   0.021   0.002   TYR B 264 
 PHE   0.019   0.002   PHE A 280 
 TRP   0.026   0.002   TRP R 170 
 HIS   0.005   0.001   HIS R 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8467)
  covalent geometry    : angle       0.73920 (11489)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.60104 (    4)
  hydrogen bonds       : bond        0.20197 (  374)
  hydrogen bonds       : angle       6.70643 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7591 (mp0)
REVERT: A   25 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8730 (tmtt)
REVERT: A   26 ILE cc_start: 0.8254 (mm) cc_final: 0.8002 (mm)
REVERT: A   33 ASP cc_start: 0.7152 (t70) cc_final: 0.6808 (t0)
REVERT: A   38 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.7051 (mtm-85)
REVERT: A  233 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7557 (ptpt)
REVERT: A  304 GLU cc_start: 0.7757 (pp20) cc_final: 0.7551 (pp20)
REVERT: A  365 ILE cc_start: 0.7120 (mm) cc_final: 0.6746 (mm)
REVERT: A  376 MET cc_start: 0.7156 (tpp) cc_final: 0.6781 (tpp)
REVERT: B   46 ARG cc_start: 0.7171 (mpt180) cc_final: 0.6513 (mpt180)
REVERT: B   49 ARG cc_start: 0.7361 (mtt-85) cc_final: 0.6972 (mpp80)
REVERT: B  318 LEU cc_start: 0.7725 (tp) cc_final: 0.7406 (tp)
REVERT: G   44 HIS cc_start: 0.6950 (m90) cc_final: 0.6694 (m90)
REVERT: N   32 TYR cc_start: 0.7542 (m-10) cc_final: 0.7287 (m-10)
REVERT: R   74 ILE cc_start: 0.7936 (mm) cc_final: 0.7486 (mm)
REVERT: R   94 MET cc_start: 0.6269 (mpp) cc_final: 0.5789 (mpp)
REVERT: R  132 HIS cc_start: 0.8164 (m90) cc_final: 0.7727 (m90)
REVERT: R  149 ILE cc_start: 0.8329 (tt) cc_final: 0.7987 (tp)
REVERT: R  151 SER cc_start: 0.6484 (p) cc_final: 0.6228 (p)
REVERT: R  244 ARG cc_start: 0.7548 (ttt90) cc_final: 0.7177 (ttt-90)
REVERT: R  248 ILE cc_start: 0.8985 (pt) cc_final: 0.8699 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1107
  time to fit residues: 36.7437
Evaluate side-chains
  231 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 236 GLN
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 132 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.187644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.158999 restraints weight = 14409.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.164548 restraints weight = 8086.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.168411 restraints weight = 5185.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.171156 restraints weight = 3669.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.172928 restraints weight = 2783.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8469  Z= 0.148
  Angle     :  0.643   8.980  11493  Z= 0.332
  Chirality :  0.044   0.161   1296
  Planarity :  0.005   0.052   1452
  Dihedral  :  6.308  67.861   1158
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.99 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.48 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.14 (0.27), residues: 1022
  helix:  0.96 (0.26), residues: 395
  sheet: -0.51 (0.39), residues: 191
  loop : -0.79 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 314 
 TYR   0.015   0.002   TYR A 253 
 PHE   0.020   0.002   PHE R  82 
 TRP   0.032   0.002   TRP R 170 
 HIS   0.005   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8467)
  covalent geometry    : angle       0.64311 (11489)
  SS BOND              : bond        0.00276 (    2)
  SS BOND              : angle       0.52852 (    4)
  hydrogen bonds       : bond        0.04612 (  374)
  hydrogen bonds       : angle       5.20654 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 236
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8702 (tmtt)
REVERT: A   26 ILE cc_start: 0.8160 (mm) cc_final: 0.7951 (mm)
REVERT: A  209 GLU cc_start: 0.7652 (mp0) cc_final: 0.7202 (mp0)
REVERT: A  233 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7622 (ptpt)
REVERT: A  255 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7659 (mtm-85)
REVERT: A  267 TRP cc_start: 0.7497 (t-100) cc_final: 0.7015 (t-100)
REVERT: A  365 ILE cc_start: 0.7283 (mm) cc_final: 0.7034 (mm)
REVERT: A  376 MET cc_start: 0.7158 (tpp) cc_final: 0.6736 (tpp)
REVERT: B  214 ARG cc_start: 0.7462 (mmp80) cc_final: 0.7123 (mmp80)
REVERT: B  262 MET cc_start: 0.6267 (pmm) cc_final: 0.5693 (pmm)
REVERT: B  318 LEU cc_start: 0.7694 (tp) cc_final: 0.7305 (tp)
REVERT: B  323 ASP cc_start: 0.8572 (p0) cc_final: 0.8302 (p0)
REVERT: N   51 ILE cc_start: 0.5930 (OUTLIER) cc_final: 0.5600 (mt)
REVERT: N   68 PHE cc_start: 0.6161 (m-10) cc_final: 0.5885 (m-10)
REVERT: R   30 VAL cc_start: 0.8719 (t) cc_final: 0.8437 (m)
