Starting phenix.real_space_refine
on Wed Sep 17 10:17:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yut_39582/09_2025/8yut_39582.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5212      2.51       5
     N    1440      2.21       5
     O    1522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8229
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1891
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          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: 2302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2302
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'A1D67': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.14, per 1000 atoms: 0.26
  Number of scatterers: 8229
  At special positions: 0
  Unit cell: (86.19, 117.624, 116.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1522      8.00
     N    1440      7.00
     C    5212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, 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=2.02
    Simple disulfide: pdb=" SG  CYS R  91 " - pdb=" SG  CYS R 174 " distance=2.04

  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: 0.67
  Conformation dependent library (CDL) restraints added in 437.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 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:
      32 helices and 10 sheets defined
      43.7% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 4.103A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.887A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.595A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.879A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.862A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.513A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.879A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.102A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 14 through 46
    Processing helix  chain 'R' and resid 47 through 50
    Processing helix  chain 'R' and resid 54 through 71
    Processing helix  chain 'R' and resid 71 through 82
      removed outlier: 3.750A  pdb=" N   ILE R  77 " --> pdb=" O   PRO R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 122
      removed outlier: 3.877A  pdb=" N   ILE R  93 " --> pdb=" O   VAL R  89 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP R 122 " --> pdb=" O   CYS R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 130
    Processing helix  chain 'R' and resid 131 through 151
    Processing helix  chain 'R' and resid 151 through 156
    Processing helix  chain 'R' and resid 179 through 191
    Processing helix  chain 'R' and resid 191 through 220
      removed outlier: 3.892A  pdb=" N   SER R 220 " --> pdb=" O   ILE R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 261
      removed outlier: 3.500A  pdb=" N   ALA R 242 " --> pdb=" O   ALA R 238 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE R 243 " --> pdb=" O   VAL R 239 " (cutoff:3.500A)
      Proline residue:  R 249  - end of helix
    Processing helix  chain 'R' and resid 262 through 265
    Processing helix  chain 'R' and resid 266 through 280
      removed outlier: 3.703A  pdb=" N   ASN R 280 " --> pdb=" O   LEU R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 288
    Processing helix  chain 'R' and resid 292 through 305
      removed outlier: 4.439A  pdb=" N   PHE R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.149A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 9.698A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.534A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.547A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.695A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.968A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 4.085A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.796A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.167A  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: 6.637A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.668A  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: 3.734A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.501A  pdb=" N   GLY N  10 " --> pdb=" O   GLN N 123 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1248 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: 1.37

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1633
        1.33 -     1.45: 2032
        1.45 -     1.57: 4645
        1.57 -     1.69: 4
        1.69 -     1.81: 74
  Bond restraints: 8388
  Sorted by residual:
  bond pdb=" C06 A1D67 R 401 "
       pdb=" S01 A1D67 R 401 "