REVERT: R   64 ASN cc_start: 0.7447 (m-40) cc_final: 0.7110 (t0)
REVERT: R   74 ILE cc_start: 0.8053 (mm) cc_final: 0.7648 (mm)
REVERT: R   94 MET cc_start: 0.6147 (mpp) cc_final: 0.5757 (mpp)
REVERT: R  149 ILE cc_start: 0.8536 (tt) cc_final: 0.8225 (tp)
  outliers start: 21
  outliers final: 14
  residues processed: 244
  average time/residue: 0.1054
  time to fit residues: 34.2759
Evaluate side-chains
  245 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 230
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  377 ASN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain R residue   86 LEU
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  178 SER
Chi-restraints excluded: chain R residue  267 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0470
   chunk 57 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 236 GLN
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 277 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.186294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.157710 restraints weight = 14124.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.163276 restraints weight = 7944.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.167090 restraints weight = 5087.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.169503 restraints weight = 3594.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.171627 restraints weight = 2784.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8469  Z= 0.155
  Angle     :  0.612   7.557  11493  Z= 0.319
  Chirality :  0.043   0.172   1296
  Planarity :  0.004   0.047   1452
  Dihedral  :  6.107  68.373   1158
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.99 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 15.16 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.27), residues: 1022
  helix:  1.16 (0.27), residues: 395
  sheet: -0.48 (0.39), residues: 191
  loop : -0.83 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 332 
 TYR   0.013   0.001   TYR N  32 
 PHE   0.021   0.002   PHE N 103 
 TRP   0.020   0.002   TRP R 170 
 HIS   0.012   0.002   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8467)
  covalent geometry    : angle       0.61188 (11489)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.31198 (    4)
  hydrogen bonds       : bond        0.04335 (  374)
  hydrogen bonds       : angle       5.03510 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 237
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7170 (mp0)
REVERT: A   25 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8690 (tmtt)
REVERT: A   26 ILE cc_start: 0.8286 (mm) cc_final: 0.8067 (mm)
REVERT: A   38 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7230 (mtm-85)
REVERT: A  207 ILE cc_start: 0.7849 (mt) cc_final: 0.7629 (mm)
REVERT: A  209 GLU cc_start: 0.7730 (mp0) cc_final: 0.7247 (mp0)
REVERT: A  233 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7545 (ptpt)
REVERT: A  255 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7697 (mtm-85)
REVERT: A  267 TRP cc_start: 0.7511 (t-100) cc_final: 0.7071 (t-100)
REVERT: A  272 LEU cc_start: 0.8452 (mt) cc_final: 0.8213 (mt)
REVERT: A  365 ILE cc_start: 0.7421 (mm) cc_final: 0.7181 (mm)
REVERT: A  376 MET cc_start: 0.7132 (tpp) cc_final: 0.6758 (tpp)
REVERT: B  214 ARG cc_start: 0.7411 (mmp80) cc_final: 0.7015 (mmp80)
REVERT: B  318 LEU cc_start: 0.7742 (tp) cc_final: 0.7252 (tp)
REVERT: B  323 ASP cc_start: 0.8472 (p0) cc_final: 0.8203 (p0)
REVERT: N   51 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5691 (mt)
REVERT: R   30 VAL cc_start: 0.8738 (t) cc_final: 0.8450 (m)
REVERT: R   64 ASN cc_start: 0.7553 (m-40) cc_final: 0.7241 (t0)
REVERT: R   94 MET cc_start: 0.6374 (mpp) cc_final: 0.6055 (mpp)
REVERT: R  149 ILE cc_start: 0.8558 (tt) cc_final: 0.8243 (tp)
REVERT: R  244 ARG cc_start: 0.7739 (ttt90) cc_final: 0.7422 (ttt-90)
  outliers start: 36
  outliers final: 23
  residues processed: 252
  average time/residue: 0.1095
  time to fit residues: 36.2604
Evaluate side-chains
  255 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 230
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  377 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  178 SER
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  267 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0970
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
** N  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.185702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.157248 restraints weight = 14234.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.162767 restraints weight = 7959.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.166556 restraints weight = 5080.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.168930 restraints weight = 3590.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.171047 restraints weight = 2783.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6283
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8469  Z= 0.160
  Angle     :  0.622   9.111  11493  Z= 0.323
  Chirality :  0.044   0.151   1296
  Planarity :  0.004   0.046   1452
  Dihedral  :  6.076  71.308   1158
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.89 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.95 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.27), residues: 1022
  helix:  1.16 (0.27), residues: 396
  sheet: -0.59 (0.37), residues: 206
  loop : -0.92 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 332 
 TYR   0.016   0.001   TYR B  85 
 PHE   0.021   0.001   PHE N 103 
 TRP   0.019   0.002   TRP R 170 
 HIS   0.013   0.002   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8467)
  covalent geometry    : angle       0.62178 (11489)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       0.32298 (    4)
  hydrogen bonds       : bond        0.04200 (  374)
  hydrogen bonds       : angle       5.04873 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 240
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7212 (mp0)
REVERT: A   25 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8627 (tmtt)
REVERT: A   26 ILE cc_start: 0.8236 (mm) cc_final: 0.7994 (mm)
REVERT: A   38 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7233 (mtm-85)
REVERT: A  207 ILE cc_start: 0.7890 (mt) cc_final: 0.7609 (mm)
REVERT: A  209 GLU cc_start: 0.7722 (mp0) cc_final: 0.7217 (mp0)
REVERT: A  220 HIS cc_start: 0.7885 (t-170) cc_final: 0.7677 (t-90)
REVERT: A  267 TRP cc_start: 0.7471 (t-100) cc_final: 0.7082 (t-100)
REVERT: A  332 ARG cc_start: 0.7219 (ttp80) cc_final: 0.6847 (ttm-80)
REVERT: A  365 ILE cc_start: 0.7492 (mm) cc_final: 0.7256 (mm)
REVERT: A  376 MET cc_start: 0.7200 (tpp) cc_final: 0.6789 (tpp)
REVERT: B   78 LYS cc_start: 0.6779 (mmmm) cc_final: 0.6445 (mmmm)
REVERT: B   90 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8414 (p)
REVERT: B  262 MET cc_start: 0.6151 (pmm) cc_final: 0.5688 (pmm)
REVERT: B  339 TRP cc_start: 0.5933 (OUTLIER) cc_final: 0.4523 (m100)
REVERT: N   51 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5935 (mt)
REVERT: R   64 ASN cc_start: 0.7485 (m-40) cc_final: 0.7187 (t0)
REVERT: R   75 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7525 (tp)
REVERT: R   79 PHE cc_start: 0.7163 (m-10) cc_final: 0.6954 (m-10)
REVERT: R   94 MET cc_start: 0.6198 (mpp) cc_final: 0.5822 (mpp)
REVERT: R  112 ILE cc_start: 0.7705 (tp) cc_final: 0.7299 (tp)
REVERT: R  135 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7112 (mppt)
REVERT: R  149 ILE cc_start: 0.8641 (tt) cc_final: 0.8341 (tp)
REVERT: R  244 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7360 (ttt-90)
REVERT: R  259 ASN cc_start: 0.7828 (p0) cc_final: 0.7595 (p0)
  outliers start: 35
  outliers final: 23
  residues processed: 256
  average time/residue: 0.1049
  time to fit residues: 35.6466
Evaluate side-chains
  265 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 237
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  355 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  377 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue   75 LEU
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  267 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0040
   chunk 85 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 6 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
A 377 ASN
B 155 ASN
N  53 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.187859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.159032 restraints weight = 14285.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.164682 restraints weight = 8018.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.168475 restraints weight = 5128.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.171086 restraints weight = 3637.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.172799 restraints weight = 2780.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6240
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8469  Z= 0.122
  Angle     :  0.601   9.433  11493  Z= 0.310
  Chirality :  0.043   0.146   1296
  Planarity :  0.004   0.055   1452
  Dihedral  :  5.702  69.813   1158
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.01 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 19.18 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.27), residues: 1022