    ideal  model  delta    sigma   weight residual
    1.746  1.509  0.237 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" C10 A1D67 R 401 "
       pdb=" S01 A1D67 R 401 "
    ideal  model  delta    sigma   weight residual
    1.740  1.536  0.204 2.00e-02 2.50e+03 1.04e+02
  bond pdb=" C08 A1D67 R 401 "
       pdb=" N02 A1D67 R 401 "
    ideal  model  delta    sigma   weight residual
    1.377  1.567 -0.190 2.00e-02 2.50e+03 9.00e+01
  bond pdb=" C15 CLR R 402 "
       pdb=" C16 CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.541  1.696 -0.155 2.00e-02 2.50e+03 6.02e+01
  bond pdb=" C11 CLR R 402 "
       pdb=" C9  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.533  1.681 -0.148 2.00e-02 2.50e+03 5.49e+01
  ... (remaining 8383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.68: 11307
        3.68 -     7.37: 60
        7.37 -    11.05: 5
       11.05 -    14.74: 0
       14.74 -    18.42: 1
  Bond angle restraints: 11373
  Sorted by residual:
  angle pdb=" C06 A1D67 R 401 "
        pdb=" S01 A1D67 R 401 "
        pdb=" C10 A1D67 R 401 "
      ideal   model   delta    sigma   weight residual
      89.27  107.69  -18.42 3.00e+00 1.11e-01 3.77e+01
  angle pdb=" N   ILE R 227 "
        pdb=" CA  ILE R 227 "
        pdb=" C   ILE R 227 "
      ideal   model   delta    sigma   weight residual
     108.12  115.68   -7.56 1.44e+00 4.82e-01 2.76e+01
  angle pdb=" C   THR R 235 "
        pdb=" N   LEU R 236 "
        pdb=" CA  LEU R 236 "
      ideal   model   delta    sigma   weight residual
     120.28  114.52    5.76 1.34e+00 5.57e-01 1.85e+01
  angle pdb=" N   ARG R 228 "
        pdb=" CA  ARG R 228 "
        pdb=" C   ARG R 228 "
      ideal   model   delta    sigma   weight residual
     108.20  115.37   -7.17 1.71e+00 3.42e-01 1.76e+01
  angle pdb=" C   MET R 240 "
        pdb=" N   GLY R 241 "
        pdb=" CA  GLY R 241 "
      ideal   model   delta    sigma   weight residual
     119.99  124.70   -4.71 1.13e+00 7.83e-01 1.74e+01
  ... (remaining 11368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4821
       17.69 -    35.39: 194
       35.39 -    53.08: 30
       53.08 -    70.78: 7
       70.78 -    88.47: 6
  Dihedral angle restraints: 5058
    sinusoidal: 2029
      harmonic: 3029
  Sorted by residual:
  dihedral pdb=" CA  TYR R 299 "
           pdb=" C   TYR R 299 "
           pdb=" N   GLN R 300 "
           pdb=" CA  GLN R 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.99   19.01     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PHE B 241 "
           pdb=" C   PHE B 241 "
           pdb=" N   ALA B 242 "
           pdb=" CA  ALA B 242 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CB  CYS R  91 "
           pdb=" SG  CYS R  91 "
           pdb=" SG  CYS R 174 "
           pdb=" CB  CYS R 174 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.49  -31.49     1      1.00e+01 1.00e-02 1.41e+01
  ... (remaining 5055 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1056
       0.063 -    0.125: 187
       0.125 -    0.188: 43
       0.188 -    0.251: 11
       0.251 -    0.313: 4
  Chirality restraints: 1301
  Sorted by residual:
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA  LEU B 318 "
            pdb=" N   LEU B 318 "
            pdb=" C   LEU B 318 "
            pdb=" CB  LEU B 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  LEU R 236 "
            pdb=" N   LEU R 236 "
            pdb=" C   LEU R 236 "
            pdb=" CB  LEU R 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1298 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 229 "    0.015 2.00e-02 2.50e+03   3.16e-02 1.00e+01
        pdb=" C   ASP A 229 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASP A 229 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A 230 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 165 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   SER R 165 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   SER R 165 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS R 166 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  67 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   SER B  67 "    0.034 2.00e-02 2.50e+03
        pdb=" O   SER B  67 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG B  68 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1299
        2.76 -     3.30: 7855
        3.30 -     3.83: 13572
        3.83 -     4.37: 16433
        4.37 -     4.90: 28411
  Nonbonded interactions: 67570
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 340 "