  helix:  1.28 (0.27), residues: 388
  sheet: -0.55 (0.37), residues: 205
  loop : -0.91 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 332 
 TYR   0.014   0.001   TYR B  85 
 PHE   0.022   0.001   PHE N 103 
 TRP   0.020   0.001   TRP R 170 
 HIS   0.013   0.001   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8467)
  covalent geometry    : angle       0.60104 (11489)
  SS BOND              : bond        0.00072 (    2)
  SS BOND              : angle       0.39223 (    4)
  hydrogen bonds       : bond        0.03770 (  374)
  hydrogen bonds       : angle       4.88425 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 242
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7160 (mp0)
REVERT: A   25 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8662 (tmtt)
REVERT: A   26 ILE cc_start: 0.8193 (mm) cc_final: 0.7955 (mm)
REVERT: A   38 ARG cc_start: 0.7545 (mtm-85) cc_final: 0.7261 (mtm-85)
REVERT: A  207 ILE cc_start: 0.7899 (mt) cc_final: 0.7574 (mm)
REVERT: A  209 GLU cc_start: 0.7606 (mp0) cc_final: 0.7208 (mp0)
REVERT: A  220 HIS cc_start: 0.7858 (t-170) cc_final: 0.7638 (t-90)
REVERT: A  233 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7514 (ptpt)
REVERT: A  267 TRP cc_start: 0.7444 (t-100) cc_final: 0.7052 (t-100)
REVERT: A  332 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6760 (ttm-80)
REVERT: B   90 VAL cc_start: 0.8660 (m) cc_final: 0.8437 (p)
REVERT: B  111 TYR cc_start: 0.5557 (m-80) cc_final: 0.5270 (m-80)
REVERT: B  195 ASP cc_start: 0.8441 (p0) cc_final: 0.8190 (p0)
REVERT: B  197 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.6893 (mmm-85)
REVERT: B  286 LEU cc_start: 0.6302 (mp) cc_final: 0.6060 (mp)
REVERT: B  323 ASP cc_start: 0.8669 (p0) cc_final: 0.8274 (p0)
REVERT: N   51 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5758 (mt)
REVERT: N   67 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.7005 (mmm-85)
REVERT: N   68 PHE cc_start: 0.6031 (m-10) cc_final: 0.5653 (m-10)
REVERT: R   64 ASN cc_start: 0.7527 (m-40) cc_final: 0.7226 (t0)
REVERT: R   94 MET cc_start: 0.6511 (mpp) cc_final: 0.6235 (mpp)
REVERT: R  112 ILE cc_start: 0.7669 (tp) cc_final: 0.7313 (tp)
REVERT: R  135 LYS cc_start: 0.7446 (mmtm) cc_final: 0.7164 (mppt)
REVERT: R  149 ILE cc_start: 0.8604 (tt) cc_final: 0.8326 (tp)
  outliers start: 38
  outliers final: 23
  residues processed: 260
  average time/residue: 0.1056
  time to fit residues: 36.1820
Evaluate side-chains
  260 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 234
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  284 GLN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  178 SER
Chi-restraints excluded: chain R residue  205 ILE
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  267 SER
Chi-restraints excluded: chain R residue  277 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0170
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.186414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.157691 restraints weight = 14297.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.163248 restraints weight = 8055.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.167003 restraints weight = 5178.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.169527 restraints weight = 3680.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.171533 restraints weight = 2854.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6256
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8469  Z= 0.131
  Angle     :  0.617   7.924  11493  Z= 0.319
  Chirality :  0.044   0.163   1296
  Planarity :  0.004   0.038   1452
  Dihedral  :  5.696  72.864   1158
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.40 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 21.18 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.27), residues: 1022
  helix:  1.24 (0.27), residues: 390
  sheet: -0.58 (0.37), residues: 204
  loop : -0.99 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 231 
 TYR   0.015   0.001   TYR R 141 
 PHE   0.025   0.001   PHE N 103 
 TRP   0.023   0.001   TRP R 170 
 HIS   0.008   0.001   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8467)
  covalent geometry    : angle       0.61666 (11489)
  SS BOND              : bond        0.00074 (    2)
  SS BOND              : angle       0.39165 (    4)
  hydrogen bonds       : bond        0.03808 (  374)
  hydrogen bonds       : angle       4.87702 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7170 (mp0)
REVERT: A   25 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8650 (tmtt)