            pdb=" ND2 ASN G  59 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OE1 GLU A 330 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OD1 ASP A 368 "
            pdb=" N   THR A 369 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.314 3.040
  ... (remaining 67565 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.390
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:7.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
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      :  0.008   0.237   8391  Z= 0.464
  Angle     :  0.812  18.419  11379  Z= 0.522
  Chirality :  0.057   0.313   1301
  Planarity :  0.004   0.047   1443
  Dihedral  : 10.592  88.470   3089
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1025
  helix:  2.03 (0.26), residues: 399
  sheet:  0.72 (0.33), residues: 228
  loop : -0.16 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG N 118 
 TYR   0.026   0.002   TYR N 115 
 PHE   0.018   0.002   PHE N  68 
 TRP   0.020   0.002   TRP R 222 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00793 ( 8388)
  covalent geometry    : angle       0.81116 (11373)
  SS BOND              : bond        0.00556 (    3)
  SS BOND              : angle       2.00879 (    6)
  hydrogen bonds       : bond        0.14847 (  438)
  hydrogen bonds       : angle       6.31666 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7004 (mtmt) cc_final: 0.6763 (mmmt)
REVERT: A  230 GLU cc_start: 0.6367 (mt-10) cc_final: 0.5506 (tt0)
REVERT: A  344 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7523 (tp30)
REVERT: A  381 ASP cc_start: 0.7554 (m-30) cc_final: 0.7338 (m-30)
REVERT: B  111 TYR cc_start: 0.8402 (m-80) cc_final: 0.8196 (m-80)
REVERT: B  188 MET cc_start: 0.8583 (mmm) cc_final: 0.8321 (mmm)
REVERT: G   21 MET cc_start: 0.6227 (ttp) cc_final: 0.5774 (tmt)
REVERT: N   21 SER cc_start: 0.8658 (t) cc_final: 0.8450 (t)
REVERT: N   34 MET cc_start: 0.7460 (mmm) cc_final: 0.7247 (mmm)
REVERT: R  198 MET cc_start: 0.8119 (mtp) cc_final: 0.7913 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.5610
  time to fit residues: 96.3465
Evaluate side-chains
  104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.5758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.194025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.153594 restraints weight = 8584.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.91
r_work: 0.3605 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8391  Z= 0.115
  Angle     :  0.512   8.945  11379  Z= 0.277
  Chirality :  0.041   0.148   1301
  Planarity :  0.004   0.071   1443
  Dihedral  :  4.859  54.367   1207
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  8.64 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.26), residues: 1025
  helix:  2.31 (0.25), residues: 409
  sheet:  1.10 (0.34), residues: 204
  loop : -0.20 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG B 197 
 TYR   0.011   0.001   TYR N  80 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 222 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8388)
  covalent geometry    : angle       0.51180 (11373)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       0.36836 (    6)
  hydrogen bonds       : bond        0.04575 (  438)
  hydrogen bonds       : angle       4.75718 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6899 (mtmt) cc_final: 0.6313 (mmmt)
REVERT: A  230 GLU cc_start: 0.7037 (mt-10) cc_final: 0.4922 (tt0)
REVERT: B  111 TYR cc_start: 0.8734 (m-80) cc_final: 0.8531 (m-80)
REVERT: B  195 ASP cc_start: 0.7005 (p0) cc_final: 0.6746 (p0)
REVERT: B  197 ARG cc_start: 0.7312 (mmm160) cc_final: 0.7056 (mmp80)
REVERT: B  217 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6120 (mmp)
REVERT: B  291 ASP cc_start: 0.6783 (m-30) cc_final: 0.6550 (p0)
REVERT: G   21 MET cc_start: 0.6300 (ttp) cc_final: 0.5410 (tmt)
REVERT: N    4 LEU cc_start: 0.7700 (mt) cc_final: 0.7430 (mt)
REVERT: N   21 SER cc_start: 0.8527 (t) cc_final: 0.8255 (t)
REVERT: N   25 SER cc_start: 0.6703 (OUTLIER) cc_final: 0.6382 (p)
REVERT: R  122 ASP cc_start: 0.8225 (p0) cc_final: 0.7768 (p0)
  outliers start: 21
  outliers final: 7
  residues processed: 132
  average time/residue: 0.5394
  time to fit residues: 75.8574
Evaluate side-chains
  107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  272 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0070
   chunk 100 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.9600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.190372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150058 restraints weight = 8454.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.90