REVERT: A   26 ILE cc_start: 0.8233 (mm) cc_final: 0.7989 (mm)
REVERT: A   38 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7243 (mtm-85)
REVERT: A  207 ILE cc_start: 0.7907 (mt) cc_final: 0.7533 (mm)
REVERT: A  209 GLU cc_start: 0.7608 (mp0) cc_final: 0.7161 (mp0)
REVERT: A  221 MET cc_start: 0.6762 (mtp) cc_final: 0.6491 (mtp)
REVERT: A  233 LYS cc_start: 0.7860 (mppt) cc_final: 0.7513 (ptpt)
REVERT: A  267 TRP cc_start: 0.7450 (t-100) cc_final: 0.6314 (t-100)
REVERT: A  332 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6764 (ttm-80)
REVERT: B   90 VAL cc_start: 0.8657 (m) cc_final: 0.8455 (p)
REVERT: B  111 TYR cc_start: 0.5634 (m-80) cc_final: 0.5316 (m-80)
REVERT: B  197 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7224 (mmm-85)
REVERT: B  339 TRP cc_start: 0.5790 (OUTLIER) cc_final: 0.4610 (m100)
REVERT: N   51 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5761 (mt)
REVERT: N   83 MET cc_start: 0.2846 (OUTLIER) cc_final: 0.2637 (mmm)
REVERT: R   64 ASN cc_start: 0.7549 (m-40) cc_final: 0.7273 (t0)
REVERT: R  112 ILE cc_start: 0.7708 (tp) cc_final: 0.7367 (tp)
REVERT: R  149 ILE cc_start: 0.8624 (tt) cc_final: 0.8317 (tp)
REVERT: R  155 THR cc_start: 0.7800 (t) cc_final: 0.7456 (p)
  outliers start: 36
  outliers final: 25
  residues processed: 252
  average time/residue: 0.1058
  time to fit residues: 35.4168
Evaluate side-chains
  263 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 234
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  277 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0970
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0170
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.4416

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.187141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.158471 restraints weight = 14415.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.164092 restraints weight = 8098.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.167834 restraints weight = 5169.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.170280 restraints weight = 3650.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.172089 restraints weight = 2820.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8469  Z= 0.129
  Angle     :  0.633  11.369  11493  Z= 0.322
  Chirality :  0.044   0.181   1296
  Planarity :  0.004   0.038   1452
  Dihedral  :  5.664  74.692   1158
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.31 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.63 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.23 (0.27), residues: 1022
  helix:  1.08 (0.26), residues: 396
  sheet: -0.59 (0.37), residues: 204
  loop : -1.05 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 231 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.021   0.001   PHE N 103 
 TRP   0.026   0.002   TRP R 170 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8467)
  covalent geometry    : angle       0.63293 (11489)
  SS BOND              : bond        0.00077 (    2)
  SS BOND              : angle       0.43111 (    4)
  hydrogen bonds       : bond        0.03797 (  374)
  hydrogen bonds       : angle       4.89399 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 236
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7185 (mp0)
REVERT: A   25 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8620 (tmtt)
REVERT: A   26 ILE cc_start: 0.8228 (mm) cc_final: 0.7918 (mm)
REVERT: A   27 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7239 (mm-30)
REVERT: A   38 ARG cc_start: 0.7492 (mtm-85) cc_final: 0.7178 (mtm-85)
REVERT: A  207 ILE cc_start: 0.7811 (mt) cc_final: 0.7455 (mm)
REVERT: A  209 GLU cc_start: 0.7609 (mp0) cc_final: 0.7181 (mp0)
REVERT: A  220 HIS cc_start: 0.7943 (t-170) cc_final: 0.7674 (t70)
REVERT: A  231 ARG cc_start: 0.7404 (ptt90) cc_final: 0.7182 (ptt-90)
REVERT: A  233 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7499 (ptpt)
REVERT: A  267 TRP cc_start: 0.7523 (t-100) cc_final: 0.6503 (t-100)
REVERT: A  332 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6814 (ttm-80)
REVERT: B  111 TYR cc_start: 0.5616 (m-80) cc_final: 0.5347 (m-80)
REVERT: B  197 ARG cc_start: 0.7756 (mmm-85) cc_final: 0.7299 (mmm-85)
REVERT: B  323 ASP cc_start: 0.8641 (p0) cc_final: 0.8299 (p0)
REVERT: N   83 MET cc_start: 0.2915 (OUTLIER) cc_final: 0.2395 (mmm)
REVERT: R   64 ASN cc_start: 0.7543 (m-40) cc_final: 0.7261 (m-40)
REVERT: R  112 ILE cc_start: 0.7662 (tp) cc_final: 0.7308 (tp)
REVERT: R  135 LYS cc_start: 0.7417 (mmtm) cc_final: 0.7102 (mppt)
REVERT: R  149 ILE cc_start: 0.8646 (tt) cc_final: 0.8357 (tp)