r_work: 0.3548 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8391  Z= 0.127
  Angle     :  0.526   8.400  11379  Z= 0.282
  Chirality :  0.042   0.187   1301
  Planarity :  0.003   0.044   1443
  Dihedral  :  4.635  44.002   1207
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.44 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.26), residues: 1025
  helix:  2.39 (0.25), residues: 414
  sheet:  1.15 (0.35), residues: 197
  loop : -0.09 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 197 
 TYR   0.018   0.002   TYR B 105 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.012   0.001   TRP R 275 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8388)
  covalent geometry    : angle       0.52588 (11373)
  SS BOND              : bond        0.00355 (    3)
  SS BOND              : angle       0.35674 (    6)
  hydrogen bonds       : bond        0.04594 (  438)
  hydrogen bonds       : angle       4.57220 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6884 (mtmt) cc_final: 0.6292 (mmmt)
REVERT: B   45 MET cc_start: 0.8479 (mtt) cc_final: 0.8079 (mtt)
REVERT: B  186 ASP cc_start: 0.8152 (m-30) cc_final: 0.7631 (m-30)
REVERT: B  217 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7159 (ppp)
REVERT: B  219 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6718 (mtm-85)
REVERT: B  259 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7524 (mt0)
REVERT: G   21 MET cc_start: 0.6497 (ttp) cc_final: 0.5579 (tmt)
REVERT: N    4 LEU cc_start: 0.7999 (mt) cc_final: 0.7502 (mt)
REVERT: N   21 SER cc_start: 0.8676 (t) cc_final: 0.8451 (t)
REVERT: N   25 SER cc_start: 0.7472 (OUTLIER) cc_final: 0.7268 (p)
REVERT: N  110 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8242 (m)
REVERT: R  122 ASP cc_start: 0.8299 (p0) cc_final: 0.7819 (p0)
REVERT: R  201 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7866 (m)
  outliers start: 23
  outliers final: 10
  residues processed: 125
  average time/residue: 0.5083
  time to fit residues: 67.9872
Evaluate side-chains
  114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  201 THR
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.0010
   chunk 77 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.191988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.151378 restraints weight = 8615.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.01
r_work: 0.3589 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8391  Z= 0.101
  Angle     :  0.486  11.531  11379  Z= 0.256
  Chirality :  0.041   0.286   1301
  Planarity :  0.003   0.042   1443
  Dihedral  :  4.434  46.618   1207
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.12 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.26), residues: 1025
  helix:  2.67 (0.25), residues: 409
  sheet:  1.21 (0.35), residues: 199
  loop : -0.01 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 317 
 TYR   0.011   0.001   TYR N  80 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.013   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8388)
  covalent geometry    : angle       0.48386 (11373)
  SS BOND              : bond        0.00343 (    3)
  SS BOND              : angle       1.87355 (    6)
  hydrogen bonds       : bond        0.04014 (  438)
  hydrogen bonds       : angle       4.33732 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5822 (OUTLIER) cc_final: 0.5521 (p0)
REVERT: A  230 GLU cc_start: 0.8212 (mt-10) cc_final: 0.6371 (tm-30)
REVERT: A  268 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6959 (tp30)
REVERT: B  186 ASP cc_start: 0.8050 (m-30) cc_final: 0.7617 (m-30)
REVERT: B  217 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7297 (ppp)
REVERT: G   21 MET cc_start: 0.6487 (ttp) cc_final: 0.5570 (tmt)
REVERT: N    4 LEU cc_start: 0.8034 (mt) cc_final: 0.7528 (mt)
REVERT: N   21 SER cc_start: 0.8584 (t) cc_final: 0.8373 (t)
REVERT: N  110 VAL cc_start: 0.8477 (t) cc_final: 0.8202 (m)
REVERT: R  122 ASP cc_start: 0.8301 (p0) cc_final: 0.7815 (p0)
REVERT: R  240 MET cc_start: 0.7540 (tpt) cc_final: 0.7280 (tpt)
  outliers start: 25
  outliers final: 11
  residues processed: 116
  average time/residue: 0.4927
  time to fit residues: 61.4754
Evaluate side-chains
  110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain R residue  201 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 94 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.186968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.145604 restraints weight = 8579.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.02
r_work: 0.3492 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8391  Z= 0.160
  Angle     :  0.576  12.299  11379  Z= 0.303
  Chirality :  0.044   0.311   1301
  Planarity :  0.004   0.042   1443
  Dihedral  :  4.869  45.503   1207
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 11.78 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.26), residues: 1025
  helix:  2.62 (0.25), residues: 409
  sheet:  1.11 (0.35), residues: 189
  loop : -0.05 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.016   0.002   TYR B 105 
 PHE   0.016   0.002   PHE B 151 
 TRP   0.012   0.002   TRP R 275 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8388)
  covalent geometry    : angle       0.56749 (11373)
  SS BOND              : bond        0.01218 (    3)
  SS BOND              : angle       4.35456 (    6)
  hydrogen bonds       : bond        0.04839 (  438)
  hydrogen bonds       : angle       4.55796 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6907 (mtmt) cc_final: 0.6303 (mmmt)
REVERT: A  229 ASP cc_start: 0.5702 (OUTLIER) cc_final: 0.5399 (p0)
REVERT: A  268 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6892 (tp30)
REVERT: A  344 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: B  186 ASP cc_start: 0.8266 (m-30) cc_final: 0.8022 (m-30)
REVERT: B  217 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7305 (ppp)
REVERT: B  259 GLN cc_start: 0.7970 (tt0) cc_final: 0.7702 (tt0)
REVERT: G   21 MET cc_start: 0.6433 (ttp) cc_final: 0.5438 (tmt)
REVERT: R  122 ASP cc_start: 0.8405 (p0) cc_final: 0.7936 (p0)
REVERT: R  240 MET cc_start: 0.7743 (tpt) cc_final: 0.7521 (mmm)
  outliers start: 27
  outliers final: 14
  residues processed: 114
  average time/residue: 0.4832
  time to fit residues: 59.4189
Evaluate side-chains
  110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.188382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147352 restraints weight = 8512.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.01
r_work: 0.3529 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8391  Z= 0.124
  Angle     :  0.526  13.546  11379  Z= 0.276
  Chirality :  0.042   0.233   1301
  Planarity :  0.003   0.043   1443
  Dihedral  :  4.687  46.932   1207
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.23 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1025
  helix:  2.62 (0.25), residues: 415
  sheet:  1.01 (0.34), residues: 209
  loop : -0.09 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.011   0.001   TYR B 105 
 PHE   0.015   0.002   PHE A 212 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8388)
  covalent geometry    : angle       0.51879 (11373)
  SS BOND              : bond        0.00658 (    3)
  SS BOND              : angle       3.87700 (    6)
  hydrogen bonds       : bond        0.04335 (  438)
  hydrogen bonds       : angle       4.37498 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5541 (OUTLIER) cc_final: 0.5255 (p0)
REVERT: A  344 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: B   45 MET cc_start: 0.8518 (mtt) cc_final: 0.8128 (mtt)
REVERT: B   59 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7737 (m-80)
REVERT: B   78 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8572 (tppt)
REVERT: B  186 ASP cc_start: 0.8217 (m-30) cc_final: 0.7984 (m-30)
REVERT: B  217 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7378 (ppp)
REVERT: B  259 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7731 (tt0)
REVERT: G   21 MET cc_start: 0.6413 (ttp) cc_final: 0.5433 (tmt)
REVERT: N    3 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7006 (pp30)
REVERT: R  122 ASP cc_start: 0.8365 (p0) cc_final: 0.7831 (p0)
REVERT: R  240 MET cc_start: 0.7752 (tpt) cc_final: 0.7501 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 107
  average time/residue: 0.5136
  time to fit residues: 58.8575
Evaluate side-chains
  114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain R residue  171 THR
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0470
   chunk 96 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    1.3482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.186987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.145634 restraints weight = 8560.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.02
r_work: 0.3506 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8391  Z= 0.143
  Angle     :  0.557  13.932  11379  Z= 0.290
  Chirality :  0.043   0.334   1301
  Planarity :  0.003   0.042   1443
  Dihedral  :  4.806  46.467   1207
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 11.78 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.26), residues: 1025