REVERT: R  155 THR cc_start: 0.7799 (t) cc_final: 0.7455 (p)
REVERT: R  193 LEU cc_start: 0.7774 (mm) cc_final: 0.7564 (mm)
  outliers start: 38
  outliers final: 32
  residues processed: 249
  average time/residue: 0.1042
  time to fit residues: 34.4800
Evaluate side-chains
  268 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 233
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  178 SER
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  267 SER
Chi-restraints excluded: chain R residue  277 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 99 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 92 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0030
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 213 GLN
A 284 GLN
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.186432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.157330 restraints weight = 14268.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.162906 restraints weight = 8110.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.166605 restraints weight = 5235.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.169267 restraints weight = 3740.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.170821 restraints weight = 2872.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6274
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8469  Z= 0.137
  Angle     :  0.642  11.018  11493  Z= 0.326
  Chirality :  0.044   0.226   1296
  Planarity :  0.004   0.039   1452
  Dihedral  :  5.728  76.663   1158
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.31 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 21.85 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.30 (0.27), residues: 1022
  helix:  0.99 (0.26), residues: 397
  sheet: -0.63 (0.37), residues: 205
  loop : -1.08 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 231 
 TYR   0.011   0.001   TYR A 381 
 PHE   0.021   0.001   PHE N 103 
 TRP   0.025   0.002   TRP R 170 
 HIS   0.003   0.001   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8467)
  covalent geometry    : angle       0.64166 (11489)
  SS BOND              : bond        0.00087 (    2)
  SS BOND              : angle       0.39990 (    4)
  hydrogen bonds       : bond        0.03826 (  374)
  hydrogen bonds       : angle       4.91469 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 234
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7227 (mp0)
REVERT: A   25 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8654 (tmtt)
REVERT: A   26 ILE cc_start: 0.8228 (mm) cc_final: 0.7933 (mm)
REVERT: A   38 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7189 (mtm-85)
REVERT: A   49 ASP cc_start: 0.7591 (t0) cc_final: 0.7387 (t0)
REVERT: A  207 ILE cc_start: 0.7783 (mt) cc_final: 0.7401 (mm)
REVERT: A  209 GLU cc_start: 0.7607 (mp0) cc_final: 0.7176 (mp0)
REVERT: A  220 HIS cc_start: 0.7963 (t-170) cc_final: 0.7677 (t70)
REVERT: A  233 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7531 (ptpt)
REVERT: A  267 TRP cc_start: 0.7495 (t-100) cc_final: 0.6513 (t-100)
REVERT: A  376 MET cc_start: 0.7110 (tpp) cc_final: 0.6705 (tpp)
REVERT: B  111 TYR cc_start: 0.5706 (m-80) cc_final: 0.5388 (m-80)
REVERT: B  154 ASP cc_start: 0.6535 (t0) cc_final: 0.6225 (t0)
REVERT: B  197 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7420 (mmm-85)
REVERT: R   64 ASN cc_start: 0.7535 (m-40) cc_final: 0.7304 (m-40)
REVERT: R  112 ILE cc_start: 0.7665 (tp) cc_final: 0.7322 (tp)
REVERT: R  149 ILE cc_start: 0.8626 (tt) cc_final: 0.8339 (tp)
REVERT: R  155 THR cc_start: 0.7805 (t) cc_final: 0.7464 (p)
  outliers start: 40
  outliers final: 30
  residues processed: 248
  average time/residue: 0.1078
  time to fit residues: 35.5020
Evaluate side-chains
  262 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 230
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  277 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 284 GLN
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.185031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.156562 restraints weight = 14203.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.161958 restraints weight = 8161.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165611 restraints weight = 5318.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.167892 restraints weight = 3813.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.169759 restraints weight = 2989.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6301
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8469  Z= 0.162
  Angle     :  0.683  11.148  11493  Z= 0.345
  Chirality :  0.046   0.234   1296