  helix:  2.60 (0.25), residues: 415
  sheet:  1.00 (0.34), residues: 207
  loop : -0.15 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.014   0.002   TYR B 105 
 PHE   0.016   0.002   PHE B 234 
 TRP   0.011   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8388)
  covalent geometry    : angle       0.54992 (11373)
  SS BOND              : bond        0.00480 (    3)
  SS BOND              : angle       3.78881 (    6)
  hydrogen bonds       : bond        0.04622 (  438)
  hydrogen bonds       : angle       4.46429 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.6896 (mtmt) cc_final: 0.6266 (mmmt)
REVERT: A  229 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5323 (p0)
REVERT: A  268 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.5629 (tp30)
REVERT: A  344 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8222 (mm-30)
REVERT: B   59 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7708 (m-80)
REVERT: B  217 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7287 (ppp)
REVERT: B  259 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7728 (tt0)
REVERT: B  268 ASN cc_start: 0.7462 (m-40) cc_final: 0.7146 (p0)
REVERT: G   21 MET cc_start: 0.6475 (ttp) cc_final: 0.5476 (tmt)
REVERT: R  122 ASP cc_start: 0.8393 (p0) cc_final: 0.7869 (p0)
  outliers start: 33
  outliers final: 20
  residues processed: 111
  average time/residue: 0.4942
  time to fit residues: 58.5905
Evaluate side-chains
  117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain R residue  141 LEU
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 64 optimal weight:    0.0270
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6838

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.189393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.148237 restraints weight = 8578.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.02
r_work: 0.3544 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8391  Z= 0.105
  Angle     :  0.505  14.586  11379  Z= 0.262
  Chirality :  0.041   0.309   1301
  Planarity :  0.003   0.042   1443
  Dihedral  :  4.593  46.618   1207
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.91 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.26), residues: 1025
  helix:  2.74 (0.25), residues: 415
  sheet:  0.98 (0.34), residues: 214
  loop : -0.04 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 317 
 TYR   0.009   0.001   TYR N  80 
 PHE   0.016   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8388)
  covalent geometry    : angle       0.50030 (11373)
  SS BOND              : bond        0.00371 (    3)
  SS BOND              : angle       2.98442 (    6)
  hydrogen bonds       : bond        0.04075 (  438)
  hydrogen bonds       : angle       4.30522 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5631 (OUTLIER) cc_final: 0.5342 (p0)
REVERT: A  230 GLU cc_start: 0.8449 (mt-10) cc_final: 0.6591 (tm-30)
REVERT: A  268 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5525 (tp30)
REVERT: B   59 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7730 (m-80)
REVERT: B  153 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7700 (p0)
REVERT: B  217 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7345 (ppp)
REVERT: B  259 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7671 (tt0)
REVERT: B  268 ASN cc_start: 0.7439 (m-40) cc_final: 0.7128 (p0)
REVERT: G   21 MET cc_start: 0.6410 (ttp) cc_final: 0.5444 (tmt)
REVERT: N    3 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6854 (pp30)
REVERT: R  122 ASP cc_start: 0.8340 (p0) cc_final: 0.7833 (p0)
  outliers start: 23
  outliers final: 13
  residues processed: 109
  average time/residue: 0.4901
  time to fit residues: 57.3068
Evaluate side-chains
  116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0980
   chunk 86 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.188606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148174 restraints weight = 8552.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 1.99
r_work: 0.3554 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8391  Z= 0.102
  Angle     :  0.500  14.269  11379  Z= 0.260
  Chirality :  0.041   0.281   1301
  Planarity :  0.003   0.044   1443
  Dihedral  :  4.517  45.684   1207
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.02 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.26), residues: 1025
  helix:  2.82 (0.25), residues: 415
  sheet:  0.99 (0.34), residues: 214
  loop : -0.04 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 197 
 TYR   0.009   0.001   TYR N  80 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8388)
  covalent geometry    : angle       0.49565 (11373)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       2.87793 (    6)
  hydrogen bonds       : bond        0.03989 (  438)
  hydrogen bonds       : angle       4.23897 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5527 (p0)
REVERT: A  230 GLU cc_start: 0.8393 (mt-10) cc_final: 0.6449 (tt0)
REVERT: A  268 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5459 (tp30)
REVERT: B   59 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7709 (m-80)
REVERT: B  153 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7687 (p0)
REVERT: B  217 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7288 (ppp)
REVERT: B  259 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7655 (tt0)
REVERT: G   21 MET cc_start: 0.6407 (ttp) cc_final: 0.5425 (tmt)
REVERT: N    3 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6816 (pp30)
REVERT: R  122 ASP cc_start: 0.8313 (p0) cc_final: 0.7818 (p0)
  outliers start: 22
  outliers final: 14
  residues processed: 105
  average time/residue: 0.5031
  time to fit residues: 56.5615
Evaluate side-chains
  114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  247 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   77 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0470
   chunk 44 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0050
   overall best weight:    0.4092

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.190368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150643 restraints weight = 8523.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 1.98
r_work: 0.3583 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8391  Z= 0.092
  Angle     :  0.484  14.455  11379  Z= 0.249
  Chirality :  0.041   0.269   1301
  Planarity :  0.003   0.041   1443
  Dihedral  :  4.377  44.517   1207
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.02 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.27), residues: 1025
  helix:  2.94 (0.25), residues: 411
  sheet:  0.98 (0.34), residues: 219
  loop :  0.08 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.009   0.001   TYR N  80 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 8388)
  covalent geometry    : angle       0.48019 (11373)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       2.52646 (    6)
  hydrogen bonds       : bond        0.03737 (  438)
  hydrogen bonds       : angle       4.12801 ( 1248)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASP cc_start: 0.5664 (OUTLIER) cc_final: 0.5373 (p0)
REVERT: A  268 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5446 (tp30)
REVERT: B   59 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7703 (m-80)
REVERT: B  153 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7579 (p0)
REVERT: G   21 MET cc_start: 0.6387 (ttp) cc_final: 0.5395 (tmt)
REVERT: N    3 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6834 (pp30)
REVERT: R  122 ASP cc_start: 0.8234 (p0) cc_final: 0.7788 (p0)
  outliers start: 23
  outliers final: 14
  residues processed: 106
  average time/residue: 0.4751
  time to fit residues: 54.0542
Evaluate side-chains
  111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  234 TRP
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   77 ASN
Chi-restraints excluded: chain R residue  226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0030
   chunk 25 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.190576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149749 restraints weight = 8531.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.03
r_work: 0.3556 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8391  Z= 0.104
  Angle     :  0.508  14.207  11379  Z= 0.259
  Chirality :  0.042   0.351   1301
  Planarity :  0.003   0.041   1443
  Dihedral  :  4.416  43.323   1207
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.36 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.26), residues: 1025
  helix:  3.03 (0.25), residues: 405
  sheet:  0.95 (0.34), residues: 214
  loop :  0.04 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 317 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8388)
  covalent geometry    : angle       0.50396 (11373)
  SS BOND              : bond        0.00302 (    3)
  SS BOND              : angle       2.77443 (    6)
  hydrogen bonds       : bond        0.03913 (  438)
  hydrogen bonds       : angle       4.16984 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 3054.91 seconds
wall clock time: 52 minutes 25.79 seconds (3145.79 seconds total)