  Planarity :  0.004   0.041   1452
  Dihedral  :  5.947  78.802   1158
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.60 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.30 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.26), residues: 1022
  helix:  0.98 (0.27), residues: 392
  sheet: -0.81 (0.36), residues: 211
  loop : -1.04 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 332 
 TYR   0.016   0.001   TYR A 381 
 PHE   0.021   0.002   PHE N 103 
 TRP   0.025   0.002   TRP R 170 
 HIS   0.004   0.001   HIS R 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 8467)
  covalent geometry    : angle       0.68279 (11489)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       0.38745 (    4)
  hydrogen bonds       : bond        0.04047 (  374)
  hydrogen bonds       : angle       5.02900 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 234
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7207 (mp0)
REVERT: A   25 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8648 (tmtt)
REVERT: A   26 ILE cc_start: 0.8247 (mm) cc_final: 0.7930 (mm)
REVERT: A   38 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.7142 (mtm-85)
REVERT: A   49 ASP cc_start: 0.7618 (t0) cc_final: 0.7410 (t0)
REVERT: A  207 ILE cc_start: 0.7801 (mt) cc_final: 0.7415 (mm)
REVERT: A  209 GLU cc_start: 0.7552 (mp0) cc_final: 0.7135 (mp0)
REVERT: A  220 HIS cc_start: 0.7993 (t-170) cc_final: 0.7730 (t70)
REVERT: A  233 LYS cc_start: 0.7904 (mppt) cc_final: 0.7554 (ptpt)
REVERT: A  267 TRP cc_start: 0.7553 (t-100) cc_final: 0.6602 (t-100)
REVERT: A  332 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6888 (ttm-80)
REVERT: A  376 MET cc_start: 0.7090 (tpp) cc_final: 0.6706 (tpp)
REVERT: B   49 ARG cc_start: 0.6460 (mtt-85) cc_final: 0.6057 (mtt-85)
REVERT: B  111 TYR cc_start: 0.5815 (m-80) cc_final: 0.5511 (m-80)
REVERT: B  197 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7446 (mmm-85)
REVERT: B  339 TRP cc_start: 0.5869 (OUTLIER) cc_final: 0.4780 (m100)
REVERT: N   83 MET cc_start: 0.2376 (mmm) cc_final: 0.1622 (tpt)
REVERT: R   64 ASN cc_start: 0.7539 (m-40) cc_final: 0.7323 (m-40)
REVERT: R  112 ILE cc_start: 0.7701 (tp) cc_final: 0.7349 (tp)
REVERT: R  149 ILE cc_start: 0.8668 (tt) cc_final: 0.8360 (tp)
REVERT: R  155 THR cc_start: 0.7867 (t) cc_final: 0.7514 (p)
REVERT: R  193 LEU cc_start: 0.7853 (mm) cc_final: 0.7625 (mm)
  outliers start: 40
  outliers final: 32
  residues processed: 251
  average time/residue: 0.1009
  time to fit residues: 33.8974
Evaluate side-chains
  273 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  170 TRP
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  267 SER
Chi-restraints excluded: chain R residue  277 ASN
Chi-restraints excluded: chain R residue  288 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0050
   chunk 84 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0980
   chunk 89 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.187419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.159070 restraints weight = 14112.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.164539 restraints weight = 8050.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.168180 restraints weight = 5217.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.170575 restraints weight = 3727.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.172331 restraints weight = 2900.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6255
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8469  Z= 0.138
  Angle     :  0.682  11.370  11493  Z= 0.344
  Chirality :  0.045   0.231   1296
  Planarity :  0.004   0.052   1452
  Dihedral  :  5.874  79.653   1158
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.52 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 24.08 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1022
  helix:  0.98 (0.27), residues: 392
  sheet: -0.72 (0.36), residues: 209
  loop : -1.13 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 231 
 TYR   0.011   0.001   TYR A 381 
 PHE   0.024   0.001   PHE N 103 
 TRP   0.029   0.002   TRP A 271 
 HIS   0.008   0.001   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8467)
  covalent geometry    : angle       0.68189 (11489)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.42350 (    4)
  hydrogen bonds       : bond        0.03895 (  374)
  hydrogen bonds       : angle       5.02825 ( 1068)

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

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

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2044 Ramachandran restraints generated.
    1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 242
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: A   25 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8653 (tmtt)
REVERT: A   26 ILE cc_start: 0.8225 (mm) cc_final: 0.7882 (mm)
REVERT: A   38 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7121 (mtm-85)
REVERT: A   49 ASP cc_start: 0.7613 (t0) cc_final: 0.7389 (t0)
REVERT: A  207 ILE cc_start: 0.7789 (mt) cc_final: 0.7392 (mm)
REVERT: A  209 GLU cc_start: 0.7507 (mp0) cc_final: 0.7110 (mp0)
REVERT: A  220 HIS cc_start: 0.7957 (t-170) cc_final: 0.7714 (t70)
REVERT: A  227 GLN cc_start: 0.7255 (pm20) cc_final: 0.6641 (pm20)
REVERT: A  233 LYS cc_start: 0.7881 (mppt) cc_final: 0.7487 (ptpt)
REVERT: A  267 TRP cc_start: 0.7503 (t-100) cc_final: 0.6559 (t-100)
REVERT: A  332 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6677 (ttm-80)
REVERT: A  376 MET cc_start: 0.7050 (tpp) cc_final: 0.6663 (tpp)
REVERT: B   49 ARG cc_start: 0.6344 (mtt-85) cc_final: 0.5955 (mtt-85)
REVERT: B   96 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7863 (mtm110)
REVERT: B  111 TYR cc_start: 0.5707 (m-80) cc_final: 0.5386 (m-80)
REVERT: B  154 ASP cc_start: 0.6584 (t0) cc_final: 0.6290 (t0)
REVERT: B  197 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7463 (mmm-85)
REVERT: B  314 ARG cc_start: 0.5617 (ttp80) cc_final: 0.4978 (ttp80)
REVERT: B  325 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.5000 (mmp)
REVERT: N   32 TYR cc_start: 0.6573 (m-10) cc_final: 0.6325 (m-80)
REVERT: N   83 MET cc_start: 0.3193 (mmm) cc_final: 0.2367 (tpt)
REVERT: R   64 ASN cc_start: 0.7536 (m-40) cc_final: 0.7286 (m-40)
REVERT: R  112 ILE cc_start: 0.7658 (tp) cc_final: 0.7348 (tp)
REVERT: R  149 ILE cc_start: 0.8639 (tt) cc_final: 0.8330 (tp)
REVERT: R  166 TRP cc_start: 0.6629 (t-100) cc_final: 0.6019 (t-100)
REVERT: R  193 LEU cc_start: 0.7766 (mm) cc_final: 0.7553 (mm)
  outliers start: 31
  outliers final: 28
  residues processed: 254
  average time/residue: 0.1016
  time to fit residues: 34.1366
Evaluate side-chains
  266 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   85 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  166 CYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 LYS
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  124 ILE
Chi-restraints excluded: chain R residue  261 TRP
Chi-restraints excluded: chain R residue  277 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 284 GLN
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 180 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.185338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.156892 restraints weight = 14199.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.162335 restraints weight = 8167.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.165922 restraints weight = 5315.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.168531 restraints weight = 3800.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.170380 restraints weight = 2931.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6289
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8469  Z= 0.165
  Angle     :  0.698  10.962  11493  Z= 0.358
  Chirality :  0.046   0.234   1296
  Planarity :  0.004   0.055   1452
  Dihedral  :  6.003  84.339   1158
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.40 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 24.86 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1022
  helix:  0.86 (0.27), residues: 393
  sheet: -0.62 (0.36), residues: 211
  loop : -1.12 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 231 
 TYR   0.017   0.001   TYR A 350 
 PHE   0.022   0.002   PHE N  68 
 TRP   0.052   0.002   TRP A 271 
 HIS   0.007   0.001   HIS R 180 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8467)
  covalent geometry    : angle       0.69772 (11489)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       0.38251 (    4)
  hydrogen bonds       : bond        0.04111 (  374)
  hydrogen bonds       : angle       5.11236 ( 1068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1655.47 seconds
wall clock time: 29 minutes 23.06 seconds (1763.06 seconds total)